


Остановите войну!
for scientists:


default search action
Bioinformatics, Volume 31
Volume 31, Number 1, January 2015
Genome Analysis
- Vinita Periwal
, Vinod Scaria
:
Insights into structural variations and genome rearrangements in prokaryotic genomes. 1-9
Genome Analysis
- Pablo Cingolani, Rob Sladek, Mathieu Blanchette:
BigDataScript: a scripting language for data pipelines. 10-16 - Ka-Chun Wong
, Yue Li, Chengbin Peng, Zhaolei Zhang:
SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles. 17-24 - Liping Li, Enguo Chen, Chun Yang, Jun Zhu, Pushkala Jayaraman
, Jeff de Pons, Catherine C. Kaczorowski
, Howard J. Jacob, Andrew S. Greene
, Matthew R. Hodges, Allen W. Cowley Jr., Mingyu Liang, Haiming Xu, Pengyuan Liu, Yan Lu:
Improved rat genome gene prediction by integration of ESTs with RNA-Seq information. 25-32 - P. R. Shidhi, Prashanth Suravajhala
, Aysha Nayeema, Achuthsankar S. Nair, Shailja Singh, Pawan K. Dhar:
Making novel proteins from pseudogenes. 33-39
- Mufleh Al-Shatnawi, M. Omair Ahmad, M. N. Shanmukha Swamy:
Prediction of Indel flanking regions in protein sequences using a variable-order Markov model. 40-47 - Mahmoud M. Ibrahim
, Scott A. Lacadie, Uwe Ohler:
JAMM: a peak finder for joint analysis of NGS replicates. 48-55 - Darren T. Houniet, Thahira J. Rahman, Saeed Al Turki, Matthew E. Hurles, Yaobo Xu, Judith A. Goodship, Bernard D. Keavney
, Mauro F. Santibanez-Koref:
Using population data for assessing next-generation sequencing performance. 56-61
- Hongwei Wang
, Qiang Sun
, Wenyuan Zhao, Lishuang Qi, Yunyan Gu, Pengfei Li, Mengmeng Zhang, Yang Li, Shu-Lin Liu, Zheng Guo:
Individual-level analysis of differential expression of genes and pathways for personalized medicine. 62-68 - Antti Häkkinen
, Andre S. Ribeiro
:
Estimation of GFP-tagged RNA numbers from temporal fluorescence intensity data. 69-75 - Sheng Qin, Fei Ma, Liming Chen
:
Gene regulatory networks by transcription factors and microRNAs in breast cancer. 76-83 - Yaomin Xu, Xingyi Guo, Jiayang Sun
, Zhongming Zhao:
Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation. 84-93
- Bie M. P. Verbist, Kim Thys, Joke Reumers
, Yves Wetzels, Koen Van der Borght, Willem Talloen, Jeroen Aerssens
, Lieven Clement, Olivier Thas
:
VirVarSeq: a low-frequency virus variant detection pipeline for Illumina sequencing using adaptive base-calling accuracy filtering. 94-101
- Yotsawat Pomyen
, Marcelo Segura, Timothy M. D. Ebbels
, Hector C. Keun:
Over-representation of correlation analysis (ORCA): a method for identifying associations between variable sets. 102-108
Genome Analysis
- Julien Lajugie, Nicolas Fourel, Eric E. Bouhassira
:
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface. 109-111
- Pierre Lindenbaum, Richard Redon
:
mod_bio: Apache modules for Next-Generation sequencing data. 112-113 - Mick Watson
, Marian Thomson, Judith E. Risse, Richard Talbot, Javier Santoyo-Lopez
, Karim Gharbi
, Mark L. Blaxter
:
poRe: an R package for the visualization and analysis of nanopore sequencing data. 114-115 - Kenichi Chiba, Yuichi Shiraishi, Yasunobu Nagata, Kenichi Yoshida, Seiya Imoto, Seishi Ogawa, Satoru Miyano
:
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data. 116-118 - Wei Chen
, Xitong Zhang, Jordan Brooker, Hao Lin
, Liqing Zhang, Kuo-Chen Chou:
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions. 119-120
- Anna Katharina Hildebrandt, Daniel Stöckel, Nina M. Fischer, Luis de la Garza, Jens Krüger, Stefan Nickels, Marc Röttig, Charlotta Schärfe, Marcel Schumann, Philipp Thiel, Hans-Peter Lenhof, Oliver Kohlbacher, Andreas Hildebrandt
:
ballaxy: web services for structural bioinformatics. 121-122 - Iain H. Moal
, Brian Jiménez-García
, Juan Fernández-Recio
:
CCharPPI web server: computational characterization of protein-protein interactions from structure. 123-125 - Gregory B. Quinn, Chunxiao Bi, Cole H. Christie, Kyle Pang, Andreas Prlic
, Takanori Nakane
, Christine Zardecki
, Maria Voigt, Helen M. Berman, Philip E. Bourne, Peter W. Rose
:
RCSB PDB Mobile: iOS and Android mobile apps to provide data access and visualization to the RCSB Protein Data Bank. 126-127
- Steffen Sass, Florian Buettner, Nikola S. Müller, Fabian J. Theis
:
RAMONA: a Web application for gene set analysis on multilevel omics data. 128-130
- Murat Can Cobanoglu, Zoltán N. Oltvai, D. Lansing Taylor
, Ivet Bahar:
BalestraWeb: efficient online evaluation of drug-target interactions. 131-133 - John H. Morris
, Allan Wu, Roxanne A. Yamashita, Aron Marchler-Bauer
, Thomas E. Ferrin:
cddApp: a Cytoscape app for accessing the NCBI conserved domain database. 134-136
- Niya Wang, Ting Gong, Robert Clarke
, Lulu Chen, Ie-Ming Shih, Zhen Zhang, Douglas A. Levine
, Jianhua Xuan, Yue Joseph Wang:
UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples. 137-139
- Manuel Corpas
, Rafael C. Jiménez
, Erik Bongcam-Rudloff, Aidan Budd, Michelle D. Brazas
, Pedro L. Fernandes
, Bruno A. Gaëta, Celia W. G. van Gelder
, Eija Korpelainen
, Fran Lewitter, Annette McGrath
, Daniel MacLean
, Patricia M. Palagi
, Kristian Rother, Jan Taylor, Allegra Via, Mick Watson
, Maria Victoria Schneider, Teresa K. Attwood:
The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers. 140-142 - Andrew D. Yates
, Kathryn Beal, Stephen Keenan
, William M. McLaren
, Miguel Pignatelli, Graham R. S. Ritchie, Magali Ruffier
, Kieron R. Taylor
, Alessandro Vullo
, Paul Flicek
:
The Ensembl REST API: Ensembl Data for Any Language. 143-145
Databases and Ontologies
- Ilan Samish
, Philip E. Bourne, Rafael J. Najmanovich
:
Editor's Choice: Achievements and challenges in structural bioinformatics and computational biophysics. 146-150
Volume 31, Number 2, January 2015
Genome Analysis
- Tatsiana Vaitsiakhovich, Dmitriy Drichel
, Christine Herold, André Lacour
, Tim Becker
:
METAINTER: meta-analysis of multiple regression models in genome-wide association studies. 151-157 - Naruekamol 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. 158-165 - Simon Anders
, Paul Theodor Pyl
, Wolfgang Huber
:
HTSeq - a Python framework to work with high-throughput sequencing data. 166-169 - Tae-Hyuk Ahn
, Juanjuan Chai, Chongle Pan
:
Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance. 170-177 - Sha He, Hai Zhang, Haihua Liu
, Hao Zhu:
LongTarget: a tool to predict lncRNA DNA-binding motifs and binding sites via Hoogsteen base-pairing analysis. 178-186
- Vassily Trubetskoy
, Alex Rodriguez, Uptal J. Dave, Nicholas Campbell, Emily L. Crawford, Edwin H. Cook Jr., 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. 187-193 - Xiang 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. 194-200
- Ian Walsh
, Manuel Giollo, Tomás Di Domenico
, Carlo Ferrari
, Olav Zimmermann, Silvio C. E. Tosatto
:
Comprehensive large-scale assessment of intrinsic protein disorder. 201-208
- Marcus A. Badgeley
, Stuart C. Sealfon
, Maria D. Chikina:
Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation. 209-215 - Timo 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. 216-224 - Hachem Saddiki, Jon McAuliffe, Patrick Flaherty:
GLAD: a mixed-membership model for heterogeneous tumor subtype classification. 225-232 - Hao Wu
, Chi Wang, Zhijin Wu
:
PROPER: comprehensive power evaluation for differential expression using RNA-seq. 233-241
- Khalifeh 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. 242-245 - Matteo Giulietti
, Sara Armida Milantoni, Tatiana Armeni
, Giovanni Principato
, Francesco Piva
:
ExportAid: database of RNA elements regulating nuclear RNA export in mammals. 246-251 - Chunhong 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. 252-258
Genome Analysis
- Thomas W. Winkler, Zoltán Kutalik, Mathias Gorski, Claudio Lottaz, Florian Kronenberg
, Iris M. Heid:
EasyStrata: evaluation and visualization of stratified genome-wide association meta-analysis data. 259-261 - Lili Wang, Takuya Matsushita, Lohith Madireddy, Parvin Mousavi
, Sergio Baranzini
:
PINBPA: Cytoscape app for network analysis of GWAS data. 262-264
- Heejoon Chae, SungMin Rhee
, Kenneth P. Nephew, Sun Kim:
BioVLAB-MMIA-NGS: microRNA-mRNA integrated analysis using high-throughput sequencing data. 265-267 - Reece 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. 268-270 - Ishita K. Khan, Qing Wei, Meghana Chitale, Daisuke Kihara:
PFP/ESG: automated protein function prediction servers enhanced with Gene Ontology visualization tool. 271-272
- Bahman Afsari, Elana J. Fertig
, Donald Geman, Luigi Marchionni
:
switchBox: an R package for k-Top Scoring Pairs classifier development. 273-274
- Yunfei Guo, David V. Conti, Kai Wang
:
Enlight: web-based integration of GWAS results with biological annotations. 275-276
- Daniel 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. 277-278 - Dong-Sheng Cao
, Nan Xiao
, Qing-Song Xu, Alex F. Chen:
Rcpi: R/Bioconductor package to generate various descriptors of proteins, compounds and their interactions. 279-281
- Paul J. McMurdie
, Susan P. Holmes
:
Shiny-phyloseq: Web application for interactive microbiome analysis with provenance tracking. 282-283 - Qingli Guo
, Xiongfei Qu, Weibo Jin:
PhaseTank: genome-wide computational identification of phasiRNAs and their regulatory cascades. 284-286 - Ye Tian, Bai Zhang, Eric P. Hoffman
, Robert Clarke
, Zhen Zhang, Ie-Ming Shih, Jianhua Xuan, David M. Herrington, Yue Joseph Wang:
KDDN: an open-source Cytoscape app for constructing differential dependency networks with significant rewiring. 287-289 - Zhao Zhang
, Li Jiang, Jingjing Wang, Peizhen Gu, Ming Chen
:
MTide: an integrated tool for the identification of miRNA-target interaction in plants. 290-291
- Noa 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. 292-294 - Egle Bunkute, Christopher Cummins, Fraser J. Crofts
, Gareth Bunce, Ian T. Nabney
, Darren R. Flower:
PIP-DB: the Protein Isoelectric Point database. 295-296
Databases and Ontologies
- Karin Verspoor
, Hagit Shatkay, Lynette Hirschman, Christian Blaschke, Alfonso Valencia
:
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013. 297-298 - Nomi L. Harris, Peter J. A. Cock, Brad A. Chapman, Jeremy Goecks, Hans-Rudolf Hotz, Hilmar Lapp
:
The Bioinformatics Open Source Conference (BOSC) 2013. 299-300
Volume 31, Number 3, February 2015
Genome Analysis
- Sankar Subramanian
:
Using the plurality of codon positions to identify deleterious variants in human exomes. 301-305
- James Vlasblom, Khalid Zuberi, Harold Rodriguez, Roland Arnold
, Alla Gagarinova, Viktor Deineko, Ashwani Kumar, Elisa Leung, Kamran Rizzolo
, Bahram Samanfar, Luke Chang, Sadhna Phanse
, Ashkan Golshani, Jack Greenblatt, Walid A. Houry, Andrew Emili, Quaid Morris
, Gary D. Bader
, Mohan Babu
:
Novel function discovery with GeneMANIA: a new integrated resource for gene function prediction in Escherichia coli. 306-310
Genome Analysis
- Jonathan D. Magasin
, Dietlind L. Gerloff:
Pooled assembly of marine metagenomic datasets: enriching annotation through chimerism. 311-317 - Jing Wang, Leon Raskin, David C. Samuels
, Yu Shyr
, Yan Guo:
Genome measures used for quality control are dependent on gene function and ancestry. 318-323
- Yi-Kuo Yu, John A. Capra, Aleksandar Stojmirovic
, David Landsman
, Stephen F. Altschul:
Log-odds sequence logos. 324-331 - Andrzej Zielezinski
, Wojciech M. Karlowski
:
Integrative data analysis indicates an intrinsic disordered domain character of Argonaute-binding motifs. 332-339
- René Luijk, Jelle J. Goeman
, P. Eline Slagboom
, Bastiaan T. Heijmans, Erik W. van Zwet:
An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs. 340-345
- Katharina Nöh
, Peter Droste, Wolfgang Wiechert
:
Visual workflows for 13C-metabolic flux analysis. 346-354 - Maria Anna Rapsomaniki
, Eugenio Cinquemani, Nickolaos-Nikiforos Giakoumakis
, Panagiotis Kotsantis
, John Lygeros, Zoi Lygerou:
Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments. 355-362 - Jialu Hu
, Knut Reinert
:
LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks. 363-372 - Ralf Schmidt, Silvio Waschina
, Daniela Boettger-Schmidt, Christian Kost
, Christoph Kaleta
:
Computing autocatalytic sets to unravel inconsistencies in metabolic network reconstructions. 373-381 - Ralph Patrick
, Kim-Anh Lê Cao
, Bostjan Kobe
, Mikael Bodén
:
PhosphoPICK: modelling cellular context to map kinase-substrate phosphorylation events. 382-389 - Hamidreza Khataee, Alan Wee-Chung Liew
:
A stochastic automaton model for simulating kinesin processivity. 390-396
- Philippe Bastien
, Frédéric Bertrand
, Nicolas Meyer, Myriam Maumy-Bertrand
:
Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data. 397-404
- Zhihai Liu, Yan Li, Li Han, Jie Li, Jie Liu, Zhixiong Zhao
, Wei Nie, Yuchen Liu, Renxiao Wang
:
PDB-wide collection of binding data: current status of the PDBbind database. 405-412
Genome Analysis
- Ulrich Wittelsbürger, Bastian Pfeifer
, Martin J. Lercher
:
WhopGenome: high-speed access to whole-genome variation and sequence data in R. 413-415 - Ryan M. Ames, Simon C. Lovell
:
DupliPHY-Web: a web server for DupliPHY and DupliPHY-ML. 416-417 - Tune H. Pers
, Pascal N. Timshel
, Joel Hirschhorn
:
SNPsnap: a Web-based tool for identification and annotation of matched SNPs. 418-420 - Dina Zhabinskaya, Sally Madden, Craig J. Benham:
SIST: stress-induced structural transitions in superhelical DNA. 421-422
- Stefan Janssen
, Robert Giegerich:
The RNA shapes studio. 423-425 - Zexuan Zhu, Linsen Li, Yongpeng Zhang, Yanli Yang, Xiao Yang:
CompMap: a reference-based compression program to speed up read mapping to related reference sequences. 426-428 - Javad Nadaf, Jacek Majewski, Somayyeh Fahiminiya:
ExomeAI: detection of recurrent allelic imbalance in tumors using whole-exome sequencing data. 429-431
- Ruchi Chaudhary, David Fernández-Baca, John Gordon Burleigh:
MulRF: a software package for phylogenetic analysis using multi-copy gene trees. 432-433
- Pier Paolo Olimpieri
, Paolo Marcatili
, Anna Tramontano:
Tabhu: tools for antibody humanization. 434-435
- Marc W. Schmid
, Ueli Grossniklaus
:
Rcount: simple and flexible RNA-Seq read counting. 436-437
- Giovanni Marco Dall'Olio, Ali R. Vahdati
, Jaume Bertranpetit
, Andreas Wagner, Hafid Laayouni
:
VCF2Networks: applying genotype networks to single-nucleotide variants data. 438-439
- Heiko Giese, Jörg Ackermann, Heinrich Heide, Lea Bleier, Stefan Dröse, Ilka Wittig, Ulrich Brandt
, Ina Koch
:
NOVA: a software to analyze complexome profiling data. 440-441 - Avigail Taylor
, Julia Steinberg
, Tallulah S. Andrews
, Caleb Webber
:
GeneNet Toolbox for MATLAB: a flexible platform for the analysis of gene connectivity in biological networks. 442-444
- Steffen Priebe, Christian Kreisel, Fabian Horn
, Reinhard Guthke, Jörg Linde:
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. 445-446 - Benjamin Linard
, Alexis Allot, Raphael Schneider, Can Morel, Raymond Ripp, Marc Bigler, Julie Dawn Thompson, Olivier Poch, Odile Lecompte
:
OrthoInspector 2.0: Software and database updates. 447-448
Databases and Ontologies
- Yana Bromberg, Emidio Capriotti
:
Editor's Choice: SNP-SIG 2013: the state of the art of genomic variant interpretation. 449-450
Volume 31, Number 4, February 2015
Editorial
- Julia Hoeng, Manuel C. Peitsch
, Pablo Meyer, Igor Jurisica:
Where are we at regarding species translation? A review of the sbv IMPROVER challenge. 451-452
- Michael Biehl
, Peter J. Sadowski
, Gyan Bhanot, Erhan Bilal, Adel Dayarian, Pablo Meyer, Raquel Norel
, Kahn Rhrissorrakrai, Michael D. Zeller, Sahand Hormoz:
Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge. 453-461 - Adel Dayarian, Roberto Romero
, Zhiming Wang, Michael Biehl
, Erhan Bilal, Sahand Hormoz, Pablo Meyer, Raquel Norel
, Kahn Rhrissorrakrai, Gyan Bhanot, Feng Luo, Adi L. Tarca:
Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge. 462-470 - Kahn Rhrissorrakrai, Vincenzo Belcastro
, Erhan Bilal, Raquel Norel
, Carine Poussin, Carole Mathis, Rémi H. J. Dulize, Nikolai V. Ivanov, Leonidas G. Alexopoulos
, John Jeremy Rice, Manuel C. Peitsch
, Gustavo Stolovitzky, Pablo Meyer, Julia Hoeng:
Understanding the limits of animal models as predictors of human biology: lessons learned from the sbv IMPROVER Species Translation Challenge. 471-483 - Erhan Bilal, Theodore Sakellaropoulos, Challenge Participants, Ioannis N. Melas, Dimitris E. Messinis
, Vincenzo Belcastro
, Kahn Rhrissorrakrai, Pablo Meyer, Raquel Norel
, Anita Iskandar
, Elise Blaese, John Jeremy Rice, Manuel C. Peitsch
, Julia Hoeng, Gustavo Stolovitzky, Leonidas G. Alexopoulos
, Carine Poussin:
A crowd-sourcing approach for the construction of species-specific cell signaling networks. 484-491
- Sahand Hormoz, Gyan Bhanot, Michael Biehl
, Erhan Bilal, Pablo Meyer, Raquel Norel
, Kahn Rhrissorrakrai, Adel Dayarian:
Inter-species inference of gene set enrichment in lung epithelial cells from proteomic and large transcriptomic datasets. 492-500 - Christoph Hafemeister
, Roberto Romero
, Erhan Bilal, Pablo Meyer, Raquel Norel
, Kahn Rhrissorrakrai, Richard Bonneau, Adi L. Tarca:
Inter-species pathway perturbation prediction via data-driven detection of functional homology. 501-508
Genome Analysis
- Nilesh Khiste, Lucian Ilie
:
E-MEM: efficient computation of maximal exact matches for very large genomes. 509-514
- Chang-Chang Cao, Xiao Sun:
Accurate estimation of haplotype frequency from pooled sequencing data and cost-effective identification of rare haplotype carriers by overlapping pool sequencing. 515-522 - Yi-Fei Huang
, Geoffrey Brian Golding:
FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures. 523-531