Journal: Bioinformatics

Volume 35, Issue 3

361 -- 364Hua Yu, Lu Lu, Bingke Jiao, Chengzhi Liang. Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples
365 -- 371Nora von Thenen, Erman Ayday, A. Ercument Cicek. Re-identification of individuals in genomic data-sharing beacons via allele inference
372 -- 379Luca Parca, Bruno Ariano, Andrea Cabibbo, Marco Paoletti, Annalaura Tamburrini, Antonio Palmeri, Gabriele Ausiello, Manuela Helmer-Citterich. Kinome-wide identification of phosphorylation networks in eukaryotic proteomes
380 -- 388Wei Zheng, Qi Mao, Robert J. Genco, Jean Wactawski-Wende, Michael Buck, Yunpeng Cai, Yijun Sun. A parallel computational framework for ultra-large-scale sequence clustering analysis
389 -- 397Xinguo Lu, Xin Qian, Xing Li, Qiumai Miao, Shaoliang Peng. DMCM: a Data-adaptive Mutation Clustering Method to identify cancer-related mutation clusters
398 -- 406Xiang Cheng, Wei-Zhong Lin, Xuan Xiao, Kuo-Chen Chou. pLoc_bal-mAnimal: predict subcellular localization of animal proteins by balancing training dataset and PseAAC
407 -- 414Harun Mustafa, Ingo Schilken, Mikhail Karasikov, Carsten Eickhoff, Gunnar Rätsch, André Kahles. Dynamic compression schemes for graph coloring
415 -- 420Chen Sun, Paul Medvedev. Toward fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics
421 -- 432Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles. Scaling read aligners to hundreds of threads on general-purpose processors
433 -- 441Avdesh Mishra, Pujan Pokhrel, Md. Tamjidul Hoque. StackDPPred: a stacking based prediction of DNA-binding protein from sequence
442 -- 451Jeffrey M. Yunes, Patricia C. Babbitt. Effusion: prediction of protein function from sequence similarity networks
452 -- 461Marcin Kowiel, Dariusz Brzezinski, Przemyslaw J. Porebski, Ivan G. Shabalin, Mariusz Jaskolski, Wladek Minor. Automatic recognition of ligands in electron density by machine learning
462 -- 469Justina Jankauskaite, Brian Jiménez-García, Justas Dapkunas, Juan Fernández-Recio, Iain H. Moal. SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation
470 -- 477Rubén Sánchez García, Carlos Oscar Sánchez Sorzano, José María Carazo, Joan Segura. BIPSPI: a method for the prediction of partner-specific protein-protein interfaces
478 -- 486Rasmus Henningsson, Magnus Fontes. SMSSVD: SubMatrix Selection Singular Value Decomposition
487 -- 496Shiquan Sun, Jiaqiang Zhu, Sahar Mozaffari, Carole Ober, Mengjie Chen, Xiang Zhou. Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies
497 -- 505Alberto Valdeolivas, Laurent Tichit, Claire Navarro, Sophie Perrin, Gaëlle Odelin, Nicolas Levy, Pierre Cau, Elisabeth Remy, Anaïs Baudot. Random walk with restart on multiplex and heterogeneous biological networks
506 -- 514Bruce A. Corliss, H. Clifton Ray, James T. Patrie, Jennifer Mansour, Sam Kesting, Janice H. Park, Gustavo Rohde, Paul A. Yates, Kevin A. Janes, Shayn M. Peirce. CIRCOAST: a statistical hypothesis test for cellular colocalization with network structures
515 -- 517Caralyn Reisle, Karen L. Mungall, Caleb Choo, Daniel Paulino, Dustin W. Bleile, Amir Muhammadzadeh, Andrew J. Mungall, Richard A. Moore, Inna Shlafman, Robin Coope, Stephen Pleasance, Yussanne Ma, Steven J. M. Jones. MAVIS: merging, annotation, validation, and illustration of structural variants
518 -- 520Haiming Tang, Robert D. Finn, Paul D. Thomas. TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations
521 -- 522Hadrien Gourlé, Oskar Karlsson-Lindsjö, Juliette Hayer, Erik Bongcam-Rudloff. Simulating Illumina metagenomic data with InSilicoSeq
523 -- 525Robert Lanfear, Miriam Schalamun, David Kainer, W. Wang, Benjamin Schwessinger. MinIONQC: fast and simple quality control for MinION sequencing data
526 -- 528Emmanuel Paradis, Klaus Schliep. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R
529 -- 531Zongxiao He, Lu Wang, Andrew T. Dewan, Suzanne M. Leal. MendelProb: probability and sample size calculations for Mendelian studies of exome and whole genome sequence data
532 -- 534Kieu Trinh Do, David J. N. P. Rasp, Gabi Kastenmüller, Karsten Suhre, Jan Krumsiek. MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions
535 -- 537Iñigo Apaolaza, Luis Vitores Valcarcel, Francisco J. Planes. gMCS: fast computation of genetic minimal cut sets in large networks
538 -- 539Zainab Noor, Jemma X. Wu, Dana Pascovici, Abidali Mohamedali, Mark P. Molloy, Mark S. Baker, Shoba Ranganathan. iSwathX: an interactive web-based application for extension of DIA peptide reference libraries
540 -- 0Peter M. Bourke, Geert van Geest, Roeland E. Voorrips, Johannes Jansen, Twan Kranenburg, Arwa Shahin, Richard G. F. Visser, Paul Arens, Marinus J. M. Smulders, Chris Maliepaard. polymapR - linkage analysis and genetic map construction from F1 populations of outcrossing polyploids