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ORCIDBioinformatics, 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 A. 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 - Fei Deng, Lusheng Wang, Xiaowen Liu:
An efficient algorithm for the blocked pattern matching problem. 532-538
- Ambrish Roy, Jeffrey Skolnick:
LIGSIFT: an open-source tool for ligand structural alignment and virtual screening. 539-544