Journal: Bioinformatics

Volume 31, Issue 13

2015 -- 2240Daniel G. Hurley, Joseph Cursons, Yi Kan Wang, David M. Budden, Cristin G. Print, Edmund J. Crampin. NAIL, a software toolset for inferring, analyzing and visualizing regulatory networks
2061 -- 2065Sebastián Duchêne, Simon Y. W. Ho. Mammalian genome evolution is governed by multiple pacemakers
2066 -- 2074Kyung-Ah Sohn, Joshua W. K. Ho, Djordje Djordjevic, Hyun-hwan Jeong, Peter J. Park, Ju Han Kim. hiHMM: Bayesian non-parametric joint inference of chromatin state maps
2075 -- 2083David C. Ream, Asma R. Bankapur, Iddo Friedberg. An event-driven approach for studying gene block evolution in bacteria
2084 -- 2090Derek M. Bickhart, Jana L. Hutchison, Lingyang Xu, Robert D. Schnabel, Jeremy F. Taylor, James M. Reecy, Steven Schroeder, Curtis P. Van Tassell, Tad S. Sonstegard, George E. Liu. RAPTR-SV: a hybrid method for the detection of structural variants
2091 -- 2097Priyashree Chaudhary, Athi N. Naganathan, M. Michael Gromiha. Folding RaCe: a robust method for predicting changes in protein folding rates upon point mutations
2098 -- 2105Dong Xu, Lukasz Jaroszewski, Zhanwen Li, Adam Godzik. ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction
2106 -- 2114John Lhota, Ruth Hauptman, Thomas Hart, Clara Ng, Lei Xie. A new method to improve network topological similarity search: applied to fold recognition
2115 -- 2122Diana M. Hendrickx, Danyel G. J. Jennen, Jacob J. Briedé, Rachel Cavill, Theo M. de Kok, Jos C. S. Kleinjans. Pattern recognition methods to relate time profiles of gene expression with phenotypic data: a comparative study
2123 -- 2130Sara Ballouz, Wim Verleyen, Jesse Gillis. Guidance for RNA-seq co-expression network construction and analysis: safety in numbers
2131 -- 2140Sam Benidt, Dan Nettleton. SimSeq: a nonparametric approach to simulation of RNA-sequence datasets
2141 -- 2150Ofer Isakov, Antonio V. Bordería, David Golan, Amir Hamenahem, Gershon Celniker, Liron Yoffe, Hervé Blanc, Marco Vignuzzi, Noam Shomron. Deep sequencing analysis of viral infection and evolution allows rapid and detailed characterization of viral mutant spectrum
2151 -- 2158Yi-Hsiung Chen, Chi-Dung Yang, Ching-Ping Tseng, Hsien-Da Huang, Shinn-Ying Ho. GeNOSA: inferring and experimentally supporting quantitative gene regulatory networks in prokaryotes
2159 -- 2165Abdelmoneim Amer Desouki, Florian Jarre, Gabriel Gelius-Dietrich, Martin J. Lercher. CycleFreeFlux: efficient removal of thermodynamically infeasible loops from flux distributions
2166 -- 2173David Ochoa, David de Juan, Alfonso Valencia, Florencio Pazos. Detection of significant protein coevolution
2174 -- 2181Thomas Trolle, Imir G. Metushi, Jason A. Greenbaum, Yohan Kim, John Sidney, Ole Lund, Alessandro Sette, Bjoern Peters, Morten Nielsen. Automated benchmarking of peptide-MHC class I binding predictions
2182 -- 2189Noël Malod-Dognin, Natasa Przulj. L-GRAAL: Lagrangian graphlet-based network aligner
2190 -- 2198Murad Megjhani, Nicolas Rey-Villamizar, Amine Merouane, Yanbin Lu, Amit Mukherjee, Kristen Trett, Peter Chong, Carolyn Harris, William Shain, Badrinath Roysam. Population-scale three-dimensional reconstruction and quantitative profiling of microglia arbors
2199 -- 2201Francesco Musacchia, Swaraj Basu, Giuseppe Petrosino, Marco Salvemini, Remo Sanges. Annocript: a flexible pipeline for the annotation of transcriptomes able to identify putative long noncoding RNAs
2202 -- 2204Adrian Tan, Gonçalo R. Abecasis, Hyun Min Kang. Unified representation of genetic variants
2205 -- 2207Vincenzo Capece, Julio C. Garcia Vizcaino, Ramon Vidal, Raza-Ur Rahman, Tonatiuh Pena Centeno, Orr Shomroni, Irantzu Suberviola, André Fischer, Stefan Bonn. Oasis: online analysis of small RNA deep sequencing data
2208 -- 2210Ioannis Kirmitzoglou, Vasilis J. Promponas. LCR-eXXXplorer: a web platform to search, visualize and share data for low complexity regions in protein sequences
2211 -- 2213Benjamin Schubert, Hans-Philipp Brachvogel, Christopher Jürges, Oliver Kohlbacher. EpiToolKit - a web-based workbench for vaccine design
2214 -- 2216Amr Alhossary, Stephanus Daniel Handoko, Yuguang Mu, Chee Keong Kwoh. Fast, accurate, and reliable molecular docking with QuickVina 2
2217 -- 2219Kentaro Morimoto, Takashi Nishikaze, Akiyasu C. Yoshizawa, Shigeki Kajihara, Ken Aoshima, Yoshiya Oda, Koichi Tanaka. N-glycan structures using mass spectrometry
2220 -- 2221Fergal J. Duffy, Pauline M. Rudd. GlycoProfileAssigner: automated structural assignment with error estimation for glycan LC data
2222 -- 2224Yang Shi, Arul M. Chinnaiyan, Hui Jiang. rSeqNP: a non-parametric approach for detecting differential expression and splicing from RNA-Seq data
2225 -- 2227Bo Ding, Lina Zheng, Yun Zhu, Nan Li, Haiyang Jia, Rizi Ai, Andre Wildberg, Wei Wang. Normalization and noise reduction for single cell RNA-seq experiments
2228 -- 2231Christian Panse, Christian Trachsel, Jonas Grossmann, Ralph Schlapbach. specL - an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics
2232 -- 2234Matthias P. Gerstl, Christian Jungreuthmayer, Jürgen Zanghellini. tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks
2235 -- 2237Enrico Glaab, Reinhard Schneider 0002. RepExplore: addressing technical replicate variance in proteomics and metabolomics data analysis
2238 -- 2239Christiana N. Fogg, Diane E. Kovats. Message from the ISCB: 2015 ISCB Accomplishment by a Senior Scientist Award: Cyrus Chothia