default search action
Briefings in Bioinformatics, Volume 26
Volume 26, Number 1, 2024
- Yiwen Yang, Chengming Zhang, Zhaonan Liu, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen, Wu Wei:
MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics. - Tianjiao Zhang, Xiang Zhang, Zhenao Wu, Jixiang Ren, Zhongqian Zhao, Hongfei Zhang, Guohua Wang, Tao Wang:
VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network. - Xiaoyi Li, Kangli Zhu, Ying Zhen:
A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning. - Zhen Wang, Yizhen Feng, Qingwen Tian, Ziqi Liu, Pengju Yan, Xiaolin Li:
RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models. - James Strudwick, Laura-Jayne Gardiner, Kate Denning-James, Niina Haiminen, Ashley Evans, Jennifer Kelly, Matthew Madgwick, Filippo Utro, Ed Seabolt, Christopher Gibson, Bharat Bedi, Daniel Clayton, Ciaron Howell, Laxmi Parida, Anna Paola Carrieri:
AutoXAI4Omics: an automated explainable AI tool for omics and tabular data. - Xin Ma, Lijing Lin, Qian Zhao, Mudassar Iqbal:
TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data. - Anna Postovskaya, Koen Vercauteren, Pieter Meysman, Kris Laukens:
tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs. - Jiachen Chen, Joanne M. Murabito, Kathryn L. Lunetta:
ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks. - Yinhu Li, Guangze Pan, Shuai Wang, Zhengtu Li, Ru Yang, Yiqi Jiang, Yu Chen, Shuaicheng Li, Bairong Shen:
Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome. - Saurav Chandra Das, Wahia Tasnim, Humayan Kabir Rana, Uzzal Kumar Acharjee, Md. Manowarul Islam, Rabea Khatun:
Comprehensive bioinformatics and machine learning analyses for breast cancer staging using TCGA dataset. - Alfred Ultsch, Jörn Lötsch:
Augmenting small biomedical datasets using generative AI methods based on self-organizing neural networks. - Yuqi Miao, Huang Xu, Shuang Wang:
PartIES: a disease subtyping framework with Partition-level Integration using diffusion-Enhanced Similarities from multi-omics Data. - Elisabet Munté, Carla Roca, Jesús del Valle, Lidia Feliubadaló, Marta Pineda, Bernat Gel, Elisabeth Castellanos, Barbara Rivera, David Cordero, Víctor Moreno, Conxi Lázaro, José Marcos Moreno-Cabrera:
Detection of germline CNVs from gene panel data: benchmarking the state of the art. - Yuhan Wang, Zhikang Wang, Xuan Yu, Xiaoyu Wang, Jiangning Song, Dong-Jun Yu, Fang Ge:
MORE: a multi-omics data-driven hypergraph integration network for biomedical data classification and biomarker identification. - Hai Cui, Meiyu Duan, Haijia Bi, Xiaobo Li, Xiaodi Hou, Yi-Jia Zhang:
Heterogeneous graph contrastive learning with gradient balance for drug repositioning. - Sara Cuvertino, Terence Garner, Evgenii Martirosian, Bridgious Walusimbi, Susan J. Kimber, Siddharth Banka, Adam Stevens:
Higher order interaction analysis quantifies coordination in the epigenome revealing novel biological relationships in Kabuki syndrome. - Marin Volaric, Nevenka Mestrovic, Evelin Despot-Slade:
SatXplor - a comprehensive pipeline for satellite DNA analyses in complex genome assemblies. - Correction to: HHOMR: a hybrid high-order moment residual model for miRNA-disease association prediction.
- Yiwen Yang, Chengming Zhang, Zhaonan Liu, Kazuyuki Aihara, Chuanchao Zhang, Luonan Chen, Wu Wei:
MCGAE: unraveling tumor invasion through integrated multimodal spatial transcriptomics. - Tianjiao Zhang, Xiang Zhang, Zhenao Wu, Jixiang Ren, Zhongqian Zhao, Hongfei Zhang, Guohua Wang, Tao Wang:
VGAE-CCI: variational graph autoencoder-based construction of 3D spatial cell-cell communication network. - Xiaoyi Li, Kangli Zhu, Ying Zhen:
A versatile pipeline to identify convergently lost ancestral conserved fragments associated with convergent evolution of vocal learning. - Zhen Wang, Yizhen Feng, Qingwen Tian, Ziqi Liu, Pengju Yan, Xiaolin Li:
RNADiffFold: generative RNA secondary structure prediction using discrete diffusion models. - Junning Feng, Yong Liang, Tianwei Yu:
ADM: adaptive graph diffusion for meta-dimension reduction. - Yuejun Tan, Linhai Xie, Hong Yang, Qingyuan Zhang, Jinyuan Luo, Yanchun Zhang:
BioDSNN: a dual-stream neural network with hybrid biological knowledge integration for multi-gene perturbation response prediction. - Yuxiao Wei, Qi Zhang, Liwei Liu:
The improved de Bruijn graph for multitask learning: predicting functions, subcellular localization, and interactions of noncoding RNAs. - Long Xu, Qiang Yang, Weihe Dong, Xiaokun Li, Kuanquan Wang, Suyu Dong, Xianyu Zhang, Tiansong Yang, Gongning Luo, Xingyu Liao, Xin Gao, Guohua Wang:
Meta learning for mutant HLA class I epitope immunogenicity prediction to accelerate cancer clinical immunotherapy. - Leandro Murgas, Gianluca Pollastri, Erick Riquelme, Mauricio Sáez, Alberto J. M. Martin:
Understanding relationships between epigenetic marks and their application to robust assignment of chromatin states. - Ivan Ferrari, Federica De Grossi, Giancarlo Lai, Stefania Oliveto, Giorgia Deroma, Stefano Biffo, Nicola Manfrini:
CancerHubs: a systematic data mining and elaboration approach for identifying novel cancer-related protein interaction hubs. - Xiaolong Zhang, Xianchao Ji, Lingxiang Wang, Lianjiang Chi, Chengtao Li, Shaoqing Wen, Hua Chen:
STRsensor: a computationally efficient method for STR allele-typing from massively parallel sequencing data. - Expression of Concern: Bioinformatics in Russia: history and present-day landscape.
- Yunlong Wang, Siyuan Kong, Cong Zhou, Yanfang Wang, Yubo Zhang, Yaping Fang, Guoliang Li:
A review of deep learning models for the prediction of chromatin interactions with DNA and epigenomic profiles. - Shuailin Xue, Fangfang Zhu, Jinyu Chen, Wenwen Min:
Inferring single-cell resolution spatial gene expression via fusing spot-based spatial transcriptomics, location, and histology using GCN. - Tong Lu, Wei Guo, Wei Guo, Wangyang Meng, Tianyi Han, Zizhen Guo, Chengqiang Li, Shugeng Gao, Youqiong Ye, Hecheng Li:
A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity. - Hao Yuan, Parker Hicks, Mansooreh Ahmadian, Kayla A. Johnson, Lydia Valtadoros, Arjun Krishnan:
Annotating publicly-available samples and studies using interpretable modeling of unstructured metadata. - Zhenxian Zheng, Yingxuan Ren, Lei Chen, Angel On Ki Wong, Shumin Li, Xian Yu, Tak Wah Lam, Ruibang Luo:
Repun: an accurate small variant representation unification method for multiple sequencing platforms. - Tianyu Liu, Wenxin Long, Zhiyuan Cao, Yuge Wang, Chuan Hua He, Le Zhang, Stephen M. Strittmatter, Hongyu Zhao:
CosGeneGate selects multi-functional and credible biomarkers for single-cell analysis. - Fatma S. Ahmed, Saleh K. H. Aly, Xiangrong Liu:
NABP-BERT: NANOBODY®-antigen binding prediction based on bidirectional encoder representations from transformers (BERT) architecture. - Yong Liu, Le Zhong, Bin Yan, Zhuobin Chen, Yanjia Yu, Dan Yu, Jing Qin, Junwen Wang:
A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks. - Lubin Cui, Guiliang Guo, Michael K. Ng, Quan Zou, Yushan Qiu:
GSTRPCA: irregular tensor singular value decomposition for single-cell multi-omics data clustering. - Zheyu Ding, Rong Wei, Jianing Xia, Yonghao Mu, Jiahuan Wang, Yingying Lin:
Exploring the potential of large language model-based chatbots in challenges of ribosome profiling data analysis: a review. - Mengya Liu, Zhan-Li Sun, Zhigang Zeng, Kin-Man Lam:
Multi-kernel feature extraction with dynamic fusion and downsampled residual feature embedding for predicting rice RNA N6-methyladenine sites. - Aimin Xie, Hao Wang, Jiaxu Zhao, Zhaoyang Wang, Jinyuan Xu, Yan Xu:
scPAS: single-cell phenotype-associated subpopulation identifier. - Xizi Luo, Amadeus Song Yi Chi, Andre Huikai Lin, Tze Jet Ong, Limsoon Wong, Chowdhury Rafeed Rahman:
Benchmarking recent computational tools for DNA-binding protein identification. - Ornit Nahman, Timothy J. Few-Cooper, Shai S. Shen-Orr:
Cell-specific priors rescue differential gene expression in spatial spot-based technologies. - Xinglong Wang, Kangjie Xu, Lingling Ma, Ruoxi Sun, Kun Wang, Ruiyan Wang, Junli Zhang, Wenwen Tao, Kai Linghu, Shuyao Yu, Jingwen Zhou:
Diffusion model assisted designing self-assembling collagen mimetic peptides as biocompatible materials. - Bo Wang, Yahui Long, Yuting Bai, Jiawei Luo, Chee Keong Kwoh:
STCGAN: a novel cycle-consistent generative adversarial network for spatial transcriptomics cellular deconvolution. - Boya Ji, Xiaoqi Wang, Xiang Wang, Liwen Xu, Shaoliang Peng:
scDCA: deciphering the dominant cell communication assembly of downstream functional events from single-cell RNA-seq data. - Correction to: Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach.
- Konstantina Tzavella, Adrián Díaz, Catharina Olsen, Wim F. Vranken:
Combining evolution and protein language models for an interpretable cancer driver mutation prediction with D2Deep. - Cathal Ormond, Niamh M. Ryan, Mathieu Cap, William Byerley, Aiden P. Corvin, Elizabeth A. Heron:
BICEP: Bayesian inference for rare genomic variant causality evaluation in pedigrees. - Tianjiao Zhang, Hao Sun, Zhenao Wu, Zhongqian Zhao, Xingjie Zhao, Hongfei Zhang, Bo Gao, Guohua Wang:
GAADE: identification spatially variable genes based on adaptive graph attention network. - Shan Tharanga, Eyyüb Selim Ünlü, Yongli Hu, Muhammad Farhan Sjaugi, Muhammet A Çelik, Hilal Hekimoglu, Olivo Miotto, Muhammed Miran Öncel, Asif M. Khan:
DiMA: sequence diversity dynamics analyser for viruses. - Shyamsundar Ravishankar, Vilma Perez, Roberta Davidson, Xavier Roca-Rada, Divon Lan, Yassine Souilmi, Bastien Llamas:
Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping. - Cui-Xiang Lin, Hong-Dong Li, Jianxin Wang:
LIMO-GCN: a linear model-integrated graph convolutional network for predicting Alzheimer disease genes. - Yan-Yu Li, Fengcui Qian, Guo-Rui Zhang, Xue-Cang Li, Li-Wei Zhou, Zheng-Min Yu, Wei Liu, Qiu-Yu Wang, Chunquan Li:
FunlncModel: integrating multi-omic features from upstream and downstream regulatory networks into a machine learning framework to identify functional lncRNAs. - James Strudwick, Laura-Jayne Gardiner, Kate Denning-James, Niina Haiminen, Ashley Evans, Jennifer Kelly, Matthew Madgwick, Filippo Utro, Ed Seabolt, Christopher Gibson, Bharat Bedi, Daniel Clayton, Ciaron Howell, Laxmi Parida, Anna Paola Carrieri:
AutoXAI4Omics: an automated explainable AI tool for omics and tabular data. - Xueshi Yu, Renmin Han, Haitao Jiao, Wenjia Meng:
Few-shot classification of Cryo-ET subvolumes with deep Brownian distance covariance. - Xiaolong Wu, Lehan Zhang, Xiaochu Tong, Yitian Wang, Zimei Zhang, Xiangtai Kong, Shengkun Ni, Xiaomin Luo, Mingyue Zheng, Yun Tang, Xutong Li:
miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA. - Shuhe Liu, Zhen Wei, Daniel F. Carr, John Moraros:
Deciphering the genetic interplay between depression and dysmenorrhea: a Mendelian randomization study. - Xin Ma, Lijing Lin, Qian Zhao, Mudassar Iqbal:
TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data. - Peng Liu, Yuchen Pan, Hung-Ching Chang, Wenjia Wang, Yusi Fang, Xiangning Xue, Jian Zou, Jessica M. Toothaker, Oluwabunmi Olaloye, Eduardo Gonzalez Santiago, Black McCourt, Vanessa Mitsialis, Pietro Presicce, Suhas G. Kallapur, Scott B. Snapper, Jia-Jun Liu, George C. Tseng, Liza Konnikova, Silvia Liu:
Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating. - Yixuan Wang, Yanfang Guan, Xin Lai, Yuqian Liu, Zhili Chang, Xiaonan Wang, Quan Wang, Jingjing Liu, Jian Zhao, Shuanying Yang, Jiayin Wang, Xiaofeng Song:
THOR: a TMB heterogeneity-adaptive optimization model predicts immunotherapy response using clonal genomic features in group-structured data. - Junhang Cao, Jun Zhang, Qiyuan Yu, Junkai Ji, Jianqiang Li, Shan He, Zexuan Zhu:
TG-CDDPM: text-guided antimicrobial peptides generation based on conditional denoising diffusion probabilistic model. - Yunjian Chang, Ligang Wu:
CapHLA: a comprehensive tool to predict peptide presentation and binding to HLA class I and class II. - Pawel Dudzic, Bartosz Janusz, Tadeusz Satlawa, Dawid Chomicz, Tomasz Gawlowski, Rafal Grabowski, Przemek Józwiak, Mateusz Tarkowski, Maciej Mycielski, Sonia Wróbel, Konrad Krawczyk:
RIOT - Rapid Immunoglobulin Overview Tool - annotation of nucleotide and amino acid immunoglobulin sequences using an open germline database. - Junlei Liao, Hongyang Yi, Hao Wang, Sumei Yang, Duanmei Jiang, Xin Huang, Mingxia Zhang, Jiayin Shen, Hongzhou Lu, Yuanling Niu:
CDCM: a correlation-dependent connectivity map approach to rapidly screen drugs during outbreaks of infectious diseases. - Sergio Llaneza-Lago, William D. Fraser, Darrell Green:
Bayesian unsupervised clustering identifies clinically relevant osteosarcoma subtypes. - Dries Heylen, Murih Pusparum, Jurgis Kuliesius, Jim Wilson, Young-Chan Park, Jacek Jamiolkowski, Valentino D'onofrio, Dirk Valkenborg, Jan Aerts, Gökhan Ertaylan, Jef Hooyberghs:
Synthetic plasma pool cohort correction for affinity-based proteomics datasets allows multiple study comparison. - Yi Zhang, Yin Wang, Xinyuan Liu, Xi Feng:
CPARI: a novel approach combining cell partitioning with absolute and relative imputation to address dropout in single-cell RNA-seq data. - Nana Jin, Chuanchuan Nan, Wanyang Li, Peijing Lin, Yu Xin, Jun Wang, Yuelong Chen, Yuanhao Wang, Kaijiang Yu, Changsong Wang, Chunbo Chen, Qingshan Geng, Lixin Cheng:
PAGE-based transfer learning from single-cell to bulk sequencing enhances model generalization for sepsis diagnosis. - Qianwen Luo, Shanshan Zhang, Hamza Butt, Yin Chen, Hongmei Jiang, Lingling An:
PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data. - Ankang Wei, Zhen Xiao, Lingling Fu, Weizhong Zhao, Xingpeng Jiang:
Predicting phage-host interactions via feature augmentation and regional graph convolution. - Chi Zhang, Yiran Cheng, Kaiwen Feng, Fa Zhang, Renmin Han, Jieqing Feng:
UPicker: a semi-supervised particle picking transformer method for cryo-EM micrographs. - Jiachen Chen, Joanne M. Murabito, Kathryn L. Lunetta:
ONDSA: a testing framework based on Gaussian graphical models for differential and similarity analysis of multiple omics networks. - Yinhu Li, Guangze Pan, Shuai Wang, Zhengtu Li, Ru Yang, Yiqi Jiang, Yu Chen, Shuaicheng Li, Bairong Shen:
Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome. - Anna Postovskaya, Koen Vercauteren, Pieter Meysman, Kris Laukens:
tcrBLOSUM: an amino acid substitution matrix for sensitive alignment of distant epitope-specific TCRs. - Willem Stock, Coralie Rousseau, Glen Dierickx, Sofie D'hondt, Luz Amadei Martínez, Simon M. Dittami, Luna M. van der Loos, Olivier De Clerck:
Breaking free from references: a consensus-based approach for community profiling with long amplicon nanopore data. - Junwei Luo, Jiaojiao Wang, Jingjing Wei, Chaokun Yan, Huimin Luo:
DeepHapNet: a haplotype assembly method based on RetNet and deep spectral clustering. - Runqing Wang, Qiguo Dai, Xiaodong Duan, Quan Zou:
stHGC: a self-supervised graph representation learning for spatial domain recognition with hybrid graph and spatial regularization. - Lin Yuan, Shengguo Sun, Yufeng Jiang, Qinhu Zhang, Lan Ye, Chun-Hou Zheng, De-Shuang Huang:
scRGCL: a cell type annotation method for single-cell RNA-seq data using residual graph convolutional neural network with contrastive learning. - Jiaqi Wang, Ronggang Xi, Yi Wang, Huiyuan Gao, Ming Gao, Xiaozhe Zhang, Lihua Zhang, Yukui Zhang:
Toward molecular diagnosis of major depressive disorder by plasma peptides using a deep learning approach.
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.