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ORCIDBriefings in Bioinformatics, Volume 22
Volume 22, Number 1, January 2021
- Simona E. Rombo, Domenico Ursino:
Integrative bioinformatics and omics data source interoperability in the next-generation sequencing era - Editorial. 1-2 - Juan José Galano-Frutos
, Helena García-Cebollada, Javier Sancho:
Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. 3-19 - Mattia Forcato, Oriana Romano, Silvio Bicciato:
Computational methods for the integrative analysis of single-cell data. 20-29 - Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Stefano Ceri:
The road towards data integration in human genomics: players, steps and interactions. 30-44 - Oscar Pastor, Ana Palacio León, José Fabián Reyes Román, Alberto García Simón, Juan Carlos Casamayor Ródenas:
Using conceptual modeling to improve genome data management. 45-54 - Alba Gutiérrez-Sacristán, Carlos De Niz, Cartik Kothari, Sek Won Kong, Kenneth D. Mandl, Paul Avillach:
GenoPheno: cataloging large-scale phenotypic and next-generation sequencing data within human datasets. 55-65 - Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae:
Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. 66-76 - Susana Vinga:
Structured sparsity regularization for analyzing high-dimensional omics data. 77-87 - Matteo Comin, Barbara Di Camillo, Cinzia Pizzi, Fabio Vandin:
Comparison of microbiome samples: methods and computational challenges. 88-95 - Sergey Knyazev, Lauren Hughes, Pavel Skums, Alexander Zelikovsky:
Epidemiological data analysis of viral quasispecies in the next-generation sequencing era. 96-108 - Peter D. Karp, Peter E. Midford, Richard Billington, Anamika Kothari, Markus Krummenacker, Mario Latendresse, Wai Kit Ong, Pallavi Subhraveti, Ron Caspi, Carol A. Fulcher, Ingrid M. Keseler, Suzanne M. Paley:
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. 109-126 - Yun Zhang, Jonavelle Cuerdo, Marc K. Halushka, Matthew N. McCall:
The effect of tissue composition on gene co-expression. 127-139 - Joël Simoneau, Simon Dumontier, Ryan Gosselin, Michelle S. Scott:
Current RNA-seq methodology reporting limits reproducibility. 140-145 - Mariana Neves, Jurica Seva:
An extensive review of tools for manual annotation of documents. 146-163 - Duc Anh Nguyen, Canh Hao Nguyen, Hiroshi Mamitsuka:
A survey on adverse drug reaction studies: data, tasks and machine learning methods. 164-177 - Richa Bharti, Dominik G. Grimm:
Current challenges and best-practice protocols for microbiome analysis. 178-193 - Qiang Shi, Weiya Chen, Siqi Huang, Yan Wang, Zhidong Xue:
Deep learning for mining protein data. 194-218 - Beatriz T. Magalhães, Anália Lourenço, Nuno F. Azevedo:
Computational resources and strategies to assess single-molecule dynamics of the translation process in S. cerevisiae. 219-231 - Jinyu Chen, Louxin Zhang:
A survey and systematic assessment of computational methods for drug response prediction. 232-246 - Maryam Bagherian, Elyas Sabeti, Kai Wang, Maureen A. Sartor, Zaneta Nikolovska-Coleska, Kayvan Najarian:
Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. 247-269 - Ammu Prasanna Kumar, Chandra S. Verma, Suryani Lukman:
Structural dynamics and allostery of Rab proteins: strategies for drug discovery and design. 270-287 - Marieke Vromman, Jo Vandesompele, Pieter-Jan Volders:
Closing the circle: current state and perspectives of circular RNA databases. 288-297 - Shaofeng Lin, Chenwei Wang, Jiaqi Zhou, Ying Shi, Chen Ruan, Yiran Tu, Lan Yao, Di Peng, Yu Xue:
EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. 298-307 - Aidan R. O'Brien, Gaetan Burgio, Denis C. Bauer:
Domain-specific introduction to machine learning terminology, pitfalls and opportunities in CRISPR-based gene editing. 308-314 - Lan Huang, Dan Shao, Yan Wang, Xueteng Cui, Yufei Li, Qian Chen, Juan Cui:
Human body-fluid proteome: quantitative profiling and computational prediction. 315-333 - Han Fu, Kellie J. Archer:
High-dimensional variable selection for ordinal outcomes with error control. 334-345 - Betül Güvenç Paltun, Hiroshi Mamitsuka, Samuel Kaski:
Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches. 346-359 - Delora Baptista, Pedro G. Ferreira, Miguel Rocha:
Deep learning for drug response prediction in cancer. 360-379 - Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu:
Computational annotation of miRNA transcription start sites. 380-392 - Md. Rezaul Karim, Oya Beyan, Achille Zappa, Ivan G. Costa, Dietrich Rebholz-Schuhmann, Michael Cochez, Stefan Decker:
Deep learning-based clustering approaches for bioinformatics. 393-415 - Meichen Dong, Aatish Thennavan, Eugene Urrutia, Yun Li, Charles M. Perou, Fei Zou, Yuchao Jiang:
SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references. 416-427 - Ran Su, Huichen Wu, Xinyi Liu, Leyi Wei:
Predicting drug-induced hepatotoxicity based on biological feature maps and diverse classification strategies. 428-437 - Fei Liu, Wujie Sun, Monika Heiner, David R. Gilbert:
Hybrid modelling of biological systems using fuzzy continuous Petri nets. 438-450 - Yanyi Chu, Aman Chandra Kaushik, Xiangeng Wang, Wei Wang, Yufang Zhang, Xiaoqi Shan, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei:
DTI-CDF: a cascade deep forest model towards the prediction of drug-target interactions based on hybrid features. 451-462 - Qi Liu, Changjun Ding, Xiaoqiang Lang, Ganggang Guo, Jiafei Chen, Xiaohua Su:
Small noncoding RNA discovery and profiling with sRNAtools based on high-throughput sequencing. 463-473 - Jie Dong, Min-Feng Zhu, Yong-Huan Yun, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
BioMedR: an R/CRAN package for integrated data analysis pipeline in biomedical study. 474-484 - Xing Chen, Lian-Gang Sun, Yan Zhao:
NCMCMDA: miRNA-disease association prediction through neighborhood constraint matrix completion. 485-496 - Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Haiyang Zhong, Gaoang Wang, Xiaojun Yao, Lei Xu, Dong-Sheng Cao, Tingjun Hou:
Can machine learning consistently improve the scoring power of classical scoring functions? Insights into the role of machine learning in scoring functions. 497-514 - Le Zhang, Zichun Dai, Jun Yu, Ming Xiao:
CpG-island-based annotation and analysis of human housekeeping genes. 515-525 - Zhao-Yue Zhang, Yu-He Yang, Hui Ding, Dong Wang, Wei Chen, Hao Lin:
Design powerful predictor for mRNA subcellular location prediction in Homo sapiens. 526-535 - Jiangpeng Wu, Yifan Yang, Long Cheng, Jing Wu, Lili Xi, Ying Ma, Pengyi Zhang, Xiaoying Xu, Dekui Zhang, Shuyan Li:
GCdiscrimination: identification of gastric cancer based on a milliliter of blood. 536-544 - Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity W. Law, Sean R. Davis, Vincent J. Carey, Martin Morgan, Ralf Zimmer, Levi Waldron:
Toward a gold standard for benchmarking gene set enrichment analysis. 545-556 - Mo Zhu, Kai Kang, Kang Ning:
Meta-Prism: Ultra-fast and highly accurate microbial community structure search utilizing dual indexing and parallel computation. 557-567 - Nansu Zong, Rachael Sze Nga Wong, Yue Yu, Andrew Wen, Ming Huang, Ning Li:
Drug-target prediction utilizing heterogeneous bio-linked network embeddings. 568-580 - Xueyan Liu, Yong Xu, Ran Wang, Sheng Liu, Jun Wang, Yonglun Luo, Kwong-Sak Leung, Lixin Cheng:
A network-based algorithm for the identification of moonlighting noncoding RNAs and its application in sepsis. 581-588 - Jie Wu, Li Zhang, Qian Song, Lei Yu, Shuyuan Wang, Bo Zhang, Weida Wang, Peng Xia, Xiaowen Chen, Yun Xiao, Chaohan Xu:
Systematical identification of cell-specificity of CTCF-gene binding based on epigenetic modifications. 589-600 - Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Piero Fariselli:
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation. 601-603 - Juan José Galano-Frutos, Helena García-Cebollada, Javier Sancho:
Erratum to: Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when. 604 - Jing-Fang Yang, Fan Wang, Yuzong Chen, Ge-Fei Hao, Guangfu Yang:
Erratum to: LARMD: integration of bioinformatic resources to profile ligand-driven protein dynamics with a case on the activation of estrogen receptor. 605 - Maryam Bagherian, Elyas Sabeti, Kai Wang, Maureen A. Sartor, Zaneta Nikolovska-Coleska, Kayvan Najarian:
Erratum to: Machine learning approaches and databases for prediction of drug-target interaction: a survey paper. 606 - Minsik Oh, Sungjoon Park, Sun Kim, Heejoon Chae:
Erratum to: Machine learning-based analysis of multi-omics data on the cloud for investigating gene regulations. 607 - David Hoksza, Piotr Gawron, Marek Ostaszewski, Jan Hasenauer, Reinhard Schneider:
Closing the gap between formats for storing layout information in systems biology. 608 - Saidi Wang, Amlan Talukder, Mingyu Cha, Xiaoman Li, Haiyan Hu:
Corrigendum to: Computational annotation of miRNA transcription start sites. 609 - Maria Victoria Schneider, Rafael C. Jiménez:
Corrigendum to: Bioinformatics: scalability, capabilities and training in the data-driven era. 610 - Ziye Wang, Ying Wang, Jed A. Fuhrman, Fengzhu Sun, Shanfeng Zhu:
Corrigendum to: Assessment of metagenomic assemblers based on hybrid reads of real and simulated metagenomic sequences. 611
Volume 22, Number 2, March 2021
- Mario Cannataro, Andrew Harrison:
Bioinformatics helping to mitigate the impact of COVID-19 - Editorial. 613-615 - Matteo Chiara, Anna Maria D'Erchia, Carmela Gissi, Caterina Manzari, Antonio Parisi, Nicoletta Resta, Federico Zambelli, Ernesto Picardi, Giulio Pavesi, David Stephen Horner, Graziano Pesole:
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. 616-630 - Tao Hu, Juan Li, Hong Zhou, Cixiu Li, Edward C. Holmes, Weifeng Shi:
Bioinformatics resources for SARS-CoV-2 discovery and surveillance. 631-641 - Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Robert D. Finn, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F. Löchel, Maria Jesus Martin, Roman Martin, Julian O. Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine Niamh O'toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Pineros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna J. Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz:
Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research. 642-663 - Anna Bernasconi, Arif Canakoglu, Marco Masseroli, Pietro Pinoli, Stefano Ceri:
A review on viral data sources and search systems for perspective mitigation of COVID-19. 664-675 - Giuseppe Agapito, Chiara Pastrello, Igor Jurisica:
Comprehensive pathway enrichment analysis workflows: COVID-19 case study. 676-689 - Daniele Mercatelli, Andrew N. Holding, Federico M. Giorgi:
Web tools to fight pandemics: the COVID-19 experience. 690-700 - Francesca P. Caruso, Giovanni Scala, Luigi Cerulo, Michele Ceccarelli:
A review of COVID-19 biomarkers and drug targets: resources and tools. 701-713 - Md. Asif Ahsan, Yongjing Liu, Cong Feng, Yincong Zhou, Guangyuan Ma, Youhuang Bai, Ming Chen:
Bioinformatics resources facilitate understanding and harnessing clinical research of SARS-CoV-2. 714-725 - Serena Dotolo, Anna Marabotti, Angelo M. Facchiano, Roberto Tagliaferri:
A review on drug repurposing applicable to COVID-19. 726-741 - Vaishali P. Waman, Neeladri Sen, Mihaly Varadi, Antoine Daina, Shoshana J. Wodak, Vincent Zoete, Sameer Velankar, Christine A. Orengo:
The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. 742-768 - Ali F. Alsulami, Sherine E. Thomas, Arian R. Jamasb, Christopher A. Beaudoin, Ismail Moghul, Bridget Bannerman, Liviu Copoiu, Sundeep Chaitanya Vedithi, Pedro Torres, Tom L. Blundell:
SARS-CoV-2 3D database: understanding the coronavirus proteome and evaluating possible drug targets. 769-780 - Lucy Lu Wang, Kyle Lo:
Text mining approaches for dealing with the rapidly expanding literature on COVID-19. 781-799 - Xu Zuo, Yong Chen, Lucila Ohno-Machado, Hua Xu:
How do we share data in COVID-19 research? A systematic review of COVID-19 datasets in PubMed Central Articles. 800-811 - Arianna Dagliati, Alberto Malovini, Valentina Tibollo, Riccardo Bellazzi:
Health informatics and EHR to support clinical research in the COVID-19 pandemic: an overview. 812-822 - Valeria Seidita, Francesco Lanza, Arianna Pipitone, Antonio Chella:
Robots as intelligent assistants to face COVID-19 pandemic. 823-831 - Xiaodi Yang, Xianyi Lian, Chen Fu, Stefan Wuchty, Shiping Yang, Ziding Zhang:
HVIDB: a comprehensive database for human-virus protein-protein interactions. 832-844 - Yibo Dong, Chang Li, Kami Kim, Liwang Cui, Xiaoming Liu:
Genome annotation of disease-causing microorganisms. 845-854 - Jayanta Kumar Das, Giuseppe Tradigo, Pierangelo Veltri, Pietro H. Guzzi, Swarup Roy:
Data science in unveiling COVID-19 pathogenesis and diagnosis: evolutionary origin to drug repurposing. 855-872 - Krishan Gupta, Sanjay Kumar Mohanty, Aayushi Mittal, Siddhant Kalra, Suvendu Kumar, Tripti Mishra, Jatin Ahuja, Debarka Sengupta, Gaurav Ahuja:
The Cellular basis of loss of smell in 2019-nCoV-infected individuals. 873-881 - Zhiwei Feng, Maozi Chen, Tianjian Liang, Mingzhe Shen, Hui Chen, Xiang-Qun Xie:
Virus-CKB: an integrated bioinformatics platform and analysis resource for COVID-19 research. 882-895 - Tong Shao, Wenfang Wang, Meiyu Duan, Jiahui Pan, Zhuoyuan Xin, Baoyue Liu, Fengfeng Zhou, Guoqing Wang:
Application of Bayesian phylogenetic inference modelling for evolutionary genetic analysis and dynamic changes in 2019-nCoV. 896-904 - Wenzhong Yang, Guangxu Jin:
Origin-independent analysis links SARS-CoV-2 local genomes with COVID-19 incidence and mortality. 905-913 - Ashmita Dey, Sagnik Sen, Ujjwal Maulik:
Unveiling COVID-19-associated organ-specific cell types and cell-specific pathway cascade. 914-923 - Shifu Chen, Chang-Shou He, Yingqiang Li, Zhicheng Li, Charles E. Melançon:
A computational toolset for rapid identification of SARS-CoV-2, other viruses and microorganisms from sequencing data. 924-935 - Anjali Dhall, Sumeet Patiyal, Neelam Sharma, Salman Sadullah Usmani, Gajendra P. S. Raghava:
Computer-aided prediction and design of IL-6 inducing peptides: IL-6 plays a crucial role in COVID-19. 936-945 - Zhiwei Feng, Maozi Chen, Ying Xue, Tianjian Liang, Hui Chen, Yuehan Zhou, Thomas D. Nolin, Randall B. Smith, Xiang-Qun Xie:
MCCS: a novel recognition pattern-based method for fast track discovery of anti-SARS-CoV-2 drugs. 946-962 - Senbiao Fang, Ruoqian Zheng, Chuqi Lei, Jianxin Wang, Ruiqing Zheng, Min Li:
Key residues influencing binding affinities of 2019-nCoV with ACE2 in different species. 963-975 - Zhiting Wei, Yuli Gao, Fangliangzi Meng, Xin Chen, Yukang Gong, Chenyu Zhu, Bin Ju, Chao Zhang, Zhongmin Liu, Qi Liu:
iDMer: an integrative and mechanism-driven response system for identifying compound interventions for sudden virus outbreak. 976-987 - Jinyu Cheng, Ji Zhang, Zhongdao Wu, Xiaoqiang Sun:
Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19. 988-1005 - Yashpal Singh Malik, Mohd Ikram Ansari, Jobin Jose Kattoor, Rahul Kaushik, Shubhankar Sircar, Anbazhagan Subbaiyan, Ruchi Tiwari, Kuldeep Dhama, Souvik Ghosh, Shailly Tomar, Kam Y. J. Zhang:
Evolutionary and codon usage preference insights into spike glycoprotein of SARS-CoV-2. 1006-1022 - Burak Berber, Osman Doluca:
A comprehensive drug repurposing study for COVID19 treatment: novel putative dihydroorotate dehydrogenase inhibitors show association to serotonin-dopamine receptors. 1023-1037 - Antonio J. Pérez-Pulido, Gualberto Asencio-Cortés, Ana M. Brokate-Llanos, Gloria Brea-Calvo, Rosario Rodríguez-Griñolo, Andrés Garzón, Manuel J. Muñoz:
Serial co-expression analysis of host factors from SARS-CoV viruses highly converges with former high-throughput screenings and proposes key regulators. 1038-1052 - Yanqing Yang, Zhengdan Zhu, Xiaoyu Wang, Xinben Zhang, Kaijie Mu, Yulong Shi, Cheng Peng, Zhijian Xu, Weiliang Zhu:
Ligand-based approach for predicting drug targets and for virtual screening against COVID-19. 1053-1064 - Sanket Desai, Sonal Rashmi, Aishwarya Rane, Bhasker Dharavath, Aniket Sawant, Amit Dutt:
An integrated approach to determine the abundance, mutation rate and phylogeny of the SARS-CoV-2 genome. 1065-1075 - Akanksha Rajput, Archit Kumar, Kirti Megha, Anamika Thakur, Manoj Kumar:
DrugRepV: a compendium of repurposed drugs and chemicals targeting epidemic and pandemic viruses. 1076-1084 - Yuxuan Pang, Zhuo Wang, Jhih-Hua Jhong, Tzong-Yi Lee:
Identifying anti-coronavirus peptides by incorporating different negative datasets and imbalanced learning strategies. 1085-1095 - Qingren Meng, Yanan Chu, Changjun Shao, Jing Chen, Jian Wang, Zhancheng Gao, Jun Yu, Yu Kang:
Roles of host small RNAs in the evolution and host tropism of coronaviruses. 1096-1105 - Indrajit Saha, Nimisha Ghosh, Ayan Pradhan, Nikhil Sharma, Debasree Maity, Kaushik Mitra:
Whole genome analysis of more than 10 000 SARS-CoV-2 virus unveils global genetic diversity and target region of NSP6. 1106-1121 - Fang-Fang Yan, Feng Gao:
Comparison of the binding characteristics of SARS-CoV and SARS-CoV-2 RBDs to ACE2 at different temperatures by MD simulations. 1122-1136 - Song Zhang, Kuerbannisha Amahong, Xiuna Sun, Xichen Lian, Jin Liu, Huaicheng Sun, Yan Lou, Feng Zhu, Yunqing Qiu:
The miRNA: a small but powerful RNA for COVID-19. 1137-1149 - Danyang Ji, Mario Juhas, Chi Man Tsang, Chun Kit Kwok, Yongshu Li, Yang Zhang:
Discovery of G-quadruplex-forming sequences in SARS-CoV-2. 1150-1160 - Rong Li, Ka Wu, Yu Li, Xiao Liang, Keng Po Lai, Jian Chen:
Integrative pharmacological mechanism of vitamin C combined with glycyrrhizic acid against COVID-19: findings of bioinformatics analyses. 1161-1174 - Zulkar Nain, Humayan Kabir Rana, Pietro Liò, Sheikh Mohammed Shariful Islam, Matthew A. Summers, Mohammad Ali Moni:
Pathogenetic profiling of COVID-19 and SARS-like viruses. 1175-1196 - Safaa M. Naeem, Mai S. Mabrouk, Samir Y. Marzouk, Mohamed A. Eldosoky:
A diagnostic genomic signal processing (GSP)-based system for automatic feature analysis and detection of COVID-19. 1197-1205 - Abdul Arif Khan, Zakir Khan:
Comparative host-pathogen protein-protein interaction analysis of recent coronavirus outbreaks and important host targets identification. 1206-1214 - Tao Xu, Jingu Wang, Bingjie Hu, Guosi Zhang, Wu Zhou, Meiqin Zheng, Bo Shen, Baochang Sun, Yanjun Zhang, Yin Chen, Jian Yu, Min Liang, Jingye Pan, Chengshui Chen, Haixiao Chen, Minghua Jiang, Liangde Xu, Jia Qu, Jiang-Fan Chen:
Identification of the RNase-binding site of SARS-CoV-2 RNA for anchor primer-PCR detection of viral loading in 306 COVID-19 patients. 1215-1224 - Yanqiang Han, Zhilong Wang, Jiahao Ren, Zhiyun Wei, Jin-Jin Li:
Potential inhibitors for the novel coronavirus (SARS-CoV-2). 1225-1231 - Ying Jing, Lixia Diao, Leng Han:
Adverse events associated with potential drugs for COVID-19: a case study from real-world data. 1232-1238 - Shaolei Teng, Adebiyi Sobitan, Raina Rhoades, Dongxiao Liu, Qiyi Tang:
Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. 1239-1253 - Tasnimul Alam Taz, Kawsar Ahmed, Bikash Kumar Paul, Md. Kawsar, Nargis Aktar, S. M. Hasan Mahmud, Mohammad Ali Moni:
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. 1254-1266 - Jingzhe Shang, Na Han, Ziyi Chen, Yousong Peng, Liang Li, Hangyu Zhou, Chengyang Ji, Jing Meng, Taijiao Jiang, Aiping Wu:
Compositional diversity and evolutionary pattern of coronavirus accessory proteins. 1267-1278 - Rong Li, Yu Li, Xiao Liang, Lu Yang, Min Su, Keng Po Lai:
Network Pharmacology and bioinformatics analyses identify intersection genes of niacin and COVID-19 as potential therapeutic targets. 1279-1290 - Zheng Li, Xingye Li, Jianxiong Shen, Haining Tan, Tianhua Rong, Youxi Lin, Erwei Feng, Zhengguang Chen, Yang Jiao, Gang Liu, Lin Zhang, Matthew Tak Vai Chan, William Ka Kei Wu:
Bioinformatic analysis of SMN1-ACE/ACE2 interactions hinted at a potential protective effect of spinal muscular atrophy against COVID-19-induced lung injury. 1291-1296 - Zena Cai, Congyu Lu, Jun He, Li Liu, Yuanqiang Zou, Zheng Zhang, Zhaozhong Zhu, Xingyi Ge, Aiping Wu, Taijiao Jiang, Heping Zheng, Yousong Peng:
Identification and characterization of circRNAs encoded by MERS-CoV, SARS-CoV-1 and SARS-CoV-2. 1297-1308 - Aftab Alam, Arbaaz Khan, Nikhat Imam, Mohd Faizan Siddiqui, Mohd Waseem, Md. Zubbair Malik, Romana Ishrat:
Design of an epitope-based peptide vaccine against the SARS-CoV-2: a vaccine-informatics approach. 1309-1323 - Mohammad Ali Moni, Julian M. W. Quinn, Nese Sinmaz, Matthew A. Summers:
Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease. 1324-1337 - Pratik Goswami, Martin Bartas, Matej Lexa, Natália Bohálová, Adriana Volná, Jirí Cerven, Veronika Cervenová, Petr Pecinka, Vladimír Spunda, Miroslav Fojta, Václav Brázda:
SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. 1338-1345 - Chandra Bhushan Mishra, Preeti Pandey, Ravi Datta Sharma, Md. Zubbair Malik, Raj Kumar Mongre, Andrew M. Lynn, Rajendra Prasad, Raok Jeon, Amresh Prakash:
Identifying the natural polyphenol catechin as a multi-targeted agent against SARS-CoV-2 for the plausible therapy of COVID-19: an integrated computational approach. 1346-1360 - Shiv Bharadwaj, Amit Dubey, Umesh Yadava, Sarad Kumar Mishra, Sang Gu Kang, Vivek Dhar Dwivedi:
Exploration of natural compounds with anti-SARS-CoV-2 activity via inhibition of SARS-CoV-2 Mpro. 1361-1377 - Shasha Li, Wenli Liu, Yangzhen Chen, Liqin Wang, Wenlin An, Xiaoping An, Lihua Song, Yigang Tong, Huahao Fan, Chenyang Lu:
Transcriptome analysis of cepharanthine against a SARS-CoV-2-related coronavirus. 1378-1386 - Asif Nashiry, Shauli Sarmin Sumi, Salequl Islam, Julian M. W. Quinn, Mohammad Ali Moni:
Bioinformatics and system biology approach to identify the influences of COVID-19 on cardiovascular and hypertensive comorbidities. 1387-1401 - Shafi Mahmud, Mohammad Abu Raihan Uddin, Gobindo Kumar Paul, Sharmin Sultana Shimu, Saiful Islam, Ekhtiar Rahman, Ariful Islam, Md Samiul Islam, Maria Meha Promi, Talha Bin Emran, Md. Abu Saleh:
Virtual screening and molecular dynamics simulation study of plant-derived compounds to identify potential inhibitors of main protease from SARS-CoV-2. 1402-1414 - Md. Shahriare Satu, Md. Imran Khan, Md. Rezanur Rahman, Koushik Chandra Howlader, Shatabdi Roy, Shuvo Saha Roy, Julian M. W. Quinn, Mohammad Ali Moni:
Diseasome and comorbidities complexities of SARS-CoV-2 infection with common malignant diseases. 1415-1429 - Alisa Pavel, Giusy del Giudice, Antonio Federico, Antonio Di Lieto, Pia Anneli Sofia Kinaret, Angela Serra, Dario Greco:
Integrated network analysis reveals new genes suggesting COVID-19 chronic effects and treatment. 1430-1441 - Liang Cheng, Xudong Han, Zijun Zhu, Changlu Qi, Ping Wang, Xue Zhang:
Functional alterations caused by mutations reflect evolutionary trends of SARS-CoV-2. 1442-1450 - Tasnimul Alam Taz, Kawsar Ahmed, Bikash Kumar Paul, Fahad Ahmed Al-Zahrani, S. M. Hasan Mahmud, Mohammad Ali Moni:
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. 1451-1465 - Shisong Fang, Lin Zhang, Yingzhi Liu, Wenye Xu, Weihua Wu, Ziheng Huang, Xin Wang, Hui Liu, Ying Sun, Renli Zhang, Bo Peng, Xiaodong Liu, Xiao Sun, Jun Yu, Francis Ka-Leung Chan, Siew Chien Ng, Sunny Hei Wong, Maggie Haitian Wang, Tony Gin, Gavin Matthew Joynt, David Shu Cheong Hui, Tiejian Feng, William Ka Kei Wu, Matthew Tak Vai Chan, Xuan Zou, Junjie Xia:
Lysosome activation in peripheral blood mononuclear cells and prognostic significance of circulating LC3B in COVID-19. 1466-1475 - Ahmed Rakib, Zulkar Nain, Saad Ahmed Sami, Shafi Mahmud, Ashiqul Islam, Shahriar Ahmed, Adnan Bin Faisul Siddiqui, S. M. Omar Faruque Babu, Payar Hossain, Asif Shahriar, Firzan Nainu, Talha Bin Emran, Jesus Simal-Gandara:
A molecular modelling approach for identifying antiviral selenium-containing heterocyclic compounds that inhibit the main protease of SARS-CoV-2: an in silico investigation. 1476-1498 - Jim Warwicker:
A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium. 1499-1507 - Yu-Xi Huang, Wen-Xiao Wang, Yu-Ping Tang, Shi-Jun Yue:
Drug repurposing for COVID-19: could vitamin C combined with glycyrrhizic acid be at play by the findings of Li et al.'s database-based network pharmacology analysis? 1508-1510 - Jinyu Cheng, Ji Zhang, Zhongdao Wu, Xiaoqiang Sun:
Corrigendum to: Inferring microenvironmental regulation of gene expression from single-cell RNA sequencing data using scMLnet with an application to COVID-19. 1511-1512 - Daniel Berrar, Werner Dubitzky:
Deep learning in bioinformatics and biomedicine. 1513-1514 - Giulia Muzio, Leslie O'Bray, Karsten M. Borgwardt:
Biological network analysis with deep learning. 1515-1530 - Partho Sen, Santosh Lamichhane, Vivek Bhakta Mathema, Aidan J. McGlinchey, Alex M. Dickens, Sakda Khoomrung, Matej Oresic:
Deep learning meets metabolomics: a methodological perspective. 1531-1542 - Haiying Wang, Estelle Pujos-Guillot, Blandine Comte, Joao Luis de Miranda, Vojtech Spiwok, Ivan Chorbev, Filippo Castiglione, Paolo Tieri, Steven Watterson, Roisin McAllister, Tiago De Melo Malaquias, Massimiliano Zanin, Taranjit Singh Rai, Huiru Zheng:
Deep learning in systems medicine. 1543-1559 - Ninon Burgos, Simona Bottani, Johann Faouzi, Elina Thibeau-Sutre, Olivier Colliot:
Deep learning for brain disorders: from data processing to disease treatment. 1560-1576 - Jesse A. Livezey, Joshua I. Glaser:
Deep learning approaches for neural decoding across architectures and recording modalities. 1577-1591 - Mohamed Nadif, François Role:
Unsupervised and self-supervised deep learning approaches for biomedical text mining. 1592-1603 - Huimin Luo, Min Li, Mengyun Yang, Fang-Xiang Wu, Yaohang Li, Jianxin Wang:
Biomedical data and computational models for drug repositioning: a comprehensive review. 1604-1619 - Zainab Noor, Seong Beom Ahn, Mark S. Baker, Shoba Ranganathan, Abidali Mohamedali:
Mass spectrometry-based protein identification in proteomics - a review. 1620-1638 - Zhaoqian Liu, Anjun Ma, Ewy A. Mathé, Marlena Merling, Qin Ma, Bingqiang Liu:
Network analyses in microbiome based on high-throughput multi-omics data. 1639-1655 - ZiaurRehman Tanoli, Umair Seemab, Andreas Scherer, Krister Wennerberg, Jing Tang, Markus Vähä-Koskela:
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. 1656-1678 - Sameh K. Mohamed, Aayah Nounu, Vít Novácek:
Biological applications of knowledge graph embedding models. 1679-1693 - Daniel Toro-Domínguez, Juan Antonio Villatoro-García, Jordi Martorell-Marugan, Yolanda Román-Montoya, Marta E. Alarcón-Riquelme, Pedro Carmona-Saez:
A survey of gene expression meta-analysis: methods and applications. 1694-1705 - Liang Chen, Changliang Wang, Huiyan Sun, Juexin Wang, Yanchun Liang, Yan Wang, Garry Wong:
The bioinformatics toolbox for circRNA discovery and analysis. 1706-1728 - Jiancheng Zhong, Yusui Sun, Minzhu Xie, Wei Peng, Chushu Zhang, Fang-Xiang Wu, Jianxin Wang:
Proteoform characterization based on top-down mass spectrometry. 1729-1750 - Simon Lam, Stephen Doran, Hatice Hilal Yuksel, Ozlem Altay, Hasan Turkez, Jens Nielsen, Jan Boren, Mathias Uhlen, Adil Mardinoglu:
Addressing the heterogeneity in liver diseases using biological networks. 1751-1766 - Syed Ashiqur Rahman, Peter Giacobbi, Lee Pyles, Charles J. Mullett, Gianfranco Doretto, Donald A. Adjeroh:
Deep learning for biological age estimation. 1767-1781 - Dareen Alyousfi, Diana Baralle, Andrew Collins:
Essentiality-specific pathogenicity prioritization gene score to improve filtering of disease sequence data. 1782-1789 - Natesh Singh, Ludovic Chaput, Bruno O. Villoutreix:
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. 1790-1818 - Guanjing Hu, Corrinne E. Grover, Mark Arick II, Meiling Liu, Daniel G. Peterson, Jonathan F. Wendel:
Homoeologous gene expression and co-expression network analyses and evolutionary inference in allopolyploids. 1819-1835 - Wanshan Ning, Peiran Jiang, Yaping Guo, Chenwei Wang, Xiaodan Tan, Weizhi Zhang, Di Peng, Yu Xue:
GPS-Palm: a deep learning-based graphic presentation system for the prediction of S-palmitoylation sites in proteins. 1836-1847 - Anna Niarakis, Martin Kuiper, Marek Ostaszewski, Rahuman S. Malik-Sheriff, Cristina Casals-Casas, Denis Thieffry, Tom C. Freeman, Paul D. Thomas, Vasundra Touré, Vincent Noël, Gautier Stoll, Julio Saez-Rodriguez, Aurélien Naldi, Eugenia Oshurko, Ioannis Xenarios, Sylvain Soliman, Claudine Chaouiya, Tomás Helikar, Laurence Calzone:
Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. 1848-1859 - Song Zhang, Ying Zhou, Yanan Wang, Zhengwen Wang, Qitao Xiao, Ying Zhang, Yan Lou, Yunqing Qiu, Feng Zhu:
The mechanistic, diagnostic and therapeutic novel nucleic acids for hepatocellular carcinoma emerging in past score years. 1860-1883 - Chun Yen Lee, Yi-Ping Phoebe Chen:
Prediction of drug adverse events using deep learning in pharmaceutical discovery. 1884-1901 - Shuting Jin, Xiangxiang Zeng, Feng Xia, Wei Huang, Xiangrong Liu:
Application of deep learning methods in biological networks. 1902-1917 - Jing Li, Leyi Wei, Fei Guo, Quan Zou:
EP3: an ensemble predictor that accurately identifies type III secreted effectors. 1918-1928 - Yanyu Li, Xuecang Li, Yongsan Yang, Meng Li, Fengcui Qian, Zhidong Tang, Jianmei Zhao, Jian Zhang, Xuefeng Bai, Yong Jiang, Jianyuan Zhou, Yuexin Zhang, Liwei Zhou, Jianjun Xie, Enmin Li, Qiuyu Wang, Chunquan Li:
TRlnc: a comprehensive database for human transcriptional regulatory information of lncRNAs. 1929-1939 - Fu-Ying Dao, Hao Lv, Hasan Zulfiqar, Hui Yang, Wei Su, Hui Gao, Hui Ding, Hao Lin:
A computational platform to identify origins of replication sites in eukaryotes. 1940-1950 - Hao Wu, Dan Wang, Feng Gao:
Toward a high-quality pan-genome landscape of Bacillus subtilis by removal of confounding strains. 1951-1971 - Zhourun Wu, Qing Liao, Bin Liu:
idenPC-MIIP: identify protein complexes from weighted PPI networks using mutual important interacting partner relation. 1972-1983 - Jun Wang, Ziying Yang, Carlotta Domeniconi, Xiangliang Zhang, Guoxian Yu:
Cooperative driver pathway discovery via fusion of multi-relational data of genes, miRNAs and pathways. 1984-1999 - Yumeng Liu, Xiaolong Wang, Bin Liu:
RFPR-IDP: reduce the false positive rates for intrinsically disordered protein and region prediction by incorporating both fully ordered proteins and disordered proteins. 2000-2011 - Rasmus Froberg Brøndum, Thomas Yssing Michaelsen, Martin Bøgsted:
Regression on imperfect class labels derived by unsupervised clustering. 2012-2019 - Shiyuan Wang, Qi Zhang, Chunlu Yu, Yiyin Cao, Yongchun Zuo, Lei Yang:
Immune cell infiltration-based signature for prognosis and immunogenomic analysis in breast cancer. 2020-2031 - Weidun Xie, Jiawei Luo, Chu Pan, Ying Liu:
SG-LSTM-FRAME: a computational frame using sequence and geometrical information via LSTM to predict miRNA-gene associations. 2032-2042 - Qiu Xiao, Ning Zhang, Jiawei Luo, Jianhua Dai, Xiwei Tang:
Adaptive multi-source multi-view latent feature learning for inferring potential disease-associated miRNAs. 2043-2057 - Yayuan Peng, Manjiong Wang, Yixiang Xu, Zengrui Wu, Jiye Wang, Chao Zhang, Guixia Liu, Weihua Li, Jian Li, Yun Tang:
Drug repositioning by prediction of drug's anatomical therapeutic chemical code via network-based inference approaches. 2058-2072 - Yu Zhang, Cangzhi Jia, Melissa Jane Fullwood, Chee Keong Kwoh:
DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction. 2073-2084 - Zhen-Hao Guo, Zhu-Hong You, De-Shuang Huang, Hai-Cheng Yi, Kai Zheng, Zhan-Heng Chen, Yan-Bin Wang:
MeSHHeading2vec: a new method for representing MeSH headings as vectors based on graph embedding algorithm. 2085-2095 - Jiajie Peng, Hansheng Xue, Zhongyu Wei, Idil Tuncali, Jianye Hao, Xuequn Shang:
Integrating multi-network topology for gene function prediction using deep neural networks. 2096-2105 - Yifei Shen, Qinjie Chu, Xinxin Yin, Yinjun He, Panpan Bai, Yunfei Wang, Weijia Fang, Michael P. Timko, Longjiang Fan, Weiqin Jiang:
TOD-CUP: a gene expression rank-based majority vote algorithm for tissue origin diagnosis of cancers of unknown primary. 2106-2118 - A. Kulandaisamy, R. Sakthivel, M. Michael Gromiha:
MPTherm: database for membrane protein thermodynamics for understanding folding and stability. 2119-2125 - Fuyi Li, Jinxiang Chen, Zongyuan Ge, Ya Wen, Yanwei Yue, Morihiro Hayashida, Abdelkader Baggag, Halima Bensmail, Jiangning Song:
Computational prediction and interpretation of both general and specific types of promoters in Escherichia coli by exploiting a stacked ensemble-learning framework. 2126-2140 - Tianyi Zhao, Yang Hu, Linda R. Valsdottir, Tianyi Zang, Jiajie Peng:
Identifying drug-target interactions based on graph convolutional network and deep neural network. 2141-2150 - Hailong Zheng, Kai Song, Yelin Fu, Tianyi You, Jing Yang, Wenbing Guo, Kai Wang, Liangliang Jin, Yunyan Gu, Lishuang Qi, Wenyuan Zhao:
An absolute human stemness index associated with oncogenic dedifferentiation. 2151-2160 - Maryam Bagherian, Renaid B. Kim, Cheng Jiang, Maureen A. Sartor, Harm Derksen, Kayvan Najarian:
Coupled matrix-matrix and coupled tensor-matrix completion methods for predicting drug-target interactions. 2161-2171 - Piero Fariselli, Cristian Taccioli, Luca Pagani, Amos Maritan:
DNA sequence symmetries from randomness: the origin of the Chargaff's second parity rule. 2172-2181 - Zena Cai, Yunshi Fan, Zheng Zhang, Congyu Lu, Zhaozhong Zhu, Taijiao Jiang, Tongling Shan, Yousong Peng:
VirusCircBase: a database of virus circular RNAs. 2182-2190
Volume 22, Number 3, May 2021
- Xiaopeng Jin, Qing Liao, Bin Liu:
PL-search: a profile-link-based search method for protein remote homology detection. - Xiaohui Niu, Kaixuan Deng, Lifen Liu, Kun Yang, Xuehai Hu:
A statistical framework for predicting critical regions of p53-dependent enhancers. - Hao-Dong Xu, Ru-Ping Liang, You-Gan Wang, Jian-Ding Qiu:
mUSP: a high-accuracy map of the in situ crosstalk of ubiquitylation and SUMOylation proteome predicted via the feature enhancement approach. - Shuang Deng, Hongwan Zhang, Kaiyu Zhu, Xingyang Li, Ying Ye, Rui Li, Xuefei Liu, Dongxin Lin, Zhixiang Zuo, Jian Zheng:
M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers. - Mengying Zhang, Xiyun Jin, Junyi Li, Yi Tian, Qi Wang, Xinhui Li, Juan Xu, Yongsheng Li, Xia Li:
CeRNASeek: an R package for identification and analysis of ceRNA regulation. - Yanhong Huang, Xiao Chang, Yu Zhang, Luonan Chen, Xiaoping Liu:
Disease characterization using a partial correlation-based sample-specific network. - Hang Wei, Yong Xu, Bin Liu:
iPiDi-PUL: identifying Piwi-interacting RNA-disease associations based on positive unlabeled learning. - Ran Wei, Pengcheng Li, Funan He, Gang Wei, Zhan Zhou, Zhixi Su, Ting Ni:
Comprehensive analysis reveals distinct mutational signature and its mechanistic insights of alcohol consumption in human cancers. - Nan Sheng, Hui Cui, Tiangang Zhang, Ping Xuan:
Attentional multi-level representation encoding based on convolutional and variance autoencoders for lncRNA-disease association prediction. - Tingting Gong, Vanessa M. Hayes, Eva K. F. Chan:
Detection of somatic structural variants from short-read next-generation sequencing data. - Ye Wang, Tathagata Bhattacharya, Yuchao Jiang, Xiao Qin, Yue Wang, Yunlong Liu, Andrew J. Saykin, Li Chen:
A novel deep learning method for predictive modeling of microbiome data. - Jianteng Zhou, Jianing Gao, Huan Zhang, Daren Zhao, Ao Li, Furhan Iqbal, Qinghua Shi, Yuanwei Zhang:
PedMiner: a tool for linkage analysis-based identification of disease-associated variants using family based whole-exome sequencing data. - Rong Li, Chao Guo, Yu Li, Zuqian Qin, Wenjun Huang:
Therapeutic targets and signaling mechanisms of vitamin C activity against sepsis: a bioinformatics study. - Xiaoyu He, Shanyu Chen, Ruilin Li, Xinyin Han, Zhipeng He, Danyang Yuan, Shuying Zhang, Xiaohong Duan, Beifang Niu:
Comprehensive fundamental somatic variant calling and quality management strategies for human cancer genomes. - Qingfeng Zhang, Kai Yu, Shihua Li, Xiaolong Zhang, Qi Zhao, Xia Zhao, Zekun Liu, Han Cheng, Zexian Liu, Xiaoxing Li:
gutMEGA: a database of the human gut MEtaGenome Atlas. - Stephan Struckmann, Mathias Ernst, Sarah Fischer, Nancy Mah, Georg Fuellen, Steffen Möller:
Scoring functions for drug-effect similarity. - Jinzhuang Dou, Degang Wu, Lin Ding, Kai Wang, Minghui Jiang, Xiaoran Chai, Dermot F. Reilly, E. Shyong Tai, Jianjun Liu, Xueling Sim, Shanshan Cheng, Chaolong Wang:
Using off-target data from whole-exome sequencing to improve genotyping accuracy, association analysis and polygenic risk prediction. - Cong Feng, Min Dai, Yongjing Liu, Ming Chen:
Sequence repetitiveness quantification and de novo repeat detection by weighted k-mer coverage. - Louison Fresnais, Pedro J. Ballester:
The impact of compound library size on the performance of scoring functions for structure-based virtual screening. - Hua Tan, Pora Kim, Peiqing Sun, Xiaobo Zhou:
miRactDB characterizes miRNA-gene relation switch between normal and cancer tissues across pan-cancer. - Guo-Li Xiong, Wenling Ye, Chao Shen, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
Improving structure-based virtual screening performance via learning from scoring function components. - Xuanyi Wang, Zixuan Chai, Guizhi Pan, Youjin Hao, Bo Li, Ting Ye, Yinghong Li, Fei Long, Lixin Xia, Mingwei Liu:
ExoBCD: a comprehensive database for exosomal biomarker discovery in breast cancer. - Arif Canakoglu, Pietro Pinoli, Andrea Gulino, Luca Nanni, Marco Masseroli, Stefano Ceri:
Federated sharing and processing of genomic datasets for tertiary data analysis. - Cécile Hilpert, Geneviève Bricheux, Didier Debroas:
Reconstruction of plasmids by shotgun sequencing from environmental DNA: which bioinformatic workflow? - Jie Huang, Jiazhou Chen, Bin Zhang, Lei Zhu, Hongmin Cai:
Evaluation of gene-drug common module identification methods using pharmacogenomics data. - Jing Tang, Minjie Mou, Yunxia Wang, Yongchao Luo, Feng Zhu:
MetaFS: Performance assessment of biomarker discovery in metaproteomics. - Wei Wang, Qiuying Dai, Fang Li, Yi Xiong, Dong-Qing Wei:
MLCDForest: multi-label classification with deep forest in disease prediction for long non-coding RNAs. - Vivek Dhar Dwivedi, Aditya Arya, Pardeep Yadav, Rajesh Kumar, Vinod Kumar, Gajendra P. S. Raghava:
DenvInD: dengue virus inhibitors database for clinical and molecular research. - Yuchen Yang, Gang Li, Huijun Qian, Kirk C. Wilhelmsen, Yin Shen, Yun Li:
SMNN: batch effect correction for single-cell RNA-seq data via supervised mutual nearest neighbor detection. - Xin Wu, Hao Zheng, Zuochao Dou, Feng Chen, Jieren Deng, Xiang Chen, Shengqian Xu, Guanmin Gao, Mengmeng Li, Zhen Wang, Yuhui Xiao, Kang Xie, Shuang Wang, Huji Xu:
A novel privacy-preserving federated genome-wide association study framework and its application in identifying potential risk variants in ankylosing spondylitis. - Qiong Zhang, Mei Luo, Chun-Jie Liu, An-Yuan Guo:
CCLA: an accurate method and web server for cancer cell line authentication using gene expression profiles. - Hao Fei, Yafeng Ren, Yue Zhang, Donghong Ji, Xiaohui Liang:
Enriching contextualized language model from knowledge graph for biomedical information extraction. - Mingxuan Gao, Mingyi Ling, Xinwei Tang, Shun Wang, Xu Xiao, Ying Qiao, Wenxian Yang, Rongshan Yu:
Comparison of high-throughput single-cell RNA sequencing data processing pipelines. - Zhenyu Yue, Xinlu Chu, Junfeng Xia:
PredCID: prediction of driver frameshift indels in human cancer. - Junyi Chen, Ka-Chun Wong:
RNCE: network integration with reciprocal neighbors contextual encoding for multi-modal drug community study on cancer targets. - Pan Wang, Qi Li, Nan Sun, Yibo Gao, Jun S. Liu, Ke Deng, Jie He:
MiRACLe: an individual-specific approach to improve microRNA-target prediction based on a random contact model. - Dingfeng Wu, Wenxing Gao, Xiaoyi Li, Chuan Tian, Na Jiao, Sa Fang, Jing Xiao, Zhifeng Xu, Lixin Zhu, Guoqing Zhang, Ruixin Zhu:
Dr AFC: drug repositioning through anti-fibrosis characteristic. - Quanzhong Liu, Jinxiang Chen, Yanze Wang, Shuqin Li, Cangzhi Jia, Jiangning Song, Fuyi Li:
DeepTorrent: a deep learning-based approach for predicting DNA N4-methylcytosine sites. - Kangning Dong, Shihua Zhang:
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data. - Ruopeng Xie, Jiahui Li, Jiawei Wang, Wei Dai, André Leier, Tatiana T. Marquez-Lago, Tatsuya Akutsu, Trevor Lithgow, Jiangning Song, Yanju Zhang:
DeepVF: a deep learning-based hybrid framework for identifying virulence factors using the stacking strategy. - Wenbo Guo, Dongfang Wang, Shicheng Wang, Yiran Shan, Changyi Liu, Jin Gu:
scCancer: a package for automated processing of single-cell RNA-seq data in cancer. - A. K. M. Azad, Mojdeh Dinarvand, Alireza Nematollahi, Joshua Swift, Louise Lutze-Mann, Fatemeh Vafaee:
A comprehensive integrated drug similarity resource for in-silico drug repositioning and beyond. - Zhi-Luo Deng, Akshay Dhingra, Adrian Fritz, Jasper Götting, Philipp C. Münch, Lars Steinbrück, Thomas F. Schulz, Tina Ganzenmüller, Alice C. McHardy:
Evaluating assembly and variant calling software for strain-resolved analysis of large DNA viruses. - Xiangyu Luo, Joel Schwartz, Andrea A. Baccarelli, Zhonghua Liu:
Testing cell-type-specific mediation effects in genome-wide epigenetic studies. - Min Yuan, Xu Steven Xu, Yaning Yang, Yinsheng Zhou, Yi Li, Jinfeng Xu, Jose Pinheiro:
SCEBE: an efficient and scalable algorithm for genome-wide association studies on longitudinal outcomes with mixed-effects modeling. - Ruiling Fang, Haitao Yang, Yuzhao Gao, Hongyan Cao, Ellen L. Goode, Yuehua Cui:
Gene-based mediation analysis in epigenetic studies. - Yu-An Huang, Keith C. C. Chan, Zhu-Hong You, Pengwei Hu, Lei Wang, Zhi-An Huang:
Predicting microRNA-disease associations from lncRNA-microRNA interactions via Multiview Multitask Learning. - Jan Zaucha, Michael Heinzinger, A. Kulandaisamy, Evans Kataka, Óscar Llorian Salvádor, Petr Popov, Burkhard Rost, M. Michael Gromiha, Boris S. Zhorov, Dmitrij Frishman:
Mutations in transmembrane proteins: diseases, evolutionary insights, prediction and comparison with globular proteins. - Zhixu Qiu, Siyuan Chen, Yuhong Qi, Chunni Liu, Jingjing Zhai, Shang Xie, Chuang Ma:
Exploring transcriptional switches from pairwise, temporal and population RNA-Seq data using deepTS. - Hartmut Foerster, James N. D. Battey, Nicolas Sierro, Nikolai V. Ivanov, Lukas A. Mueller:
Metabolic networks of the Nicotiana genus in the spotlight: content, progress and outlook. - Luciano A. Abriata, Matteo Dal Peraro:
State-of-the-art web services for de novo protein structure prediction. - Wenwen Mei, Zhiwen Jiang, Yang Chen, Li Chen, Aziz Sancar, Yuchao Jiang:
Genome-wide circadian rhythm detection methods: systematic evaluations and practical guidelines. - Surui Pei, Tao Liu, Xue Ren, Weizhong Li, Chongjian Chen, Zhi Xie:
Benchmarking variant callers in next-generation and third-generation sequencing analysis. - Cindy Perscheid:
Integrative biomarker detection on high-dimensional gene expression data sets: a survey on prior knowledge approaches. - Jian Yi, Longyun Chen, Yajie Xiao, Zhikun Zhao, Xiaofan Su:
Investigations of sequencing data and sample type on HLA class Ia typing with different computational tools. - Aman Chandra Kaushik, Yanjing Wang, Xiangeng Wang, Dong-Qing Wei:
Irinotecan and vandetanib create synergies for treatment of pancreatic cancer patients with concomitant TP53 and KRAS mutations. - Yahui Long, Jiawei Luo, Yu Zhang, Yan Xia:
Predicting human microbe-disease associations via graph attention networks with inductive matrix completion. - Hsin-Yao Wang, Chia-Ru Chung, Zhuo Wang, Shangfu Li, Bo-Yu Chu, Jorng-Tzong Horng, Jang-Jih Lu, Tzong-Yi Lee:
A large-scale investigation and identification of methicillin-resistant Staphylococcus aureus based on peaks binning of matrix-assisted laser desorption ionization-time of flight MS spectra. - Minzhe Zhang, Thomas Sheffield, Xiaowei Zhan, Qiwei Li, Donghan M. Yang, Yunguan Wang, Shidan Wang, Yang Xie, Tao Wang, Guanghua Xiao:
Spatial molecular profiling: platforms, applications and analysis tools. - Veronica Porubsky, Lucian P. Smith, Herbert M. Sauro:
Publishing reproducible dynamic kinetic models. - Zhongqi Wen, Cheng Yan, Guihua Duan, Suning Li, Fang-Xiang Wu, Jianxin Wang:
A survey on predicting microbe-disease associations: biological data and computational methods. - Jiawei Li, Yuqian Pu, Jijun Tang, Quan Zou, Fei Guo:
DeepATT: a hybrid category attention neural network for identifying functional effects of DNA sequences. - Yan Zhao, Chun-Chun Wang, Xing Chen:
Microbes and complex diseases: from experimental results to computational models. - Dionysios Fanidis, Panagiotis Moulos:
Integrative, normalization-insusceptible statistical analysis of RNA-Seq data, with improved differential expression and unbiased downstream functional analysis. - Qifeng Bai, Shuoyan Tan, Tingyang Xu, Huanxiang Liu, Junzhou Huang, Xiaojun Yao:
MolAICal: a soft tool for 3D drug design of protein targets by artificial intelligence and classical algorithm. - Chen Yang, Xiaowen Huang, Yan Li, Junfei Chen, Yuanyuan Lv, Shixue Dai:
Prognosis and personalized treatment prediction in TP53-mutant hepatocellular carcinoma: an in silico strategy towards precision oncology. - Rong Li, Xue Huang, Xiao Liang, Min Su, Keng Po Lai, Jian Chen:
Integrated omics analysis reveals the alteration of gut microbe-metabolites in obese adults. - Chunlong Zhang, Ning Zhao, Xue Zhang, Jun Xiao, Junyi Li, Dezhong Lv, Weiwei Zhou, Yongsheng Li, Juan Xu, Xia Li:
SurvivalMeth: a web server to investigate the effect of DNA methylation-related functional elements on prognosis. - Haitao Yang, Zhaohong Deng, Xiaoyong Pan, Hong-Bin Shen, Kup-Sze Choi, Lei Wang, Shitong Wang, Jing Wu:
RNA-binding protein recognition based on multi-view deep feature and multi-label learning. - Denis Awany, Emile R. Chimusa:
Heritability jointly explained by host genotype and microbiome: will improve traits prediction? - Harold Duruflé, Merwann Selmani, Philippe Ranocha, Elisabeth Jamet, Christophe Dunand, Sébastien Déjean:
A powerful framework for an integrative study with heterogeneous omics data: from univariate statistics to multi-block analysis. - Amlan Talukder, Clayton Barham, Xiaoman Li, Haiyan Hu:
Interpretation of deep learning in genomics and epigenomics. - Murilo Horacio Pereira da Cruz, Douglas Silva Domingues, Priscila Tiemi Maeda Saito, Alexandre Rossi Paschoal, Pedro Henrique Bugatti:
TERL: classification of transposable elements by convolutional neural networks. - Dan Wang, Fei-Liao Lai, Feng Gao:
Ori-Finder 3: a web server for genome-wide prediction of replication origins in Saccharomyces cerevisiae. - Shuai Jiang, Hao Li, Hao Hong, Guifang Du, Xin Huang, Yu Sun, Junting Wang, Huan Tao, Kang Xu, Cheng Li, Yang Chen, Hebing Chen, Xiaochen Bo:
Spatial density of open chromatin: an effective metric for the functional characterization of topologically associated domains. - John Torcivia-Rodriguez, Raja Mazumder:
Scanning window analysis of non-coding regions within normal-tumor whole-genome sequence samples. - Gunnar Völkel, Simon Laban, Axel Fürstberger, Silke D. Kühlwein, Nensi Ikonomi, Thomas K. Hoffmann, Cornelia Brunner, Donna S. Neuberg, Verena Gaidzik, Hartmut Döhner, Johann M. Kraus, Hans A. Kestler:
Analysis, identification and visualization of subgroups in genomics. - Pawel Dabrowski-Tumanski, Pawel Rubach, Wanda Niemyska, Bartosz Ambrozy Gren, Joanna I. Sulkowska:
Topoly: Python package to analyze topology of polymers. - Hukam C. Rawal, Ulavappa B. Angadi, Tapan Kumar Mondal:
TEnGExA: an R package based tool for tissue enrichment and gene expression analysis. - Md. Mehedi Hasan, Shaherin Basith, Mst. Shamima Khatun, Gwang Lee, Balachandran Manavalan, Hiroyuki Kurata:
Meta-i6mA: an interspecies predictor for identifying DNA N6-methyladenine sites of plant genomes by exploiting informative features in an integrative machine-learning framework. - Chun-Chun Wang, Yan Zhao, Xing Chen:
Drug-pathway association prediction: from experimental results to computational models. - Huaming Chen, Fuyi Li, Lei Wang, Yaochu Jin, Chi-Hung Chi, Lukasz A. Kurgan, Jiangning Song, Jun Shen:
Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions. - Hengqiang Zhao, Shanshan Gu, Siqi Bao, Congcong Yan, Zicheng Zhang, Ping Hou, Meng Zhou, Jie Sun:
Mechanistically derived patient-level framework for precision medicine identifies a personalized immune prognostic signature in high-grade serous ovarian cancer. - Andrea Binatti, Silvia Bresolin, Stefania Bortoluzzi, Alessandro Coppe:
iWhale: a computational pipeline based on Docker and SCons for detection and annotation of somatic variants in cancer WES data. - Chao Shen, Ye Hu, Zhe Wang, Xujun Zhang, Jinping Pang, Gaoang Wang, Haiyang Zhong, Lei Xu, Dong-Sheng Cao, Tingjun Hou:
Beware of the generic machine learning-based scoring functions in structure-based virtual screening. - Haopeng Yu, Yi Zhang, Qing Sun, Huijie Gao, Shiheng Tao:
RSVdb: a comprehensive database of transcriptome RNA structure. - Shibo Wang, Yang Xu, Han Qu, Yanru Cui, Ruidong Li, John M. Chater, Lei Yu, Rui Zhou, Renyuan Ma, Yuhan Huang, Yiru Qiao, Xuehai Hu, Weibo Xie, Zhenyu Jia:
Boosting predictabilities of agronomic traits in rice using bivariate genomic selection. - Pora Kim, Hanyang Li, Junmei Wang, Zhongming Zhao:
Landscape of drug-resistance mutations in kinase regulatory hotspots. - Zhuohui Wei, Yue Zhang, Wanlin Weng, Jiazhou Chen, Hongmin Cai:
Survey and comparative assessments of computational multi-omics integrative methods with multiple regulatory networks identifying distinct tumor compositions across pan-cancer data sets. - Zheyang Zhang, Sainan Zhang, Xin Li, Zhangxiang Zhao, Changjing Chen, Juxuan Zhang, Mengyue Li, Zixin Wei, Wenbin Jiang, Bo Pan, Ying Li, Yixin Liu, Yingyue Cao, Wenyuan Zhao, Yunyan Gu, Yan Yu, Qingwei Meng, Lishuang Qi:
Reference genome and annotation updates lead to contradictory prognostic predictions in gene expression signatures: a case study of resected stage I lung adenocarcinoma. - Debby Dan Wang, Mengxu Zhu, Hong Yan:
Computationally predicting binding affinity in protein-ligand complexes: free energy-based simulations and machine learning-based scoring functions. - Yi Hsiao, Bo-Han Su, Yufeng J. Tseng:
Current development of integrated web servers for preclinical safety and pharmacokinetics assessments in drug development. - Mengyun Wu, Huangdi Yi, Shuangge Ma:
Vertical integration methods for gene expression data analysis. - Xing Chen, Tian-Hao Li, Yan Zhao, Chun-Chun Wang, Chi-Chi Zhu:
Deep-belief network for predicting potential miRNA-disease associations. - Vu Viet Hoang Pham, Xiaomei Li, Buu Minh Thanh Truong, Thin Nguyen, Lin Liu, Jiuyong Li, Thuc Duy Le:
The winning methods for predicting cellular position in the DREAM single-cell transcriptomics challenge. - Dohoon Lee, Youngjune Park, Sun Kim:
Towards multi-omics characterization of tumor heterogeneity: a comprehensive review of statistical and machine learning approaches. - Shihua Zhang, Xiaolong He, Rui Zhang, Wensheng Deng:
LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events. - Chunyu Yu, Boyan Shen, Kaiqiang You, Qi Huang, Minglei Shi, Congying Wu, Yang Chen, Chaolin Zhang, Tingting Li:
Proteome-scale analysis of phase-separated proteins in immunofluorescence images. - Fei-Fei Hu, Chun-Jie Liu, Lan-Lan Liu, Qiong Zhang, An-Yuan Guo:
Expression profile of immune checkpoint genes and their roles in predicting immunotherapy response. - Leandro A Bugnon, Cristian A. Yones, Diego H. Milone, Georgina Stegmayer:
Genome-wide discovery of pre-miRNAs: comparison of recent approaches based on machine learning. - Jike Wang, Dong-Sheng Cao, Cunchen Tang, Lei Xu, Qiaojun He, Bo Yang, Xi Chen, Huiyong Sun, Tingjun Hou:
DeepAtomicCharge: a new graph convolutional network-based architecture for accurate prediction of atomic charges. - Zi-Yi Yang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
Scopy: an integrated negative design python library for desirable HTS/VS database design. - Yulan Deng, Hao Luo, Zhenyu Yang, Lunxu Liu:
LncAS2Cancer: a comprehensive database for alternative splicing of lncRNAs across human cancers. - Soyeon Kim, Yulong Bai, Zhenjiang Fan, Brenda Diergaarde, George C. Tseng, Hyun Jung Park:
The microRNA target site landscape is a novel molecular feature associating alternative polyadenylation with immune evasion activity in breast cancer. - Hung Nguyen, Duc Tran, Bang Tran, Bahadir Pehlivan, Tin Nguyen:
A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data. - Vincenzo Bonnici, Emiliano Maresi, Rosalba Giugno:
Challenges in gene-oriented approaches for pangenome content discovery. - Anjali Garg, Neelja Singhal, Manish Kumar:
Discerning novel drug targets for treating Mycobacterium avium ss. paratuberculosis-associated autoimmune disorders: an in silico approach. - Ruidong Li, Shibo Wang, Yanru Cui, Han Qu, John M. Chater, Le Zhang, Julong Wei, Meiyue Wang, Yang Xu, Lei Yu, Jianming Lu, Yuanfa Feng, Rui Zhou, Yuhan Huang, Renyuan Ma, Jianguo Zhu, Wei-De Zhong, Zhenyu Jia:
Extended application of genomic selection to screen multiomics data for prognostic signatures of prostate cancer. - Joanna Miskiewicz, Joanna Sarzynska, Marta Szachniuk:
How bioinformatics resources work with G4 RNAs. - Arjun Bhattacharya, Alina M. Hamilton, Helena Furberg, Eugene Pietzak, Mark P. Purdue, Melissa A. Troester, Katherine A. Hoadley, Michael I. Love:
An approach for normalization and quality control for NanoString RNA expression data. - Kun Sun, Huating Wang, Hao Sun:
NAMS webserver: coding potential assessment and functional annotation of plant transcripts. - Zhaoqian Liu, Jingtong Feng, Bin Yu, Qin Ma, Bingqiang Liu:
The functional determinants in the organization of bacterial genomes. - Zhe Wang, Lei Meng, Hong Liu, Liang Shen, Hong-Fang Ji:
AlzRiskMR database: an online database for the impact of exposure factors on Alzheimer's disease. - Eva S. Deutekom, Berend Snel, Teunis J. P. van Dam:
Benchmarking orthology methods using phylogenetic patterns defined at the base of Eukaryotes. - Chuanjie Zhang, Tianhe Chen, Zongtai Li, Ao Liu, Yang Xu, Yi Gao, Danfeng Xu:
Depiction of tumor stemlike features and underlying relationships with hazard immune infiltrations based on large prostate cancer cohorts. - Zerong Wang, Dongyang Liu, Baofang Xu, Ruixia Tian, Yongchun Zuo:
Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. - Jialin Zhang, Da Xu, Kaijing Hao, Yusen Zhang, Wei Chen, Jiaguo Liu, Rui Gao, Chuanyan Wu, Yang De Marinis:
FS-GBDT: identification multicancer-risk module via a feature selection algorithm by integrating Fisher score and GBDT. - Sendong Zhao, Chang Su, Zhiyong Lu, Fei Wang:
Recent advances in biomedical literature mining. - Yi-Heng Zhu, Jun Hu, Fang Ge, Fuyi Li, Jiangning Song, Yang Zhang, Dong-Jun Yu:
Accurate multistage prediction of protein crystallization propensity using deep-cascade forest with sequence-based features. - Zicheng Zhang, Siqi Bao, Congcong Yan, Ping Hou, Meng Zhou, Jie Sun:
Computational principles and practice for decoding immune contexture in the tumor microenvironment. - Lei Zheng, Dongyang Liu, Wuritu Yang, Lei Yang, Yongchun Zuo:
RaacLogo: a new sequence logo generator by using reduced amino acid clusters. - Jen-Hao Chen, Yufeng Jane Tseng:
Different molecular enumeration influences in deep learning: an example using aqueous solubility. - Moritz Herrmann, Philipp Probst, Roman Hornung, Vindi Jurinovic, Anne-Laure Boulesteix:
Large-scale benchmark study of survival prediction methods using multi-omics data. - Yanyi Chu, Xiaoqi Shan, Tianhang Chen, Mingming Jiang, Yanjing Wang, Qiankun Wang, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei:
DTI-MLCD: predicting drug-target interactions using multi-label learning with community detection method. - Jing Chen, Lindsey J. Leach, Zewei Luo:
Letter to the Editor: Methods for mapping quantitative trait loci in autotetraploid species. - Cátia Vaz, Marta Nascimento, João A. Carriço, Tatiana Rocher, Alexandre P. Francisco:
Distance-based phylogenetic inference from typing data: a unifying view. - Piyush Agrawal, Dhruv Bhagat, Manish Mahalwal, Neelam Sharma, Gajendra P. S. Raghava:
AntiCP 2.0: an updated model for predicting anticancer peptides. - Cristian D. Loaiza, Naveen Duhan, Matthew Lister, Rakesh Kaundal:
In silico prediction of host-pathogen protein interactions in melioidosis pathogen Burkholderia pseudomallei and human reveals novel virulence factors and their targets. - Jianan Wang, Su Chen, Lili Dong, Guohua Wang:
CHTKC: a robust and efficient k-mer counting algorithm based on a lock-free chaining hash table. - Feng Huang, Xiang Yue, Zhankun Xiong, Zhouxin Yu, Shichao Liu, Wen Zhang:
Tensor decomposition with relational constraints for predicting multiple types of microRNA-disease associations. - Jieming Chen, Shravan Madireddi, Deepti Nagarkar, Maciej Migdal, Jason A. Vander Heiden, Diana Chang, Kiran Mukhyala, Suresh Selvaraj, Edward E. Kadel, Matthew J. Brauer, Sanjeev Mariathasan, Julie Hunkapiller, Suchit Jhunjhunwala, Matthew L. Albert, Christian Hammer:
In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales. - Rodrigo Madurga, Noemí García-Romero, Beatriz Jiménez, Ana Collazo, Francisco Pérez-Rodríguez, Aurelio Hernández-Laín, Carlos Fernández-Carballal, Ricardo Prat-Acín, Massimiliano Zanin, Ernestina Menasalvas, Ángel Ayuso-Sacido:
Normal tissue content impact on the GBM molecular classification. - Aleksandra E. Badaczewska-Dawid, Sebastian Kmiecik, Michal Kolinski:
Docking of peptides to GPCRs using a combination of CABS-dock with FlexPepDock refinement. - Anna Marabotti, Bernardina Scafuri, Angelo M. Facchiano:
Predicting the stability of mutant proteins by computational approaches: an overview. - Kyubum Lee, Chih-Hsuan Wei, Zhiyong Lu:
Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. - Jiangyi Shao, Bin Liu:
ProtFold-DFG: protein fold recognition by combining Directed Fusion Graph and PageRank algorithm. - Jiangyi Shao, Ke Yan, Bin Liu:
FoldRec-C2C: protein fold recognition by combining cluster-to-cluster model and protein similarity network. - Mingyi Liu, Ashok Dongre:
Proper imputation of missing values in proteomics datasets for differential expression analysis. - Peng Zhang, Mingyue Liu, Ya Cui, Pan Zheng, Yang Liu:
Microsatellite instability status differentially associates with intratumoral immune microenvironment in human cancers. - Carlos Eduardo Sequeiros-Borja, Bartlomiej Surpeta, Jan Brezovsky:
Recent advances in user-friendly computational tools to engineer protein function. - Hua-Ping Liu, Hung-Ming Lai, Zheng Guo:
Prostate cancer early diagnosis: circulating microRNA pairs potentially beyond single microRNAs upon 1231 serum samples. - Pedro G. Nachtigall, André Y. Kashiwabara, Alan M. Durham:
CodAn: predictive models for precise identification of coding regions in eukaryotic transcripts. - Xing-Xing Shi, Feng-Xu Wu, Long-Can Mei, Yu-Liang Wang, Ge-Fei Hao, Guangfu Yang:
Bioinformatics toolbox for exploring protein phosphorylation network. - Hao-Dong Xu, Peilin Jia, Zhongming Zhao:
Deep4mC: systematic assessment and computational prediction for DNA N4-methylcytosine sites by deep learning. - Meng Zhou, Zicheng Zhang, Siqi Bao, Ping Hou, Congcong Yan, Jianzhong Su, Jie Sun:
Computational recognition of lncRNA signature of tumor-infiltrating B lymphocytes with potential implications in prognosis and immunotherapy of bladder cancer. - Lei Xu, Shanshan Jiang, Jin Wu, Quan Zou:
An in silico approach to identification, categorization and prediction of nucleic acid binding proteins. - Duyen Thi Do, Trang Thanh Quynh Le, Nguyen-Quoc-Khanh Le:
Using deep neural networks and biological subwords to detect protein S-sulfenylation sites. - Xiaoqing Peng, Hong-Dong Li, Fang-Xiang Wu, Jianxin Wang:
Identifying the tissues-of-origin of circulating cell-free DNAs is a promising way in noninvasive diagnostics.
Volume 22, Number 4, July 2021
- Gaston K. Mazandu, Christopher Hooper, Kenneth Opap, Funmilayo L. Makinde, Victoria Nembaware, Nicholas E. Thomford, Emile R. Chimusa, Ambroise Wonkam, Nicola J. Mulder:
IHP-PING - generating integrated human protein-protein interaction networks on-the-fly. - Stefano Grasso, Tjeerd van Rij, Jan Maarten van Dijl:
GP4: an integrated Gram-Positive Protein Prediction Pipeline for subcellular localization mimicking bacterial sorting. - Shanwen Sun, BenZhi Dong, Quan Zou:
Revisiting genome-wide association studies from statistical modelling to machine learning. - Yuanyuan Chen, Yu Gu, Zixi Hu, Xiao Sun:
Sample-specific perturbation of gene interactions identifies breast cancer subtypes. - Bing-Liang Fan, Zheng Jiang, Jun Sun, Rong Liu:
Systematic characterization and prediction of coenzyme A-associated proteins using sequence and network information. - Xin Shao, Jie Liao, Chengyu Li, Xiaoyan Lu, Junyun Cheng, Xiaohui Fan:
CellTalkDB: a manually curated database of ligand-receptor interactions in humans and mice. - Yang Liu, Yuchen Guo, Xiaoyan Liu, Chunyu Wang, Maozu Guo:
Pathogenic gene prediction based on network embedding. - Maozi Chen, Zhiwei Feng, Siyi Wang, Weiwei Lin, Xiang-Qun Xie:
MCCS, a novel characterization method for protein-ligand complex. - Yuning Yang, Zilong Hou, Zhiqiang Ma, Xiangtao Li, Ka-Chun Wong:
iCircRBP-DHN: identification of circRNA-RBP interaction sites using deep hierarchical network. - Zhenxing Wu, Minfeng Zhu, Yu Kang, Elaine Lai-Han Leung, Tailong Lei, Chao Shen, Dejun Jiang, Zhe Wang, Dong-Sheng Cao, Tingjun Hou:
Do we need different machine learning algorithms for QSAR modeling? A comprehensive assessment of 16 machine learning algorithms on 14 QSAR data sets. - Yang Liu, Hongxia He, Zhi-Xiong Xiao, Anquan Ji, Jian Ye, Qifan Sun, Yang Cao:
A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification. - Mark F. Rogers, Tom R. Gaunt, Colin Campbell:
Prediction of driver variants in the cancer genome via machine learning methodologies. - Jens Nußberger, Frederic Boesel, Stefan Lenz, Harald Binder, Moritz Hess:
Synthetic observations from deep generative models and binary omics data with limited sample size. - Pieter Moris, Joey De Pauw, Anna Postovskaya, Sofie Gielis, Nicolas De Neuter, Wout Bittremieux, Benson Ogunjimi, Kris Laukens, Pieter Meysman:
Current challenges for unseen-epitope TCR interaction prediction and a new perspective derived from image classification. - Anyi Yang, Jingqi Chen, Xing-Ming Zhao:
nMAGMA: a network-enhanced method for inferring risk genes from GWAS summary statistics and its application to schizophrenia. - Sina Abdollahi, Peng-Chan Lin, Meng-Ru Shen, Jung-Hsien Chiang:
Precise uncertain significance prediction using latent space matrix factorization models: genomics variant and heterogeneous clinical data-driven approaches. - Chenggong Han, Qing Xie, Shili Lin:
Are dropout imputation methods for scRNA-seq effective for scHi-C data? - Tatiana Subkhankulova, Fedor Naumenko, Oleg E. Tolmachov, Yuriy L. Orlov:
Novel ChIP-seq simulating program with superior versatility: isChIP. - Sagnik Banerjee, Valeria Velásquez-Zapata, Gregory Fuerst, J. Mitch Elmore, Roger P. Wise:
NGPINT: a next-generation protein-protein interaction software. - Xiaoya Gao, Zifeng Huang, Cailing Feng, Chaohao Guan, Ruidong Li, Haiting Xie, Jian Chen, Mingchun Li, Rongfang Que, Bin Deng, Peihua Cao, Mengyan Li, Jianjun Lu, Yihong Huang, Minzi Li, Weihong Yang, Xiaohua Yang, Chunyan Wen, Xiaomei Liang, Qin Yang, Yin-Xia Chao, Ling Ling Chan, Midori A. Yenari, Kunlin Jin, Kallol Ray Chaudhuri, Jing Zhang, Eng-King Tan, Qing Wang:
Multimodal analysis of gene expression from postmortem brains and blood identifies synaptic vesicle trafficking genes to be associated with Parkinson's disease. - Sezin Kircali Ata, Min Wu, Yuan Fang, Le Ou-Yang, Chee Keong Kwoh, Xiaoli Li:
Recent advances in network-based methods for disease gene prediction. - Taj Mohammad, Yash Mathur, Md. Imtaiyaz Hassan:
InstaDock: A single-click graphical user interface for molecular docking-based virtual high-throughput screening. - Stefanie Peschel, Christian L. Müller, Erika von Mutius, Anne-Laure Boulesteix, Martin Depner:
NetCoMi: network construction and comparison for microbiome data in R. - Tian Lan, Gyorgy Hutvagner, Qing Lan, Tao Liu, Jinyan Li:
Sequencing dropout-and-batch effect normalization for single-cell mRNA profiles: a survey and comparative analysis. - Yu-Liang Wang, Fan Wang, Xing-Xing Shi, Chen-Yang Jia, Feng-Xu Wu, Ge-Fei Hao, Guangfu Yang:
Cloud 3D-QSAR: a web tool for the development of quantitative structure-activity relationship models in drug discovery. - Yongzhuang Liu, Yalin Huang, Guohua Wang, Yadong Wang:
A deep learning approach for filtering structural variants in short read sequencing data. - Chichi Dai, Pengmian Feng, Lizhen Cui, Ran Su, Wei Chen, Leyi Wei:
Iterative feature representation algorithm to improve the predictive performance of N7-methylguanosine sites. - Zhouxin Yu, Feng Huang, Xiaohan Zhao, Wenjie Xiao, Wen Zhang:
Predicting drug-disease associations through layer attention graph convolutional network. - Zhengwei Li, Jiashu Li, Ru Nie, Zhu-Hong You, Wenzheng Bao:
A graph auto-encoder model for miRNA-disease associations prediction. - Maxat Kulmanov, Fatima Zohra Smaili, Xin Gao, Robert Hoehndorf:
Semantic similarity and machine learning with ontologies. - Rui Tian, Ping Zhou, Mengyuan Li, Jinfeng Tan, Zifeng Cui, Wei Xu, Jingyue Wei, Jingjing Zhu, Zhuang Jin, Chen Cao, Weiwen Fan, Weiling Xie, Zhaoyue Huang, Hongxian Xie, Zeshan You, Gang Niu, Canbiao Wu, Xiaofang Guo, Xuchu Weng, Xun Tian, Fubing Yu, Zhiying Yu, Jiuxing Liang, Zheng Hu:
DeepHPV: a deep learning model to predict human papillomavirus integration sites. - Emmanuel Rivière, Tim H. Heupink, Nabila Ismail, Anzaan Dippenaar, Charlene Clarke, Gemeda Abebe, Peter van Heusden, Rob Warren, Conor J. Meehan, Annelies Van Rie:
Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries. - Nuojin Cheng, Ashley J. Schulte, Fadil Santosa, Jong Hyuk Kim:
Machine learning application identifies novel gene signatures from transcriptomic data of spontaneous canine hemangiosarcoma. - Yujia Xiang, Quan Zou, Lilin Zhao:
VPTMdb: a viral posttranslational modification database. - Vasundra Touré, Åsmund Flobak, Anna Niarakis, Steven Vercruysse, Martin Kuiper:
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. - A. T. Vivek, Shailesh Kumar:
Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq. - N. R. Siva Shanmugam, J. Jino Blessy, K. Veluraja, M. Michael Gromiha:
Prediction of protein-carbohydrate complex binding affinity using structural features. - Ling-Ling Zheng, Jing-Hua Xiong, Wu-Jian Zheng, Jun-Hao Wang, Zi-Liang Huang, Zhi-Rong Chen, Xin-Yao Sun, Yi-Min Zheng, Keren Zhou, Bin Li, Shun Liu, Liang-Hu Qu, Jian-Hua Yang:
ColorCells: a database of expression, classification and functions of lncRNAs in single cells. - Ying Li, Qi Zhang, Zhaoqian Liu, Cankun Wang, Siyu Han, Qin Ma, Wei Du:
Deep forest ensemble learning for classification of alignments of non-coding RNA sequences based on multi-view structure representations. - Anna Niarakis, Tomás Helikar:
A practical guide to mechanistic systems modeling in biology using a logic-based approach. - Fu-Ying Dao, Hao Lv, Dan Zhang, Zi-Mei Zhang, Li Liu, Hao Lin:
DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops. - Xiujuan Lei, Thosini Bamunu Mudiyanselage, Yuchen Zhang, Chen Bian, Wei Lan, Ning Yu, Yi Pan:
A comprehensive survey on computational methods of non-coding RNA and disease association prediction. - Yin Li, Jie Gu, Fengkai Xu, Qiaoliang Zhu, Yiwei Chen, Di Ge, Chunlai Lu:
Molecular characterization, biological function, tumor microenvironment association and clinical significance of m6A regulators in lung adenocarcinoma. - Md Shariful Islam Bhuyan, Itsik Pe'er, M. Sohel Rahman:
SICaRiO: short indel call filtering with boosting. - Pengyi Zhang, Jiangpeng Wu, Honglin Zhai, Shuyan Li:
ABCModeller: an automatic data mining tool based on a consistent voting method with a user-friendly graphical interface. - Mingguang Shi, Zhou Sheng, Hao Tang:
Prognostic outcome prediction by semi-supervised least squares classification. - Roula Tsonaka, Pietro Spitali:
Negative Binomial mixed models estimated with the maximum likelihood method can be used for longitudinal RNAseq data. - Sascha Jung, Kartikeya Singh, Antonio del Sol:
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. - Jing Meng, Brandon Victor, Zhen He, Hongde Liu, Taijiao Jiang:
DeepSSV: detecting somatic small variants in paired tumor and normal sequencing data with convolutional neural network. - Shuang Qiu, Zheng An, Renbo Tan, Ping-an He, Jingjing Jing, Hongxia Li, Shuang Wu, Ying Xu:
Understanding the unimodal distributions of cancer occurrence rates: it takes two factors for a cancer to occur. - Apurva Badkas, Sébastien De Landtsheer, Thomas Sauter:
Topological network measures for drug repositioning. - Yuanfei Dai, Chenhao Guo, Wenzhong Guo, Carsten Eickhoff:
Drug-drug interaction prediction with Wasserstein Adversarial Autoencoder-based knowledge graph embeddings. - Shan-Shan Dong, Wei-Ming He, Jing-Jing Ji, Chi Zhang, Yan Guo, Tie-Lin Yang:
LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on variant call format files. - Xiaoping Min, Congmin Ye, Xiangrong Liu, Xiangxiang Zeng:
Predicting enhancer-promoter interactions by deep learning and matching heuristic. - Ping Hou, Siqi Bao, Dandan Fan, Congcong Yan, Jianzhong Su, Jia Qu, Meng Zhou:
Machine learning-based integrative analysis of methylome and transcriptome identifies novel prognostic DNA methylation signature in uveal melanoma. - Elham Kazemi, Javaad Zargooshi, Marzieh Kaboudi, Parviz Heidari, Danial Kahrizi, Behzad Mahaki, Youkhabeh Mohammadian, Habibolah Khazaei, Kawsar Ahmed:
A genome-wide association study to identify candidate genes for erectile dysfunction. - Zhicheng Wang, Yushi Luan, Xiaoxu Zhou, Jun Cui, Feishi Luan, Jun Meng:
Optimized combination methods for exploring and verifying disease-resistant transcription factors in melon. - Mattia Furlan, Stefano de Pretis, Mattia Pelizzola:
Dynamics of transcriptional and post-transcriptional regulation. - Jinpu Cai, Yuyang Xu, Wen Zhang, Shiying Ding, Yuewei Sun, Jingyi Lyu, Meiyu Duan, Shuai Liu, Lan Huang, Fengfeng Zhou:
A comprehensive comparison of residue-level methylation levels with the regression-based gene-level methylation estimations by ReGear. - Chen Cao, Devin Kwok, Shannon Edie, Qing Li, Bowei Ding, Pathum Kossinna, Simone Campbell, Jingjing Wu, Matthew Greenberg, Quan Long:
kTWAS: integrating kernel machine with transcriptome-wide association studies improves statistical power and reveals novel genes. - Ziad Al Bkhetan, Gursharan Chana, Kotagiri Ramamohanarao, Karin Verspoor, Benjamin Goudey:
Evaluation of consensus strategies for haplotype phasing. - Zi-Yi Yang, Jie Dong, Zhi-Jiang Yang, Mingzhu Yin, Hong-Li Jiang, Ai-Ping Lu, Xiang Chen, Tingjun Hou, Dong-Sheng Cao:
ChemFLuo: a web-server for structure analysis and identification of fluorescent compounds. - Ren Qi, Jin Wu, Fei Guo, Lei Xu, Quan Zou:
A spectral clustering with self-weighted multiple kernel learning method for single-cell RNA-seq data. - Wen-Ya Zhang, Junhai Xu, Jun Wang, Yuan-Ke Zhou, Wei Chen, Pu-Feng Du:
KNIndex: a comprehensive database of physicochemical properties for k-tuple nucleotides. - Junyu Long, Shan Huang, Yi Bai, Jinzhu Mao, Anqiang Wang, Yu Lin, Xu Yang, Dongxu Wang, Jianzhen Lin, Jin Bian, Xiaobo Yang, Xinting Sang, Xi Wang, Haitao Zhao:
Transcriptional landscape of cholangiocarcinoma revealed by weighted gene coexpression network analysis. - Xiaokang Wang, Jinfeng Liu, Danwen Wang, Maohui Feng, Xiongzhi Wu:
Epigenetically regulated gene expression profiles reveal four molecular subtypes with prognostic and therapeutic implications in colorectal cancer. - Jingbo Yang, Denan Zhang, Lei Liu, Guoqi Li, Yiyang Cai, Yan Zhang, Hongbo Jin, Xiujie Chen:
Computational drug repositioning based on the relationships between substructure-indication. - Xiaohui Wu, Tao Liu, Congting Ye, Wenbin Ye, Guoli Ji:
scAPAtrap: identification and quantification of alternative polyadenylation sites from single-cell RNA-seq data. - Ying He, Zhen Shen, Qinhu Zhang, Siguo Wang, De-Shuang Huang:
A survey on deep learning in DNA/RNA motif mining. - Dipanka Sarmah, Nandadulal Bairagi, Samrat Chatterjee:
Tracing the footsteps of autophagy in computational biology. - Xiangtao Li, Shaochuan Li, Yunhe Wang, Shixiong Zhang, Ka-Chun Wong:
Identification of pan-cancer Ras pathway activation with deep learning. - Jie Huang, Stefano Pallotti, Qianling Zhou, Marcus Kleber, Xiaomeng Xin, Daniel A. King, Valerio Napolioni:
PERHAPS: Paired-End short Reads-based HAPlotyping from next-generation Sequencing data. - Jing Yang, Ling Hou, Kun-Meng Liu, Wen-Bin He, Yong Cai, Feng-Qing Yang, Yuanjia Hu:
ChemGenerator: a web server for generating potential ligands for specific targets. - Heike Deutelmoser, Dominique Scherer, Hermann Brenner, Melanie Waldenberger, Karsten Suhre, Gabi Kastenmüller, Justo Lorenzo Bermejo:
Robust Huber-LASSO for improved prediction of protein, metabolite and gene expression levels relying on individual genotype data. - Chao Hou, Haotai Xie, Yang Fu, Yao Ma, Tingting Li:
MloDisDB: a manually curated database of the relations between membraneless organelles and diseases. - Mengyun Yang, Gaoyan Wu, Qichang Zhao, Yaohang Li, Jianxin Wang:
Computational drug repositioning based on multi-similarities bilinear matrix factorization. - Pengyong Li, Yuquan Li, Chang-Yu Hsieh, Shengyu Zhang, Xianggen Liu, Huanxiang Liu, Sen Song, Xiaojun Yao:
TrimNet: learning molecular representation from triplet messages for biomedicine. - Lixin Ren, Caixia Gao, Zhana Duren, Yong Wang:
GuidingNet: revealing transcriptional cofactor and predicting binding for DNA methyltransferase by network regularization. - Yu Zhang, Cangzhi Jia, Chee Keong Kwoh:
Predicting the interaction biomolecule types for lncRNA: an ensemble deep learning approach. - Peifeng Ruan, Shuang Wang:
DiSNEP: a Disease-Specific gene Network Enhancement to improve Prioritizing candidate disease genes. - Tianyi Zhao, Yang Hu, Liang Cheng:
Deep-DRM: a computational method for identifying disease-related metabolites based on graph deep learning approaches. - Trang Le, Rachel A. Aronow, Arkadz Kirshtein, Leili Shahriyari:
A review of digital cytometry methods: estimating the relative abundance of cell types in a bulk of cells. - Elmer A. Fernández, Yamil D. Mahmoud, Florencia Veigas, Darío Rocha, Matías Miranda, Joaquín Merlo, Mónica Balzarini, Hugo D. Lujan, Gabriel A. Rabinovich, María Romina Girotti:
Unveiling the immune infiltrate modulation in cancer and response to immunotherapy by MIXTURE - an enhanced deconvolution method. - Leyi Wei, Wenjia He, Adeel Malik, Ran Su, Lizhen Cui, Balachandran Manavalan:
Computational prediction and interpretation of cell-specific replication origin sites from multiple eukaryotes by exploiting stacking framework. - Hao Lv, Fu-Ying Dao, Zheng-Xing Guan, Hui Yang, Yan-Wen Li, Hao Lin:
Deep-Kcr: accurate detection of lysine crotonylation sites using deep learning method. - Chunman Zuo, Luonan Chen:
Deep-joint-learning analysis model of single cell transcriptome and open chromatin accessibility data. - Zhourun Wu, Qing Liao, Shixi Fan, Bin Liu:
idenPC-CAP: Identify protein complexes from weighted RNA-protein heterogeneous interaction networks using co-assemble partner relation. - Ran Su, Linlin He, Tianling Liu, Xiaofeng Liu, Leyi Wei:
Protein subcellular localization based on deep image features and criterion learning strategy. - Yan Zhu, Fuyi Li, Dongxu Xiang, Tatsuya Akutsu, Jiangning Song, Cangzhi Jia:
Computational identification of eukaryotic promoters based on cascaded deep capsule neural networks. - Wei Du, Gaoyang Li, Nicholas Ho, Landon Jenkins, Drew Hockaday, Jiankang Tan, Huansheng Cao:
CyanoPATH: a knowledgebase of genome-scale functional repertoire for toxic cyanobacterial blooms. - Xiao Liang, Fuyi Li, Jinxiang Chen, Junlong Li, Hao Wu, Shuqin Li, Jiangning Song, Quanzhong Liu:
Large-scale comparative review and assessment of computational methods for anti-cancer peptide identification. - Salequl Islam, Mohammad Ali Moni, Umme Laila Urmi, Atsushi Tanaka, Hiroo Hoshino:
C-C Chemokine receptor-like 2 (CCRL2) acts as coreceptor for human immunodeficiency virus-2. - Kyoung Sik Park, Seong Hoon Kim, Jung Hun Oh, Sung Young Kim:
Highly accurate diagnosis of papillary thyroid carcinomas based on personalized pathways coupled with machine learning. - Yun Zhang, Brian D. Aevermann, Trygve E. Bakken, Jeremy A. Miller, Rebecca D. Hodge, Ed S. Lein, Richard H. Scheuermann:
FR-Match: robust matching of cell type clusters from single cell RNA sequencing data using the Friedman-Rafsky non-parametric test. - Shiyuan Wang, Yuqiang Xiong, Qi Zhang, Dongqing Su, Chunlu Yu, Yiyin Cao, Yi Pan, Qianzi Lu, Yongchun Zuo, Lei Yang:
Clinical significance and immunogenomic landscape analyses of the immune cell signature based prognostic model for patients with breast cancer. - Shuangjia Zheng, Jiahua Rao, Ying Song, Jixian Zhang, Xianglu Xiao, Evandro Fei Fang, Yuedong Yang, Zhangming Niu:
PharmKG: a dedicated knowledge graph benchmark for bomedical data mining. - Lijun Cai, Li Wang, Xiangzheng Fu, Chenxing Xia, Xiangxiang Zeng, Quan Zou:
ITP-Pred: an interpretable method for predicting, therapeutic peptides with fused features low-dimension representation. - Neelam Sharma, Sumeet Patiyal, Anjali Dhall, Akshara Pande, Chakit Arora, Gajendra P. S. Raghava:
AlgPred 2.0: an improved method for predicting allergenic proteins and mapping of IgE epitopes. - Yue Yin, Jia Li, Jin Li, Minjung Lee, Sibo Zhao, Linlang Guo, Jianfang Li, Mutian Zhang, Yun Huang, Xiao-Nan Li, Zhenzhong Deng, Deqiang Sun:
LiBis: an ultrasensitive alignment augmentation for low-input bisulfite sequencing.
Volume 22, Number 5, September 2021
- Xinyin Han, Shuying Zhang, Daniel Cui Zhou, Dongliang Wang, Xiaoyu He, Danyang Yuan, Ruilin Li, Jiayin He, Xiaohong Duan, Michael C. Wendl, Li Ding, Beifang Niu:
MSIsensor-ct: microsatellite instability detection using cfDNA sequencing data. - Yuning Yang, Shaochuan Li, Yunhe Wang, Zhiqiang Ma, Ka-Chun Wong, Xiangtao Li:
Identification of haploinsufficient genes from epigenomic data using deep forest. - Zhenzhen Han, Yang Zhang, Pengqian Wang, Qilin Tang, Kai Zhang:
Is acupuncture effective in the treatment of COVID-19 related symptoms? Based on bioinformatics/network topology strategy. - Huayu Zhang, Amy Ferguson, Grant Robertson, Muchen Jiang, Teng Zhang, Cathie Sudlow, Keith Smith, Kristiina Rannikmäe, Honghan Wu:
Benchmarking network-based gene prioritization methods for cerebral small vessel disease. - Lun Hu, Xiaojuan Wang, Yu-An Huang, Pengwei Hu, Zhu-Hong You:
A survey on computational models for predicting protein-protein interactions. - Lesong Wei, Xiucai Ye, Yuyang Xue, Tetsuya Sakurai, Leyi Wei:
ATSE: a peptide toxicity predictor by exploiting structural and evolutionary information based on graph neural network and attention mechanism. - Zhenhua Luo, Weijin Liu, Panpan Sun, Feng Wang, Xuyang Feng:
Pan-cancer analyses reveal regulation and clinical outcome association of the shelterin complex in cancer. - Ziad Al Bkhetan, Gursharan Chana, Cheng Soon Ong, Benjamin Goudey, Kotagiri Ramamohanarao:
eQTLHap: a tool for comprehensive eQTL analysis considering haplotypic and genotypic effects. - Jianyang Du, Hang Ji, Shuai Ma, Jiaqi Jin, Shan Mi, Kuiyuan Hou, Jiawei Dong, Fang Wang, Chaochao Zhang, Yuan Li, Shaoshan Hu:
m6A regulator-mediated methylation modification patterns and characteristics of immunity and stemness in low-grade glioma. - Mengyuan Zhao, Wenying He, Jijun Tang, Quan Zou, Fei Guo:
A comprehensive overview and critical evaluation of gene regulatory network inference technologies. - Robson Bonidia, Lucas Dias H. Sampaio, Douglas Silva Domingues, Alexandre Rossi Paschoal, Fabrício Martins Lopes, André C. P. L. F. de Carvalho, Danilo Sipoli Sanches:
Feature extraction approaches for biological sequences: a comparative study of mathematical features. - Qing-Wen Wu, Jun-Feng Xia, Jian-Cheng Ni, Chun-Hou Zheng:
GAERF: predicting lncRNA-disease associations by graph auto-encoder and random forest. - Tianyi Zhao, Jinxin Liu, Xi Zeng, Wei Wang, Sheng Li, Tianyi Zang, Jiajie Peng, Yang Yang:
Prediction and collection of protein-metabolite interactions. - Xiuliang Cui, Lu Han, Yang Liu, Ying Li, Wen Sun, Bin Song, Wenxia Zhou, Yongxiang Zhang, Hongyang Wang:
siGCD: a web server to explore survival interaction of genes, cells and drugs in human cancers. - Adrien Rougny, Vasundra Touré, John Albanese, Dagmar Waltemath, Denis Shirshov, Anatoly A. Sorokin, Gary D. Bader, Michael L. Blinov, Alexander Mazein:
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. - Mitra Ebrahimpoor, Jelle J. Goeman:
Inflated false discovery rate due to volcano plots: problem and solutions. - Rashedul Islam, Rajan Saha Raju, Nazia Tasnim, Istiak Hossain Shihab, Maruf Ahmed Bhuiyan, Yusha Araf, Tofazzal Islam:
Choice of assemblers has a critical impact on de novo assembly of SARS-CoV-2 genome and characterizing variants. - Weiwen Wang, Xiwen Zhang, Dao-Qing Dai:
DeFusion: a denoised network regularization framework for multi-omics integration. - Long-Can Mei, Yu-Liang Wang, Feng-Xu Wu, Fan Wang, Ge-Fei Hao, Guangfu Yang:
HISNAPI: a bioinformatic tool for dynamic hot spot analysis in nucleic acid-protein interface with a case study. - Qianqian Song, Jing Su:
DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence. - Yafei Chang, Qilian Fan, Jialin Hou, Yu Zhang, Jing Li:
A community-supported metaproteomic pipeline for improving peptide identifications in hydrothermal vent microbiota. - Yuni Zeng, Xiangru Chen, Yujie Luo, Xuedong Li, Dezhong Peng:
Deep drug-target binding affinity prediction with multiple attention blocks. - Kaili Wang, Renyi Zhou, Yaohang Li, Min Li:
DeepDTAF: a deep learning method to predict protein-ligand binding affinity. - Kenong Su, Tianwei Yu, Hao Wu:
Accurate feature selection improves single-cell RNA-seq cell clustering. - Chao Shen, Gaoqi Weng, Xujun Zhang, Elaine Lai-Han Leung, Xiaojun Yao, Jinping Pang, Xin Chai, Dan Li, Ercheng Wang, Dong-Sheng Cao, Tingjun Hou:
Accuracy or novelty: what can we gain from target-specific machine-learning-based scoring functions in virtual screening? - Nguyen-Quoc-Khanh Le, Quang-Thai Ho, Trinh-Trung-Duong Nguyen, Yu-Yen Ou:
A transformer architecture based on BERT and 2D convolutional neural network to identify DNA enhancers from sequence information. - Dropen Sheka, Nikolay Alabi, Paul M. K. Gordon:
Oxford nanopore sequencing in clinical microbiology and infection diagnostics. - Jiajie Peng, Yuxian Wang, Jiaojiao Guan, Jingyi Li, Ruijiang Han, Jianye Hao, Zhongyu Wei, Xuequn Shang:
An end-to-end heterogeneous graph representation learning-based framework for drug-target interaction prediction. - Wenyi Zhao, Jingwen Yang, Jingcheng Wu, Guoxing Cai, Yao Zhang, Jeffrey Haltom, Weijia Su, Michael J. Dong, Shuqing Chen, Jian Wu, Zhan Zhou, Xun Gu:
CanDriS: posterior profiling of cancer-driving sites based on two-component evolutionary model. - Shutao Mei, Fuyi Li, Dongxu Xiang, Rochelle Ayala, Pouya Faridi, Geoffrey I. Webb, Patricia T. Illing, Jamie Rossjohn, Tatsuya Akutsu, Nathan P. Croft, Anthony W. Purcell, Jiangning Song:
Anthem: a user customised tool for fast and accurate prediction of binding between peptides and HLA class I molecules. - Gerhard Mayer, Wolfgang Müller, Karin Schork, Julian Uszkoreit, Andreas Weidemann, Ulrike Wittig, Maja Rey, Christian Quast, Janine Felden, Frank Oliver Glöckner, Matthias Lange, Daniel Arend, Sebastian Beier, Astrid Junker, Uwe Scholz, Danuta Schüler, Hans A. Kestler, Daniel Wibberg, Alfred Pühler, Sven Twardziok, Jürgen Eils, Roland Eils, Steve Hoffmann, Martin Eisenacher, Michael Turewicz:
Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de.NBI) exemplified by selected use cases. - Matthew L. Davis, Yuan Huang, Kai Wang:
Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries. - Irina Chelysheva, Andrew J. Pollard, Daniel O'Connor:
RNA2HLA: HLA-based quality control of RNA-seq datasets. - Ye Yuan, Ziv Bar-Joseph:
Deep learning of gene relationships from single cell time-course expression data. - Jana Musilova, Karel Sedlár:
Tools for time-course simulation in systems biology: a brief overview. - Mengyuan Yang, Ke Yiya, Pora Kim, Xiaobo Zhou:
ExonSkipAD provides the functional genomic landscape of exon skipping events in Alzheimer's disease. - Ryan D. Kuster, G. Craig Yencho, Bode A. Olukolu:
ngsComposer: an automated pipeline for empirically based NGS data quality filtering. - Lijun Dou, Fenglong Yang, Lei Xu, Quan Zou:
A comprehensive review of the imbalance classification of protein post-translational modifications. - You Zou, Yuejie Zhu, Yaohang Li, Fang-Xiang Wu, Jianxin Wang:
Parallel computing for genome sequence processing. - Chunyan Li, Jianmin Wang, Zhangming Niu, Junfeng Yao, Xiangxiang Zeng:
A spatial-temporal gated attention module for molecular property prediction based on molecular geometry. - Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger:
Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. - Danyang Yuan, Xiaoyu He, Xinyin Han, Chunyan Yang, Fei Liu, Shuying Zhang, Haijing Luan, Ruilin Li, Jiayin He, Xiaohong Duan, Dongliang Wang, Qiming Zhou, Sujun Gao, Beifang Niu:
Comprehensive review and evaluation of computational methods for identifying FLT3-internal tandem duplication in acute myeloid leukaemia. - Jianjun Jiang, Lehua Cheng, Liang Yan, Mingxia Ge, Liqin Yang, Haoqiang Ying, Qingpeng Kong:
Decoding the role of long noncoding RNAs in the healthy aging of centenarians. - Xi Tang, Tao Zhang, Na Cheng, Huadong Wang, Chun-Hou Zheng, Junfeng Xia, Tiejun Zhang:
usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme. - Zhenxing Wu, Dejun Jiang, Chang-Yu Hsieh, Guangyong Chen, Ben Liao, Dong-Sheng Cao, Tingjun Hou:
Hyperbolic relational graph convolution networks plus: a simple but highly efficient QSAR-modeling method. - Ritesh Sharma, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar, Sonal Saxena, Raj Kumar Singh:
Deep-ABPpred: identifying antibacterial peptides in protein sequences using bidirectional LSTM with word2vec. - Shaolei Teng, Adebiyi Sobitan, Raina Rhoades, Dongxiao Liu, Qiyi Tang:
Corrigendum to: Systemic effects of missense mutations on SARS-CoV-2 spike glycoprotein stability and receptor-binding affinity. - Hao Wang, Jijun Tang, Yijie Ding, Fei Guo:
Exploring associations of non-coding RNAs in human diseases via three-matrix factorization with hypergraph-regular terms on center kernel alignment. - Xiang Liu, Xiangjun Wang, Jie Wu, Kelin Xia:
Hypergraph-based persistent cohomology (HPC) for molecular representations in drug design. - Fu-Ying Dao, Hao Lv, Wei Su, Zi-Jie Sun, Qin-Lai Huang, Hao Lin:
iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network. - Rita Pancsa, Wim F. Vranken, Bálint Mészáros:
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. - Zihao Wang, Yaning Wang, Tianrui Yang, Hao Xing, Yuekun Wang, Lu Gao, Xiaopeng Guo, Bing Xing, Yu Wang, Wenbin Ma:
Machine learning revealed stemness features and a novel stemness-based classification with appealing implications in discriminating the prognosis, immunotherapy and temozolomide responses of 906 glioblastoma patients. - Hong Wang, Jing Li, Siyu Wang, Xiaoyan Lu, Guosi Zhang, Youyuan Zhuang, Liansheng Li, Wencan Wang, Peng Lin, Chong Chen, Hao Wang, Qi Chen, Yongshuai Jiang, Jia Qu, Liangde Xu:
Contribution of structural accessibility to the cooperative relationship of TF-lncRNA in myopia. - Jin Liu, Ran Su, Jiahang Zhang, Leyi Wei:
Classification and gene selection of triple-negative breast cancer subtype embedding gene connectivity matrix in deep neural network. - Xiangtao Li, Shixiong Zhang, Ka-Chun Wong:
Deep embedded clustering with multiple objectives on scRNA-seq data. - Reza Mousavi, Sri Harsha Konuru, Daniel Lobo:
Inference of dynamic spatial GRN models with multi-GPU evolutionary computation. - Jiao Gong, Rong Li, Yaqiong Chen, Zhenjian Zhuo, Shuru Chen, Jing Cao, Qi Zhang, Yutian Chong, Bo Hu:
HCC subtypes based on the activity changes of immunologic and hallmark gene sets in tumor and nontumor tissues. - Pedro G. Nachtigall, Felipe G. Grazziotin, Inácio L. M. Junqueira-de-Azevedo:
MITGARD: an automated pipeline for mitochondrial genome assembly in eukaryotic species using RNA-seq data. - Zhuohan Yu, Chuang Bian, Genggeng Liu, Shixiong Zhang, Ka-Chun Wong, Xiangtao Li:
Elucidating transcriptomic profiles from single-cell RNA sequencing data using nature-inspired compressed sensing. - Kai Song, Hao Cai, Hailong Zheng, Jing Yang, Liangliang Jin, Huiting Xiao, Jiashuai Zhang, Zhangxiang Zhao, Xin Li, Wenyuan Zhao, Xia Li:
Multilevel prioritization of gene regulators associated with consensus molecular subtypes of colorectal cancer. - Christoph A. Krettler, Gerhard G. Thallinger:
A map of mass spectrometry-based in silico fragmentation prediction and compound identification in metabolomics. - Zihan Zheng, Xin Qiu, Haiyang Wu, Ling Chang, Xiangyu Tang, Liyun Zou, Jingyi Li, Yuzhang Wu, Jianzhi Zhou, Shan Jiang, Ying Wan, Qingshan Ni:
TIPS: trajectory inference of pathway significance through pseudotime comparison for functional assessment of single-cell RNAseq data. - Nan Zhang, Xizi Luo, Juanjuan Huang, Hongyan Song, Xinyue Zhang, Honglan Huang, Shishun Zhao, Guoqing Wang:
The landscape of different molecular modules in an immune microenvironment during tuberculosis infection. - Abozar Ghorbani, Samira Samarfard, Neda Eskandarzade, Alireza Afsharifar, Mohammad Hadi Eskandari, Ali Niazi, Keramatollah Izadpanah, Thomas P. Karbanowicz:
Comparative phylogenetic analysis of SARS-CoV-2 spike protein - possibility effect on virus spillover. - Tianjian Liang, Hui Chen, Jiayi Yuan, Chen Jiang, Yixuan Hao, Yuanqiang Wang, Zhiwei Feng, Xiang-Qun Xie:
IsAb: a computational protocol for antibody design. - Ottavia Spiga, Vittoria Cicaloni, Giovanna Maria Dimitri, Francesco Pettini, Daniela Braconi, Andrea Bernini, Annalisa Santucci:
Machine learning application for patient stratification and phenotype/genotype investigation in a rare disease. - Yansu Wang, Murong Zhou, Quan Zou, Lei Xu:
Machine learning for phytopathology: from the molecular scale towards the network scale. - Lei Wang, Xin Yan, Zhu-Hong You, Xi Zhou, Hao-Yuan Li, Yu-An Huang:
SGANRDA: semi-supervised generative adversarial networks for predicting circRNA-disease associations. - Yinghan Wang, Jinfeng Zeng, Chi Zhang, Cai Chen, Zekai Qiu, Jiali Pang, Yutian Xu, Zhiqi Dong, Yanxin Song, Weiying Liu, Peipei Dong, Litao Sun, Yao-Qing Chen, Yuelong Shu, Xiangjun Du:
New framework for recombination and adaptive evolution analysis with application to the novel coronavirus SARS-CoV-2. - Xiaoqing Ru, Xiucai Ye, Tetsuya Sakurai, Quan Zou:
Application of learning to rank in bioinformatics tasks. - Zhibin Lv, Feifei Cui, Quan Zou, Lichao Zhang, Lei Xu:
Anticancer peptides prediction with deep representation learning features. - Jun Zhang, Qingcai Chen, Bin Liu:
NCBRPred: predicting nucleic acid binding residues in proteins based on multilabel learning. - Panqin Wang, Qingfeng Zhang, Shihua Li, Ben Cheng, Han Xue, Zhen Wei, Tian Shao, Zexian Liu, Han Cheng, Zhenlong Wang:
iCysMod: an integrative database for protein cysteine modifications in eukaryotes. - Hui Peng, Yi Zheng, Zhixun Zhao, Jinyan Li:
Multigene editing: current approaches and beyond. - Lena M. Davidson, Mary Regina Boland:
Towards deep phenotyping pregnancy: a systematic review on artificial intelligence and machine learning methods to improve pregnancy outcomes. - Md Rabiul Auwul, Md. Rezanur Rahman, Esra Gov, Md Shahjaman, Mohammad Ali Moni:
Bioinformatics and machine learning approach identifies potential drug targets and pathways in COVID-19. - Wenming Wu, Zaiyi Liu, Xiaoke Ma:
jSRC: a flexible and accurate joint learning algorithm for clustering of single-cell RNA-sequencing data. - S. M. Hasan Mahmud, Wenyu Chen, Yongsheng Liu, Md. Abdul Awal, Kawsar Ahmed, Md. Habibur Rahman, Mohammad Ali Moni:
PreDTIs: prediction of drug-target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. - Shijie Qin, Weijun Xu, Canbiao Wang, Sizhu Jiang, Wei Dai, Yang Yang, Jiawei Shen, Ping Jin, Fei Ma, Xinyi Xia:
Analyzing master regulators and scRNA-seq of COVID-19 patients reveals an underlying anti-SARS-CoV-2 mechanism of ZNF proteins. - Yuchen Yang, Gang Li, Yifang Xie, Li Wang, Taylor M. Lagler, Yingxi Yang, Jiandong Liu, Li Qian, Yun Li:
iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinement. - Fenglong Yang, Quan Zou:
DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data. - Long-Chen Shen, Yan Liu, Jiangning Song, Dong-Jun Yu:
SAResNet: self-attention residual network for predicting DNA-protein binding. - Stephen Doran, Muhammad Arif, Simon Lam, Abdulahad Bayraktar, Hasan Turkez, Mathias Uhlen, Jan Boren, Adil Mardinoglu:
Multi-omics approaches for revealing the complexity of cardiovascular disease. - Olga Lazareva, Jan Baumbach, Markus List, David B. Blumenthal:
On the limits of active module identification. - Adrien Oliva, Raymond Tobler, Alan Cooper, Bastien Llamas, Yassine Souilmi:
Systematic benchmark of ancient DNA read mapping. - Mengchi Wang, Vu Ngo, Wei Wang:
Deciphering the genetic code of DNA methylation. - Junwei Luo, Yawei Wei, Mengna Lyu, Zhengjiang Wu, Xiaoyan Liu, Huimin Luo, Chaokun Yan:
A comprehensive review of scaffolding methods in genome assembly. - Jianbo Fu, Ying Zhang, Jin Liu, Xichen Lian, Jing Tang, Feng Zhu:
Pharmacometabonomics: data processing and statistical analysis. - Beihong Ji, Xibing He, Jingchen Zhai, Yuzhao Zhang, Viet Hoang Man, Junmei Wang:
Machine learning on ligand-residue interaction profiles to significantly improve binding affinity prediction. - Fenglong Yang, Quan Zou, Bo Gao:
GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed. - Ying Zhang, Yuxin Song, Jin Gao, Hengyu Zhang, Ning Yang, Runqing Yang:
Hierarchical mixed-model expedites genome-wide longitudinal association analysis. - Yangjun Zhang, Xiaoliang Wu, Jingzhen Li, Kui Sun, Heng Li, Libin Yan, Chen Duan, Haoran Liu, Ke Chen, Zhangqun Ye, Mugen Liu, Hua Xu:
Comprehensive characterization of alternative splicing in renal cell carcinoma. - Ping Xuan, Yu Zhang, Hui Cui, Tiangang Zhang, Maozu Guo, Toshiya Nakaguchi:
Integrating multi-scale neighbouring topologies and cross-modal similarities for drug-protein interaction prediction. - Jing Xu, Fuyi Li, André Leier, Dongxu Xiang, Hsin-Hui Shen, Tatiana T. Marquez-Lago, Jian Li, Dong-Jun Yu, Jiangning Song:
Comprehensive assessment of machine learning-based methods for predicting antimicrobial peptides. - Tan-Hoang Nguyen, Xin He, Ruth C. Brown, Bradley Todd Webb, Kenneth S. Kendler, Vladimir I. Vladimirov, Brien P. Riley, Silviu-Alin Bacanu:
DECO: a framework for jointly analyzing de novo and rare case/control variants, and biological pathways. - Alexander Mazein, Adrien Rougny, Jonathan R. Karr, Julio Saez-Rodriguez, Marek Ostaszewski, Reinhard Schneider:
Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling. - Qing Ye, Xin Chai, Dejun Jiang, Liu Yang, Chao Shen, Xujun Zhang, Dan Li, Dong-Sheng Cao, Tingjun Hou:
Identification of active molecules against Mycobacterium tuberculosis through machine learning. - Hailin Hu, Xianggen Liu, An Xiao, Yangyang Li, Chengdong Zhang, Tao Jiang, Dan Zhao, Sen Song, Jianyang Zeng:
Riboexp: an interpretable reinforcement learning framework for ribosome density modeling. - A. K. M. Azad, Salem A. Alyami:
Discovering novel cancer bio-markers in acquired lapatinib resistance using Bayesian methods. - Dan Huang, Xiansong Wang, Yingzhi Liu, Ziheng Huang, Xiaoxu Hu, Wei Hu, Qing Li, Hung Chan, Yidan Zou, Idy H. T. Ho, Yan Wang, Alfred S. L. Cheng, Wei Kang, Ka F. To, Maggie H. T. Wang, Sunny Hei Wong, Jun Yu, Tony Gin, Qingpeng Zhang, Zheng Li, Jianxiong Shen, Lin Zhang, Matthew Tak Vai Chan, Xiaodong Liu, William Ka Kei Wu:
Multi-omic analysis suggests tumor suppressor genes evolved specific promoter features to optimize cancer resistance. - Jim Clauwaert, Gerben Menschaert, Willem Waegeman:
Explainability in transformer models for functional genomics. - Pedro G. Nachtigall, Rhett M. Rautsaw, Schyler A. Ellsworth, Andrew J. Mason, Darin R. Rokyta, Christopher L. Parkinson, Inácio L. M. Junqueira-de-Azevedo:
ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics. - Yongxin Zhao, Zheng Kuang, Ying Wang, Lei Li, Xiaozeng Yang:
MicroRNA annotation in plants: current status and challenges. - Marzia Settino, Mario Cannataro:
MMRFBiolinks: an R-package for integrating and analyzing MMRF-CoMMpass data. - Chiwen Qu, Lupeng Zhang, Jinlong Li, Fang Deng, Yifan Tang, Xiaomin Zeng, Xiaoning Peng:
Improving feature selection performance for classification of gene expression data using Harris Hawks optimizer with variable neighborhood learning. - Xianyi Lian, Xiaodi Yang, Shiping Yang, Ziding Zhang:
Current status and future perspectives of computational studies on human-virus protein-protein interactions. - Yongcui Wang, Yingxi Yang, Shilong Chen, Jiguang Wang:
DeepDRK: a deep learning framework for drug repurposing through kernel-based multi-omics integration. - Ju Xiang, Jiashuai Zhang, Ruiqing Zheng, Xingyi Li, Min Li:
NIDM: network impulsive dynamics on multiplex biological network for disease-gene prediction. - Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, Quan Zou:
Critical downstream analysis steps for single-cell RNA sequencing data. - Menglan Cai, Canh Hao Nguyen, Hiroshi Mamitsuka, Limin Li:
XGSEA: CROSS-species gene set enrichment analysis via domain adaptation. - Jingru Wang, Jin Li, Kun Yue, Li Wang, Yuyun Ma, Qing Li:
NMCMDA: neural multicategory MiRNA-disease association prediction. - Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Sonia Longhi, Kam Y. J. Zhang, Sandeep Bhatia:
Insights into the evolutionary forces that shape the codon usage in the viral genome segments encoding intrinsically disordered protein regions. - Xiang Liu, Huitao Feng, Jie Wu, Kelin Xia:
Persistent spectral hypergraph based machine learning (PSH-ML) for protein-ligand binding affinity prediction. - Zi-Ang Shen, Tao Luo, Yuan-Ke Zhou, Han Yu, Pu-Feng Du:
NPI-GNN: Predicting ncRNA-protein interactions with deep graph neural networks. - Yumeng Yan, Sheng-You Huang:
Accurate prediction of inter-protein residue-residue contacts for homo-oligomeric protein complexes. - Xin Wang, Yang Yang, Jian Liu, Guohua Wang:
The stacking strategy-based hybrid framework for identifying non-coding RNAs. - Yan Liu, Yi-Heng Zhu, Xiaoning Song, Jiangning Song, Dong-Jun Yu:
Why can deep convolutional neural networks improve protein fold recognition? A visual explanation by interpretation. - Yiliang Zhang, Youshu Cheng, Wei Jiang, Yixuan Ye, Qiongshi Lu, Hongyu Zhao:
Comparison of methods for estimating genetic correlation between complex traits using GWAS summary statistics. - Sascha Jung, Kartikeya Singh, Antonio del Sol:
Corrigendum to: FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. - Houcemeddine Turki, Mohamed Ali Hadj Taieb, Mohamed Ben Aouicha:
Developing intuitive and explainable algorithms through inspiration from human physiology and computational biology. - Qinhu Zhang, Siguo Wang, Zhanheng Chen, Ying He, Qi Liu, De-Shuang Huang:
Locating transcription factor binding sites by fully convolutional neural network. - Sijia Wu, Mengyuan Yang, Pora Kim, Xiaobo Zhou:
ADeditome provides the genomic landscape of A-to-I RNA editing in Alzheimer's disease. - Zi-Yi Yang, Zhi-Jiang Yang, Yue Zhao, Ming-Zhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao:
PySmash: Python package and individual executable program for representative substructure generation and application. - Yinyin Wang, Hongbin Yang, Linxiao Chen, Mohieddin Jafari, Jing Tang:
Network-based modeling of herb combinations in traditional Chinese medicine. - Lihong Huang, Bin Hong, Wenxian Yang, Liansheng Wang, Rongshan Yu:
Snipe: highly sensitive pathogen detection from metagenomic sequencing data. - Priya Gupta, Debasisa Mohanty:
SMMPPI: a machine learning-based approach for prediction of modulators of protein-protein interactions and its application for identification of novel inhibitors for RBD: hACE2 interactions in SARS-CoV-2. - Md. Habibur Rahman, Humayan Kabir Rana, Silong Peng, Xiyuan Hu, Chen Chen, Julian M. W. Quinn, Mohammad Ali Moni:
Bioinformatics and machine learning methodologies to identify the effects of central nervous system disorders on glioblastoma progression. - Li Guo, Yongsheng Li, Kara M. Cirillo, Robert A. Marick, Zhe Su, Xing Yin, Xu Hua, Gordon B. Mills, Nidhi Sahni, S. Stephen Yi:
mi-IsoNet: systems-scale microRNA landscape reveals rampant isoform-mediated gain of target interaction diversity and signaling specificity. - Rajesh Pal, Amit Kumar, Gauri Misra:
Exploring TEAD2 as a drug target for therapeutic intervention of cancer: A multi-computational case study. - Hui Hu, Qiong Zhang, Fei-Fei Hu, Chun-Jie Liu, An-Yuan Guo:
A comprehensive survey for human transcription factors on expression, regulation, interaction, phenotype and cancer survival. - Foysal Ahammad, Rahat Alam, Rasel Mahmud, Shahina Akhter, Enamul Kabir Talukder, Al Mahmud Tonmoy, Salman Fahim, Khalid Al-Ghamdi, Abdus Samad, Ishtiaq Qadri:
Pharmacoinformatics and molecular dynamics simulation-based phytochemical screening of neem plant (Azadiractha indica) against human cancer by targeting MCM7 protein. - Kaiyin Zhou, Yuxing Wang, Kevin Bretonnel Cohen, Jin-Dong Kim, Xiaohang Ma, Zhixue Shen, Xiangyu Meng, Jingbo Xia:
Bridging heterogeneous mutation data to enhance disease gene discovery. - Cathal Ormond, Niamh M. Ryan, Aiden P. Corvin, Elizabeth A. Heron:
Converting single nucleotide variants between genome builds: from cautionary tale to solution. - Li Fu, Zi-Yi Yang, Zhi-Jiang Yang, Ming-Zhu Yin, Ai-Ping Lu, Xiang Chen, Shao Liu, Tingjun Hou, Dong-Sheng Cao:
QSAR-assisted-MMPA to expand chemical transformation space for lead optimization. - Hao Li, Junyao Hou, Ziyu Chen, Jingyu Zeng, Yu Ni, Yayu Li, Xia Xiao, Yaqi Zhou, Ning Zhang, Deyu Long, Hongfei Liu, Luyu Yang, Xinyue Bai, Qun Li, Tongtong Li, Dongxue Che, Leijie Li, Xiaodan Wang, Peng Zhang, Mingzhi Liao:
FifBase: a comprehensive fertility-associated indicators factor database for domestic animals. - Shien Huang, Xinyu He, Guohua Wang, Ergude Bao:
AlignGraph2: similar genome-assisted reassembly pipeline for PacBio long reads. - Jesús San Fabián, Salama Omar, José Manuel García de la Vega:
Computational approaches to amino acid side-chain conformation using combined NMR theoretical and experimental results: leucine-67 in Desulfovibrio vulgaris flavodoxin. - Siqi Xu, Wing Kam Fung, Zhonghua Liu:
MRCIP: a robust Mendelian randomization method accounting for correlated and idiosyncratic pleiotropy. - Chunli Zheng, Yue Xiao, Chuang Chen, Jinglin Zhu, Ruijie Yang, Jiangna Yan, Ruifei Huang, Wei Xiao, Yonghua Wang, Chao Huang:
Systems pharmacology: a combination strategy for improving efficacy of PD-1/PD-L1 blockade. - Masood ur Rehman Kayani, Wanqiu Huang, Ru Feng, Lei Chen:
Genome-resolved metagenomics using environmental and clinical samples. - Yushan Qiu, Wai-Ki Ching, Quan Zou:
Prediction of RNA-binding protein and alternative splicing event associations during epithelial-mesenchymal transition based on inductive matrix completion. - Joseph Glessner, Xiurui Hou, Cheng Zhong, Jie Zhang, Munir Khan, Fabian Brand, Peter Krawitz, Patrick Sleiman, Hakon Hakonarson, Zhi Wei:
DeepCNV: a deep learning approach for authenticating copy number variations. - Jing Li, Lichao Zhang, Shida He, Fei Guo, Quan Zou:
SubLocEP: a novel ensemble predictor of subcellular localization of eukaryotic mRNA based on machine learning. - Yuqi Sheng, Ying Jiang, Yang Yang, Xiangmei Li, Jiayue Qiu, Jiashuo Wu, Liang Cheng, Junwei Han:
CNA2Subpathway: identification of dysregulated subpathway driven by copy number alterations in cancer. - Ziyi Chen, Aiping Wu:
Progress and challenge for computational quantification of tissue immune cells. - Heng Du, Chenguang Diao, Pengju Zhao, Lei Zhou, Jianfeng Liu:
Integrated hybrid de novo assembly technologies to obtain high-quality pig genome using short and long reads. - Adam Nunn, Christian Otto, Peter F. Stadler, David Langenberger:
Erratum to: Comprehensive benchmarking of software for mapping whole genome bisulfite data: from read alignment to DNA methylation analysis. - Roberto Del Amparo, Catarina Branco, Jesús Arenas, Alberto Vicens, Miguel Arenas:
Analysis of selection in protein-coding sequences accounting for common biases. - Anqiang Jia, Ling Xu, Yi Wang:
Venn diagrams in bioinformatics. - Olufemi Aromolaran, Damilare Aromolaran, Itunuoluwa Isewon, Jelili Oyelade:
Machine learning approach to gene essentiality prediction: a review. - Yunlong Wang, Yaqi Liu, Qian Xu, Yao Xu, Kai Cao, Nan Deng, Ruimin Wang, Xueying Zhang, Ruiqin Zheng, Guoliang Li, Yaping Fang:
TAD boundary and strength prediction by integrating sequence and epigenetic profile information. - Xuan Liu, Sara J. C. Gosline, Lance T. Pflieger, Pierre Wallet, Archana Iyer, Justin Guinney, Andrea H. Bild, Jeffrey T. Chang:
Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.
Volume 22, Number 6, November 2021
- Zulkar Nain, Shital K. Barman, Md Moinuddin Sheam, Shifath Bin Syed, Abdus Samad, Julian M. W. Quinn, Mohammad Minnatul Karim, Mahbubul Kabir Himel, Rajib Kanti Roy, Mohammad Ali Moni, Sudhangshu Kumar Biswas:
Transcriptomic studies revealed pathophysiological impact of COVID-19 to predominant health conditions. - Bulat Zagidullin, Ziyan Wang, Yuanfang Guan, Esa Pitkänen, Jing Tang:
Comparative analysis of molecular fingerprints in prediction of drug combination effects. - Anson T. Ku, Scott Wilkinson, Adam G. Sowalsky:
Comparison of approaches to transcriptomic analysis in multi-sampled tumors. - Pengfei Pei, Hongbo Qin, Jialin Chen, Fengli Wang, Chengzhi He, Shiting He, Bixia Hong, Ke Liu, Renzhong Qiao, Huahao Fan, Yigang Tong, Long Chen, Shi-Zhong Luo:
Corrigendum to: Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein. - Arnold K. Nyamabo, Hui Yu, Jian-Yu Shi:
SSI-DDI: substructure-substructure interactions for drug-drug interaction prediction. - Wenjiang Zheng, Hui Wu, Ting Wang, Shaofeng Zhan, Xiaohong Liu:
Quercetin for COVID-19 and DENGUE co-infection: a potential therapeutic strategy of targeting critical host signal pathways triggered by SARS-CoV-2 and DENV. - Shaherin Basith, Md. Mehedi Hasan, Gwang Lee, Leyi Wei, Balachandran Manavalan:
Integrative machine learning framework for the identification of cell-specific enhancers from the human genome. - Xuan Liu, Wenbo Chen, Yu Fang, Siqi Yang, Liuping Chang, Xingyu Chen, Haidong Ye, Xinyu Tang, Shan Zhong, Wen Zhang, Zhiqiang Dong, Leng Han, Chunjiang He:
ADEIP: an integrated platform of age-dependent expression and immune profiles across human tissues. - Subhayan Chattopadhyay, Jenny Karlsson, Anders Valind, Natalie Andersson, David Gisselsson:
Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST. - Marios Tomazou, Marilena M. Bourdakou, George Minadakis, Margarita Zachariou, Anastasis Oulas, Evangelos Karatzas, Eleni M. Loizidou, Andrea C. Kakouri, Christiana C. Christodoulou, Kyriaki Savva, Maria Zanti, Anna Onisiforou, Sotiroula Afxenti, Jan Richter, Christina G. Christodoulou, Theodoros C. Kyprianou, George Kolios, Nikolas Dietis, George M. Spyrou:
Multi-omics data integration and network-based analysis drives a multiplex drug repurposing approach to a shortlist of candidate drugs against COVID-19. - Zhiqiang Yan, Jianting An, Yong Peng, Siming Kong, Qiang Liu, Ming Yang, Qilong He, Shi Song, Yidong Chen, Wei Chen, Rong Li, Jie Qiao, Liying Yan:
DevOmics: an integrated multi-omics database of human and mouse early embryo. - Fei Qin, Xizhi Luo, Guoshuai Cai, Feifei Xiao:
Shall genomic correlation structure be considered in copy number variants detection? - Florian Borchert, Andreas Mock, Aurelie Tomczak, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna-Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P. Schapranow:
Knowledge bases and software support for variant interpretation in precision oncology. - Jingzhe Lu, Xu Wang, Keyong Sun, Xun Lan:
Chrom-Lasso: a lasso regression-based model to detect functional interactions using Hi-C data. - Janak Sunuwar, Rajeev K. Azad:
A machine learning framework to predict antibiotic resistance traits and yet unknown genes underlying resistance to specific antibiotics in bacterial strains. - Nabil Ibtehaz, Ishtiaque Ahmed, Md. Sabbir Ahmed, M. Sohel Rahman, Rajeev K. Azad, Md. Shamsuzzoha Bayzid:
SSG-LUGIA: Single Sequence based Genome Level Unsupervised Genomic Island Prediction Algorithm. - Chunmei Cui, Yuan Zhou, Qinghua Cui:
Defining the functional divergence of orthologous genes between human and mouse in the context of miRNA regulation. - Furong Tang, Lichao Zhang, Lei Xu, Quan Zou, Hailin Feng:
The accurate prediction and characterization of cancerlectin by a combined machine learning and GO analysis. - Bosheng Song, Fen Li, Yuansheng Liu, Xiangxiang Zeng:
Deep learning methods for biomedical named entity recognition: a survey and qualitative comparison. - Philip Davies, Matt Jones, Juntai Liu, Daniel Hebenstreit:
Anti-bias training for (sc)RNA-seq: experimental and computational approaches to improve precision. - Carlos A. Ortiz-Mahecha, William A. Agudelo, Manuel A. Patarroyo, Manuel-Elkin Patarroyo, Carlos F. Suárez:
MHCBI: a pipeline for calculating peptide-MHC binding energy using semi-empirical quantum mechanical methods with explicit/implicit solvent models. - Junjie Wee, Kelin Xia:
Forman persistent Ricci curvature (FPRC)-based machine learning models for protein-ligand binding affinity prediction. - Limin Jiang, Hui Yu, Jiawei Li, Jijun Tang, Yan Guo, Fei Guo:
Predicting MHC class I binder: existing approaches and a novel recurrent neural network solution. - Yuxuan Pang, Lantian Yao, Jhih-Hua Jhong, Zhuo Wang, Tzong-Yi Lee:
AVPIden: a new scheme for identification and functional prediction of antiviral peptides based on machine learning approaches. - Shuquan Rao, Ancha V. Baranova, Hongbao Cao, Jiu Chen, Xiangrong Zhang, Fuquan Zhang:
Corrigendum to: Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption. - Betül Güvenç Paltun, Samuel Kaski, Hiroshi Mamitsuka:
Machine learning approaches for drug combination therapies. - Margo VanOeffelen, Marcus Nguyen, Derya Aytan-Aktug, Thomas S. Brettin, Emily M. Dietrich, Ronald W. Kenyon, Dustin Machi, Chunhong Mao, Robert Olson, Gordon D. Pusch, Maulik Shukla, Rick Stevens, Veronika Vonstein, Andrew S. Warren, Alice R. Wattam, Hyun Seung Yoo, James J. Davis:
A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes. - Qiujie Lv, Guanxing Chen, Lu Zhao, Weihe Zhong, Calvin Yu-Chian Chen:
Mol2Context-vec: learning molecular representation from context awareness for drug discovery. - Ying Zhang, Yan Liu, Jian Xu, Xiaoyu Wang, Xinxin Peng, Jiangning Song, Dong-Jun Yu:
Leveraging the attention mechanism to improve the identification of DNA N6-methyladenine sites. - Shuo Shi, Qiheng Qian, Shuhuan Yu, Qi Wang, Jinyue Wang, Jingyao Zeng, Zhenglin Du, Jing-Fa Xiao:
RefRGim: an intelligent reference panel reconstruction method for genotype imputation with convolutional neural networks. - Maria Bernard, Olivier Rué, Mahendra Mariadassou, Géraldine Pascal:
FROGS: a powerful tool to analyse the diversity of fungi with special management of internal transcribed spacers. - Shuquan Rao, Ancha V. Baranova, Hongbao Cao, Jiu Chen, Xiangrong Zhang, Fuquan Zhang:
Genetic mechanisms of COVID-19 and its association with smoking and alcohol consumption. - Chun-Chun Wang, Chendi Han, Qi Zhao, Xing Chen:
Circular RNAs and complex diseases: from experimental results to computational models. - Pengyong Li, Jun Wang, Yixuan Qiao, Hao Chen, Yihuan Yu, Xiaojun Yao, Peng Gao, Guotong Xie, Sen Song:
An effective self-supervised framework for learning expressive molecular global representations to drug discovery. - Patrick Brendan Timmons, Chandralal M. Hewage:
APPTEST is a novel protocol for the automatic prediction of peptide tertiary structures. - Kewalin Samart, Phoebe Tuyishime, Arjun Krishnan, Janani Ravi:
Reconciling multiple connectivity scores for drug repurposing. - Aman Chandra Kaushik, Qiqi Wu, Li Lin, Haibo Li, Longqi Zhao, Zilu Wen, Yanzheng Song, Qihang Wu, Jin Wang, Xiaokui Guo, Hualin Wang, Xiaoli Yu, Dongqing Wei, Shulin Zhang:
Exosomal ncRNAs profiling of mycobacterial infection identified miRNA-185-5p as a novel biomarker for tuberculosis. - Chenxing Zhang, Lin Gao, Bingbo Wang, Yong Gao:
Improving Single-Cell RNA-seq Clustering by Integrating Pathways. - Yanqiang Han, Zhilong Wang, Zhiyun Wei, Jinyun Liu, Jinjin Li:
Machine learning builds full-QM precision protein force fields in seconds. - Hongjian Li, Gang Lu, Kam-Heung Sze, Xianwei Su, Wai-Yee Chan, Kwong-Sak Leung:
Machine-learning scoring functions trained on complexes dissimilar to the test set already outperform classical counterparts on a blind benchmark. - Wei Zhang, Qiaozhen Meng, Jijun Tang, Fei Guo:
Exploring effectiveness of ab-initio protein-protein docking methods on a novel antibacterial protein complex dataset. - Haochen Zhao, Kai Zheng, Yaohang Li, Jianxin Wang:
A novel graph attention model for predicting frequencies of drug-side effects from multi-view data. - Seyoon Ko, Ginny X. Li, Hyungwon Choi, Joong-Ho Won:
Computationally scalable regression modeling for ultrahigh-dimensional omics data with ParProx. - Jiaqi Li, Lei Wei, Xianglin Zhang, Wei Zhang, Haochen Wang, Bixi Zhong, Zhen Xie, Hairong Lv, Xiaowo Wang:
DISMIR: Deep learning-based noninvasive cancer detection by integrating DNA sequence and methylation information of individual cell-free DNA reads. - Raghvendra Mall, Mohamad Saad, Jessica Roelands, Darawan Rinchai, Khalid Kunji, Hossam Almeer, Wouter Hendrickx, Francesco M. Marincola, Michele Ceccarelli, Davide Bedognetti:
Network-based identification of key master regulators associated with an immune-silent cancer phenotype. - Ye Wang, Yuchao Jiang, Bing Yao, Kun Huang, Yunlong Liu, Yue Wang, Xiao Qin, Andrew J. Saykin, Li Chen:
WEVar: a novel statistical learning framework for predicting noncoding regulatory variants. - Sagnik Sen, Ashmita Dey, Sanghamitra Bandhyopadhyay, Vladimir N. Uversky, Ujjwal Maulik:
Understanding structural malleability of the SARS-CoV-2 proteins and relation to the comorbidities. - Md. Rezanur Rahman, Tania Islam, Md Shahjaman, Md. Rafiqul Islam, Salvo Danilo Lombardo, Placido Bramanti, Rosella Ciurleo, Alessia Bramanti, Andrey Tchorbanov, Francesco Fisicaro, Paolo Fagone, Ferdinando Nicoletti, Manuela Pennisi:
Discovering common pathogenetic processes between COVID-19 and diabetes mellitus by differential gene expression pattern analysis. - Jakub M. Bartoszewicz, Ulrich Genske, Bernhard Y. Renard:
Deep learning-based real-time detection of novel pathogens during sequencing. - Yu Zhang, Yichao Cai, Xavier Roca, Chee Keong Kwoh, Melissa Jane Fullwood:
Chromatin loop anchors predict transcript and exon usage. - Qi An, Liang Yu:
A heterogeneous network embedding framework for predicting similarity-based drug-target interactions. - Nikhita Gogate, Daniel Lyman, Amanda Bell, Edmund Cauley, Keith A. Crandall, Ashia Joseph, Robel Y. Kahsay, Darren A. Natale, Lynn M. Schriml, Sabyasach Sen, Raja Mazumder:
COVID-19 biomarkers and their overlap with comorbidities in a disease biomarker data model. - Jiahua He, Sheng-You Huang:
EMNUSS: a deep learning framework for secondary structure annotation in cryo-EM maps. - Bethan Yates, Kristian A. Gray, Tamsin E. M. Jones, Elspeth A. Bruford:
Updates to HCOP: the HGNC comparison of orthology predictions tool. - Cheng-Peng Gui, Jin-Huan Wei, Yu-Hang Chen, Liang-Min Fu, Yi-Ming Tang, Jia-Zheng Cao, Wei Chen, Jun-Hang Luo:
A new thinking: extended application of genomic selection to screen multiomics data for development of novel hypoxia-immune biomarkers and target therapy of clear cell renal cell carcinoma. - Ai Ni, Li-Xuan Qin:
Performance evaluation of transcriptomics data normalization for survival risk prediction. - Haluk Dogan, Zeynep Hakguder, Roland Madadjim, Stephen Scott, Massimiliano Pierobon, Juan Cui:
Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning. - Ali F. Alsulami, Pedro H. M. Torres, Ismail Moghul, Sheikh Mohammed Arif, Amanda K. Chaplin, Sundeep Chaitanya Vedithi, Tom L. Blundell:
COSMIC Cancer Gene Census 3D database: understanding the impacts of mutations on cancer targets. - Yin Jin, Zheng Wang, An-Yu Dong, Yuan-Qin Huang, Ge-Fei Hao, Bao-An Song:
Web repositories of natural agents promote pests and pathogenic microbes management. - Peilin Jia, Astrid Marilyn Manuel, Brisa S. Fernandes, Yulin Dai, Zhongming Zhao:
Distinct effect of prenatal and postnatal brain expression across 20 brain disorders and anthropometric social traits: a systematic study of spatiotemporal modularity. - Zhao-Yu Fang, Cui-Xiang Lin, Yun-Pei Xu, Hong-Dong Li, Qing-Song Xu:
REBET: a method to determine the number of cell clusters based on batch effect removal. - Jing Xing, Shreya Paithankar, Ke Liu, Katie Uhl, Xiaopeng Li, Meehyun Ko, Seungtaek Kim, Jeremy Haskins, Bin Chen:
Published anti-SARS-CoV-2 in vitro hits share common mechanisms of action that synergize with antivirals. - Ruiqi Lyu, Jianle Sun, Dong Xu, Qianxue Jiang, Chaochun Wei, Yue Zhang:
GESLM algorithm for detecting causal SNPs in GWAS with multiple phenotypes. - Jie Sheng, Wei Vivian Li:
Selecting gene features for unsupervised analysis of single-cell gene expression data. - Eloise Withnell, Xiaoyu Zhang, Kai Sun, Yike Guo:
XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data. - Chen Lyu, Manyan Huang, Nianjun Liu, Zhongxue Chen, Philip J. Lupo, Benjamin Tycko, John S. Witte, Charlotte A. Hobbs, Ming Li:
Detecting methylation quantitative trait loci using a methylation random field method. - Trinh-Trung-Duong Nguyen, Duc-Khanh Nguyen, Yu-Yen Ou:
Addressing data imbalance problems in ligand-binding site prediction using a variational autoencoder and a convolutional neural network. - Pedro H. M. Torres, Artur D. Rossi, Tom L. Blundell:
ProtCHOIR: a tool for proteome-scale generation of homo-oligomers. - Md Asif Nashiry, Shauli Sarmin Sumi, Mohammad Umer Sharif Shohan, Salem A. Alyami, A. K. M. Azad, Mohammad Ali Moni:
Bioinformatics and system biology approaches to identify the diseasome and comorbidities complexities of SARS-CoV-2 infection with the digestive tract disorders. - Jiajun Yang, Dongyang Wang, Yanbo Yang, Wenqian Yang, Weiwei Jin, Xiaohui Niu, Jing Gong:
A systematic comparison of normalization methods for eQTL analysis. - Jian Chen, Xiaojun Qian, Yifu He, Xinghua Han, Yueyin Pan:
An artificial neural network model based on DNA damage response genes to predict outcomes of lower-grade glioma patients. - Qian Gao, Yu Zhang, Jie Liang, Hongwei Sun, Tong Wang:
High-dimensional generalized propensity score with application to omics data. - Yu Cheng, Yongshun Gong, Yuansheng Liu, Bosheng Song, Quan Zou:
Molecular design in drug discovery: a comprehensive review of deep generative models. - Matee Ullah, Ke Han, Fazal Hadi, Jian Xu, Jiangning Song, Dong-Jun Yu:
PScL-HDeep: image-based prediction of protein subcellular location in human tissue using ensemble learning of handcrafted and deep learned features with two-layer feature selection. - Zhengfeng Wang, Xiujuan Lei:
Prediction of RBP binding sites on circRNAs using an LSTM-based deep sequence learning architecture. - Zhi-Kai Yang, Lingyu Pan, Yanming Zhang, Hao Luo, Feng Gao:
Data-driven identification of SARS-CoV-2 subpopulations using PhenoGraph and binary-coded genomic data. - Anna Onisiforou, George M. Spyrou:
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. - Lin Li, Canping Chen, Xiaosheng Wang:
DITHER: an algorithm for Defining IntraTumor Heterogeneity based on EntRopy. - Yixuan Huang, Peng Zhang:
Corrigendum to: Evaluation of machine learning approaches for cell-type identification from single-cell transcriptomics data. - Satyajit Mahapatra, Sitanshu Sekhar Sahu:
Improved prediction of protein-protein interaction using a hybrid of functional-link Siamese neural network and gradient boosting machines. - Xuan Xiao, Yu-Tao Shao, Xiang Cheng, Biljana Stamatovic:
iAMP-CA2L: a new CNN-BiLSTM-SVM classifier based on cellular automata image for identifying antimicrobial peptides and their functional types. - Yaxuan Cui, Shaoqiang Zhang, Ying Liang, Xiangyun Wang, Thomas N. Ferraro, Yong Chen:
Consensus clustering of single-cell RNA-seq data by enhancing network affinity. - Khandakar Tanvir Ahmed, Jiao Sun, William Chen, Irene Martinez, Sze Cheng, Wencai Zhang, Jeongsik Yong, Wei Zhang:
In silico model for miRNA-mediated regulatory network in cancer. - Xingjian Chen, Lingjing Liu, Weitong Zhang, Jianyi Yang, Ka-Chun Wong:
Human host status inference from temporal microbiome changes via recurrent neural networks. - Yan Liu, Ke Han, Yi-Heng Zhu, Ying Zhang, Long-Chen Shen, Jiangning Song, Dong-Jun Yu:
Improving protein fold recognition using triplet network and ensemble deep learning. - Margaret Staton, Ethalinda Cannon, Lacey-Anne Sanderson, Jill L. Wegrzyn, Tavis K. Anderson, Sean Buehler, Irene Cobo-Simón, Kay Faaberg, Emily S. Grau, Valentin Guignon, Jessica Gunoskey, Blake Inderski, Sook Jung, Kelly Lager, Dorrie Main, Monica Poelchau, Risharde Ramnath, Peter Richter, Joe West, Stephen P. Ficklin:
Tripal, a community update after 10 years of supporting open source, standards-based genetic, genomic and breeding databases. - Md. Mehedi Hasan, Md. Ashad Alam, Watshara Shoombuatong, Hong-Wen Deng, Balachandran Manavalan, Hiroyuki Kurata:
NeuroPred-FRL: an interpretable prediction model for identifying neuropeptide using feature representation learning. - Brian B. Nadel, Meritxell Oliva, Benjamin L. Shou, Keith Mitchell, Feiyang Ma, Dennis J. Montoya, Alice Mouton, Sarah Kim-Hellmuth, Barbara E. Stranger, Matteo Pellegrini, Serghei Mangul:
Systematic evaluation of transcriptomics-based deconvolution methods and references using thousands of clinical samples. - Shiwei Wang, Qi Sun, Youjun Xu, Jianfeng Pei, Luhua Lai:
A transferable deep learning approach to fast screen potential antiviral drugs against SARS-CoV-2. - Bingxing An, Mang Liang, Tianpeng Chang, Xinghai Duan, Lili Du, Lingyang Xu, Lupei Zhang, Xue Gao, Junya Li, Huijiang Gao:
KCRR: a nonlinear machine learning with a modified genomic similarity matrix improved the genomic prediction efficiency. - Linhui Xie, Bing He, Pradeep Varathan, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Paul Salama, Jingwen Yan:
Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease. - Gerald van Eeden, Caitlin Uren, Gian van der Spuy, Gerard Tromp, Marlo Möller:
Local ancestry inference in heterogeneous populations - Are recent recombination events more relevant? - Yichen Guo, Ke Yan, Hongwu Lv, Bin Liu:
PreTP-EL: prediction of therapeutic peptides based on ensemble learning. - Yan Liu, Yuzhao Gao, Ruiling Fang, Hongyan Cao, Jian Sa, Jianrong Wang, Hongqi Liu, Tong Wang, Yuehua Cui:
Identifying complex gene-gene interactions: a mixed kernel omnibus testing approach. - Aditya K. Padhi, Ashutosh Kumar, Ken-ichi Haruna, Haruna Sato, Hiroko Tamura, Satoru Nagatoishi, Kouhei Tsumoto, Atushi Yamaguchi, Fumie Iraha, Mihoko Takahashi, Kensaku Sakamoto, Kam Y. J. Zhang:
An integrated computational pipeline for designing high-affinity nanobodies with expanded genetic codes. - Yumei Li, Qing Sunny Shen, Qi Peng, Wanqiu Ding, Jie Zhang, Xiaoming Zhong, Ni A. An, Mingjun Ji, Wei-Zhen Zhou, Chuan-Yun Li:
Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure. - Ettore Mosca, Matteo Bersanelli, Tommaso Matteuzzi, Noemi Di Nanni, Gastone C. Castellani, Luciano Milanesi, Daniel Remondini:
Characterization and comparison of gene-centered human interactomes. - Etienne Boileau, Janine Altmüller, Isabel S. Naarmann-de Vries, Christoph Dieterich:
A comparison of metabolic labeling and statistical methods to infer genome-wide dynamics of RNA turnover. - Xin Chen, Wei Gao, Jie Li, Dongfang You, Zhaolei Yu, Mingzhi Zhang, Fang Shao, Yongyue Wei, Ruyang Zhang, Theis Lange, Qianghu Wang, Feng Chen, Xiang Lu, Yang Zhao:
A predictive paradigm for COVID-19 prognosis based on the longitudinal measure of biomarkers. - Patrick Brendan Timmons, Chandralal M. Hewage:
ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides. - Serena Dotolo, Anna Marabotti, Anna Maria Rachiglio, Riziero Esposito Abate, Marco Benedetto, Fortunato Ciardiello, Antonella De Luca, Nicola Normanno, Angelo M. Facchiano, Roberto Tagliaferri:
A multiple network-based bioinformatics pipeline for the study of molecular mechanisms in oncological diseases for personalized medicine. - Wenlong Jia, Chang Xu, Shuai Cheng Li:
Resolving complex structures at oncovirus integration loci with conjugate graph. - Kath Nicholls, Chris Wallace:
Comparison of sparse biclustering algorithms for gene expression datasets. - Qi Wang, Zhaoqian Liu, Bo Yan, Wen-Chi Chou, Laurence Ettwiller, Qin Ma, Bingqiang Liu:
A novel computational framework for genome-scale alternative transcription units prediction. - Shahid Iqbal, Fuyi Li, Tatsuya Akutsu, David B. Ascher, Geoffrey I. Webb, Jiangning Song:
Assessing the performance of computational predictors for estimating protein stability changes upon missense mutations. - Ting Yu, Renmin Han, Zhaoyuan Fang, Zengchao Mu, Hongyu Zheng, Juntao Liu:
TransRef enables accurate transcriptome assembly by redefining accurate neo-splicing graphs. - Haocheng Ding, Lingsong Meng, Andrew C. Liu, Michelle L. Gumz, Andrew J. Bryant, Colleen A. Mcclung, George C. Tseng, Karyn A. Esser, Zhiguang Huo:
Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications. - Thomas Haschka, Jean Baptiste Morlot, Leopold Carron, Julien Mozziconacci:
Improving distance measures between genomic tracks with mutual proximity. - Shuhui Liu, Yupei Zhang, Xuequn Shang, Zhaolei Zhang:
ProTICS reveals prognostic impact of tumor infiltrating immune cells in different molecular subtypes. - Deborah F. Nacer, Helena Liljedahl, Anna Karlsson, David Lindgren, Johan Staaf:
Pan-cancer application of a lung-adenocarcinoma-derived gene-expression-based prognostic predictor. - Danielle Maeser, Robert F. Gruener, Rong Stephanie Huang:
oncoPredict: an R package for predicting in vivo or cancer patient drug response and biomarkers from cell line screening data. - R. Prabakaran, Puneet Rawat, Sandeep Kumar, M. Michael Gromiha:
Evaluation of in silico tools for the prediction of protein and peptide aggregation on diverse datasets. - Tyrone Chen, Melcy Philip, Kim-Anh Lê Cao, Sonika Tyagi:
A multi-modal data harmonisation approach for discovery of COVID-19 drug targets. - Angelo Fortunato, Diego Mallo, Shawn M. Rupp, Lorraine M. King, Timothy Hardman, Joseph Y. Lo, Allison H. Hall, Jeffrey R. Marks, Eun-Sil Shelley Hwang, Carlo C. Maley:
A new method to accurately identify single nucleotide variants using small FFPE breast samples. - Congting Ye, Danhui Zhao, Wenbin Ye, Xiaohui Wu, Guoli Ji, Qingshun Quinn Li, Juncheng Lin:
QuantifyPoly(A): reshaping alternative polyadenylation landscapes of eukaryotes with weighted density peak clustering. - Yong-Zi Chen, Zhuo-Zhi Wang, Yanan Wang, Guoguang Ying, Zhen Chen, Jiangning Song:
nhKcr: a new bioinformatics tool for predicting crotonylation sites on human nonhistone proteins based on deep learning. - Lu Liu, Xikang Feng, Haimei Li, Shuai Cheng Li, Qiujin Qian, Yufeng Wang:
Deep learning model reveals potential risk genes for ADHD, especially Ephrin receptor gene EPHA5. - Liye He, Daria Bulanova, Jaana Oikkonen, Antti Häkkinen, Kaiyang Zhang, Shuyu Zheng, Wenyu Wang, Erdogan Pekcan Erkan, Olli Carpén, Titta Joutsiniemi, Sakari Hietanen, Johanna Hynninen, Kaisa Huhtinen, Sampsa Hautaniemi, Anna Vähärautio, Jing Tang, Krister Wennerberg, Tero Aittokallio:
Network-guided identification of cancer-selective combinatorial therapies in ovarian cancer. - Yuzhao Zhang, Xibing He, Jingchen Zhai, Beihong Ji, Viet Hoang Man, Junmei Wang:
In silico binding profile characterization of SARS-CoV-2 spike protein and its mutants bound to human ACE2 receptor. - Vishakha Gautam, Aayushi Mittal, Siddhant Kalra, Sanjay Kumar Mohanty, Krishan Gupta, Komal Rani, Srivatsava Naidu, Tripti Mishra, Debarka Sengupta, Gaurav Ahuja:
EcTracker: Tracking and elucidating ectopic expression leveraging large-scale scRNA-seq studies. - Yan Huang, Pingping Wang, Wenyang Zhou, Meng Luo, Zhaochun Xu, Rui Cheng, Chang Xu, Xiyun Jin, Yiqun Li, Qinghua Jiang:
Comprehensive analysis of partial methylation domains in colorectal cancer based on single-cell methylation profiles. - Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Yuedong Yang:
scAdapt: virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species. - Fuyi Li, Xudong Guo, Peipei Jin, Jinxiang Chen, Dongxu Xiang, Jiangning Song, Lachlan J. M. Coin:
Porpoise: a new approach for accurate prediction of RNA pseudouridine sites. - Thomas Gaudelet, Ben Day, Arian R. Jamasb, Jyothish Soman, Cristian Regep, Gertrude Liu, Jeremy B. R. Hayter, Richard Vickers, Charles Roberts, Jian Tang, David Roblin, Tom L. Blundell, Michael M. Bronstein, Jake P. Taylor-King:
Utilizing graph machine learning within drug discovery and development. - Yue Zhao, Xiang-Gui Wang, Zhong-Ye Ma, Guo-Li Xiong, Zhi-Jiang Yang, Yan Cheng, Ai-Ping Lu, Zhi-Jun Huang, Dong-Sheng Cao:
Systematic comparison of ligand-based and structure-based virtual screening methods on poly (ADP-ribose) polymerase-1 inhibitors. - Jing-Yi Li, Shen Jin, Xin-Ming Tu, Yang Ding, Ge Gao:
Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network. - Hideki Yamaguchi, Yutaka Saito:
Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins. - Mauro de Medeiros Oliveira, Ígor Bonadio, Alicia Lie de Melo, Glaucia Mendes Souza, Alan Mitchell Durham:
TSSFinder - fast and accurate ab initio prediction of the core promoter in eukaryotic genomes. - Dalwinder Singh, Akansha Madhawan, Joy Roy:
Identification of multiple RNAs using feature fusion. - Leiv Rønneberg, Andrea Cremaschi, Robert Hanes, Jorrit M. Enserink, Manuela Zucknick:
bayesynergy: flexible Bayesian modelling of synergistic interaction effects in in vitro drug combination experiments. - Wei Wang, Wei Liu:
PCLasso: a protein complex-based, group lasso-Cox model for accurate prognosis and risk protein complex discovery. - Kexin Chen, Haoming Xu, Yiming Lei, Pietro Lió, Yuan Li, Hongyan Guo, Mohammad Ali Moni:
Integration and interplay of machine learning and bioinformatics approach to identify genetic interaction related to ovarian cancer chemoresistance. - Forrest C. Koch, Gavin J. Sutton, Irina Voineagu, Fatemeh Vafaee:
Supervised application of internal validation measures to benchmark dimensionality reduction methods in scRNA-seq data. - Yang Yang, Timothy M. Walker, Samaneh Kouchaki, Chenyang Wang, Timothy E. A Peto, Derrick W. Crook, David A. Clifton:
An end-to-end heterogeneous graph attention network for Mycobacterium tuberculosis drug-resistance prediction. - Jian Zhang, Sina Ghadermarzi, Akila Katuwawala, Lukasz A. Kurgan:
DNAgenie: accurate prediction of DNA-type-specific binding residues in protein sequences. - Hongchao Liu, Huihui Yin, Guangyu Li, Junling Li, Xiaoyue Wang:
Aperture: alignment-free detection of structural variations and viral integrations in circulating tumor DNA. - Funmilayo L. Makinde, Milaine S. S. Tchamga, James Jafali, Segun A. Fatumo, Emile R. Chimusa, Nicola J. Mulder, Gaston K. Mazandu:
Reviewing and assessing existing meta-analysis models and tools. - Yushan Qiu, Wai-Ki Ching, Quan Zou:
Matrix factorization-based data fusion for the prediction of RNA-binding proteins and alternative splicing event associations during epithelial-mesenchymal transition. - Hossein Sharifi-Noghabi, Soheil Jahangiri-Tazehkand, Petr Smirnov, Casey Hon, Anthony Mammoliti, Sisira Kadambat Nair, Arvind Singh Mer, Martin Ester, Benjamin Haibe-Kains:
Drug sensitivity prediction from cell line-based pharmacogenomics data: guidelines for developing machine learning models. - Shokouh Rezaei, Yahya Sefidbakht, Vuk Uskokovic:
Tracking the pipeline: immunoinformatics and the COVID-19 vaccine design. - Meng Zou, Zhana Duren, Qiuyue Yuan, Henry Li, Andrew Paul Hutchins, Wing Hung Wong, Yong Wang:
MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting. - Bonil Koo, Je-Keun Rhee:
Prediction of tumor purity from gene expression data using machine learning. - Florian Borchert, Andreas Mock, Aurelie Tomczak, Jonas Hügel, Samer Alkarkoukly, Alexander Knurr, Anna-Lena Volckmar, Albrecht Stenzinger, Peter Schirmacher, Jürgen Debus, Dirk Jäger, Thomas Longerich, Stefan Fröhling, Roland Eils, Nina Bougatf, Ulrich Sax, Matthieu-P. Schapranow:
Knowledge bases and software support for variant interpretation in precision oncology. - Yongzhuang Liu, Xiaoliang Wu, Yadong Wang:
An integrated approach for copy number variation discovery in parent-offspring trios. - Pengfei Pei, Hongbo Qin, Jialin Chen, Fengli Wang, Chengzhi He, Shiting He, Bixia Hong, Ke Liu, Renzhong Qiao, Huahao Fan, Yigang Tong, Long Chen, Shi-Zhong Luo:
Computational design of ultrashort peptide inhibitors of the receptor-binding domain of the SARS-CoV-2 S protein. - Luyao Qin, Xiao Ding, Yongjie Li, Qingfeng Chen, Jing Meng, Taijiao Jiang:
Co-mutation modules capture the evolution and transmission patterns of SARS-CoV-2. - Amarinder Singh Thind, Isha Monga, Prasoon Kumar Thakur, Pallawi Kumari, Kiran Dindhoria, Monika Krzak, Marie Ranson, Bruce Ashford:
Demystifying emerging bulk RNA-Seq applications: the application and utility of bioinformatic methodology. - Xiaoqi Wang, Bin Xin, Weihong Tan, Zhijian Xu, Kenli Li, Fei Li, Wu Zhong, Shaoliang Peng:
DeepR2cov: deep representation learning on heterogeneous drug networks to discover anti-inflammatory agents for COVID-19. - Qiu Xiao, Yu Fu, Yide Yang, Jianhua Dai, Jiawei Luo:
NSL2CD: identifying potential circRNA-disease associations based on network embedding and subspace learning. - Xiao Cao, Wenjia He, Zitan Chen, Yifan Li, Kexin Wang, Hongbo Zhang, Lesong Wei, Lizhen Cui, Ran Su, Leyi Wei:
PSSP-MVIRT: peptide secondary structure prediction based on a multi-view deep learning architecture. - Limin Jiang, Yan Guo, Hui Yu, Kendal Hoff, Xun Ding, Wei Zhou, Jeremy Edwards:
Detecting SARS-CoV-2 and its variant strains with a full genome tiling array. - Xi Tang, Tao Zhang, Na Cheng, Huadong Wang, Chun-Hou Zheng, Junfeng Xia, Tiejun Zhang:
Erratum: usDSM: a novel method for deleterious synonymous mutation prediction using undersampling scheme. - Bingbo Wang, Xianan Dong, Jie Hu, Xiujuan Ma, Chao Han, Yajun Wang, Lin Gao:
The peripheral and core regions of virus-host network of COVID-19. - Fan Hu, Lei Wang, Yishen Hu, Dongqi Wang, Weijie Wang, Jianbing Jiang, Nan Li, Peng Yin:
A novel framework integrating AI model and enzymological experiments promotes identification of SARS-CoV-2 3CL protease inhibitors and activity-based probe. - Mingming Jiang, Bowen Zhao, Shenggan Luo, Qiankun Wang, Yanyi Chu, Tianhang Chen, Xueying Mao, Yatong Liu, Yanjing Wang, Xue Jiang, Dong-Qing Wei, Yi Xiong:
NeuroPpred-Fuse: an interpretable stacking model for prediction of neuropeptides by fusing sequence information and feature selection methods. - Ronald Yurko, Kathryn Roeder, Bernie Devlin, Max G'Sell:
An approach to gene-based testing accounting for dependence of tests among nearby genes. - Gunnar Völkel, Simon Laban, Axel Fürstberger, Silke D. Kühlwein, Nensi Ikonomi, Thomas K. Hoffmann, Cornelia Brunner, Donna S. Neuberg, Verena Gaidzik, Hartmut Döhner, Johann M. Kraus, Hans A. Kestler:
Erratum to: Analysis, identification and visualization of subgroups in genomics. - Hansi Zheng, Amlan Talukder, Xiaoman Li, Haiyan Hu:
A systematic evaluation of the computational tools for lncRNA identification. - Alok Sharma, Artem Lysenko, Keith A. Boroevich, Edwin Vans, Tatsuhiko Tsunoda:
DeepFeature: feature selection in nonimage data using convolutional neural network. - Fengqing Lu, Mufei Li, Xiaoping Min, Chunyan Li, Xiangxiang Zeng:
De novo generation of dual-target ligands using adversarial training and reinforcement learning. - Jiaxing Chen, Chinwang Cheong, Liang Lan, Xin Zhou, Jiming Liu, Aiping Lyu, William K. Cheung, Lu Zhang:
DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data. - Pengfei Liang, Lei Zheng, Chunshen Long, Wuritu Yang, Lei Yang, Yongchun Zuo:
HelPredictor models single-cell transcriptome to predict human embryo lineage allocation. - Yile Huang, Yulong Qiao, Yu Zhao, Yuying Li, Jie Yuan, Jiajian Zhou, Hao Sun, Huating Wang:
Large scale RNA-binding proteins/LncRNAs interaction analysis to uncover lncRNA nuclear localization mechanisms. - Valentina Galata, Susheel Bhanu Busi, Benoît Josef Kunath, Laura de Nies, Magdalena Calusinska, Rashi Halder, Patrick May, Paul Wilmes, Cedric Christian Laczny:
Functional meta-omics provide critical insights into long- and short-read assemblies. - Zilong Hou, Yuning Yang, Hui Li, Ka-Chun Wong, Xiangtao Li:
iDeepSubMito: identification of protein submitochondrial localization with deep learning. - Yunda Si, Chengfei Yan:
Improved protein contact prediction using dimensional hybrid residual networks and singularity enhanced loss function. - Zhaochun Xu, Meng Luo, Weizhong Lin, Guangfu Xue, Pingping Wang, Xiyun Jin, Chang Xu, Wenyang Zhou, Yideng Cai, Wenyi Yang, Huan Nie, Qinghua Jiang:
DLpTCR: an ensemble deep learning framework for predicting immunogenic peptide recognized by T cell receptor. - Jing Qin, Yaohua Hu, Jen-Chih Yao, Ricky Wai Tak Leung, Yongqiang Zhou, Yiming Qin, Junwen Wang:
Cell fate conversion prediction by group sparse optimization method utilizing single-cell and bulk OMICs data. - E. Sacristán-Horcajada, S. González-de la Fuente, Ramón Peiró-Pastor, Fernando Carrasco-Ramiro, R. Amils, J. M. Requena, J. Berenguer, B. Aguado:
ARAMIS: From systematic errors of NGS long reads to accurate assemblies. - Xiyun Jin, Wenyang Zhou, Meng Luo, Pingping Wang, Zhaochun Xu, Kexin Ma, Huimin Cao, Chang Xu, Yan Huang, Rui Cheng, Lixing Xiao, Xiaoyu Lin, Fenglan Pang, Yiqun Li, Huan Nie, Qinghua Jiang:
Global characterization of B cell receptor repertoire in COVID-19 patients by single-cell V(D)J sequencing. - Hilal Tayara, Ibrahim Abdelbaky, Kil To Chong:
Recent omics-based computational methods for COVID-19 drug discovery and repurposing. - Yanyi Chu, Xuhong Wang, Qiuying Dai, Yanjing Wang, Qiankun Wang, Shaoliang Peng, Xiaoyong Wei, Jingfei Qiu, Dennis Russell Salahub, Yi Xiong, Dong-Qing Wei:
MDA-GCNFTG: identifying miRNA-disease associations based on graph convolutional networks via graph sampling through the feature and topology graph. - Aleksandra A. Galitsyna, Mikhail S. Gelfand:
Single-cell Hi-C data analysis: safety in numbers. - Xiao-Chen Zhang, Chengkun Wu, Zhi-Jiang Yang, Zhen-Xing Wu, Jia-Cai Yi, Chang-Yu Hsieh, Tingjun Hou, Dong-Sheng Cao:
MG-BERT: leveraging unsupervised atomic representation learning for molecular property prediction. - Xiting Wang, Meng Liu, Yiling Zhang, Shuangshuang He, Caimeng Qin, Yu Li, Tao Lu:
Deep fusion learning facilitates anatomical therapeutic chemical recognition in drug repurposing and discovery. - Hao Lv, Lei Shi, Joshua William Berkenpas, Fu-Ying Dao, Hasan Zulfiqar, Hui Ding, Yang Zhang, Liming Yang, Renzhi Cao:
Application of artificial intelligence and machine learning for COVID-19 drug discovery and vaccine design. - Kunjie Fan, Lijun Cheng, Lang Li:
Artificial intelligence and machine learning methods in predicting anti-cancer drug combination effects. - Stefano Castellana, Tommaso Biagini, Luca Parca, Francesco Petrizzelli, Salvatore Daniele Bianco, Angelo Luigi Vescovi, Massimo Carella, Tommaso Mazza:
A comparative benchmark of classic DNA motif discovery tools on synthetic data. - Nam Nhut Phan, Amrita Chattopadhyay, Tsui-Ting Lee, Hsiang-I Yin, Tzu-Pin Lu, Liang-Chuan Lai, Hsiao-Lin Hwa, Mong-Hsun Tsai, Eric Y. Chuang:
High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data. - Xing Chen, Chi Zhou, Chun-Chun Wang, Yan Zhao:
Predicting potential small molecule-miRNA associations based on bounded nuclear norm regularization. - Chayanit Piyawajanusorn, Linh C. Nguyen, Ghita Ghislat, Pedro J. Ballester:
A gentle introduction to understanding preclinical data for cancer pharmaco-omic modeling. - Zhiyu Hao, Jin Gao, Yuxin Song, Runqing Yang, Di Liu:
Genome-wide hierarchical mixed model association analysis. - Chi-Chi Zhu, Chun-Chun Wang, Yan Zhao, Mingcheng Zuo, Xing Chen:
Identification of miRNA-disease associations via multiple information integration with Bayesian ranking. - Teemu J. Rintala, Antonio Federico, Leena Latonen, Dario Greco, Vittorio Fortino:
A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery. - Liujing Wang, Jun Liu, Yuhao Xia, Jiakang Xu, Xiaogen Zhou, Guijun Zhang:
Distance-guided protein folding based on generalized descent direction. - Yoshihiro Noguchi, Tomoya Tachi, Hitomi Teramachi:
Detection algorithms and attentive points of safety signal using spontaneous reporting systems as a clinical data source. - Lu Wang, Boran Gao, Yue Fan, Fuzhong Xue, Xiang Zhou:
Mendelian randomization under the omnigenic architecture. - Chengkun Wu, Xiao-Chen Zhang, Zhi-Jiang Yang, Ai-Ping Lu, Tingjun Hou, Dong-Sheng Cao:
Learning to SMILES: BAN-based strategies to improve latent representation learning from molecules. - Zhenla Jiang, Jianrong Xu, Aixia Yan, Ling Wang:
A comprehensive comparative assessment of 3D molecular similarity tools in ligand-based virtual screening. - Eitamar Tripto, Yaron Orenstein:
A comparative analysis of RNA-binding proteins binding models learned from RNAcompete, RNA Bind-n-Seq and eCLIP data. - Yongqing Zhang, Zixuan Wang, Yuanqi Zeng, Jiliu Zhou, Quan Zou:
High-resolution transcription factor binding sites prediction improved performance and interpretability by deep learning method. - Guangyuan Li, Balaji Iyer, V. B. Surya Prasath, Yizhao Ni, Nathan Salomonis:
DeepImmuno: deep learning-empowered prediction and generation of immunogenic peptides for T-cell immunity. - Hideki Yamaguchi, Yutaka Saito:
Erratum to: Evotuning protocols for Transformer-based variant effect prediction on multi-domain proteins. - Dandan Lu, Yue Zhang, Ling Zhang, Haiyan Wang, Wanlin Weng, Li Li, Hongmin Cai:
Methods of privacy-preserving genomic sequencing data alignments. - Yan Li, Shao-Wu Zhang:
Resilience function uncovers the critical transitions in cancer initiation. - Jialong Liang, Kun Zhang, Jie Yang, Xianfeng Li, Qinglan Li, Yan Wang, Wanshi Cai, Huajing Teng, Zhongsheng Sun:
A new approach to decode DNA methylome and genomic variants simultaneously from double strand bisulfite sequencing. - Yosef Masoudi-Sobhanzadeh, Aysan Salemi, Mohammad M. Pourseif, Behzad Jafari, Yadollah Omidi, Ali Masoudi-Nejad:
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. - Ruihan Luo, Chuang Ge, Xiao Xiao, Jing Song, Shiqi Miao, Yongyao Tang, Jiayi Lai, Weiqi Nian, Fangzhou Song, Longke Ran:
Identification of genetic variations associated with drug resistance in non-small cell lung cancer patients undergoing systemic treatment. - Wenying He, Jijun Tang, Quan Zou, Fei Guo:
MMFGRN: a multi-source multi-model fusion method for gene regulatory network reconstruction. - Hehe Wu, Xiaoyong Pan, Yang Yang, Hong-Bin Shen:
Recognizing binding sites of poorly characterized RNA-binding proteins on circular RNAs using attention Siamese network. - Lu Huo, Jiao Jiao Li, Ling Chen, Zuguo Yu, Gyorgy Hutvagner, Jinyan Li:
Single-cell multi-omics sequencing: application trends, COVID-19, data analysis issues and prospects. - Dalwinder Singh, Akansha Madhawan, Joy Roy:
Erratum to: Identification of multiple RNAs using feature fusion. - Ritesh Sharma, Sameer Shrivastava, Sanjay Kumar Singh, Abhinav Kumar, Sonal Saxena, Raj Kumar Singh:
AniAMPpred: artificial intelligence guided discovery of novel antimicrobial peptides in animal kingdom. - Yue Zhang, Jianyuan Lin, Lianmin Zhao, Xiangxiang Zeng, Xiangrong Liu:
A novel antibacterial peptide recognition algorithm based on BERT. - Sho Tsukiyama, Md. Mehedi Hasan, Satoshi Fujii, Hiroyuki Kurata:
LSTM-PHV: prediction of human-virus protein-protein interactions by LSTM with word2vec. - Miklos Diossy, Zsofia Sztupinszki, Marcin Krzystanek, Judit Börcsök, Aron C. Eklund, István Csabai, Anders Gorm Pedersen, Zoltan Szallasi:
Strand Orientation Bias Detector to determine the probability of FFPE sequencing artifacts. - Bowen Song, Kunqi Chen, Yujiao Tang, Zhen Wei, Jionglong Su, João Pedro de Magalhães, Daniel J. Rigden, Jia Meng:
ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. - Tamar Sofer, Nuzulul Kurniansyah, François Aguet, Kristin G. Ardlie, Peter Durda, Deborah A. Nickerson, Joshua D. Smith, Yongmei Liu, Sina Gharib, Susan Redline, Stephen S. Rich, Jerome I. Rotter, Kent D. Taylor:
Benchmarking association analyses of continuous exposures with RNA-seq in observational studies. - Le Ou-Yang, Dehan Cai, Xiao-Fei Zhang, Hong Yan:
WDNE: an integrative graphical model for inferring differential networks from multi-platform gene expression data with missing values. - Xinru Tang, Jiawei Luo, Cong Shen, Zihan Lai:
Multi-view Multichannel Attention Graph Convolutional Network for miRNA-disease association prediction. - Lijun Cai, Changcheng Lu, Junlin Xu, Yajie Meng, Peng Wang, Xiangzheng Fu, Xiangxiang Zeng, Yansen Su:
Drug repositioning based on the heterogeneous information fusion graph convolutional network. - Phasit Charoenkwan, Wararat Chiangjong, Chanin Nantasenamat, Md. Mehedi Hasan, Balachandran Manavalan, Watshara Shoombuatong:
StackIL6: a stacking ensemble model for improving the prediction of IL-6 inducing peptides.
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