Journal: Bioinformatics

Volume 31, Issue 2

151 -- 157Tatsiana Vaitsiakhovich, Dmitriy Drichel, Christine Herold, André Lacour, Tim Becker. METAINTER: meta-analysis of multiple regression models in genome-wide association studies
158 -- 165Naruekamol Pookhao, Michael B. Sohn, Qike Li, Isaac Jenkins, Ruofei Du, Hongmei Jiang, Lingling An. A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes
166 -- 169Simon Anders, Paul Theodor Pyl, Wolfgang Huber. HTSeq - a Python framework to work with high-throughput sequencing data
170 -- 177Tae-Hyuk Ahn, Juanjuan Chai, Chongle Pan. Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance
178 -- 186Sha He, Hai Zhang, Haihua Liu, Hao Zhu. LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis
187 -- 193Vassily Trubetskoy, Alex Rodriguez, Uptal Dave, Nicholas Campbell, Emily L. Crawford, Edwin H. Cook, James S. Sutcliffe, Ian T. Foster, Ravi K. Madduri, Nancy J. Cox, Lea K. Davis. Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes
194 -- 200Xiang Chen, Shao-Ping Shi, Sheng-Bao Suo, Hao-Dong Xu, Jian-Ding Qiu. Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity
201 -- 208Ian Walsh, Manuel Giollo, Tomás Di Domenico, Carlo Ferrari, Olav Zimmermann, Silvio C. E. Tosatto. Comprehensive large-scale assessment of intrinsic protein disorder
209 -- 215Marcus A. Badgeley, Stuart C. Sealfon, Maria D. Chikina. Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation
216 -- 224Timo Itzel, Peter Scholz, Thorsten Maass, Markus Krupp, Jens U. Marquardt, Susanne Strand, Diana Becker, Frank Staib, Harald Binder, Stephanie Roessler, Xin Wei Wang, Snorri Thorgeirsson, Martina Müller, Peter R. Galle, Andreas Teufel. Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis
225 -- 232Hachem Saddiki, Jon McAuliffe, Patrick Flaherty. GLAD: a mixed-membership model for heterogeneous tumor subtype classification
233 -- 241Hao Wu, Chi Wang, Zhijin Wu. PROPER: comprehensive power evaluation for differential expression using RNA-seq
242 -- 245Khalifeh AlJadda, Melody P. Porterfield, Robert Bridger, Christian Heiss, Michael Tiemeyer, Lance Wells, John A. Miller, William S. York, René Ranzinger. EUROCarbDB(CCRC): a EUROCarbDB node for storing glycomics standard data
246 -- 251Matteo Giulietti, Sara Armida Milantoni, Tatiana Armeni, Giovanni Principato, Francesco Piva. ExportAid: database of RNA elements regulating nuclear RNA export in mammals
252 -- 258Chunhong Mao, David Abraham, Alice R. Wattam, Meredith J. C. Wilson, Maulik Shukla, Hyun Seung Yoo, Bruno W. S. Sobral. Curation, integration and visualization of bacterial virulence factors in PATRIC
259 -- 261Thomas W. Winkler, Zoltan Kutalik, Mathias Gorski, Claudio Lottaz, Florian Kronenberg, Iris M. Heid. EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data
262 -- 264Lili Wang, Takuya Matsushita, Lohith Madireddy, Parvin Mousavi, Sergio Baranzini. PINBPA: Cytoscape app for network analysis of GWAS data
265 -- 267Heejoon Chae, SungMin Rhee, Kenneth P. Nephew, Sun Kim. BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data
268 -- 270Reece K. Hart, Rudolph Rico, Emily Hare, John Garcia, Jody Westbrook, Vincent A. Fusaro. A Python package for parsing, validating, mapping and formatting sequence variants using HGVS nomenclature
271 -- 272Ishita K. Khan, Qing Wei, Meghana Chitale, Daisuke Kihara. PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool
273 -- 274Bahman Afsari, Elana J. Fertig, Donald Geman, Luigi Marchionni. switchBox: an R package for k-Top Scoring Pairs classifier development
275 -- 276Yunfei Guo, David V. Conti, Kai Wang. Enlight: web-based integration of GWAS results with biological annotations
277 -- 278Daniel 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
279 -- 281Dong-Sheng Cao, Nan Xiao, Qing-Song Xu, Alex F. Chen. Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions
282 -- 283Paul J. McMurdie, Susan Holmes. Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking
284 -- 286Qingli Guo, Xiongfei Qu, Weibo Jin. PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades
287 -- 289Ye Tian, Bai Zhang, Eric P. Hoffman, Robert Clarke, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Wang. KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring
290 -- 291Zhao Zhang, Li Jiang, Jingjing Wang, Peizhen Gu, Ming Chen. MTide: an integrated tool for the identification of miRNA-target interaction in plants
292 -- 294Noa Maatuk, Yitav Glantz-Gashai, Maya Rotman, Meirav Baydany, Gennadiy Fonar, Amir Shechvitz, Karin Shemer, Aviva Peleg, Eli Reuveni, Abraham O. Samson. PHI-DAC: protein homology database through dihedral angle conservation
295 -- 296Egle Bunkute, Christopher Cummins, Fraser J. Crofts, Gareth Bunce, Ian T. Nabney, Darren R. Flower. PIP-DB: the Protein Isoelectric Point database
297 -- 298Karin Verspoor, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia. Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013
299 -- 300Nomi L. Harris, Peter J. A. Cock, Brad A. Chapman, Jeremy Goecks, Hans-Rudolf Hotz, Hilmar Lapp. The Bioinformatics Open Source Conference (BOSC) 2013