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ORCIDBioinformatics, Volume 32
Volume 32, Number 1, January 2016
Genome Analysis
- Zi Yang, George Michailidis:
A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data. 1-8
- Adam Krejci, Ted R. Hupp
, Matej Lexa, Borivoj Vojtesek, Petr Müller:
Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets. 9-16 - Paul M. Bodily, M. Stanley Fujimoto, Quinn Snell, Dan Ventura, Mark J. Clement:
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction. 17-24
- Maciej Dziubinski, Pawel Daniluk, Bogdan Lesyng:
ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins. 25-34
- Benoît Liquet, Pierre Lafaye de Micheaux, Boris P. Hejblum, Rodolphe Thiébaut:
Group and sparse group partial least square approaches applied in genomics context. 35-42 - Brendan A. Veeneman, Sudhanshu Shukla, Saravana M. Dhanasekaran, Arul M. Chinnaiyan, Alexey I. Nesvizhskii:
Two-pass alignment improves novel splice junction quantification. 43-49
- Kevin He, Yanming Li, Ji Zhu, Hongliang Liu, Jeffrey E. Lee, Christopher I. Amos, Terry Hyslop, Jiashun Jin, Huazhen Lin, Qinyi Wei, Yi Li:
Component-wise gradient boosting and false discovery control in survival analysis with high-dimensional covariates. 50-57 - Paulo C. Rodrigues, Andreia Monteiro, Vanda M. Lourenço:
A robust AMMI model for the analysis of genotype-by-environment data. 58-66
- Qiaozi Gao, Elisabeth Ostendorf, Jeffrey A. Cruz, Rong Jin, David M. Kramer, Jin Chen:
Inter-functional analysis of high-throughput phenotype data by non-parametric clustering and its application to photosynthesis. 67-76 - Begüm Genç, Ugur Dogrusoz:
An algorithm for automated layout of process description maps drawn in SBGN. 77-84 - Isidro Cortes-Ciriano, Gerard J. P. van Westen, Guillaume Bouvier, Michael Nilges, John P. Overington, Andreas Bender, Thérèse E. Malliavin:
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel. 85-95 - Eunjee Lee, Koichi Ito, Yong Zhao, Eric E. Schadt, Hanna Y. Irie, Jun Zhu:
Inferred miRNA activity identifies miRNA-mediated regulatory networks underlying multiple cancers. 96-105
- Emily K. Mallory, Ce Zhang, Christopher Ré, Russ B. Altman:
Large-scale extraction of gene interactions from full-text literature using DeepDive. 106-113
- Wei Shao, Mingxia Liu, Daoqiang Zhang:
Human cell structure-driven model construction for predicting protein subcellular location from biological images. 114-121 - Hendrik Schäfer, Tim Schäfer, Jörg Ackermann, Norbert Dichter, Claudia Döring, Sylvia Hartmann, Martin-Leo Hansmann, Ina Koch:
CD30 cell graphs of Hodgkin lymphoma are not scale-free - an image analysis approach. 122-129
Genome Analysis
- Utkarsh J. Dang, Geoffrey Brian Golding:
markophylo: Markov chain analysis on phylogenetic trees. 130-132 - Jonathan S. Packer, Evan K. Maxwell, Colm O'Dushlaine, Alexander E. Lopez, Frederick E. Dewey, Rostislav Chernomorsky, Aris Baras, John D. Overton, Lukas Habegger, Jeffrey G. Reid:
CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data. 133-135
- Karel Brinda, Valentina Boeva, Gregory Kucherov:
RNF: a general framework to evaluate NGS read mappers. 136-139 - Arna Óskarsdóttir, Gísli Másson, Páll Melsted:
BamHash: a checksum program for verifying the integrity of sequence data. 140-141 - Richard M. Leggett, Darren Heavens, Mario Cáccamo, Matthew D. Clark, Robert P. Davey:
NanoOK: multi-reference alignment analysis of nanopore sequencing data, quality and error profiles. 142-144
- Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, Michael T. Wolfinger:
SHAPE directed RNA folding. 145-147
- Diego A. Hartasánchez, Marina Brasó-Vives, Juanma Fuentes-Díaz, Oriol Vallès-Codina, Arcadi Navarro:
SeDuS: segmental duplication simulator. 148-150 - Wei-Yi Cheng, Jörg Hakenberg, Shuyu Dan Li, Rong Chen:
DIVAS: a centralized genetic variant repository representing 150 000 individuals from multiple disease cohorts. 151-153
- Christian Jungreuthmayer, Stefan Neubauer, Teresa Mairinger, Jürgen Zanghellini, Stephan Hann:
ICT: isotope correction toolbox. 154-156
- Noah Fahlgren, Steven T. Hill, James C. Carrington, Alberto Carbonell:
P-SAMS: a web site for plant artificial microRNA and synthetic trans-acting small interfering RNA design. 157-158 - William Gilpin:
PyPDB: a Python API for the Protein Data Bank. 159-160
Volume 32, Number 2, January 2016
Sequence Analysis
- Jimmy Caroli, Cristian Taccioli, A. De La Fuente, P. Serafini, Silvio Bicciato:
APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data. 161-164 - Van-Minh Bui, Cheng-Tsung Lu, Trang-Thi Ho, Tzong-Yi Lee:
MDD-SOH: exploiting maximal dependence decomposition to identify S-sulfenylation sites with substrate motifs. 165-172 - Zhiying Wang, Tsachy Weissman, Olgica Milenkovic:
smallWig: parallel compression of RNA-seq WIG files. 173-180
- Bernhard Knapp, Samuel Demharter, Charlotte M. Deane, Peter Minary:
Exploring peptide/MHC detachment processes using hierarchical natural move Monte Carlo. 181-186 - Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, Jing Qin:
Pseudoknots in RNA folding landscapes. 187-194
- Thomas J. Hardcastle:
Generalized empirical Bayesian methods for discovery of differential data in high-throughput biology. 195-202
- Recep Colak, TaeHyung Kim, Hilal Kazan, Yoomi Oh, Miguel Cruz, Adan Valladares-Salgado, Jesus Peralta, Jorge Escobedo, Esteban J. Parra, Philip M. Kim, Anna Goldenberg:
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis. 203-210 - Shuang Wang, Yuchen Zhang, Wenrui Dai, Kristin E. Lauter, Miran Kim, Yuzhe Richard Tang, Hongkai Xiong, Xiaoqian Jiang:
HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS. 211-218
- Miquel Marin-Riera, Miguel Brun-Usan, Roland Zimm, Tommi Välikangas, Isaac Salazar-Ciudad:
Computational modeling of development by epithelia, mesenchyme and their interactions: a unified model. 219-225 - Yong-Cui Wang, Shi-Long Chen, Nai-Yang Deng, Yong Wang:
Computational probing protein-protein interactions targeting small molecules. 226-234 - Francesco Napolitano, Francesco Sirci, Diego Carrella, Diego di Bernardo:
Drug-set enrichment analysis: a novel tool to investigate drug mode of action. 235-241 - Allison N. Tegge, Nicholas Sharp, T. M. Murali:
Xtalk: a path-based approach for identifying crosstalk between signaling pathways. 242-251 - Pengyi Yang, Sean J. Humphrey, David E. James, Yee Hwa Yang, Raja Jothi:
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data. 252-259 - Jiyang Yu, José Silva, Andrea Califano:
ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling. 260-267
- Nathaniel G. Mahieu, Jonathan L. Spalding, Gary J. Patti:
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis. 268-275 - Suwisa Kaewphan, Sofie Van Landeghem, Tomoko Ohta, Yves Van de Peer, Filip Ginter, Sampo Pyysalo:
Cell line name recognition in support of the identification of synthetic lethality in cancer from text. 276-282
Genome Analysis
- Tomaz Berisa, Joseph K. Pickrell:
Approximately independent linkage disequilibrium blocks in human populations. 283-285 - Belinda Phipson, Jovana Maksimovic, Alicia Oshlack:
missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform. 286-288 - Bernat Gel, Anna Díez-Villanueva, Eduard Serra, Marcus Buschbeck, Miguel A. Peinado, Roberto Malinverni:
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. 289-291 - Konstantin Okonechnikov, Ana Conesa, Fernando García-Alcalde:
Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. 292-294 - Donghyung Lee, Vernell S. Williamson, T. Bernard Bigdeli, Brien P. Riley, Bradley Todd Webb, Ayman H. Fanous, Kenneth S. Kendler, Vladimir I. Vladimirov, Silviu-Alin Bacanu:
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts. 295-297
- James Dunbar, Charlotte M. Deane:
ANARCI: antigen receptor numbering and receptor classification. 298-300 - Paul Hodor, Amandeep Chawla, Andrew Clark, Lauren Neal:
cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud. 301-303 - Sergey Sheetlin, Yonil Park, Martin C. Frith, John L. Spouge:
ALP & FALP: C++ libraries for pairwise local alignment E-values. 304-305
- Devin K. Schweppe, Juan D. Chavez, James E. Bruce:
XLmap: an R package to visualize and score protein structure models based on sites of protein cross-linking. 306-308
- Max Franz, Christian Tannus Lopes, Gerardo Huck, Yue Dong, Selçuk Onur Sümer, Gary D. Bader:
Cytoscape.js: a graph theory library for visualisation and analysis. 309-311
- James M. Melott, John N. Weinstein, Bradley M. Broom:
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. 312-314
- Andreas Bartschat, Eduard Hübner, Markus Reischl, Ralf Mikut, Johannes Stegmaier:
XPIWIT - an XML pipeline wrapper for the Insight Toolkit. 315-317 - Pavel Krízek, Tomás Lukes, Martin Ovesný, Karel Fliegel, Guy M. Hagen:
SIMToolbox: a MATLAB toolbox for structured illumination fluorescence microscopy. 318-320
Volume 32, Number 3, February 2016
Genome Analysis
- Ka-Chun Wong, Yue Li, Chengbin Peng:
Identification of coupling DNA motif pairs on long-range chromatin interactions in human K562 cells. 321-324
- Michael Knudsen, Dan Søndergaard, Claus Tofting-Olesen, Frederik T. Hansen, Ditlev Egeskov Brodersen, Christian N. S. Pedersen:
Computational discovery of specificity-conferring sites in non-ribosomal peptide synthetases. 325-329
Genome Analysis
- Shaolong Cao, Huaizhen Qin, Alexej Gossmann, Hong-Wen Deng, Yu-Ping Wang:
Unified tests for fine-scale mapping and identifying sparse high-dimensional sequence associations. 330-337
- Swati Kaushik, Anu G. Nair, Eshita Mutt, Hari Prasanna Subramanian, Ramanathan Sowdhamini:
Rapid and enhanced remote homology detection by cascading hidden Markov model searches in sequence space. 338-344 - Juliana S. Bernardes, Fabio R. J. Vieira, Gerson Zaverucha, Alessandra Carbone:
A multi-objective optimization approach accurately resolves protein domain architectures. 345-353 - Genivaldo Gueiros Z. Silva, Kevin T. Green, Bas E. Dutilh, Robert A. Edwards:
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. 354-361 - Bin Liu, Longyun Fang, Ren Long, Xun Lan, Kuo-Chen Chou:
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k-tuple nucleotide composition. 362-369
- Peter Brown, Wayne Pullan, Yuedong Yang, Yaoqi Zhou:
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. 370-377 - Haiyou Deng, Ya Jia, Yang Zhang:
3DRobot: automated generation of diverse and well-packed protein structure decoys. 378-387
- Isik Baris Fidaner, Ayca Cankorur-Cetinkaya, Duygu Dikicioglu, Betül Kirdar, Ali Taylan Cemgil, Stephen G. Oliver:
CLUSTERnGO: a user-defined modelling platform for two-stage clustering of time-series data. 388-397
- Mehrshad Khosraviani, Morteza Saheb Zamani, Gholamreza Bidkhori:
FogLight: an efficient matrix-based approach to construct metabolic pathways by search space reduction. 398-408 - Tin Chi Nguyen, Rebecca Tagett, Michele Donato, Cristina Mitrea, Sorin Draghici:
A novel bi-level meta-analysis approach: applied to biological pathway analysis. 409-416 - Jeremy Hyrkas, Sophie Clayton, Francois Ribalet, Daniel Halperin, E. Virginia Armbrust, Bill Howe:
Scalable clustering algorithms for continuous environmental flow cytometry. 417-423 - Marcel Mischnik, Francesca Sacco, Jürgen Cox, Hans-Christoph Schneider, Matthias Schäfer, Manfred Hendlich, Daniel Crowther, Matthias Mann, Thomas Klabunde:
IKAP: A heuristic framework for inference of kinase activities from Phosphoproteomics data. 424-431
- Simon Baker, Ilona Silins, Yufan Guo, Imran Ali, Johan Högberg, Ulla Stenius, Anna Korhonen:
Automatic semantic classification of scientific literature according to the hallmarks of cancer. 432-440
Genome Analysis
- Mitchell J. Sullivan, Nathan L. Bachmann, Peter Timms, Adam Polkinghorne:
HapFlow: visualizing haplotypes in sequencing data. 441-443
- Johannes Köster:
Rust-Bio: a fast and safe bioinformatics library. 444-446 - Ibrahim Tanyalcin, Carla Al Assaf, Alexander Gheldof, Katrien Stouffs, Willy Lissens, Anna C. Jansen:
I-PV: a CIRCOS module for interactive protein sequence visualization. 447-449 - Parth Patel, S. Deepthi Ramachandruni, Atul Kakrana, Mayumi Nakano, Blake C. Meyers:
miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis. 450-452 - Ivan Borozan, Vincent Ferretti:
CSSSCL: a python package that uses combined sequence similarity scores for accurate taxonomic classification of long and short sequence reads. 453-455 - Jérôme Mariette, Frédéric Escudié, Philippe Bardou, Nabihoudine Ibouniyamine, Céline Noirot, Marie-Stéphane Trotard, Christine Gaspin, Christophe Klopp:
Jflow: a workflow management system for web applications. 456-458
- Danny Incarnato, Francesco Neri, Francesca Anselmi, Salvatore Oliviero:
RNA structure framework: automated transcriptome-wide reconstruction of RNA secondary structures from high-throughput structure probing data. 459-461 - Chao Wang, Haicang Zhang, Wei-Mou Zheng, Dong Xu, Jianwei Zhu, Bing Wang, Kang Ning, Shiwei Sun, Shuai Cheng Li, Dongbo Bu:
FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. 462-464
- Christoph Müssel, Florian Schmid, Tamara J. Blätte, Martin Hopfensitz, Ludwig Lausser, Hans A. Kestler:
BiTrinA - multiscale binarization and trinarization with quality analysis. 465-468
- Jun Chen, Allan C. Just, Joel Schwartz, Lifang Hou, Nadereh Jafari, Zhifu Sun, Jean-Pierre A. Kocher, Andrea A. Baccarelli, Xihong Lin:
CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies. 469-471
- Weizhong Tu, Haoran Zhang, Juan Liu, Qian-Nan Hu:
BioSynther: a customized biosynthetic potential explorer. 472-473
- Tim Schäfer, Andreas Scheck, Daniel Bruneß, Patrick May, Ina Koch:
The new protein topology graph library web server. 474-476 - Gaston K. Mazandu, Emile R. Chimusa, Mamana Mbiyavanga, Nicola J. Mulder:
A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool. 477-479
Volume 32, Number 4, February 2016
Structural Bioinformatics
- Guido Capitani, Jose M. Duarte, Kumaran Baskaran, Spencer Bliven, Joseph C. Somody:
Understanding the fabric of protein crystals: computational classification of biological interfaces and crystal contacts. 481-489
Genome Analysis
- Haoyang Zeng, Tatsunori B. Hashimoto, Daniel D. Kang, David K. Gifford:
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding. 490-496 - Uwe Baier, Timo Beller, Enno Ohlebusch:
Graphical pan-genome analysis with compressed suffix trees and the Burrows-Wheeler transform. 497-504
- M. Kroon, Eric-Wubbo Lameijer, N. Lakenberg, Jayne Y. Hehir-Kwa, D. T. Thung, P. Eline Slagboom, Joost N. Kok, Kai Ye:
Detecting dispersed duplications in high-throughput sequencing data using a database-free approach. 505-510 - Massimo Andreatta, Morten Nielsen:
Gapped sequence alignment using artificial neural networks: application to the MHC class I system. 511-517
- Sarah Bastkowski, Vincent Moulton, Andreas Spillner, Taoyang Wu:
The minimum evolution problem is hard: a link between tree inference and graph clustering problems. 518-522
- Alex Lewin, Habib Saadi, James E. Peters, Aida Moreno-Moral, James C. Lee, Kenneth G. C. Smith, Enrico Petretto, Leonardo Bottolo, Sylvia Richardson:
MT-HESS: an efficient Bayesian approach for simultaneous association detection in OMICS datasets, with application to eQTL mapping in multiple tissues. 523-532 - Sheida Nabavi, Daniel Schmolze, Mayinuer Maitituoheti, Sadhika Malladi, Andrew H. Beck:
EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes. 533-541
- Qiongshi Lu, Xinwei Yao, Yiming Hu, Hongyu Zhao:
GenoWAP: GWAS signal prioritization through integrated analysis of genomic functional annotation. 542-548 - Emile R. Chimusa, Mamana Mbiyavanga, Gaston K. Mazandu, Nicola J. Mulder:
ancGWAS: a post genome-wide association study method for interaction, pathway and ancestry analysis in homogeneous and admixed populations. 549-556 - Po-Ju Yao, Ren-Hua Chung:
SeqSIMLA2_exact: simulate multiple disease sites in large pedigrees with given disease status for diseases with low prevalence. 557-562
- Martin Scharm, Olaf Wolkenhauer, Dagmar Waltemath:
An algorithm to detect and communicate the differences in computational models describing biological systems. 563-570 - Thorsten Will, Volkhard Helms:
PPIXpress: construction of condition-specific protein interaction networks based on transcript expression. 571-578
- Chen Wang, Gang Hu, Kui Wang, Michal Brylinski, Lei Xie, Lukasz A. Kurgan:
PDID: database of molecular-level putative protein-drug interactions in the structural human proteome. 579-586
Genome Analysis
- Nathan C. Sheffield, Christoph Bock:
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor. 587-589 - Heng Li:
BGT: efficient and flexible genotype query across many samples. 590-592 - Kathleen Oros Klein, Stepan Grinek, Sasha Bernatsky, Luigi Bouchard, Antonio Ciampi, Ines Colmegna, Jean-Philippe Fortin, Long Gao, Marie-France Hivert, Marie Hudson, Michael S. Kobor, Aurélie Labbe, Julia L. MacIsaac, Michael J. Meaney, Alexander M. Morin, Kieran J. O'Donnell, Tomi Pastinen, Marinus H. Van Ijzendoorn, Gregory Voisin, Celia M. T. Greenwood:
funtooNorm: an R package for normalization of DNA methylation data when there are multiple cell or tissue types. 593-595 - Jeffrey Staples, Lynette Ekunwe, Ethan M. Lange, James G. Wilson, Deborah A. Nickerson, Jennifer E. Below:
PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes. 596-598 - Cyril Denby Wilkes, Olivier Arnaiz, Linda Sperling:
ParTIES: a toolbox for Paramecium interspersed DNA elimination studies. 599-601
- Mayya Sedova, Lukasz Jaroszewski, Adam Godzik:
Protael: protein data visualization library for the web. 602-604 - Yu-Wei Wu, Blake A. Simmons, Steven W. Singer:
MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. 605-607
- François Chevenet, Jean-Philippe Doyon, Céline Scornavacca, Edwin Jacox, Emmanuelle Jousselin, Vincent Berry:
SylvX: a viewer for phylogenetic tree reconciliations. 608-610
- Hyojung Ryu, Gyutae Lim, Bong Hyun Sung, Jinhyuk Lee:
NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores. 611-613 - Lin Wang, Min Zhang, Emil Alexov:
DelPhiPKa web server: predicting pKa of proteins, RNAs and DNAs. 614-615 - Alexey G. Kikhney, Alejandro Panjkovich, Anna V. Sokolova, Dmitri I. Svergun:
DARA: a web server for rapid search of structural neighbours using solution small angle X-ray scattering data. 616-618 - Hirofumi Suzuki, Takeshi Kawabata, Haruki Nakamura:
Omokage search: shape similarity search service for biomolecular structures in both the PDB and EMDB. 619-620 - Matthieu Chartier, Etienne Adriansen, Rafael Najmanovich:
IsoMIF Finder: online detection of binding site molecular interaction field similarities. 621-623
- Ming-Huei Chen, Qiong Yang:
RVFam: an R package for rare variant association analysis with family data. 624-626 - António Múrias dos Santos, Maria Pilar Cabezas, Ana Isabel Tavares, Raquel Xavier, Madalena Branco:
tcsBU: a tool to extend TCS network layout and visualization. 627-628
- Bruce E. Shapiro, Eric Mjolsness:
Pycellerator: an arrow-based reaction-like modelling language for biological simulations. 629-631 - Jan Winter, Marco Breinig, Florian Heigwer, Dirk Brügemann, Svenja Leible, Oliver Pelz, Tianzuo Zhan, Michael Boutros:
caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens. 632-634
- Juan J. Diaz-Montana, Owen J. L. Rackham, Norberto Díaz-Díaz, Enrico Petretto:
Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data. 635-637
- Caterina Barillari, Diana S. M. Ottoz, Juan Mariano Fuentes-Serna, Chandrasekhar Ramakrishnan, Bernd Rinn, Fabian Rudolf:
openBIS ELN-LIMS: an open-source database for academic laboratories. 638-640
Volume 32, Number 5, March 2016
Genome Analysis
- Feng Liu, Chao Ren, Hao Li, Pingkun Zhou, Xiaochen Bo, Wenjie Shu:
De novo identification of replication-timing domains in the human genome by deep learning. 641-649 - Zheng Xu, Guosheng Zhang, Fulai Jin, Mengjie Chen, Terrence S. Furey, Patrick F. Sullivan, Zhaohui S. Qin, Ming Hu, Yun Li:
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data. 650-656 - Tomasz Konopka, Sebastian M. B. Nijman:
Comparison of genetic variants in matched samples using thesaurus annotation. 657-663 - Wonyul Lee, Jeffrey S. Morris:
Identification of differentially methylated loci using wavelet-based functional mixed models. 664-672
- Lorena Pantano, Marc R. Friedländer, Geòrgia Escaramís, Esther Lizano, Joan Pallarès-Albanell, Isidre Ferrer, Xavier Estivill, Eulalia Martí:
Specific small-RNA signatures in the amygdala at premotor and motor stages of Parkinson's disease revealed by deep sequencing analysis. 673-681
- Ben Li, Zhaonan Sun, Qing He, Yu Zhu, Zhaohui S. Qin:
Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes. 682-689 - Charlotte Siska, Russell Bowler, Katerina J. Kechris:
The discordant method: a novel approach for differential correlation. 690-696 - Valerio Cestarelli, Giulia Fiscon, Giovanni Felici, Paola Bertolazzi, Emanuel Weitschek:
CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules. 697-704 - Qi Shen, Jiyuan Hu, Ning Jiang, Xiaohua Hu, Zewei Luo, Hong Zhang:
contamDE: differential expression analysis of RNA-seq data for contaminated tumor samples. 705-712
- Wei Hao, Minsun Song, John D. Storey:
Probabilistic models of genetic variation in structured populations applied to global human studies. 713-721
- Eduardo Palma, Lilian Salinas, Julio Aracena:
Enumeration and extension of non-equivalent deterministic update schedules in Boolean networks. 722-729 - Matthias P. Gerstl, Steffen Klamt, Christian Jungreuthmayer, Jürgen Zanghellini:
Exact quantification of cellular robustness in genome-scale metabolic networks. 730-737 - Marie Denis, Mahlet G. Tadesse:
Evaluation of hierarchical models for integrative genomic analyses. 738-746
- A. Mazouchi, Joshua N. Milstein:
Fast Optimized Cluster Algorithm for Localizations (FOCAL): a spatial cluster analysis for super-resolved microscopy. 747-754 - Hao-Chih Lee, Tao Liao, Yongjie Jessica Zhang, Ge Yang:
Shape component analysis: structure-preserving dimension reduction on biological shape spaces. 755-763
Genome Analysis
- Minh Duc Cao, Devika Ganesamoorthy, Matthew A. Cooper, Lachlan J. M. Coin:
Realtime analysis and visualization of MinION sequencing data with npReader. 764-766 - Katharina Jasmin Hoff, Simone Lange, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke:
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS. 767-769
- André Kahles, Jonas Behr, Gunnar Rätsch:
MMR: a tool for read multi-mapper resolution. 770-772 - Carmen Maria Livi, Petr Klus, Riccardo Delli Ponti, Gian Gaetano Tartaglia:
catRAPID signature: identification of ribonucleoproteins and RNA-binding regions. 773-775 - Sumit Mukherjee, Supratim Sengupta:
Riboswitch Scanner: an efficient pHMM-based web-server to detect riboswitches in genomic sequences. 776-778 - Sneha Mitra, Leelavati Narlikar:
No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites. 779-781 - Dietmar Rieder, Thomas Amort, Elisabeth Kugler, Alexandra Lusser, Zlatko Trajanoski:
meRanTK: methylated RNA analysis ToolKit. 782-785
- Brant C. Faircloth:
PHYLUCE is a software package for the analysis of conserved genomic loci. 786-788 - Sebastian Höhna, Michael R. May, Brian R. Moore:
TESS: an R package for efficiently simulating phylogenetic trees and performing Bayesian inference of lineage diversification rates. 789-791
- Florian Kaiser, Alexander Eisold, Sebastian Bittrich, Dirk Labudde:
Fit3D: a web application for highly accurate screening of spatial residue patterns in protein structure data. 792-794
- Matthias Steinrücken, Ethan M. Jewett, Yun S. Song:
SpectralTDF: transition densities of diffusion processes with time-varying selection parameters, mutation rates and effective population sizes. 795-797
- Brandon R. Thomas, Lily A. Chylek, Joshua Colvin, Suman Sirimulla, Andrew H. A. Clayton, William S. Hlavacek, Richard G. Posner:
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments. 798-800
Volume 32, Number 6, March 2016
Genome Analysis
- Mookyung Cheon, Choongrak Kim, Iksoo Chang:
Uncovering multiloci-ordering by algebraic property of Laplacian matrix and its Fiedler vector. 801-807 - Kyle S. Smith, Vinod Kumar Yadav, Shanshan Pei, Daniel A. Pollyea, Craig T. Jordan, Subhajyoti De:
SomVarIUS: somatic variant identification from unpaired tissue samples. 808-813
- Gearoid Fox, Fabian Sievers, Desmond G. Higgins:
Using de novo protein structure predictions to measure the quality of very large multiple sequence alignments. 814-820 - Enrique Audain, Yassel Ramos, Henning Hermjakob, Darren R. Flower, Yasset Pérez-Riverol:
Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. 821-827 - Goro Terai, Satoshi Kamegai, Kiyoshi Asai:
CDSfold: an algorithm for designing a protein-coding sequence with the most stable secondary structure. 828-834 - Filippo Utro, Valeria Di Benedetto, Davide F. V. Corona, Raffaele Giancarlo:
The intrinsic combinatorial organization and information theoretic content of a sequence are correlated to the DNA encoded nucleosome organization of eukaryotic genomes. 835-842
- Rhys Heffernan, Abdollah Dehzangi, James G. Lyons, Kuldip K. Paliwal, Alok Sharma, Jihua Wang, Abdul Sattar, Yaoqi Zhou, Yuedong Yang:
Highly accurate sequence-based prediction of half-sphere exposures of amino acid residues in proteins. 843-849
- Sangjin Kim, Paul Schliekelman:
Prioritizing hypothesis tests for high throughput data. 850-858 - Pierre Pudlo, Jean-Michel Marin, Arnaud Estoup, Jean-Marie Cornuet, Mathieu Gautier, Christian P. Robert:
Reliable ABC model choice via random forests. 859-866
- Matthew B. Biggs, Jason A. Papin:
Metabolic network-guided binning of metagenomic sequence fragments. 867-874 - S. M. Minhaz Ud-Dean, Rudiyanto Gunawan:
Optimal design of gene knockout experiments for gene regulatory network inference. 875-883 - Aristidis G. Vrahatis, Konstantina Dimitrakopoulou, Panos Balomenos, Athanasios K. Tsakalidis, Anastasios Bezerianos:
CHRONOS: a time-varying method for microRNA-mediated subpathway enrichment analysis. 884-892 - Martin Pirkl, Elisabeth Hand, Dieter Kube, Rainer Spang:
Analyzing synergistic and non-synergistic interactions in signalling pathways using Boolean Nested Effect Models. 893-900
- Yusuke Komiyama, Masaki Banno, Kokoro Ueki, Gul Saad, Kentaro Shimizu:
Automatic generation of bioinformatics tools for predicting protein-ligand binding sites. 901-907 - Goksel Misirli, Matteo Cavaliere, William Waites, Matthew R. Pocock, Curtis Madsen, Owen Gilfellon, Ricardo Honorato-Zimmer, Paolo Zuliani, Vincent Danos, Anil Wipat:
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. 908-917
- Samuel Croset, Joachim Rupp, Martin Romacker:
Flexible data integration and curation using a graph-based approach. 918-925
Genome Analysis
- Xuefeng Wang, Mengjie Chen, Xiaoqing Yu, Natapol Pornputtapong, Hao Chen, Nancy Ruonan Zhang, R. Scott Powers, Michael Krauthammer:
Global copy number profiling of cancer genomes. 926-928 - Michael Richter, Ramon Rosselló-Mora, Frank Oliver Glöckner, Jörg Peplies:
JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. 929-931
- Joanna Lange, Lucjan Stanislaw Wyrwicz, Gert Vriend:
KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins. 932-936 - Kun Yang, Giovanni Stracquadanio, Jingchuan Luo, Jef D. Boeke, Joel S. Bader:
BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts. 937-939
- Nan Li, Richard I. Ainsworth, Meixin Wu, Bo Ding, Wei Wang:
MIEC-SVM: automated pipeline for protein peptide/ligand interaction prediction. 940-942
- Wentao Yang, Katja Dierking, Hinrich Schulenburg:
WormExp: a web-based application for a Caenorhabditis elegans-specific gene expression enrichment analysis. 943-945
- Yan Wen, Wenyu Wang, Xiong Guo, Feng Zhang:
PAPA: a flexible tool for identifying pleiotropic pathways using genome-wide association study summaries. 946-948 - Tokhir Dadaev, Daniel A. Leongamornlert, Edward J. Saunders, Rosalind A. Eeles, Zsofia Kote-Jarai:
LocusExplorer: a user-friendly tool for integrated visualization of human genetic association data and biological annotations. 949-951
- Ying-Wooi Wan, Genevera I. Allen, Zhandong Liu:
TCGA2STAT: simple TCGA data access for integrated statistical analysis in R. 952-954
- Filippo Piccinini, Alexa Kiss, Péter Horváth:
CellTracker (not only) for dummies. 955-957 - Dominic Waithe, Mathias P. Clausen, Erdinc Sezgin, Christian Eggeling:
FoCuS-point: software for STED fluorescence correlation and time-gated single photon counting. 958-960
Volume 32, Number 7, April 2016
Genome Analysis
- Birte Kehr, Páll Melsted, Bjarni V. Halldórsson:
PopIns: population-scale detection of novel sequence insertions. 961-967 - Simona Constantinescu, Ewa Szczurek, Pejman Mohammadi, Jörg Rahnenführer, Niko Beerenwinkel:
TiMEx: a waiting time model for mutually exclusive cancer alterations. 968-975 - Monica Golumbeanu, Pejman Mohammadi, Niko Beerenwinkel:
BMix: probabilistic modeling of occurring substitutions in PAR-CLIP data. 976-983 - Daria Iakovishina, Isabelle Janoueix-Lerosey, Emmanuel Barillot, Mireille Régnier, Valentina Boeva:
SV-Bay: structural variant detection in cancer genomes using a Bayesian approach with correction for GC-content and read mappability. 984-992
- Jie Ren, Kai Song, Minghua Deng, Gesine Reinert, Charles H. Cannon, Fengzhu Sun:
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics. 993-1000 - Yuzhen Ye, Haixu Tang:
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis. 1001-1008
Genome Analysis
- Dmitry Antipov, Anton I. Korobeynikov, Jeffrey S. McLean, Pavel A. Pevzner:
hybridSPAdes: an algorithm for hybrid assembly of short and long reads. 1009-1015 - Lee Mendelowitz, David C. Schwartz, Mihai Pop:
Maligner: a fast ordered restriction map aligner. 1016-1022
- Kevin Vervier, Pierre Mahé, Maud Tournoud, Jean-Baptiste Veyrieras, Jean-Philippe Vert:
Large-scale machine learning for metagenomics sequence classification. 1023-1032
- Laura DiChiacchio, Michael F. Sloma, David H. Mathews:
AccessFold: predicting RNA-RNA interactions with consideration for competing self-structure. 1033-1039
- Martina Fischer, Bernhard Y. Renard:
iPQF: a new peptide-to-protein summarization method using peptide spectra characteristics to improve protein quantification. 1040-1047
- Anna Paola Carrieri, Filippo Utro, Laxmi Parida:
Sampling ARG of multiple populations under complex configurations of subdivision and admixture. 1048-1056
- Zhanchao Li, Meng-Hua Huang, Wen-Qian Zhong, Zhi-Qing Liu, Yun Xie, Zong Dai, Xiaoyong Zou:
Identification of drug-target interaction from interactome network with 'guilt-by-association' principle and topology features. 1057-1064
- Wim Verleyen, Sara Ballouz, Jesse A. Gillis:
Positive and negative forms of replicability in gene network analysis. 1065-1073
- Suzanne M. Paley, Markus Krummenacker, Peter D. Karp:
Representation and inference of cellular architecture for metabolic reconstruction and modeling. 1074-1079
Genome Analysis
- Nour-al-dain Marzouka, Jessica Nordlund, Christofer L. Bäcklin, Gudmar Lönnerholm, Ann-Christine Syvänen, Jonas Carlsson Almlöf:
CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array. 1080-1082 - Thomas Lacroix, Sylvie Thérond, Marc Rugeri, Pierre Nicolas, Annie Gendrault, Valentin Loux, Jean-François Gibrat:
Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT. 1083-1084 - Andrea Franceschini, Jianyi Lin, Christian von Mering, Lars Juhl Jensen:
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. 1085-1087 - Alla Mikheenko, Vladislav Saveliev, Alexey A. Gurevich:
MetaQUAST: evaluation of metagenome assemblies. 1088-1090 - Denis Seyres, Elodie Darbo, Laurent Perrin, Carl Herrmann, Aitor González:
LedPred: an R/bioconductor package to predict regulatory sequences using support vector machines. 1091-1093
- Jun Cheng, Franziska Metge, Christoph Dieterich:
Specific identification and quantification of circular RNAs from sequencing data. 1094-1096
- Deena M. A. Gendoo, Natchar Ratanasirigulchai, Markus S. Schröder, Laia Paré, Joel S. Parker, Aleix Prat, Benjamin Haibe-Kains:
Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer. 1097-1099 - Chee Lee, Snehal Patil, Maureen A. Sartor:
RNA-Enrich: a cut-off free functional enrichment testing method for RNA-seq with improved detection power. 1100-1102
- Rongfeng Cui, Molly Schumer, Gil G. Rosenthal:
Admix'em: a flexible framework for forward-time simulations of hybrid populations with selection and mate choice. 1103-1105 - Gilles Guillot, Hákon Jónsson, Antoine Hinge, Nabil Manchih, Ludovic Orlando:
Accurate continuous geographic assignment from low- to high-density SNP data. 1106-1108
- Lars Barquist, Matthew Mayho, Carla A. Cummins, Amy K. Cain, Christine J. Boinett, Andrew J. Page, Gemma C. Langridge, Michael A. Quail, Jacqueline A. Keane, Julian Parkhill:
The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries. 1109-1111
- Christopher Schmied, Peter Steinbach, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak:
An automated workflow for parallel processing of large multiview SPIM recordings. 1112-1114
Sequence Analysis
- Sebastian Deorowicz, Szymon Grabowski, Idoia Ochoa, Mikel Hernaez, Tsachy Weissman:
Comment on: 'ERGC: an efficient referential genome compression algorithm'. 1115-1117 - Subrata Saha, Sanguthevar Rajasekaran:
Authors' response to 'Comment on: ERGC: An efficient Referential Genome Compression Algorithm'. 1118-1119
Sequence Analysis
- Paulo Gaspar, José Luís Oliveira, Jörg Frommlet, Manuel A. S. Santos, Gabriela R. Moura:
Corrigendum: EuGene: maximizing synthetic gene design for heterologous expression. 1120
Volume 32, Number 8, April 2016
Genome Analysis
- Yoli Shavit, Barnabas James Walker, Pietro Liò:
Hierarchical block matrices as efficient representations of chromosome topologies and their application for 3C data integration. 1121-1129
- Yongzhuang Liu, Jian Liu, Jianguo Lu, Jiajie Peng, Liran Juan, Xiaolin Zhu, Bingshan Li, Yadong Wang:
Joint detection of copy number variations in parent-offspring trios. 1130-1137 - Thomas Wolf, Vladimir Shelest, Neetika Nath, Ekaterina Shelest:
CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes. 1138-1143 - Fatma-Elzahraa Eid, Mahmoud ElHefnawi, Lenwood S. Heath:
DeNovo: virus-host sequence-based protein-protein interaction prediction. 1144-1150 - Hwee Kim, Yo-Sub Han:
OMPPM: online multiple palindrome pattern matching. 1151-1157
- Christoph Peters, Konstantinos D. Tsirigos, Nanjiang Shu, Arne Elofsson:
Improved topology prediction using the terminal hydrophobic helices rule. 1158-1162 - Edoardo Milanetti, Domenico Raimondo, Anna Tramontano:
Prediction of the permeability of neutral drugs inferred from their solvation properties. 1163-1169
- Jiao Yuan, Peng Zhang, Ya Cui, Jiajia Wang, Geir Skogerbø, Da-Wei Huang, Runsheng Chen, Shunmin He:
Computational identification of piRNA targets on mouse mRNAs. 1170-1177
- Il-Youp Kwak, Wei Pan:
Adaptive gene- and pathway-trait association testing with GWAS summary statistics. 1178-1184
- Jiajie Peng, Tao Wang, Jixuan Wang, Yadong Wang, Jin Chen:
Extending gene ontology with gene association networks. 1185-1194 - Vladimir Gligorijevic, Noël Malod-Dognin, Natasa Przulj:
Fuse: multiple network alignment via data fusion. 1195-1203 - Helge Hass, Clemens Kreutz, Jens Timmer, Daniel Kaschek:
Fast integration-based prediction bands for ordinary differential equation models. 1204-1210
Genome Analysis
- Tsu-Pei Chiu, Federico Comoglio, Tianyin Zhou, Lin Yang, Renato Paro, Remo Rohs:
DNAshapeR: an R/Bioconductor package for DNA shape prediction and feature encoding. 1211-1213 - Li Chen, Zhaohui S. Qin:
traseR: an R package for performing trait-associated SNP enrichment analysis in genomic intervals. 1214-1216 - Charles E. Grant, James Johnson, Timothy L. Bailey, William Stafford Noble:
MCAST: scanning for cis-regulatory motif clusters. 1217-1219
- Xiaoyu Chen, Ole Schulz-Trieglaff, Richard Shaw, Bret Barnes, Felix Schlesinger, Morten Källberg, Anthony J. Cox, Semyon Kruglyak, Christopher T. Saunders:
Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications. 1220-1222 - Sandeep K. Kushwaha, Pallavi Chauhan, Katarina Hedlund, Dag G. Ahrén:
NBSPred: a support vector machine-based high-throughput pipeline for plant resistance protein NBSLRR prediction. 1223-1225 - Youri Hoogstrate, René Böttcher, Saskia D. Hiltemann, Peter J. van der Spek, Guido Jenster, Andrew Stubbs:
FuMa: reporting overlap in RNA-seq detected fusion genes. 1226-1228 - R. Gonzalo Parra, Cristian Oscar Rohr, Daniel Koile, Carolina Perez-Castro, Patricio Yankilevich:
INSECT 2.0: a web-server for genome-wide cis-regulatory modules prediction. 1229-1231 - Robert T. Good, Temi Varghese, John Golz, Derek A. Russell, Alexie Papanicolaou, Owain Edwards, Charles Robin:
OfftargetFinder: a web tool for species-specific RNAi design. 1232-1234
- Leandro E. Lombardi, Marcelo A. Marti, Luciana Capece:
CG2AA: backmapping protein coarse-grained structures. 1235-1237 - Daniel Sundfeld, Jakob Hull Havgaard, Alba Cristina Magalhaes Alves de Melo, Jan Gorodkin:
Foldalign 2.5: multithreaded implementation for pairwise structural RNA alignment. 1238-1240
- Philipp Angerer, Laleh Haghverdi, Maren Büttner, Fabian J. Theis, Carsten Marr, Florian A. Büttner:
destiny: diffusion maps for large-scale single-cell data in R. 1241-1243 - Petr Smirnov, Zhaleh Safikhani, Nehme Hachem, Dong Wang, Adrian She, Catharina Olsen, Mark Freeman, Heather Marie Selby, Deena M. A. Gendoo, Patrick Grossmann, Andrew H. Beck, Hugo J. W. L. Aerts, Mathieu Lupien, Anna Goldenberg, Benjamin Haibe-Kains:
PharmacoGx: an R package for analysis of large pharmacogenomic datasets. 1244-1246
- Gilderlanio S. Araújo, Lucas Henrique C. Lima, Silvana Schneider, Thiago P. Leal, Ana Paula Couto da Silva, Pedro O. S. Vaz de Melo, Eduardo Tarazona-Santos, Marília O. Scliar, Maíra R. Rodrigues:
Integrating, summarizing and visualizing GWAS-hits and human diversity with DANCE (Disease-ANCEstry networks). 1247-1249 - Michael Matschiner:
Fitchi: haplotype genealogy graphs based on the Fitch algorithm. 1250-1252 - Daniel Bottomly, Shannon K. McWeeney, Beth Wilmot:
HitWalker2: visual analytics for precision medicine and beyond. 1253-1255
- Ahmadreza Ghaffarizadeh, Samuel H. Friedman, Paul Macklin:
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations. 1256-1258 - Maximilian Malek, Rashid Ibragimov, Mario Albrecht, Jan Baumbach:
CytoGEDEVO - global alignment of biological networks with Cytoscape. 1259-1261 - Augustin Luna, Özgün Babur, Bülent Arman Aksoy, Emek Demir, Chris Sander:
PaxtoolsR: pathway analysis in R using Pathway Commons. 1262-1264 - Jan Bert Van Klinken, Ko Willems van Dijk:
FluxModeCalculator: an efficient tool for large-scale flux mode computation. 1265-1266
- Alastair P. Droop:
qsubsec: a lightweight template system for defining sun grid engine workflows. 1267-1268 - Dennis Goldfarb, Wei Wang, Michael B. Major:
MSAcquisitionSimulator: data-dependent acquisition simulator for LC-MS shotgun proteomics. 1269-1271
- Augustin Luna, Vinodh N. Rajapakse, Fabricio G. Sousa, Jianjiong Gao, Nikolaus Schultz, Sudhir Varma, William C. Reinhold, Chris Sander, Yves Pommier:
rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. 1272-1274 - Damion M. Dooley, Aaron J. Petkau, Gary H. Van Domselaar, William W. L. Hsiao:
Sequence database versioning for command line and Galaxy bioinformatics servers. 1275-1277
- Zsuzsanna Püspöki, Daniel Sage, John Paul Ward, Michael Unser:
SpotCaliper: fast wavelet-based spot detection with accurate size estimation. 1278-1280
Volume 32, Number 9, May 2016
Phylogenetics
- Sebastián Duchêne, Charles S. P. Foster, Simon Y. W. Ho:
Estimating the number and assignment of clock models in analyses of multigene datasets. 1281-1285
Genome Analysis
- Tuan Trieu, Jianlin Cheng:
MOGEN: a tool for reconstructing 3D models of genomes from chromosomal conformation capturing data. 1286-1292 - Sean Simmons, Bonnie Berger:
Realizing privacy preserving genome-wide association studies. 1293-1300 - Yao-Ting Huang, Chen-Fu Liao:
Integration of string and de Bruijn graphs for genome assembly. 1301-1307
- Tanzy M. T. Love, Sung Yong Park, Elena E. Giorgi, Wendy J. Mack, Alan S. Perelson, Ha Youn Lee:
SPMM: estimating infection duration of multivariant HIV-1 infections. 1308-1315 - Xiaowei Wang:
Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies. 1316-1322 - Maria Hauser, Martin Steinegger, Johannes Söding:
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets. 1323-1330
- Diego Darriba, Michael Weiß, Alexandros Stamatakis:
Prediction of missing sequences and branch lengths in phylogenomic data. 1331-1337
- Amir Nikooienejad, Wenyi Wang, Valen E. Johnson:
Bayesian variable selection for binary outcomes in high-dimensional genomic studies using non-local priors. 1338-1345
- Antti Häkkinen, Andre S. Ribeiro:
Characterizing rate limiting steps in transcription from RNA production times in live cells. 1346-1352 - Michal P. Switnicki, Malene Juul, Tobias Madsen, Karina D. Sørensen, Jakob Skou Pedersen:
PINCAGE: probabilistic integration of cancer genomics data for perturbed gene identification and sample classification. 1353-1365
- Dmitry Prokopenko, Julian Hecker, Edwin K. Silverman, Marcello Pagano, Markus M. Nöthen, Christian Dina, Christoph Lange, Heide Loehlein Fier:
Utilizing the Jaccard index to reveal population stratification in sequencing data: a simulation study and an application to the 1000 Genomes Project. 1366-1372
- Jonathan H. Young, Michael Peyton, Hyun Seok Kim, Elizabeth McMillan, John D. Minna, Michael A. White, Edward M. Marcotte:
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. 1373-1379
- Ahmad Pesaranghader, Stan Matwin, Marina Sokolova, Robert G. Beiko:
simDEF: definition-based semantic similarity measure of gene ontology terms for functional similarity analysis of genes. 1380-1387 - Paul Blomstedt, Ritabrata Dutta, Sohan Seth, Alvis Brazma, Samuel Kaski:
Modelling-based experiment retrieval: a case study with gene expression clustering. 1388-1394
- Raphaël Marée, Loic Rollus, Benjamin Stevens, Renaud Hoyoux, Gilles Louppe, Remy Vandaele, Jean-Michel Begon, Philipp Kainz, Pierre Geurts, Louis Wehenkel:
Collaborative analysis of multi-gigapixel imaging data using Cytomine. 1395-1401
Genome Analysis
- Frederic Commo, Justin Guinney, Charles Ferté, Brian M. Bot, Celine Lefebvre, Jean-Charles Soria, Fabrice André:
rCGH: a comprehensive array-based genomic profile platform for precision medicine. 1402-1404
- Clovis Galiez, Christophe N. Magnan, François Coste, Pierre Baldi:
VIRALpro: a tool to identify viral capsid and tail sequences. 1405-1407 - Ning Leng, Jeea Choi, Li-Fang Chu, James A. Thomson, Christina Kendziorski, Ron M. Stewart:
OEFinder: a user interface to identify and visualize ordering effects in single-cell RNA-seq data. 1408-1410
- Karolis Uziela, Björn Wallner:
ProQ2: estimation of model accuracy implemented in Rosetta. 1411-1413 - Josef Laimer, Julia Hiebl-Flach, Daniel Lengauer, Peter Lackner:
MAESTROweb: a web server for structure-based protein stability prediction. 1414-1416
- Tikira Temu, Matthias Mann, Markus Räschle, Jürgen Cox:
Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry. 1417-1419
- Seung Hwan Lee, Julius H. J. Van der Werf:
MTG2: an efficient algorithm for multivariate linear mixed model analysis based on genomic information. 1420-1422 - Xiaowei Zhan, Youna Hu, Bingshan Li, Gonçalo R. Abecasis, Dajiang J. Liu:
RVTESTS: an efficient and comprehensive tool for rare variant association analysis using sequence data. 1423-1426
- Oliver Philipp, Heinz D. Osiewacz, Ina Koch:
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. 1427-1429
- Angie S. Hinrichs, Brian J. Raney, Matthew L. Speir, Brooke L. Rhead, Jonathan Casper, Donna Karolchik, Robert M. Kuhn, Kate R. Rosenbloom, Ann S. Zweig, David Haussler, W. James Kent:
UCSC Data Integrator and Variant Annotation Integrator. 1430-1432
- Jian Yang, Gaofeng Deng, Haoyang Cai:
ChromothripsisDB: a curated database of chromothripsis. 1433-1435 - Catherine Mooney, Brett A. Becker, Rana Raoof, David C. Henshall:
EpimiRBase: a comprehensive database of microRNA-epilepsy associations. 1436-1438
- Andrea Vargas, Marc Angeli, Chiara Pastrello, Rosanne McQuaid, Han Li, Andrea Jurisicova, Igor Jurisica:
Robust quantitative scratch assay. 1439-1440
Volume 32, Number 10, May 2016
Sequence Analysis
- Luis Sánchez-Pulido, Chris P. Ponting:
Vasohibins: new transglutaminase-like cysteine proteases possessing a non-canonical Cys-His-Ser catalytic triad. 1441-1445
Genome Analysis
- Yongseok Park, Hao Wu:
Differential methylation analysis for BS-seq data under general experimental design. 1446-1453
- Christian D. Schenkelberg, Christopher Bystroff:
Protein backbone ensemble generation explores the local structural space of unseen natural homologs. 1454-1461 - Benjamin Thomas Viart, C. Dias-Lopes, Edgar Ernesto Gonzalez Kozlova, C. F. B. Oliveira, C. Nguyen, G. Neshich, Carlos Chávez-Olórtegui, F. Molina, Liza Figueredo Felicori:
EPI-peptide designer: a tool for designing peptide ligand libraries based on epitope-paratope interactions. 1462-1470 - Sanjay Agravat, Xuezheng Song, Teerapat Rojsajjakul, Richard D. Cummings, David F. Smith:
Computational approaches to define a human milk metaglycome. 1471-1478
- Halit Ongen, Alfonso Buil, Andrew Anand Brown, Emmanouil T. Dermitzakis, Olivier Delaneau:
Fast and efficient QTL mapper for thousands of molecular phenotypes. 1479-1485
- Gabriel H. Murillo, Na You, Xiaoquan Su, Wei Cui, Muredach P. Reilly, Mingyao Li, Kang Ning, Xinping Cui:
MultiGeMS: detection of SNVs from multiple samples using model selection on high-throughput sequencing data. 1486-1492 - Christian Benner, Chris C. A. Spencer, Aki S. Havulinna, Veikko Salomaa, Samuli Ripatti, Matti Pirinen:
FINEMAP: efficient variable selection using summary data from genome-wide association studies. 1493-1501
- Daniel Stöckel, Tim Kehl, Patrick Trampert, Lara Schneider, Christina Backes, Nicole Ludwig, Andreas Gerasch, Michael Kaufmann, Manfred Gessler, Norbert M. Graf, Eckart Meese, Andreas Keller, Hans-Peter Lenhof:
Multi-omics enrichment analysis using the GeneTrail2 web service. 1502-1508 - Zhen Niu, Deborah Chasman, Amie J. Eisfeld, Yoshihiro Kawaoka, Sushmita Roy:
Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions. 1509-1517 - Muaaz Gul Awan, Fahad Saeed:
MS-REDUCE: an ultrafast technique for reduction of big mass spectrometry data for high-throughput processing. 1518-1526
- Martin Strazar, Marinka Zitnik, Blaz Zupan, Jernej Ule, Tomaz Curk:
Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. 1527-1535
- Raymond G. Cavalcante, Snehal Patil, Terry E. Weymouth, Kestutis G. Bendinskas, Alla Karnovsky, Maureen A. Sartor:
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. 1536-1543
- Lei Du, Heng Huang, Jingwen Yan, Sungeun Kim, Shannon L. Risacher, Mark Inlow, Jason H. Moore, Andrew J. Saykin, Li Shen:
Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method. 1544-1551
Genome Analysis
- Ahmad Vaez, Peter J. van der Most, Bram P. Prins, Harold Snieder, Edwin R. van den Heuvel, Behrooz Z. Alizadeh, Ilja M. Nolte:
lodGWAS: a software package for genome-wide association analysis of biomarkers with a limit of detection. 1552-1554 - Ge Tan, Boris Lenhard:
TFBSTools: an R/bioconductor package for transcription factor binding site analysis. 1555-1556 - Karl W. Kroll, Ann-Katherin Eisfeld, Gerard Lozanski, Clara D. Bloomfield, John C. Byrd, James S. Blachly:
MuCor: mutation aggregation and correlation. 1557-1558
- Monica-Andreea Dragan, Ismail Moghul, Anurag Priyam, Claudio Bustos, Yannick Wurm:
GeneValidator: identify problems with protein-coding gene predictions. 1559-1561 - Jorge González-Domínguez, Bertil Schmidt:
ParDRe: faster parallel duplicated reads removal tool for sequencing studies. 1562-1564 - Erik Scott Wright, Kalin H. Vetsigian:
DesignSignatures: a tool for designing primers that yields amplicons with distinct signatures. 1565-1567
- Matías R. Machado, Sergio Pantano:
SIRAH tools: mapping, backmapping and visualization of coarse-grained models. 1568-1570 - Sikander Hayat, Christoph Peters, Nanjiang Shu, Konstantinos D. Tsirigos, Arne Elofsson:
Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins. 1571-1573 - Shuai Li, Qiancheng Shen, Minyi Su, Xinyi Liu, Shaoyong Lu, Zhongjie Chen, Renxiao Wang, Jian Zhang:
Alloscore: a method for predicting allosteric ligand-protein interactions. 1574-1576
- Michael Turewicz, Maike Ahrens, Caroline May, Katrin Marcus, Martin Eisenacher:
PAA: an R/bioconductor package for biomarker discovery with protein microarrays. 1577-1579
- Kelly M. Burkett, Brad McNeney, Jinko Graham:
Sampletrees and Rsampletrees: sampling gene genealogies conditional on SNP genotype data. 1580-1582 - Johannes Rainer, Daniel Taliun, Yuri D'Elia, Cristian Pattaro, Francisco S. Domingues, Christian X. Weichenberger:
FamAgg: an R package to evaluate familial aggregation of traits in large pedigrees. 1583-1585
- Frank T. Bergmann, Sven Sahle, Christoph Zimmer:
Piecewise parameter estimation for stochastic models in COPASI. 1586-1588 - Daniel K. Witvliet, Alexey Strokach, Andrés Felipe Giraldo-Forero, Joan Teyra, Recep Colak, Philip M. Kim:
ELASPIC web-server: proteome-wide structure-based prediction of mutation effects on protein stability and binding affinity. 1589-1591
- Magnus D. Vigeland, Kristina S. Gjøtterud, Kaja K. Selmer:
FILTUS: a desktop GUI for fast and efficient detection of disease-causing variants, including a novel autozygosity detector. 1592-1594
- Yining Liu, Min Zhao:
lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes. 1595-1597 - Michael J. Meyer, Philip Geske, Haiyuan Yu:
BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers. 1598-1600
Volume 32, Number 11, June 2016
Genome Analysis
- Caleb Weinreb, Benjamin J. Raphael:
Identification of hierarchical chromatin domains. 1601-1609 - Yuri Pirola, Simone Zaccaria, Riccardo Dondi, Gunnar W. Klau, Nadia Pisanti, Paola Bonizzoni:
HapCol: accurate and memory-efficient haplotype assembly from long reads. 1610-1617 - Faezeh Dorri, Lee Mendelowitz, Héctor Corrada Bravo:
methylFlow: cell-specific methylation pattern reconstruction from high-throughput bisulfite-converted DNA sequencing. 1618-1624
- Bo Liu, Dengfeng Guan, Mingxiang Teng, Yadong Wang:
rHAT: fast alignment of noisy long reads with regional hashing. 1625-1631 - Hongyi Xin, Sunny Nahar, Richard L. Zhu, John Emmons, Gennady Pekhimenko, Carl Kingsford, Can Alkan, Onur Mutlu:
Optimal seed solver: optimizing seed selection in read mapping. 1632-1642 - Sunho Park, Seung-Jun Kim, Donghyeon Yu, Samuel Peña-Llopis, Jianjiong Gao, Jinsuk Park, Beibei Chen, Jessie Norris, Xinlei Wang, Min Chen, Min-Su Kim, Jeongsik Yong, Zabi Wardak, Kevin Choe, Michael Story, Timothy K. Starr, Jae-Ho Cheong, TaeHyun Hwang:
An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types. 1643-1651 - Kana Shimizu, Koji Nuida, Gunnar Rätsch:
Efficient privacy-preserving string search and an application in genomics. 1652-1661 - Aryan Arbabi, Ladislav Rampásek, Michael Brudno:
Cell-free DNA fragment-size distribution analysis for non-invasive prenatal CNV prediction. 1662-1669 - Dilip A. Durai, Marcel H. Schulz:
Informed kmer selection for de novo transcriptome assembly. 1670-1677
- Ali May, Bernd W. Brandt, Mohammed El-Kebir, Gunnar W. Klau, Egija Zaura, Wim Crielaard, Jaap Heringa, Sanne Abeln:
metaModules identifies key functional subnetworks in microbiome-related disease. 1678-1685
- Lin Huang, Bo Wang, Ruitang Chen, Sivan Bercovici, Serafim Batzoglou:
Reveel: large-scale population genotyping using low-coverage sequencing data. 1686-1696
Genome Analysis
- Anna Hakobyan, Lilit Nersisyan, Arsen Arakelyan:
Quantitative trait association study for mean telomere length in the South Asian genomes. 1697-1700
Genome Analysis
- Fangfang Liu, Chong Wang, Zuowei Wu, Qijing Zhang, Peng Liu:
A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data. 1701-1708
- Seungpyo Hong, Dongsup Kim:
Library of binding protein scaffolds (LibBP): a computational platform for selection of binding protein scaffolds. 1709-1715
- Vered Madar, Sandra Batista:
FastLSU: a more practical approach for the Benjamini-Hochberg FDR controlling procedure for huge-scale testing problems. 1716-1723 - Jinyu Chen, Shihua Zhang:
Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data. 1724-1732
- Mattia Zampieri, Uwe Sauer:
Model-based media selection to minimize the cost of metabolic cooperation in microbial ecosystems. 1733-1739
Genome Analysis
- Ya Cui, Xiaowei Chen, Huaxia Luo, Zhen Fan, Jianjun Luo, Shunmin He, Haiyan Yue, Peng Zhang, Runsheng Chen:
BioCircos.js: an interactive Circos JavaScript library for biological data visualization on web applications. 1740-1742 - Claus Børnich, Ivar Grytten, Eivind Hovig, Jonas Paulsen, Martin Cech, Geir Kjetil Sandve:
Galaxy Portal: interacting with the galaxy platform through mobile devices. 1743-1745
- Bart Mesuere, Toon Willems, Felix Van der Jeugt, Bart Devreese, Peter Vandamme, Peter Dawyndt:
Unipept web services for metaproteomics analysis. 1746-1748
- Vagheesh Narasimhan, Petr Danecek, Aylwyn Scally, Yali Xue, Chris Tyler-Smith, Richard Durbin:
BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data. 1749-1751
- Zhihong Liu, Peng Ding, Xin Yan, Minghao Zheng, Huihao Zhou, Yuehua Xu, Yunfei Du, Qiong Gu, Jun Xu:
ASDB: a resource for probing protein functions with small molecules. 1752-1754 - Javier Otegui, Robert P. Guralnick:
The geospatial data quality REST API for primary biodiversity data. 1755-1757
Databases and Ontologies
- Christiana N. Fogg, Diane E. Kovats:
Message from the ISCB: 2016 ISCB Accomplishment by a Senior Scientist Award Given to Søren Brunak. 1758-1759 - Christiana N. Fogg, Diane E. Kovats:
Message from the ISCB: 2016 Outstanding Contributions to ISCB Award: Burkhard Rost. 1760
Volume 32, Number 12, June 2016
Editorial
- Pierre Baldi, Teresa M. Przytycka:
ISMB 2016 Proceedings. 1-2
- Forest Agostinelli, Nicholas Ceglia, Babak Shahbaba, Paolo Sassone-Corsi, Pierre Baldi:
What time is it? Deep learning approaches for circadian rhythms. 8-17 - Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu:
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. 18-27 - Céline Brouard, Huibin Shen, Kai Dührkop, Florence d'Alché-Buc, Sebastian Böcker, Juho Rousu:
Fast metabolite identification with Input Output Kernel Regression. 28-36 - Dan He, David Kuhn, Laxmi Parida:
Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction. 37-43
- Yue Deng, Steven J. Altschuler, Lani F. Wu:
PHOCOS: inferring multi-feature phenotypic crosstalk networks. 44-51 - Oren Z. Kraus, Lei Jimmy Ba, Brendan J. Frey:
Classifying and segmenting microscopy images with deep multiple instance learning. 52-59
- Reza Haydarlou, Annika Jacobsen, Nicola Bonzanni, K. Anton Feenstra, Sanne Abeln, Jaap Heringa:
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. 60-69 - Shengwen Peng, Ronghui You, Hongning Wang, Chengxiang Zhai, Hiroshi Mamitsuka, Shanfeng Zhu:
DeepMeSH: deep semantic representation for improving large-scale MeSH indexing. 70-79
- A. Grant Schissler, Qike Li, James L. Chen, Colleen Kenost, Ikbel Achour, Dean Billheimer, Haiquan Li, Walter W. Piegorsch, Yves A. Lussier:
Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. 80-89 - Marinka Zitnik, Blaz Zupan:
Jumping across biomedical contexts using compressive data fusion. 90-100 - Benjamin S. Glicksberg, Li Li, Marcus A. Badgeley, Khader Shameer, Roman Kosoy, Noam D. Beckmann, Nam Pho, Jörg Hakenberg, Meng Ma, Kristin L. Ayers, Gabriel E. Hoffman, Shuyu Dan Li, Eric E. Schadt, Chirag J. Patel, Rong Chen, Joel T. Dudley:
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks. 101-110
- Xihao Hu, Christina Huan Shi, Kevin Y. Yip:
A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps. 111-120 - Haoyang Zeng, Matthew D. Edwards, Ge Liu, David K. Gifford:
Convolutional neural network architectures for predicting DNA-protein binding. 121-127 - Kyuri Jo, Inuk Jung, Ji Hwan Moon, Sun Kim:
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. 128-136 - Jiangwen Sun, Zongliang Jiang, Xiuchun Tian, Jinbo Bi:
A cross-species bi-clustering approach to identifying conserved co-regulated genes. 137-146 - Hande Topa, Antti Honkela:
Analysis of differential splicing suggests different modes of short-term splicing regulation. 147-155 - Dat Duong, Jennifer Zou, Farhad Hormozdiari, Jae Hoon Sul, Jason Ernst, Buhm Han, Eleazar Eskin:
Using genomic annotations increases statistical power to detect eGenes. 156-163 - Seunghak Lee, Soonho Kong, Eric P. Xing:
A network-driven approach for genome-wide association mapping. 164-173
- Bo Liu, Dixian Zhu, Yadong Wang:
deBWT: parallel construction of Burrows-Wheeler Transform for large collection of genomes with de Bruijn-branch encoding. 174-182 - Tzu-Yu Liu, Yun S. Song:
Prediction of ribosome footprint profile shapes from transcript sequences. 183-191 - Avi Srivastava, Hirak Sarkar, Nitish Gupta, Rob Patro:
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes. 192-200 - Rayan Chikhi, Antoine Limasset, Paul Medvedev:
Compacting de Bruijn graphs from sequencing data quickly and in low memory. 201-208 - Carly E. Schaeffer, Nathaniel D. Figueroa, Xiaolin Liu, John E. Karro:
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats. 209-215 - Volodymyr Kuleshov, Michael P. Snyder, Serafim Batzoglou:
Genome assembly from synthetic long read clouds. 216-224
- Yufeng Wu:
An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree. 225-233 - Shilpa Garg, Marcel Martin, Tobias Marschall:
Read-based phasing of related individuals. 234-242
- Shahin Mohammadi, Ananth Grama:
A convex optimization approach for identification of human tissue-specific interactomes. 243-252 - Siddhartha Jain, Joel Arrais, Narasimhan J. Venkatachari, Velpandi Ayyavoo, Ziv Bar-Joseph:
Reconstructing the temporal progression of HIV-1 immune response pathways. 253-261 - Sankar Basu, Björn Wallner:
Finding correct protein-protein docking models using ProQDock. 262-270 - Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan:
An integer programming framework for inferring disease complexes from network data. 271-277 - Yasuo Tabei, Yoshihiro Yamanishi, Masaaki Kotera:
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. 278-287 - Jukka Intosalmi, Kari Nousiainen, Helena Ahlfors, Harri Lähdesmäki:
Data-driven mechanistic analysis method to reveal dynamically evolving regulatory networks. 288-296 - Ewa Szczurek, Niko Beerenwinkel:
Linear effects models of signaling pathways from combinatorial perturbation data. 297-305
- Alvin Farrel, Jonathan Murphy, Jun-tao Guo:
Structure-based prediction of transcription factor binding specificity using an integrative energy function. 306-313 - Michal Jamróz, Andrzej Kolinski, Daisuke Kihara:
Ensemble-based evaluation for protein structure models. 314-321 - Shengjie Wang, John T. Halloran, Jeff A. Bilmes, William S. Noble:
Faster and more accurate graphical model identification of tandem mass spectra using trellises. 322-331 - Xuefeng Cui, Zhiwu Lu, Sheng Wang, Jim Jing-Yan Wang, Xin Gao:
CMsearch: simultaneous exploration of protein sequence space and structure space improves not only protein homology detection but also protein structure prediction. 332-340 - Fanchi Meng, Lukasz A. Kurgan:
DFLpred: High-throughput prediction of disordered flexible linker regions in protein sequences. 341-350
- Yaron Orenstein, Yuhao Wang, Bonnie Berger:
RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data. 351-359 - Juan Antonio García-Martín, Iván Dotú, Javier Fernandez-Chamorro, Gloria Lozano, Jorge Ramajo, Encarnacion Martinez-Salas, Peter Clote:
RNAiFold2T: Constraint Programming design of thermo-IRES switches. 360-368 - Mariko Tsuchiya, Kojiro Amano, Masaya Abe, Misato Seki, Sumitaka Hase, Kengo Sato, Yasubumi Sakakibara:
SHARAKU: an algorithm for aligning and clustering read mapping profiles of deep sequencing in non-coding RNA processing. 369-377 - Xiaodong Cui, Jia Meng, Shaowu Zhang, Yidong Chen, Yufei Huang:
A novel algorithm for calling mRNA m6A peaks by modeling biological variances in MeRIP-seq data. 378-385
Systems Biology
- Monica Chagoyen, Florencio Pazos:
Characterization of clinical signs in the human interactome. 1761-1765
Genome Analysis
- Yingying Wei, Hao Wu:
Measuring the spatial correlations of protein binding sites. 1766-1772 - Shicai Fan, Chengzhe Li, Rizi Ai, Mengchi Wang, Gary S. Firestein, Wei Wang:
Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. 1773-1778
- Magali Jaillard, Maud Tournoud, Faustine Meynier, Jean-Baptiste Veyrieras:
Optimization of alignment-based methods for taxonomic binning of metagenomics reads. 1779-1787 - Zhen Zhang, Jianxin Wang, Junwei Luo, Xiaojun Ding, Jiancheng Zhong, Jun Wang, Fang-Xiang Wu, Yi Pan:
Sprites: detection of deletions from sequencing data by re-aligning split reads. 1788-1796 - Daniele Raimondi, Andrea M. Gazzo, Marianne Rooman, Tom Lenaerts, Wim F. Vranken:
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects. 1797-1804
- Juan P. Bustamante, María E. Szretter, Mariela Sued, Marcelo A. Marti, Dario A. Estrin, Leonardo Boechi:
A quantitative model for oxygen uptake and release in a family of hemeproteins. 1805-1813
- Victor L. Jong, Putri W. Novianti, Kit C. B. Roes, Marinus J. C. Eijkemans:
Selecting a classification function for class prediction with gene expression data. 1814-1822 - Jie Zhang, Zhi Wei:
An empirical Bayes change-point model for identifying 3′ and 5′ alternative splicing by next-generation RNA sequencing. 1823-1831 - Yifei Chen, Yi Li, Rajiv Narayan, Aravind Subramanian, Xiaohui Xie:
Gene expression inference with deep learning. 1832-1839 - André Kahles, Cheng Soon Ong, Yi Zhong, Gunnar Rätsch:
SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data. 1840-1847
- Pei-Yuan Sung, Yi-Ting Wang, Ya-Wen Yu, Ren-Hua Chung:
An efficient gene-gene interaction test for genome-wide association studies in trio families. 1848-1855 - Jin Liu, Xiang Wan, Shuangge Ma, Can Yang:
EPS: an empirical Bayes approach to integrating pleiotropy and tissue-specific information for prioritizing risk genes. 1856-1864
- Shobhit Jain, Gary D. Bader:
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast. 1865-1872
- Justin Wagner, Joseph N. Paulson, Xiao Wang, Bobby Bhattacharjee, Héctor Corrada Bravo:
Privacy-preserving microbiome analysis using secure computation. 1873-1879
Sequence Analysis
- Hao Wang, Joel McManus, Carl Kingsford:
Isoform-level ribosome occupancy estimation guided by transcript abundance with Ribomap. 1880-1882 - Alastair P. Droop:
fqtools: an efficient software suite for modern FASTQ file manipulation. 1883-1884
- José Augusto Salim, Luiz C. Borro, Ivan Mazoni, Inácio Yano, José G. Jardine, Goran Neshich:
Multiple structure single parameter: analysis of a single protein nano environment descriptor characterizing a shared loci on structurally aligned proteins. 1885-1887 - Sabine C. Mueller, Christina Backes, Alexander Greß, Nina Baumgarten, Olga V. Kalinina, Andreas Moll, Oliver Kohlbacher, Eckart Meese, Andreas Keller:
BALL-SNPgp - from genetic variants toward computational diagnostics. 1888-1890
- Florian Schmid, Matthias Schmid, Christoph Müssel, J. Eric Sträng, Christian Buske, Lars Bullinger, Johann M. Kraus, Hans A. Kestler:
GiANT: gene set uncertainty in enrichment analysis. 1891-1894
- Michael Degiorgio, Christian D. Huber, Melissa J. Hubisz, Ines Hellmann, Rasmus Nielsen:
SweepFinder2: increased sensitivity, robustness and flexibility. 1895-1897 - Luke Jostins, Gilean McVean:
Trinculo: Bayesian and frequentist multinomial logistic regression for genome-wide association studies of multi-category phenotypes. 1898-1900 - Andrey Ziyatdinov, Helena Brunel, Angel Martinez-Perez, Alfonso Buil, Alexandre Perera, José Manuel Soria:
solarius: an R interface to SOLAR for variance component analysis in pedigrees. 1901-1902 - Paul R. Staab, Dirk Metzler:
Coala: an R framework for coalescent simulation. 1903-1904
- Harold F. Gómez, Michael Hucka, Sarah M. Keating, German Nudelman, Dagmar Iber, Stuart C. Sealfon:
MOCCASIN: converting MATLAB ODE models to SBML. 1905-1906
- Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu:
Beyond accuracy: creating interoperable and scalable text-mining web services. 1907-1910 - Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti:
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. 1911-1913
- Pengbo Wen, Peng Xiao, Junfeng Xia:
dbDSM: a manually curated database for deleterious synonymous mutations. 1914-1916
- Jonathan W. Armond, Elina Vladimirou, Andrew D. McAinsh, Nigel J. Burroughs:
KiT: a MATLAB package for kinetochore tracking. 1917-1919
Volume 32, Number 13, July 2016
Genome Analysis
- Volkan Sevim, Ali Bashir, Chen-Shan Chin, Karen H. Miga:
Alpha-CENTAURI: assessing novel centromeric repeat sequence variation with long read sequencing. 1921-1924
Genome Analysis
- Kristoffer Sahlin, Rayan Chikhi, Lars Arvestad:
Assembly scaffolding with PE-contaminated mate-pair libraries. 1925-1932
- Kazutaka Katoh, Daron M. Standley:
A simple method to control over-alignment in the MAFFT multiple sequence alignment program. 1933-1942 - Yuval Elhanati, Quentin Marcou, Thierry Mora, Aleksandra M. Walczak:
repgenHMM: a dynamic programming tool to infer the rules of immune receptor generation from sequence data. 1943-1951 - François D. Richard, Ronnie Alves, Andrey V. Kajava:
Tally: a scoring tool for boundary determination between repetitive and non-repetitive protein sequences. 1952-1958
- Alexander Lachmann, Federico M. Giorgi, Mariano J. Alvarez, Andrea Califano:
Detection and removal of spatial bias in multiwell assays. 1959-1965 - Sunghwan Kim, Chien-Wei Lin, George C. Tseng:
MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. 1966-1973
- Kevin Sharp, Warren Kretzschmar, Olivier Delaneau, Jonathan Marchini:
Phasing for medical sequencing using rare variants and large haplotype reference panels. 1974-1980 - Anna Cichonska, Juho Rousu, Pekka Marttinen, Antti J. Kangas, Pasi Soininen, Terho Lehtimäki, Olli T. Raitakari, Marjo-Riitta Järvelin, Veikko Salomaa, Mika Ala-Korpela, Samuli Ripatti, Matti Pirinen:
metaCCA: summary statistics-based multivariate meta-analysis of genome-wide association studies using canonical correlation analysis. 1981-1989 - Laura Buzdugan, Markus Kalisch, Arcadi Navarro, Daniel Schunk, Ernst Fehr, Peter Bühlmann:
Assessing statistical significance in multivariable genome wide association analysis. 1990-2000
- Luis Tobalina, Jon Pey, Francisco J. Planes:
Direct calculation of minimal cut sets involving a specific reaction knock-out. 2001-2007 - Alexander Eng, Elhanan Borenstein:
An algorithm for designing minimal microbial communities with desired metabolic capacities. 2008-2016
- Jeongbin Park, Jin-Soo Kim, Sangsu Bae:
Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9. 2017-2023
Genome Analysis
- Kenneth A. Watanabe, Kaiwang Ma, Arielle Homayouni, Paul J. Rushton, Qingxi J. Shen:
Transcript structure and domain display: a customizable transcript visualization tool. 2024-2025 - James G. Lamine, Randall J. DeJong, Serita M. Nelesen:
PhamDB: a web-based application for building Phamerator databases. 2026-2028 - Jeremiah A. Wala, Cheng-Zhong Zhang, Matthew Meyerson, Rameen Beroukhim:
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules. 2029-2031
- Yang Yang, Abhishek Niroula, Bairong Shen, Mauno Vihinen:
PON-Sol: prediction of effects of amino acid substitutions on protein solubility. 2032-2034 - Susan K. Van Riper, LeeAnn Higgins, John V. Carlis, Timothy J. Griffin:
RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification. 2035-2037 - Federico Mattiello, Bie M. P. Verbist, Karoline Faust, Jeroen Raes, William D. Shannon, Luc Bijnens, Olivier Thas:
A web application for sample size and power calculation in case-control microbiome studies. 2038-2040 - Chuming Chen, Hongzhan Huang, Raja Mazumder, Darren A. Natale, Peter B. McGarvey, Jian Zhang, Shawn W. Polson, Yuqi Wang, Cathy H. Wu:
Computational clustering for viral reference proteomes. 2041-2043 - Benjamin Schubert, Mathias Walzer, Hans-Philipp Brachvogel, András Szolek, Christopher Mohr, Oliver Kohlbacher:
FRED 2: an immunoinformatics framework for Python. 2044-2046 - Samuel M. Nicholls, Amanda Clare, Joshua C. Randall:
Goldilocks: a tool for identifying genomic regions that are 'just right'. 2047-2049 - Baekdoo Kim, Thahmina Ali, Samuel Hosmer, Konstantinos Krampis:
Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization. 2050-2052 - Alexander Ekstrom, Yanbin Yin:
ORFanFinder: automated identification of taxonomically restricted orphan genes. 2053-2055
- Edwin Jacox, Cédric Chauve, Gergely J. Szöllosi, Yann Ponty, Céline Scornavacca:
ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony. 2056-2058
- Debswapna Bhattacharya, Badri Adhikari, Jilong Li, Jianlin Cheng:
FRAGSION: ultra-fast protein fragment library generation by IOHMM sampling. 2059-2061 - Alejandro Panjkovich, Dmitri I. Svergun:
SASpy: a PyMOL plugin for manipulation and refinement of hybrid models against small angle X-ray scattering data. 2062-2064
- Syed Asad Rahman, Gilliean Torrance, Lorenzo Baldacci, Sergio Martínez Cuesta, Franz Fenninger, Nimish Gopal, Saket Choudhary, John W. May, Gemma L. Holliday, Christoph Steinbeck, Janet M. Thornton:
Reaction Decoder Tool (RDT): extracting features from chemical reactions. 2065-2066 - Ahmed Mohamed, Canh Hao Nguyen, Hiroshi Mamitsuka:
NMRPro: an integrated web component for interactive processing and visualization of NMR spectra. 2067-2068
- Yuanwei Zhang, Qiguang Zang, Bo Xu, Wei Zheng, Rongjun Ban, Huan Zhang, Yifan Yang, QiaoMei Hao, Furhan Iqbal, Ao Li, Qinghua Shi:
IsomiR Bank: a research resource for tracking IsomiRs. 2069-2071 - Karthik Gangavarapu, Vyshakh Babji, Tobias Meißner, Andrew I. Su, Benjamin M. Good:
Branch: an interactive, web-based tool for testing hypotheses and developing predictive models. 2072-2074
- Laurent Gole, Kok Haur Ong, Thomas Boudier, Weimiao Yu, Sohail Ahmed:
OpenSegSPIM: a user-friendly segmentation tool for SPIM data. 2075-2077
- Ognjen Arandjelovic:
On the discovery of hospital admission patterns - a clarification. 2078 - Guillermo López-Campos, Fernando José Martín-Sánchez, Kathleen Gray:
Comment on 'Discovering hospital admission patterns using models learnt from electronic hospital records'. The importance of using the right codes. 2079-2080
Data and Text Mining
- Sungchul Kim, Lee Sael, Hwanjo Yu:
A mutation profile for top-k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization. 2081
Volume 32, Number 14, July 2016
Systems Biology
- Yuta Narushima, Hiroko Kozuka-Hata, Kouhei Tsumoto, Jun-Ichiro Inoue, Masaaki Oyama:
Quantitative phosphoproteomics-based molecular network description for high-resolution kinase-substrate interactome analysis. 2083-2088
Genome Analysis
- Nowlan H. Freese, David C. Norris, Ann E. Loraine:
Integrated genome browser: visual analytics platform for genomics. 2089-2095 - Filipe G. Vieira, Anders Albrechtsen, Rasmus Nielsen:
Estimating IBD tracts from low coverage NGS data. 2096-2102
- Heng Li:
Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. 2103-2110
- Yann Christinat, Rafal Pawlowski, Wilhelm Krek:
jSplice: a high-performance method for accurate prediction of alternative splicing events and its application to large-scale renal cancer transcriptome data. 2111-2119 - Heeju Noh, Rudiyanto Gunawan:
Inferring gene targets of drugs and chemical compounds from gene expression profiles. 2120-2127 - Trung-Nghia Vu, Quin F. Wills, Krishna R. Kalari, Nifang Niu, Liewei Wang, Mattias Rantalainen, Yudi Pawitan:
Beta-Poisson model for single-cell RNA-seq data analyses. 2128-2135
- André Lacour, David Ellinghaus, Stefan Schreiber, Andre Franke, Tim Becker:
Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci. 2136-2142
- Pei Chen, Rui Liu, Yongjun Li, Luonan Chen:
Detecting critical state before phase transition of complex biological systems by hidden Markov model. 2143-2150 - Jie Chen, Alfred O. Hero III, Indika Rajapakse:
Spectral identification of topological domains. 2151-2158 - Vincenzo Bonnici, Federico Busato, Giovanni Micale, Nicola Bombieri, Alfredo Pulvirenti, Rosalba Giugno:
APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks. 2159-2166
- Charles Blatti, Saurabh Sinha:
Characterizing gene sets using discriminative random walks with restart on heterogeneous biological networks. 2167-2175
- Chao Pang, David van Enckevort, Mark de Haan, Fleur D. L. Kelpin, Jonathan Jetten, Dennis Hendriksen, Tommy de Boer, Bart Charbon, Erwin Winder, K. Joeri van der Velde, Dany Doiron, Isabel Fortier, Hans L. Hillege, Morris A. Swertz:
MOLGENIS/connect: a system for semi-automatic integration of heterogeneous phenotype data with applications in biobanks. 2176-2183
- Ying-Ying Xu, Fan Yang, Hong-Bin Shen:
Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction. 2184-2192
Genome Analysis
- Anestis Touloumis, John C. Marioni, Simon Tavaré:
HDTD: analyzing multi-tissue gene expression data. 2193-2195
- Dongwon Lee:
LS-GKM: a new gkm-SVM for large-scale datasets. 2196-2198 - Andreas Bremges, Esther Singer, Tanja Woyke, Alexander Sczyrba:
MeCorS: Metagenome-enabled error correction of single cell sequencing reads. 2199-2201 - Birte Kehr, Páll Melsted:
chopBAI: BAM index reduction solves I/O bottlenecks in the joint analysis of large sequencing cohorts. 2202-2204 - Mahmoud Ghandi, Morteza Mohammad Noori, Narges Ghareghani, Dongwon Lee, Levi A. Garraway, Michael A. Beer:
gkmSVM: an R package for gapped-kmer SVM. 2205-2207 - Christopher J. R. Illingworth:
SAMFIRE: multi-locus variant calling for time-resolved sequence data. 2208-2209 - Elena Bushmanova, Dmitry Antipov, Alla L. Lapidus, Vladimir Suvorov, Andrey D. Prjibelski:
rnaQUAST: a quality assessment tool for de novo transcriptome assemblies. 2210-2212
- Oz Solomon, Eran Eyal, Ninette Amariglio, Ron Unger, Gidi Rechavi:
e23D: database and visualization of A-to-I RNA editing sites mapped to 3D protein structures. 2213-2215 - Hui Liu, Tingjun Hou:
CaFE: a tool for binding affinity prediction using end-point free energy methods. 2216-2218
- Aaron Diaz, Siyuan J. Liu, Carmen Sandoval, Alex A. Pollen, Tom J. Nowakowski, Daniel A. Lim, Arnold Kriegstein:
SCell: integrated analysis of single-cell RNA-seq data. 2219-2220 - Xiao Huo, Sheng'en Hu, Chengchen Zhao, Yong Zhang:
Dr.seq: a quality control and analysis pipeline for droplet sequencing. 2221-2223
- Sophie Limou, Andrew M. Taverner, Cheryl A. Winkler:
Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project. 2224-2226 - Qian S. Zhang, Brian L. Browning, Sharon R. Browning:
ASAFE: ancestry-specific allele frequency estimation. 2227-2229 - Haiming Tang, Paul D. Thomas:
PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation. 2230-2232
- Alexander Lachmann, Federico M. Giorgi, Gonzalo López, Andrea Califano:
ARACNe-AP: gene network reverse engineering through adaptive partitioning inference of mutual information. 2233-2235
- Núria Queralt-Rosinach, Janet Piñero González, Àlex Bravo, Ferran Sanz, Laura I. Furlong:
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. 2236-2238
- Leonid Andronov, Yves Lutz, Jean-Luc Vonesch, Bruno P. Klaholz:
SharpViSu: integrated analysis and segmentation of super-resolution microscopy data. 2239-2241
- Brendan O'Fallon:
TreesimJ: a flexible, forward time population genetic simulator. 2242
Volume 32, Number 15, August 2016
Sequence Analysis
- Can Firtina, Can Alkan:
On genomic repeats and reproducibility. 2243-2247
Genome Analysis
- Yusuke Matsui, Masahiro Mizuta, Satoshi Ito, Satoru Miyano, Teppei Shimamura:
D3M: detection of differential distributions of methylation levels. 2248-2255 - Mikhail G. Dozmorov, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren:
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets. 2256-2263
- Tunca Dogan, Alistair MacDougall, Rabie Saidi, Diego Poggioli, Alex Bateman, Claire O'Donovan, Maria Jesus Martin:
UniProt-DAAC: domain architecture alignment and classification, a new method for automatic functional annotation in UniProtKB. 2264-2271 - Vitor Piro, Martin S. Lindner, Bernhard Y. Renard:
DUDes: a top-down taxonomic profiler for metagenomics. 2272-2280 - Ishita K. Khan, Daisuke Kihara:
Genome-scale prediction of moonlighting proteins using diverse protein association information. 2281-2288
- Daniel Zaidman, Haim J. Wolfson:
PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm. 2289-2296 - Sumanta Mukherjee, Chiranjib Bhattacharyya, Nagasuma Chandra:
HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials. 2297-2305
- Rudy Arthur, Jared O'Connell, Ole Schulz-Trieglaff, Anthony J. Cox:
Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions. 2306-2312
- Hao Zhu, Markus R. Owen, Yanlan Mao:
The spatiotemporal order of signaling events unveils the logic of development signaling. 2313-2320 - Sabrina Hross, Jan Hasenauer:
Analysis of CFSE time-series data using division-, age- and label-structured population models. 2321-2329 - Pedro A. Saa, Lars Keld Nielsen:
ll-ACHRB: a scalable algorithm for sampling the feasible solution space of metabolic networks. 2330-2337 - Zichen Wang, Neil R. Clark, Avi Ma'ayan:
Drug-induced adverse events prediction with the LINCS L1000 data. 2338-2345
- Ying Yang, Xiaotao Jiang, Benli Chai, Liping Ma, Bing Li, Anni Zhang, James R. Cole, James M. Tiedje, Tong Zhang:
ARGs-OAP: online analysis pipeline for antibiotic resistance genes detection from metagenomic data using an integrated structured ARG-database. 2346-2351
- Ahmed Fakhry, Hanchuan Peng, Shuiwang Ji:
Deep models for brain EM image segmentation: novel insights and improved performance. 2352-2358
Genome Analysis
- Christian Arnold, Pooja Bhat, Judith B. Zaugg:
SNPhood: investigate, quantify and visualise the epigenomic neighbourhood of SNPs using NGS data. 2359-2360 - Mariusz Butkiewicz, Jessica Cooke Bailey, Alex T. Frase, Scott M. Dudek, Brian L. Yaspan, Marylyn D. Ritchie, Sarah A. Pendergrass, Jonathan L. Haines:
Pathway analysis by randomization incorporating structure - PARIS: an update. 2361-2363 - Joshua Millstein, Gary K. Chen, Carrie V. Breton:
cit: hypothesis testing software for mediation analysis in genomic applications. 2364-2365 - Karen Y. Oróstica, Ricardo A. Verdugo:
chromPlot: visualization of genomic data in chromosomal context. 2366-2368 - Yun Heo, Anand Ramachandran, Wen-mei W. Hwu, Jian Ma, Deming Chen:
BLESS 2: accurate, memory-efficient and fast error correction method. 2369-2371 - Zuguang Gu, Roland Eils, Matthias Schlesner:
HilbertCurve: an R/Bioconductor package for high-resolution visualization of genomic data. 2372-2374 - Eric Roller, Sergii Ivakhno, Steve Lee, Thomas Royce, Stephen Tanner:
Canvas: versatile and scalable detection of copy number variants. 2375-2377 - Dan Vanderkam, Bülent Arman Aksoy, Isaac Hodes, Jaclyn Perrone, Jeff Hammerbacher:
pileup.js: a JavaScript library for interactive and in-browser visualization of genomic data. 2378-2379
- Vladimir Novichkov, Anna Kaznadzey, Natalia Alexandrova, Denis Kaznadzey:
NSimScan: DNA comparison tool with increased speed, sensitivity and accuracy. 2380-2381 - Yi Wang, Vijay K. Tiwari, Nidhi Rawat, Bikram S. Gill, Naxin Huo, Frank M. You, Devin Coleman-Derr, Yong Qiang Gu:
GSP: a web-based platform for designing genome-specific primers in polyploids. 2382-2383 - Christian Haider, Marina Kavic, Erik L. L. Sonnhammer:
TreeDom: a graphical web tool for analysing domain architecture evolution. 2384-2385
- Erney Ramírez-Aportela, José Ramón López-Blanco, Pablo Chacón:
FRODOCK 2.0: fast protein-protein docking server. 2386-2388
- Lyndal Henden, David Wakeham, Melanie Bahlo:
XIBD: software for inferring pairwise identity by descent on the X chromosome. 2389-2391 - Nadezhda M. Belonogova, Gulnara R. Svishcheva, Tatiana I. Axenovich:
FREGAT: an R package for region-based association analysis. 2392-2393
- Martin Lindén, Vladimir Curic, Alexis Boucharin, David Fange, Johan Elf:
Simulated single molecule microscopy with SMeagol. 2394-2395 - Abdelrahman Hosny, Paola Vera-Licona, Reinhard C. Laubenbacher, Thibauld Favre:
AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms. 2396-2398 - Sufang Wang, Michael Gribskov, Tony R. Hazbun, Pete E. Pascuzzi:
CellMiner Companion: an interactive web application to explore CellMiner NCI-60 data. 2399-2401
- Yuriy Hulovatyy, Huili Chen, Tijana Milenkovic:
Exploring the structure and function of temporal networks with dynamic graphlets. 2402
Volume 32, Number 16, August 2016
Genome Analysis
- Xu Hua, Luxiao Chen, Jin Wang, Jie Li, Edgar Wingender:
Identifying cell-specific microRNA transcriptional start sites. 2403-2410
- Bin Liu, Ren Long, Kuo-Chen Chou:
iDHS-EL: identifying DNase I hypersensitive sites by fusing three different modes of pseudo nucleotide composition into an ensemble learning framework. 2411-2418 - Aleksander Jankowski, Jerzy Tiuryn, Shyam Prabhakar:
Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data. 2419-2426 - En-Shiun Annie Lee, Fiona J. Whelan, Dawn M. E. Bowdish, Andrew K. C. Wong:
Partitioning and correlating subgroup characteristics from Aligned Pattern Clusters. 2427-2434
- Jing Yang, Qi-Yu Jin, Biao Zhang, Hong-Bin Shen:
R2C: improving ab initio residue contact map prediction using dynamic fusion strategy and Gaussian noise filter. 2435-2443 - Naama Hurwitz, Dina Schneidman-Duhovny, Haim J. Wolfson:
Memdock: an α-helical membrane protein docking algorithm. 2444-2450 - Daisuke Kuroda, Jeffrey J. Gray:
Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking. 2451-2456
- Kerstin Bunte, Eemeli Leppäaho, Inka Saarinen, Samuel Kaski:
Sparse group factor analysis for biclustering of multiple data sources. 2457-2463
- Eva-Maria Geissen, Jan Hasenauer, Stephanie Heinrich, Silke Hauf, Fabian J. Theis, Nicole Radde:
MEMO: multi-experiment mixture model analysis of censored data. 2464-2472
- Gianni Monaco, Hao Chen, Michael Poidinger, Jinmiao Chen, João Pedro de Magalhães, Anis Larbi:
flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. 2473-2480
- Venetia Pliatsika, Phillipe Loher, Aristeidis G. Telonis, Isidore Rigoutsos:
MINTbase: a framework for the interactive exploration of mitochondrial and nuclear tRNA fragments. 2481-2489
- Subhadip Basu, Dariusz Plewczynski, Satadal Saha, Matylda Roszkowska, Marta Magnowska, Ewa Baczynska, Jakub Wlodarczyk:
2dSpAn: semiautomated 2-d segmentation, classification and analysis of hippocampal dendritic spine plasticity. 2490-2498
Genome Analysis
- Tarun Mall, John Eckstein, David C. Norris, Hiral Vora, Nowlan H. Freese, Ann E. Loraine:
ProtAnnot: an App for Integrated Genome Browser to display how alternative splicing and transcription affect proteins. 2499-2501 - Hyungro Lee, Min Su Lee, Wazim Mohammed Ismail, Mina Rho, Geoffrey C. Fox, Sangyoon Oh, Haixu Tang:
MGEScan: a Galaxy-based system for identifying retrotransposons in genomes. 2502-2504 - Eugene Andres Houseman, Kevin C. Johnson, Brock C. Christensen:
OxyBS: estimation of 5-methylcytosine and 5-hydroxymethylcytosine from tandem-treated oxidative bisulfite and bisulfite DNA. 2505-2507 - William Chow, Kim Brügger, Mario Cáccamo, Ian Sealy, James W. Torrance, Kerstin Howe:
gEVAL - a web-based browser for evaluating genome assemblies. 2508-2510 - E. C. Schofield, Tim Carver, Premanand Achuthan, P. Freire-Pritchett, Mikhail Spivakov, John A. Todd, Oliver S. Burren:
CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets. 2511-2513 - Peng Jiang, James A. Thomson, Ron M. Stewart:
Quality control of single-cell RNA-seq by SinQC. 2514-2516 - Alexander J. Titus, Eugene Andres Houseman, Kevin C. Johnson, Brock C. Christensen:
methyLiftover: cross-platform DNA methylation data integration. 2517-2519 - Jens Roat Kultima, Luís Pedro Coelho, Kristoffer Forslund, Jaime Huerta-Cepas, Simone S. Li, Marja Driessen, Anita Yvonne Voigt, Georg Zeller, Shinichi Sunagawa, Peer Bork:
MOCAT2: a metagenomic assembly, annotation and profiling framework. 2520-2523 - Miguel Pignatelli:
TnT: a set of libraries for visualizing trees and track-based annotations for the web. 2524-2525
- Yousong Peng, Lei Yang, Honglei Li, Yuanqiang Zou, Lizong Deng, Aiping Wu, Xiangjun Du, Dayan Wang, Yuelong Shu, Taijiao Jiang:
PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences. 2526-2527 - Romain Fenouil, Nicolas Descostes, Lionel Spinelli, Frederic Koch, Muhammad Ahmad Maqbool, Touati Benoukraf, Pierre Cauchy, Charlène Innocenti, Pierre Ferrier, Jean-Christophe Andrau:
Pasha: a versatile R package for piling chromatin HTS data. 2528-2530
- Kota Kasahara, Neetha Mohan, Ikuo Fukuda, Haruki Nakamura:
mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories. 2531-2533 - Hui-Chun Lu, Julián Herrera Braga, Franca Fraternali:
PinSnps: structural and functional analysis of SNPs in the context of protein interaction networks. 2534-2536 - Jimmy C. F. Ngai, Pui-In Mak, Shirley W. I. Siu:
ProtPOS: a python package for the prediction of protein preferred orientation on a surface. 2537-2538 - Erik Walinda, Daichi Morimoto, Mayu Nishizawa, Masahiro Shirakawa, Kenji Sugase:
Efficient identification and analysis of chemical exchange in biomolecules by R1ρ relaxation dispersion with Amaterasu. 2539-2541 - Castrense Savojardo, Piero Fariselli, Pier Luigi Martelli, Rita Casadio:
INPS-MD: a web server to predict stability of protein variants from sequence and structure. 2542-2544 - Zachary Ziegler, Molly Schmidt, Thomas Gurry, Virginia Burger, Collin M. Stultz:
Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins. 2545-2547 - Guillaume Postic, Yassine Ghouzam, Jean-Christophe Gelly:
OREMPRO web server: orientation and assessment of atomistic and coarse-grained structures of membrane proteins. 2548-2550
- Abhinav Nellore, Christopher Wilks, Kasper D. Hansen, Jeffrey T. Leek, Ben Langmead:
Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. 2551-2553
- Linda Odenthal-Hesse, Julien Y. Dutheil, Fabian Klötzl, Bernhard Haubold:
hotspot: software to support sperm-typing for investigating recombination hotspots. 2554-2555 - Christine B. Peterson, M. Bogomolov, Yoav Benjamini, Chiara Sabatti:
TreeQTL: hierarchical error control for eQTL findings. 2556-2558
- Timo Lubitz, Jens Hahn, Frank T. Bergmann, Elad Noor, Edda Klipp, Wolfram Liebermeister:
SBtab: a flexible table format for data exchange in systems biology. 2559-2561
- Petar Velickovic, Pietro Liò:
Muxstep: an open-source C ++ multiplex HMM library for making inferences on multiple data types. 2562-2564
- Marta Rosikiewicz, Marc Robinson-Rechavi:
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. 2565
Volume 32, Number 17, September 2016
Editorial
- Jaap Heringa, Marcel J. T. Reinders, Sanne Abeln, Jeroen de Ridder:
ECCB 2016: The 15th European Conference on Computational Biology. 389-392
- Michael Lenz, Nadia J. T. Roumans, Roel G. Vink, Marleen A. van Baak, Edwin C. M. Mariman, Ilja C. W. Arts, Theo M. de Kok, Gökhan Ertaylan:
Estimating real cell size distribution from cross-section microscopy imaging. 396-404 - Chantriolnt-Andreas Kapourani, Guido Sanguinetti:
Higher order methylation features for clustering and prediction in epigenomic studies. 405-412 - Nanne Aben, Daniel J. Vis, Magali Michaut, Lodewyk F. A. Wessels:
TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types. 413-420 - Charles J. Labuzzetta, Margaret L. Antonio, Patricia M. Watson, Robert C. Wilson, Lauren A. Laboissonniere, Jeffrey M. Trimarchi, Baris Genc, P. Hande Ozdinler, Dennis K. Watson, Paul E. Anderson:
Complementary feature selection from alternative splicing events and gene expression for phenotype prediction. 421-429 - William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg:
Combining dependent P-values with an empirical adaptation of Brown's method. 430-436 - Sunjoo Bang, Jae-Hoon Kim, Hyunjung Shin:
Causality modeling for directed disease network. 437-444 - Thanh Le Van, Matthijs van Leeuwen, Ana Carolina Fierro, Dries De Maeyer, Jimmy Van den Eynden, Lieven P. C. Verbeke, Luc De Raedt, Kathleen Marchal, Siegfried Nijssen:
Simultaneous discovery of cancer subtypes and subtype features by molecular data integration. 445-454 - Muhammad Ammad-ud-din, Suleiman A. Khan, Disha Malani, Astrid Murumägi, Olli-P. Kallioniemi, Tero Aittokallio, Samuel Kaski:
Drug response prediction by inferring pathway-response associations with kernelized Bayesian matrix factorization. 455-463 - Dalia Cohn-Alperovich, Alona Rabner, Ilona Kifer, Yael Mandel-Gutfreund, Zohar Yakhini:
Mutual enrichment in aggregated ranked lists with applications to gene expression regulation. 464-472 - Georg Summer, Thomas Kelder, Marijana Radonjic, Marc van Bilsen, Suzan Wopereis, Stephane Heymans:
The Network Library: a framework to rapidly integrate network biology resources. 473-478 - Kedar Tatwawadi, Mikel Hernaez, Idoia Ochoa, Tsachy Weissman:
GTRAC: fast retrieval from compressed collections of genomic variants. 479-486
- Siavash Sheikhizadeh, M. Eric Schranz, Mehmet Akdel, Dick de Ridder, Sandra Smit:
PanTools: representation, storage and exploration of pan-genomic data. 487-493 - Ilan Shomorony, Samuel H. Kim, Thomas A. Courtade, David N. C. Tse:
Information-optimal genome assembly via sparse read-overlap graphs. 494-502 - Andreas D. M. Gunawan, Bingxin Lu, Louxin Zhang:
A program for verification of phylogenetic network models. 503-510 - Tarmo Äijö, Xiaojing Yue, Anjana Rao, Harri Lähdesmäki:
LuxGLM: a probabilistic covariate model for quantification of DNA methylation modifications with complex experimental designs. 511-519 - Jikai Lei, Yanni Sun:
Assemble CRISPRs from metagenomic sequencing data. 520-528 - Nan Du, Yanni Sun:
Improve homology search sensitivity of PacBio data by correcting frameshifts. 529-537 - Ariya Shajii, Deniz Yörükoglu, Yun William Yu, Bonnie Berger:
Fast genotyping of known SNPs through approximate k-mer matching. 538-544 - Ehsan Haghshenas, Faraz Hach, Süleyman Cenk Sahinalp, Cédric Chauve:
CoLoRMap: Correcting Long Reads by Mapping short reads. 545-551 - Olga V. Matveeva, Yury D. Nechipurenko, Evgeniy Riabenko, Chikako Ragan, Nafisa N. Nazipova, Aleksey Y. Ogurtsov, Svetlana A. Shabalina:
Optimization of signal-to-noise ratio for efficient microarray probe design. 552-558 - Shay Ben-Elazar, Benny Chor, Zohar Yakhini:
Extending partial haplotypes to full genome haplotypes using chromosome conformation capture data. 559-566 - Samuele Girotto, Cinzia Pizzi, Matteo Comin:
MetaProb: accurate metagenomic reads binning based on probabilistic sequence signatures. 567-575 - Omer S. Alkhnbashi, Shiraz A. Shah, Roger A. Garrett, Sita J. Saunders, Fabrizio Costa, Rolf Backofen:
Characterizing leader sequences of CRISPR loci. 576-585
- Sungyoung Lee, Sungkyoung Choi, Young Jin Kim, Bong-Jo Kim, Heungsun Hwang, Taesung Park:
Pathway-based approach using hierarchical components of collapsed rare variants. 586-594 - Kathrin Trappe, Tobias Marschall, Bernhard Y. Renard:
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries. 595-604 - Wenbao Yu, Seungyeoun Lee, Taesung Park:
A unified model based multifactor dimensionality reduction framework for detecting gene-gene interactions. 605-610 - Jaehoon Lee, Young Jin Kim, Juyoung Lee, Bong-Jo Kim, Seungyeoun Lee, Taesung Park:
Gene-set association tests for next-generation sequencing data. 611-619 - Djordje Djordjevic, Kenro Kusumi, Joshua Wing Kei Ho:
XGSA: A statistical method for cross-species gene set analysis. 620-628 - Tuomo Hartonen, Biswajyoti Sahu, Kashyap Dave, Teemu Kivioja, Jussi Taipale:
PeakXus: comprehensive transcription factor binding site discovery from ChIP-Nexus and ChIP-Exo experiments. 629-638 - Ritambhara Singh, Jack Lanchantin, Gabriel Robins, Yanjun Qi:
DeepChrome: deep-learning for predicting gene expression from histone modifications. 639-648 - I. Gregor, Alexander Schönhuth, Alice Carolyn McHardy:
Snowball: strain aware gene assembly of metagenomes. 649-657
- Somaye Hashemifar, Jianzhu Ma, Hammad Naveed, Stefan Canzar, Jinbo Xu:
ModuleAlign: module-based global alignment of protein-protein interaction networks. 658-664 - Konstantinos D. Tsirigos, Arne Elofsson, Pantelis G. Bagos:
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins. 665-671 - Sheng Wang, Jianzhu Ma, Jinbo Xu:
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields. 672-679 - Robert Vaser, Dario Pavlovic, Mile Sikic:
SWORD - a highly efficient protein database search. 680-684 - Olga S. Voitenko, Andi Dhroso, Anna Feldmann, Dmitry Korkin, Olga V. Kalinina:
Patterns of amino acid conservation in human and animal immunodeficiency viruses. 685-692 - Émilie Neveu, David W. Ritchie, Petr Popov, Sergei Grudinin:
PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation. 693-701 - Thang V. Pham, Connie R. Jimenez:
Simulated linear test applied to quantitative proteomics. 702-709 - Thach Nguyen, Michael Habeck:
A probabilistic model for detecting rigid domains in protein structures. 710-717
- Bernhard Steiert, Jens Timmer, Clemens Kreutz:
L1 regularization facilitates detection of cell type-specific parameters in dynamical systems. 718-726 - Hesam Montazeri, Jack Kuipers, Roger D. Kouyos, Jürg Böni, Sabine Yerly, Thomas Klimkait, Vincent Aubert, Huldrych F. Günthard, Niko Beerenwinkel, The Swiss Hiv Cohort Study:
Large-scale inference of conjunctive Bayesian networks. 727-735 - Mark D. M. Leiserson, Matthew A. Reyna, Benjamin J. Raphael:
A weighted exact test for mutually exclusive mutations in cancer. 736-745 - Matthew Ruffalo, Ziv Bar-Joseph:
Genome wide predictions of miRNA regulation by transcription factors. 746-754 - Max Sajitz-Hermstein, Nadine Töpfer, Sabrina Kleessen, Alisdair R. Fernie, Zoran Nikoloski:
iReMet-flux: constraint-based approach for integrating relative metabolite levels into a stoichiometric metabolic models. 755-762 - Hung-Cuong Trinh, Yung-Keun Kwon:
Edge-based sensitivity analysis of signaling networks by using Boolean dynamics. 763-771 - Pauline Traynard, Adrien Fauré, François Fages, Denis Thieffry:
Logical model specification aided by model-checking techniques: application to the mammalian cell cycle regulation. 772-780 - Konstantinos Koutroumpas, Paolo Ballarini, Irene Votsi, Paul-Henry Cournède:
Bayesian parameter estimation for the Wnt pathway: an infinite mixture models approach. 781-789 - Daniel Sánchez-Taltavull, Matthew MacLeod, Theodore J. Perkins:
On cross-conditional and fluctuation correlations in competitive RNA networks. 790-797
Genome Analysis
- Jiarui Ding, Sohrab P. Shah, Anne Condon:
densityCut: an efficient and versatile topological approach for automatic clustering of biological data. 2567-2576 - Elias Dohmen, Lukas P. M. Kremer, Erich Bornberg-Bauer, Carsten Kemena:
DOGMA: domain-based transcriptome and proteome quality assessment. 2577-2581 - Ivan Sovic, Kresimir Krizanovic, Karolj Skala, Mile Sikic:
Evaluation of hybrid and non-hybrid methods for de novo assembly of nanopore reads. 2582-2589 - Liam Harold Childs, Soulafa Mamlouk, Jörgen Brandt, Christine Sers, Ulf Leser:
SoFIA: a data integration framework for annotating high-throughput datasets. 2590-2597 - T. Bernard Bigdeli, Donghyung Lee, Bradley Todd Webb, Brien P. Riley, Vladimir I. Vladimirov, Ayman H. Fanous, Kenneth S. Kendler, Silviu-Alin Bacanu:
A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans. 2598-2603 - Raivo Kolde, Kaspar Märtens, Kaie Lokk, Sven Laur, Jaak Vilo:
seqlm: an MDL based method for identifying differentially methylated regions in high density methylation array data. 2604-2610 - Eric Z. Chen, Hongzhe Li:
A two-part mixed-effects model for analyzing longitudinal microbiome compositional data. 2611-2617 - Zheng-Zheng Tang, Guanhua Chen, Alexander V. Alekseyenko:
PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances. 2618-2625
- Sudhakar Sahoo, Michal P. Switnicki, Jakob Skou Pedersen:
ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction. 2626-2635 - Ganapathi Varma Saripella, Erik L. L. Sonnhammer, Kristoffer Forslund:
Benchmarking the next generation of homology inference tools. 2636-2641
- Gelio Alves, Yi-Kuo Yu:
Confidence assignment for mass spectrometry based peptide identifications via the extreme value distribution. 2642-2649 - David W. Ritchie:
Calculating and scoring high quality multiple flexible protein structure alignments. 2650-2658
- Liang Niu, Zongli Xu, Jack A. Taylor:
RCP: a novel probe design bias correction method for Illumina Methylation BeadChip. 2659-2663
- Huimin Luo, Jianxin Wang, Min Li, Junwei Luo, Xiaoqing Peng, Fang-Xiang Wu, Yi Pan:
Drug repositioning based on comprehensive similarity measures and Bi-Random walk algorithm. 2664-2671 - Francesco Pappalardo, Epifanio Fichera, Nicoletta Paparone, Alessandro Lombardo, Marzio Pennisi, Giulia Russo, Marco Leotta, Alessandro Pedretti, Francesco De Fiore, Santo Motta:
A computational model to predict the immune system activation by citrus-derived vaccine adjuvants. 2672-2680 - Daniel Lobo, Junji Morokuma, Michael Levin:
Computational discovery and in vivo validation of hnf4 as a regulatory gene in planarian regeneration. 2681-2685
- Jonathan D. Wren:
Bioinformatics programs are 31-fold over-represented among the highest impact scientific papers of the past two decades. 2686-2691
Genome Analysis
- Zheng Xu, Guosheng Zhang, Cong Wu, Yun Li, Ming Hu:
FastHiC: a fast and accurate algorithm to detect long-range chromosomal interactions from Hi-C data. 2692-2695
- Elena Yavorska Harris, Rachid Ounit, Stefano Lonardi:
BRAT-nova: fast and accurate mapping of bisulfite-treated reads. 2696-2698 - Paul P. S. Wang, Wendy T. Parker, Susan Branford, Andreas W. Schreiber:
BAM-matcher: a tool for rapid NGS sample matching. 2699-2701 - Ben J. Woodcroft, Joel A. Boyd, Gene W. Tyson:
OrfM: a fast open reading frame predictor for metagenomic data. 2702-2703 - Bianca K. Stöcker, Johannes Köster, Sven Rahmann:
SimLoRD: Simulation of Long Read Data. 2704-2706 - Brandon D. Pickett, S. M. Karlinsey, C. E. Penrod, Michael J. Cormier, Mark T. W. Ebbert, Dennis K. Shiozawa, C. J. Whipple, Perry G. Ridge:
SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences. 2707-2709
- Marianna Sakka, Grigorios Tzortzis, Michalis D. Mantzaris, Nick Bekas, Tahsin F. Kellici, Aristidis Likas, Dimitrios Galaris, Ioannis P. Gerothanassis, Andreas G. Tzakos:
PRESS: PRotEin S-Sulfenylation server. 2710-2712
- Ivan H. Goenawan, Kenneth Bryan, David J. Lynn:
DyNet: visualization and analysis of dynamic molecular interaction networks. 2713-2715 - Devin K. Schweppe, Chunxiang Zheng, Juan D. Chavez, Arti T. Navare, Xia Wu, Jimmy K. Eng, James E. Bruce:
XLinkDB 2.0: integrated, large-scale structural analysis of protein crosslinking data. 2716-2718
- Maciej J. Swat, Pierre Grenon, Sarala M. Wimalaratne:
ProbOnto: ontology and knowledge base of probability distributions. 2719-2721 - Anna Lukasik, Maciej Wójcikowski, Piotr Zielenkiewicz:
Tools4miRs - one place to gather all the tools for miRNA analysis. 2722-2724 - Julia Varga, László Dobson, Gábor E. Tusnády:
TOPDOM: database of conservatively located domains and motifs in proteins. 2725-2726
- Li Teng, Bing He, Jiahui Wang, Kai Tan:
4DGenome: a comprehensive database of chromatin interactions. 2727
Volume 32, Number 18, September 2016
Genome Analysis
- Mulin Jun Li, Zhicheng Pan, Zipeng Liu, Jiexing Wu, Panwen Wang, Yun Zhu, Feng Xu, Zhengyuan Xia, Pak Chung Sham, Jean-Pierre A. Kocher, Miao-Xin Li, Jun S. Liu, Junwen Wang:
Predicting regulatory variants with composite statistic. 2729-2736 - Xiaonan Hu, Wei Zhang, Sanguo Zhang, Shuangge Ma, Qizhai Li:
Group-combined P-values with applications to genetic association studies. 2737-2743
- Mindaugas Margelevicius:
Bayesian nonparametrics in protein remote homology search. 2744-2752 - Kira Vyatkina, Si Wu, Lennard J. Dekker, Martijn M. VanDuijn, Xiaowen Liu, Nikola Tolic, Theo M. Luider, Ljiljana Pasa-Tolic, Pavel A. Pevzner:
Top-down analysis of protein samples by de novo sequencing techniques. 2753-2759 - Vladimir Ulyantsev, Sergey Kazakov, Veronika B. Dubinkina, Alexander V. Tyakht, Dmitry G. Alexeev:
MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data. 2760-2767 - Jun Ding, Xiaoman Li, Haiyan Hu:
TarPmiR: a new approach for microRNA target site prediction. 2768-2775 - Thomas Hrabe, Lukasz Jaroszewski, Adam Godzik:
Revealing aperiodic aspects of solenoid proteins from sequence information. 2776-2782 - Abdullah-Al Mamun, Soumitra Pal, Sanguthevar Rajasekaran:
KCMBT: a k-mer Counter based on Multiple Burst Trees. 2783-2790
- Debswapna Bhattacharya, Renzhi Cao, Jianlin Cheng:
UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. 2791-2799
- Paul Florian Thaben, Pål O. Westermark:
Differential rhythmicity: detecting altered rhythmicity in biological data. 2800-2808 - Francisco García-García, Joaquin Panadero, Joaquín Dopazo, David Montaner:
Integrated gene set analysis for microRNA studies. 2809-2816
- Aaron A. Behr, Katherine Z. Liu, Gracie Liu-Fang, Priyanka Nakka, Sohini Ramachandran:
pong: fast analysis and visualization of latent clusters in population genetic data. 2817-2823
- Jung Eun Shim, Insuk Lee:
Weighted mutual information analysis substantially improves domain-based functional network models. 2824-2830 - Hongyi Zhou, Jeffrey Skolnick:
A knowledge-based approach for predicting gene-disease associations. 2831-2838
- Robert Leaman, Zhiyong Lu:
TaggerOne: joint named entity recognition and normalization with semi-Markov Models. 2839-2846
Genome Analysis
- Zuguang Gu, Roland Eils, Matthias Schlesner:
Complex heatmaps reveal patterns and correlations in multidimensional genomic data. 2847-2849
- Yana Valasatava, Antonio Rosato, Lucia Banci, Claudia Andreini:
MetalPredator: a web server to predict iron-sulfur cluster binding proteomes. 2850-2852
- Shravan Sukumar, Xiaolei Zhu, Spencer S. Ericksen, Julie C. Mitchell:
DBSI server: DNA binding site identifier. 2853-2855
- Umesh K. Nandal, Antoine H. C. van Kampen, Perry D. Moerland:
compendiumdb: an R package for retrieval and storage of functional genomics data. 2856-2857 - David J. Arenillas, Alistair R. R. Forrest, Hideya Kawaji, Timo Lassmann, Wyeth W. Wasserman, Anthony Mathelier:
CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs. 2858-2860
- Yuri Tani Utsunomiya, Marco Milanesi, Adam T. H. Utsunomiya, Paolo Ajmone-Marsan, José Fernando Garcia:
GHap: an R package for genome-wide haplotyping. 2861-2862
- Sisi Fan, Quentin Geissmann, Eszter Lakatos, Saulius Lukauskas, Angelique Ale, Ann C. Babtie, Paul D. W. Kirk, Michael P. H. Stumpf:
MEANS: python package for Moment Expansion Approximation, iNference and Simulation. 2863-2865 - Giovanni Y. Di Veroli, Chiara Fornari, Dennis Wang, Séverine Mollard, Jo L. Bramhall, Frances M. Richards, Duncan I. Jodrell:
Combenefit: an interactive platform for the analysis and visualization of drug combinations. 2866-2868 - Samy Deghou, Georg Zeller, Murat Iskar, Marja Driessen, Mercedes Castillo, Vera van Noort, Peer Bork:
CART - a chemical annotation retrieval toolkit. 2869-2871 - Giorgio Valentini, Giuliano Armano, Marco Frasca, Jianyi Lin, Marco Mesiti, Matteo Re:
RANKS: a flexible tool for node label ranking and classification in biological networks. 2872-2874 - Daniel Weindl, André Wegner, Karsten Hiller:
MIA: non-targeted mass isotopolome analysis. 2875-2876 - Michael J. O'Connell, Eric F. Lock:
R.JIVE for exploration of multi-source molecular data. 2877-2879 - James C. Schaff, Dan Vasilescu, Ion I. Moraru, Leslie M. Loew, Michael L. Blinov:
Rule-based modeling with Virtual Cell. 2880-2882
- Philippe Thomas, Tim Rocktäschel, Jörg Hakenberg, Yvonne Lichtblau, Ulf Leser:
SETH detects and normalizes genetic variants in text. 2883-2885 - Kyubum Lee, Won-Ho Shin, Byounggun Kim, Sunwon Lee, Yonghwa Choi, Sunkyu Kim, Minji Jeon, Aik Choon Tan, Jaewoo Kang:
HiPub: translating PubMed and PMC texts to networks for knowledge discovery. 2886-2888
- Sayoni Das, David A. Lee, Ian Sillitoe, Natalie L. Dawson, Jonathan G. Lees, Christine A. Orengo:
Functional classification of CATH superfamilies: a domain-based approach for protein function annotation. 2889
Volume 32, Number 19, October 2016
Systems Biology
- Zijian Ding, Songpeng Zu, Jin Gu:
Evaluating the molecule-based prediction of clinical drug responses in cancer. 2891-2895
Genome Analysis
- Pol Cuscó, Guillaume J. Filion:
Zerone: a ChIP-seq discretizer for multiple replicates with built-in quality control. 2896-2902 - Micol Marchetti-Bowick, Junming Yin, Judie A. Howrylak, Eric P. Xing:
A time-varying group sparse additive model for genome-wide association studies of dynamic complex traits. 2903-2910 - Yuta Suzuki, Jonas Korlach, Stephen W. Turner, Tatsuya Tsukahara, Junko Taniguchi, Wei Qu, Kazuki Ichikawa, Jun Yoshimura, Hideaki Yurino, Yuji Takahashi, Jun Mitsui, Hiroyuki Ishiura, Shoji Tsuji, Hiroyuki Takeda, Shinichi Morishita:
AgIn: measuring the landscape of CpG methylation of individual repetitive elements. 2911-2919
- Panu Somervuo, Sonja Koskela, Juho Pennanen, R. Henrik Nilsson, Otso Ovaskainen:
Unbiased probabilistic taxonomic classification for DNA barcoding. 2920-2927
- Markus Fricke, Manja Marz:
Prediction of conserved long-range RNA-RNA interactions in full viral genomes. 2928-2935 - Lijun Quan, Qiang Lv, Yang Zhang:
STRUM: structure-based prediction of protein stability changes upon single-point mutation. 2936-2946 - Nouf S. Al-Numair, Luis Lopes, Petros Syrris, Lorenzo Monserrat, Perry Elliott, Andrew C. R. Martin:
The structural effects of mutations can aid in differential phenotype prediction of beta-myosin heavy chain (Myosin-7) missense variants. 2947-2955
- Jing Yang, Christopher A. Penfold, Murray R. Grant, Magnus Rattray:
Inferring the perturbation time from biological time course data. 2956-2964 - Yuanhua Huang, Guido Sanguinetti:
Statistical modeling of isoform splicing dynamics from RNA-seq time series data. 2965-2972 - John E. Reid, Lorenz Wernisch:
Pseudotime estimation: deconfounding single cell time series. 2973-2980
- Kun Ming Kenneth Lim, Chenhao Li, Kern Rei Chng, Niranjan Nagarajan:
@MInter: automated text-mining of microbial interactions. 2981-2987 - Fabio Fabris, Alex Alves Freitas:
New KEGG pathway-based interpretable features for classifying ageing-related mouse proteins. 2988-2995 - Guangyuan Fu, Jun Wang, Bo Yang, Guo-Xian Yu:
NegGOA: negative GO annotations selection using ontology structure. 2996-3004
- Christopher B. Barnett, Kiyoko F. Aoki-Kinoshita, Kevin J. Naidoo:
The Glycome Analytics Platform: an integrative framework for glycobioinformatics. 3005-3011
Genome Analysis
- Zachary L. Skidmore, Alex H. Wagner, Robert Lesurf, Katie M. Campbell, Jason Kunisaki, Obi L. Griffith, Malachi Griffith:
GenVisR: Genomic Visualizations in R. 3012-3014 - F. Anthony San Lucas, Smruthy Sivakumar, Selina Vattathil, Jerry Fowler, Eduardo Vilar, Paul Scheet:
Rapid and powerful detection of subtle allelic imbalance from exome sequencing data with hapLOHseq. 3015-3017 - Tomasz Stokowy, Mateusz Garbulowski, Torunn Fiskerstrand, Rita Holdhus, Kornel Labun, Pawel Sztromwasser, Christian Gilissen, Alexander Hoischen, Gunnar Houge, Kjell Petersen, Inge Jonassen, Vidar M. Steen:
RareVariantVis: new tool for visualization of causative variants in rare monogenic disorders using whole genome sequencing data. 3018-3020 - Maria Nattestad, Michael C. Schatz:
Assemblytics: a web analytics tool for the detection of variants from an assembly. 3021-3023
- Zhong Wang, André L. Martins, Charles G. Danko:
RTFBSDB: an integrated framework for transcription factor binding site analysis. 3024-3026
- Astrid Cruaud, Mathieu Gautier, Jean-Pierre Rossi, Jean-Yves Rasplus, Jérôme Gouzy:
RADIS: analysis of RAD-seq data for interspecific phylogeny. 3027-3028
- Billy Heung Wing Chang, Weidong Tian:
GSA-Lightning: ultra-fast permutation-based gene set analysis. 3029-3031
- Pier Francesco Palamara:
ARGON: fast, whole-genome simulation of the discrete time Wright-fisher process. 3032-3034 - Russell Corbett-Detig, Matt Jones:
SELAM: simulation of epistasis and local adaptation during admixture with mate choice. 3035-3037 - Daniel Edsgärd, Björn Reinius, Rickard Sandberg:
scphaser: haplotype inference using single-cell RNA-seq data. 3038-3040
- Francisco Salavert, Luz Garcia-Alonso, Rubén Sánchez, Roberto Alonso, Marta Bleda, Ignacio Medina, Joaquín Dopazo:
Web-based network analysis and visualization using CellMaps. 3041-3043
- Sun Kim, Lana Yeganova, W. John Wilbur:
Meshable: searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms. 3044-3046 - Philip Ewels, Måns Magnusson, Sverker Lundin, Max Käller:
MultiQC: summarize analysis results for multiple tools and samples in a single report. 3047-3048
- Vijay Barve, Javier Otegui:
bdvis: visualizing biodiversity data in R. 3049-3050
- Forest Agostinelli, Nicholas Ceglia, Babak Shahbaba, Paolo Sassone-Corsi, Pierre Baldi:
What time is it? Deep learning approaches for circadian rhythms. 3051
Volume 32, Number 20, October 2016
Sequence Analysis
- Anna A. Deeva, Evgenia A. Temlyakova, Anatoly A. Sorokin, Elena V. Nemtseva, Valentina A. Kratasyuk:
Structural distinctions of fast and slow bacterial luciferases revealed by phylogenetic analysis. 3053-3057
Genome Analysis
- Jianwei Zhang, Dave Kudrna, Ting Mu, Weiming Li, Dario Copetti, Yeisoo Yu, Jose Luis Goicoechea, Yang Lei, Rod A. Wing:
Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences. 3058-3064 - Jacob Shujui Hsu, Johnny S. H. Kwan, Zhicheng Pan, Maria-Mercè Garcia-Barcelo, Pak Chung Sham, Miao-Xin Li:
Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes. 3065-3071 - Junho Kim, Ju Heon Maeng, Jae Seok Lim, Hyeonju Son, Junehawk Lee, Jeong Ho Lee, Sangwoo Kim:
Vecuum: identification and filtration of false somatic variants caused by recombinant vector contamination. 3072-3080
- Hákon Guðbjartsson, Guðmundur Fr. Georgsson, Sigurjón Axel Guðjónsson, Ragnar þór Valdimarsson, Jóhann H. Sigurðsson, Sigmar K. Stefánsson, Gísli Másson, Gísli Magnússon, Vilmundur Pálmason, Kári Stefánsson:
GORpipe: a query tool for working with sequence data based on a Genomic Ordered Relational (GOR) architecture. 3081-3088 - John P. Barton, Eleonora De Leonardis, Alice Coucke, Simona Cocco:
ACE: adaptive cluster expansion for maximum entropy graphical model inference. 3089-3097 - Bram Gerritsen, Aridaman Pandit, Arno C. Andeweg, Rob J. De Boer:
RTCR: a pipeline for complete and accurate recovery of T cell repertoires from high throughput sequencing data. 3098-3106 - Ping-Ping Wen, Shaoping Shi, Hao-Dong Xu, Li-na Wang, Jian-Ding Qiu:
Accurate in silico prediction of species-specific methylation sites based on information gain feature optimization. 3107-3115 - Wangren Qiu, Bi-Qian Sun, Xuan Xiao, Zhao-Chun Xu, Kuo-Chen Chou:
iPTM-mLys: identifying multiple lysine PTM sites and their different types. 3116-3123 - Daniel L. Greenfield, Oliver Stegle, Alban Rrustemi:
GeneCodeq: quality score compression and improved genotyping using a Bayesian framework. 3124-3132 - Jianhua Jia, Liuxia Zhang, Zi Liu, Xuan Xiao, Kuo-Chen Chou:
pSumo-CD: predicting sumoylation sites in proteins with covariance discriminant algorithm by incorporating sequence-coupled effects into general PseAAC. 3133-3141
- Pradeep Anand Ravindranath, Michel F. Sanner:
AutoSite: an automated approach for pseudo-ligands prediction - from ligand-binding sites identification to predicting key ligand atoms. 3142-3149
- Haixiang Zhang, Yinan Zheng, Zhou Zhang, Tao Gao, Brian Joyce, Grace Yoon, Wei Zhang, Joel Schwartz, Allan C. Just, Elena Colicino, Pantel Vokonas, Lihui Zhao, Jinchi Lv, Andrea A. Baccarelli, Lifang Hou, Lei Liu:
Estimating and testing high-dimensional mediation effects in epigenetic studies. 3150-3154
- Lei Meng, Aaron Striegel, Tijana Milenkovic:
Local versus global biological network alignment. 3155-3164 - Jing Ma, Ali Shojaie, George Michailidis:
Network-based pathway enrichment analysis with incomplete network information. 3165-3174
- Dhanya Sridhar, Shobeir Fakhraei, Lise Getoor:
A probabilistic approach for collective similarity-based drug-drug interaction prediction. 3175-3182 - Na Le Dang, Tyler B. Hughes, Varun Krishnamurthy, S. Joshua Swamidass:
A simple model predicts UGT-mediated metabolism. 3183-3189
Genome Analysis
- Kai Kruse, Clemens B. Hug, Benjamín Hernández-Rodríguez, Juan M. Vaquerizas:
TADtool: visual parameter identification for TAD-calling algorithms. 3190-3192 - Bai-Han Zhu, Ying-Nan Song, Wei Xue, Gui-Cai Xu, Jun Xiao, Ming-Yuan Sun, Xiaowen Sun, Jiongtang Li:
PEP_scaffolder: using (homologous) proteins to scaffold genomes. 3193-3195
- Ewa A. Bergmann, Bo-Juen Chen, Kanika Arora, Vladimir Vacic, Michael C. Zody:
Conpair: concordance and contamination estimator for matched tumor-normal pairs. 3196-3198
- Vittorio Fortino, Roberto Tagliaferri, Dario Greco:
CONDOP: an R package for CONdition-Dependent Operon Predictions. 3199-3200 - Steffi Grote, Kay Prüfer, Janet Kelso, Michael Dannemann:
ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain. 3201-3203
- Simon Dellicour, Rebecca Rose, Nuno R. Faria, Philippe Lemey, Oliver G. Pybus:
SERAPHIM: studying environmental rasters and phylogenetically informed movements. 3204-3206
- James R. Staley, James A. Blackshaw, Mihir A. Kamat, Steve Ellis, Praveen Surendran, Benjamin B. Sun, Dirk S. Paul, Daniel Freitag, Stephen Burgess, John Danesh, Robin Young, Adam S. Butterworth:
PhenoScanner: a database of human genotype-phenotype associations. 3207-3209
- David Dao, Adam Fraser, Jane Hung, Vebjorn Ljosa, Shantanu Singh, Anne E. Carpenter:
CellProfiler Analyst: interactive data exploration, analysis and classification of large biological image sets. 3210-3212
- Vikas Bansal, Ondrej Libiger:
A statistical method for the detection of variants from next-generation resequencing of DNA poolsA probabilistic method for the detection and genotyping of small indels from population-scale sequence data. 3213
Volume 32, Number 21, November 2016
Genome Analysis
- Sara El-Metwally, Magdi Zakaria, Taher Hamza:
LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads. 3215-3223
- Bo Liu, Hongzhe Guo, Michael Brudno, Yadong Wang:
deBGA: read alignment with de Bruijn graph-based seed and extension. 3224-3232 - Qamar M. Sheikh, Derek Gatherer, Pedro A. Reche, Darren R. Flower:
Towards the knowledge-based design of universal influenza epitope ensemble vaccines. 3233-3239 - Gongyi Huang, Shaoli Wang, Xueqin Wang, Na You:
An empirical Bayes method for genotyping and SNP detection using multi-sample next-generation sequencing data. 3240-3245 - Kazunori D. Yamada, Kentaro Tomii, Kazutaka Katoh:
Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees. 3246-3251
- Marco Barsacchi, Eva Maria Novoa, Manolis Kellis, Alessio Bechini:
SwiSpot: modeling riboswitches by spotting out switching sequences. 3252-3259 - Xiuzhen Hu, Qiwen Dong, Jianyi Yang, Yang Zhang:
Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. 3260-3269 - Pawel Krupa, Magdalena A. Mozolewska, Marta Wisniewska, Yanping Yin, Yi He, Adam K. Sieradzan, Robert Ganzynkowicz, Agnieszka G. Lipska, Agnieszka S. Karczynska, Magdalena Slusarz, Rafal Slusarz, Artur Gieldon, Cezary Czaplewski, Dawid Jagiela, Bartlomiej Zaborowski, Harold A. Scheraga, Adam Liwo:
Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. 3270-3278
- Xuebei An, Jianhua Hu, Kim-Anh Do:
SIFORM: shared informative factor models for integration of multi-platform bioinformatic data. 3279-3290 - Zhi Liu, Tuantuan Gui, Zhen Wang, Hong Li, Yunhe Fu, Xiao Dong, Yixue Li:
cisASE: a likelihood-based method for detecting putative cis-regulated allele-specific expression in RNA sequencing data. 3291-3297
- A. Macé, M. A. Tuke, Jacques S. Beckmann, L. Lin, S. Jacquemont, Michael N. Weedon, Alexandre Reymond, Zoltán Kutalik:
New quality measure for SNP array based CNV detection. 3298-3305
- Yat Hin Chan, Jukka Intosalmi, Sini Rautio, Harri Lähdesmäki:
A subpopulation model to analyze heterogeneous cell differentiation dynamics. 3306-3313
- Tomer Illouz, Ravit Madar, Charlotte Clague, Kathleen J. Griffioen, Yoram Louzoun, Eitan Okun:
Unbiased classification of spatial strategies in the Barnes maze. 3314-3320
Genome Analysis
- Alla Mikheenko, Gleb Valin, Andrey D. Prjibelski, Vladislav Saveliev, Alexey A. Gurevich:
Icarus: visualizer for de novo assembly evaluation. 3321-3323 - Hamid Younesy, Cydney B. Nielsen, Matthew C. Lorincz, Steven J. M. Jones, Mohammad M. Karimi, Torsten Möller:
ChAsE: chromatin analysis and exploration tool. 3324-3326 - Thomas Weinmaier, Alexander Platzer, Jeroen Frank, Hans-Jörg Hellinger, Patrick Tischler, Thomas Rattei:
ConsPred: a rule-based (re-)annotation framework for prokaryotic genomes. 3327-3329 - Jakob Dohrmann, Rahul Singh:
The SMAL web server: global multiple network alignment from pairwise alignments. 3330-3332 - Mingyang Cai, Fan Gao, Wange Lu, Kai Wang:
w4CSeq: software and web application to analyze 4C-seq data. 3333-3335 - Jian Ma, Johannes Köster, Qian Qin, Shengen Hu, Wei Li, Chenhao Chen, Qingyi Cao, Jinzeng Wang, Shenglin Mei, Qi Liu, Han Xu, Xiaole Shirley Liu:
CRISPR-DO for genome-wide CRISPR design and optimization. 3336-3338
- Altan Kara, Martin J. Vickers, Martin T. Swain, David E. Whitworth, Narcis Fernandez-Fuentes:
MetaPred2CS: a sequence-based meta-predictor for protein-protein interactions of prokaryotic two-component system proteins. 3339-3341
- Bing Xia, Sandor Vajda, Dima Kozakov:
Accounting for pairwise distance restraints in FFT-based protein-protein docking. 3342-3344
- Alexey Stupnikov, Shailesh Tripathi, Ricardo de Matos Simoes, Darragh G. McArt, Manuel Salto-Tellez, Galina V. Glazko, Matthias Dehmer, Frank Emmert-Streib:
samExploreR: exploring reproducibility and robustness of RNA-seq results based on SAM files. 3345-3347
- Xiaoyu Wang, James Y. Dai:
TwoPhaseInd: an R package for estimating gene-treatment interactions and discovering predictive markers in randomized clinical trials. 3348-3350
- Gang Wu, Ron C. Anafi, Michael Hughes, Karl Kornacker, John B. Hogenesch:
MetaCycle: an integrated R package to evaluate periodicity in large scale data. 3351-3353 - Guillaume Devailly, Anna Mantsoki, Anagha Joshi:
Heat*seq: an interactive web tool for high-throughput sequencing experiment comparison with public data. 3354-3356 - Eva Balsa-Canto, David Henriques, Attila Gábor, Julio R. Banga:
AMIGO2, a toolbox for dynamic modeling, optimization and control in systems biology. 3357-3359 - Irene Otero-Muras, David Henriques, Julio R. Banga:
SYNBADm: a tool for optimization-based automated design of synthetic gene circuits. 3360-3362 - David G. P. van IJzendoorn, Kimberly Glass, John Quackenbush, Marieke L. Kuijjer:
PyPanda: a Python package for gene regulatory network reconstruction. 3363-3365 - Leonard A. Harris, Justin S. Hogg, José Juan Tapia, John A. P. Sekar, Sanjana Gupta, Ilya Korsunsky, Arshi Arora, Dipak Barua, Robert P. Sheehan, James R. Faeder:
BioNetGen 2.2: advances in rule-based modeling. 3366-3368 - Maureen R. Smith, Redmond P. Smyth, Roland Marquet, Max von Kleist:
MIMEAnTo: profiling functional RNA in mutational interference mapping experiments. 3369-3370
- Edgar Mixcoha, Roberto Rosende, Rebeca García-Fandiño, Ángel Piñeiro:
Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins. 3371-3373
Volume 32, Number 22, November 2016
Phylogenetics
- Sebastián Duchêne, Jemma L. Geoghegan, Edward C. Holmes, Simon Y. W. Ho:
Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods. 3375-3379
Genome Analysis
- Dmitry Antipov, Nolan Hartwick, Max W. Shen, Mikhail Raiko, Alla L. Lapidus, Pavel A. Pevzner:
plasmidSPAdes: assembling plasmids from whole genome sequencing data. 3380-3387 - Stefanie König, Lars Romoth, Lizzy Gerischer, Mario Stanke:
Simultaneous gene finding in multiple genomes. 3388-3395 - Yalu Wen, Fushun Chen, Qingzheng Zhang, Yan Zhuang, Zhiguang Li:
Detection of differentially methylated regions in whole genome bisulfite sequencing data using local Getis-Ord statistics. 3396-3404
- Subrata Saha, Sanguthevar Rajasekaran:
NRGC: a novel referential genome compression algorithm. 3405-3412
- Véronique Hourdel, Stevenn Volant, Darragh P. O'Brien, Alexandre Chenal, Julia Chamot-Rooke, Marie-Agnès Dillies, Sébastien Brier:
MEMHDX: an interactive tool to expedite the statistical validation and visualization of large HDX-MS datasets. 3413-3419 - George A. Cortina, Peter M. Kasson:
Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance. 3420-3427
- Mengyin Lu, Matthew Stephens:
Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances. 3428-3434
- Yun Hao, Nicholas P. Tatonetti:
Predicting G protein-coupled receptor downstream signaling by tissue expression. 3435-3443
- Zhehuan Zhao, Zhihao Yang, Ling Luo, Hongfei Lin, Jian Wang:
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network. 3444-3453 - Shu Tadaka, Kengo Kinoshita:
NCMine: Core-peripheral based functional module detection using near-clique mining. 3454-3460 - Daniyar Bakirov, Alex Pappachen James, Amin Zollanvari:
An efficient method to estimate the optimum regularization parameter in RLDA. 3461-3468 - Yi Wang, Ling Xu, Yong Qiang Gu, Devin Coleman-Derr:
MetaCoMET: a web platform for discovery and visualization of the core microbiome. 3469-3470
- Yukako Tohsato, Kenneth H. L. Ho, Koji Kyoda, Shuichi Onami:
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena. 3471-3479
- Jian Fang, Dongdong Lin, S. Charles Schulz, Zongben Xu, Vince D. Calhoun, Yu-Ping Wang:
Joint sparse canonical correlation analysis for detecting differential imaging genetics modules. 3480-3488
Genome Analysis
- Samuele Bovo, Pietro Di Lena, Pier Luigi Martelli, Piero Fariselli, Rita Casadio:
NET-GE: a web-server for NETwork-based human gene enrichment. 3489-3491
- Hamid Mohamadi, Justin Chu, Benjamin P. Vandervalk, Inanç Birol:
ntHash: recursive nucleotide hashing. 3492-3494 - Qiang Kou, Likun Xun, Xiaowen Liu:
TopPIC: a software tool for top-down mass spectrometry-based proteoform identification and characterization. 3495-3497 - Chia-Hua Chang, Min-Te Chou, Yi-Chung Wu, Ting-Wei Hong, Yun-Lung Li, Chia-Hsiang Yang, Jui-Hung Hung:
sBWT: memory efficient implementation of the hardware-acceleration-friendly Schindler transform for the fast biological sequence mapping. 3498-3500 - Guy Yachdav, Sebastian Wilzbach, Benedikt Rauscher, Robert Sheridan, Ian Sillitoe, James B. Procter, Suzanna E. Lewis, Burkhard Rost, Tatyana Goldberg:
MSAViewer: interactive JavaScript visualization of multiple sequence alignments. 3501-3503 - Samuel A. Lambert, Mihai Albu, Timothy R. Hughes, Hamed Shateri Najafabadi:
Motif comparison based on similarity of binding affinity profiles. 3504-3506 - Haifeng Chen, Andrew D. Smith, Ting Chen:
WALT: fast and accurate read mapping for bisulfite sequencing. 3507-3509
- Lars Skjærven, Shashank Jariwala, Xin-Qiu Yao, Barry J. Grant:
Online interactive analysis of protein structure ensembles with Bio3D-web. 3510-3512
- Aika Terada, Ryo Yamada, Koji Tsuda, Jun Sese:
LAMPLINK: detection of statistically significant SNP combinations from GWAS data. 3513-3515 - Diego Ortega-Del Vecchyo, Clare D. Marsden, Kirk E. Lohmueller:
PReFerSim: fast simulation of demography and selection under the Poisson Random Field model. 3516-3518
- Giovanni Stracquadanio, Kun Yang, Jef D. Boeke, Joel S. Bader:
BioPartsDB: a synthetic biology workflow web-application for education and research. 3519-3521 - Tadi Venkata Sivakumar, Varun Giri, Jin Hwan Park, Tae Yong Kim, Anirban Bhaduri:
ReactPRED: a tool to predict and analyze biochemical reactions. 3522-3524
- Richard A. Schäfer, Björn Voß:
VisualGraphX: interactive graph visualization within Galaxy. 3525-3527 - Li Chen, Yongyi Yu, Xinchen Zhang, Chen Liu, Chuyu Ye, Longjiang Fan:
PcircRNA_finder: a software for circRNA prediction in plants. 3528-3529
- Mark R. Winter, Walter C. Mankowski, Eric Wait, Sally Temple, Andrew R. Cohen:
LEVER: software tools for segmentation, tracking and lineaging of proliferating cells. 3530-3531 - David Legland, Ignacio Arganda-Carreras, Philippe Andrey:
MorphoLibJ: integrated library and plugins for mathematical morphology with ImageJ. 3532-3534
Volume 32, Number 23, December 2016
Genome Analysis
- Niels W. Hanson, Kishori M. Konwar, Steven J. Hallam:
LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes. 3535-3542 - Tianshun Gao, Bing He, Sheng Liu, Heng Zhu, Kai Tan, Jiang Qian:
EnhancerAtlas: a resource for enhancer annotation and analysis in 105 human cell/tissue types. 3543-3551 - Alexander V. Alekseyenko:
Multivariate Welch t-test on distances. 3552-3558
- Ruoyan Chen, Yu-Lung Lau, Yan Zhang, Wanling Yang:
SRinversion: a tool for detecting short inversions by splitting and re-aligning poorly mapped and unmapped sequencing reads. 3559-3565 - Nicole E. Wheeler, Lars Barquist, Robert A. Kingsley, Paul P. Gardner:
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes. 3566-3574
- Krishna Choudhary, Nathan P. Shih, Fei Deng, Mirko Ledda, Bo Li, Sharon Aviran:
Metrics for rapid quality control in RNA structure probing experiments. 3575-3583 - Jing Lu, Heather A. Carlson:
ChemTreeMap: an interactive map of biochemical similarity in molecular datasets. 3584-3592
- Ei-Wen Yang, Tao Jiang:
SDEAP: a splice graph based differential transcript expression analysis tool for population data. 3593-3602
- Xiang Zhan, Santhosh Girirajan, Ni Zhao, Michael C. Wu, Debashis Ghosh:
A novel copy number variants kernel association test with application to autism spectrum disorders studies. 3603-3610
- Steven B. Cogill, Liangjiang Wang:
Support vector machine model of developmental brain gene expression data for prioritization of Autism risk gene candidates. 3611-3618 - Dong Xu, Meizhuo Zhang, Yanping Xie, Fan Wang, Ming Chen, Kenny Q. Zhu, Jia Wei:
DTMiner: identification of potential disease targets through biomedical literature mining. 3619-3626 - Gianluca Corrado, Toma Tebaldi, Fabrizio Costa, Paolo Frasconi, Andrea Passerini:
RNAcommender: genome-wide recommendation of RNA-protein interactions. 3627-3634 - Serguei V. S. Pakhomov, Gregory P. Finley, Reed McEwan, Yan Wang, Genevieve B. Melton:
Corpus domain effects on distributional semantic modeling of medical terms. 3635-3644 - Vedrana Vidulin, Tomislav Smuc, Fran Supek:
Extensive complementarity between gene function prediction methods. 3645-3653
- Shicai Wang, Mihaela A. Mares, Yike Guo:
CGDM: collaborative genomic data model for molecular profiling data using NoSQL. 3654-3660
Genome Analysis
- Louis-Philippe Lemieux Perreault, Marc-André Legault, Géraldine Asselin, Marie-Pierre Dubé:
genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools. 3661-3663 - Rickard Hammarén, Chandan Pal, Johan Bengtsson-Palme:
FARAO: the flexible all-round annotation organizer. 3664-3666 - Zongli Xu, Jack A. Taylor, Yuet-Kin Leung, Shuk-Mei Ho, Liang Niu:
oxBS-MLE: an efficient method to estimate 5-methylcytosine and 5-hydroxymethylcytosine in paired bisulfite and oxidative bisulfite treated DNA. 3667-3669
- Jamie Waese, Asher Pasha, Tingting Wang, Anna van Weringh, David S. Guttman, Nicholas J. Provart:
Gene Slider: sequence logo interactive data-visualization for education and research. 3670-3672
- Erwin Holzhauser, Ping Ge, Shaojie Zhang:
WebSTAR3D: a web server for RNA 3D structural alignment. 3673-3675 - Li C. Xue, João P. G. L. M. Rodrigues, Panagiotis L. Kastritis, Alexandre M. J. J. Bonvin, Anna Vangone:
PRODIGY: a web server for predicting the binding affinity of protein-protein complexes. 3676-3678
- Jasmine Dumas, Michael A. Gargano, Garrett M. Dancik:
shinyGEO: a web-based application for analyzing gene expression omnibus datasets. 3679-3681 - Thomas Eder, Florian Grebien, Thomas Rattei:
NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies. 3682-3684
- Zhou Lan, Yize Zhao, Jian Kang, Tianwei Yu:
Bayesian network feature finder (BANFF): an R package for gene network feature selection. 3685-3687
- Stephen G. Gaffney, Jeffrey P. Townsend:
PathScore: a web tool for identifying altered pathways in cancer data. 3688-3690
- Jan R. Detrez, Jean-Marie Vanderwinden, Michaël Barbier, Marlies Verschuuren, Rony Nuydens, Xavier Langlois, Jean-Pierre Timmermans, Winnok De Vos:
BiDiFuse: a FIJI plugin for fusing bi-directionally recorded microscopic image volumes. 3691-3693
Bioimage Informatics
- X. Hu, Q. Dong, J. Yang, Y. Zhang:
Recognizing metal and acid radical ion-binding sites by integrating ab initio modeling with template-based transferals. 3694
Volume 32, Number 24, December 2016
Genome Analysis
- Hua-Jun Wu, Franziska Michor:
A computational strategy to adjust for copy number in tumor Hi-C data. 3695-3701 - Rolf Hilker, Kai Bernd Stadermann, Oliver Schwengers, Evgeny Anisiforov, Sebastian Jaenicke, Bernd Weisshaar, Tobias Zimmermann, Alexander Goesmann:
ReadXplorer 2 - detailed read mapping analysis and visualization from one single source. 3702-3708 - Rodrigo Cánovas, Alistair Moffat, Andrew Turpin:
CSAM: Compressed SAM format. 3709-3716 - Jack P. Hou, Amin Emad, Gregory J. Puleo, Jian Ma, Olgica Milenkovic:
A new correlation clustering method for cancer mutation analysis. 3717-3728
- Lisle E. Mose, Sara R. Selitsky, Lisa M. Bixby, David L. Marron, Michael D. Iglesia, Jonathan S. Serody, Charles M. Perou, Benjamin Vincent, Joel S. Parker:
Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V'DJer. 3729-3734 - Minzhu Xie, Qiong Wu, Jianxin Wang, Tao Jiang:
H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids. 3735-3744 - Weizhong Lin, Dong Xu:
Imbalanced multi-label learning for identifying antimicrobial peptides and their functional types. 3745-3752
- Cristina Frías-López, José F. Sánchez-Herrero, Sara Guirao-Rico, Elisa Mora, Miquel A. Arnedo, Alejandro Sánchez-Gracia, Julio Rozas:
DOMINO: development of informative molecular markers for phylogenetic and genome-wide population genetic studies in non-model organisms. 3753-3759
- Jinchao Yu, Raphaël Guérois:
PPI4DOCK: large scale assessment of the use of homology models in free docking over more than 1000 realistic targets. 3760-3767 - Jianzhao Gao, Yuedong Yang, Yaoqi Zhou:
Predicting the errors of predicted local backbone angles and non-local solvent- accessibilities of proteins by deep neural networks. 3768-3773 - Qiwei Li, David B. Dahl, Marina Vannucci, Hyun Joo, Jerry W. Tsai:
KScons: a Bayesian approach for protein residue contact prediction using the knob-socket model of protein tertiary structure. 3774-3781
- Yiyi Liu, Hongyu Zhao:
Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes. 3782-3789 - Eoin C. Whelan, Alexander C. Nwala, Christopher Osgood, Stephan Olariu:
Selective mutation accumulation: a computational model of the paternal age effect. 3790-3797 - Andy L. Olivares, Miguel Ángel González Ballester, Jérôme Noailly:
Virtual exploration of early stage atherosclerosis. 3798-3806 - Pedro A. Saa, Lars Keld Nielsen:
Fast-SNP: a fast matrix pre-processing algorithm for efficient loopless flux optimization of metabolic models. 3807-3814
- Sara Hillenmeyer, Lea K. Davis, Eric R. Gamazon, Edwin H. Cook Jr., Nancy J. Cox, Russ B. Altman:
STAMS: STRING-assisted module search for genome wide association studies and application to autism. 3815-3822
Sequence Analysis
- Rachid Ounit, Stefano Lonardi:
Higher classification sensitivity of short metagenomic reads with CLARK-S. 3823-3825 - Jorge González-Domínguez, Yongchao Liu, Juan Touriño, Bertil Schmidt:
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems. 3826-3828 - Bayo Lau, Marghoob Mohiyuddin, John C. Mu, Li Tai Fang, Narges Bani Asadi, Carolina Dallett, Hugo Y. K. Lam:
LongISLND: in silico sequencing of lengthy and noisy datatypes. 3829-3832
- Andreas Prlic, Tara Kalro, Roshni Bhattacharya, Cole H. Christie, Stephen K. Burley, Peter W. Rose:
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank. 3833-3835
- Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson:
BatchQC: interactive software for evaluating sample and batch effects in genomic data. 3836-3838
- Andrew D. Kern, Daniel R. Schrider:
Discoal: flexible coalescent simulations with selection. 3839-3841
- Amit Frishberg, Avital Brodt, Yael Steuerman, Irit Gat-Viks:
ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data. 3842-3843 - Aristidis G. Vrahatis, Panos Balomenos, Athanasios K. Tsakalidis, Anastasios Bezerianos:
DEsubs: an R package for flexible identification of differentially expressed subpathways using RNA-seq experiments. 3844-3846 - Jamie Soul, Sara L. Dunn, Tim E. Hardingham, Ray P. Boot-Handford, Jean-Marc Schwartz:
PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations. 3847-3849
- Joseph Ward, Christian Cole, Melanie Febrer, Geoffrey J. Barton:
AlmostSignificant: simplifying quality control of high-throughput sequencing data. 3850-3851
- Eisuke Hayakawa, Yoshinori Fujimura, Daisuke Miura:
MSIdV: a versatile tool to visualize biological indices from mass spectrometry imaging data. 3852-3854
Bioimage Informatics
- Arnon Mazza, Konrad Klockmeier, Erich E. Wanker, Roded Sharan:
An integer programming framework for inferring disease complexes from network data. 3855
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