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Bioinformatics, Volume 30
Volume 30, Number 1, January 2014
- Christos Kozanitis, Andrew Heiberg, George Varghese, Vineet Bafna
:
Using Genome Query Language to uncover genetic variation. 1-8
- Sven H. Giese
, Franziska Zickmann, Bernhard Y. Renard
:
Specificity control for read alignments using an artificial reference genome-guided false discovery rate. 9-16 - Daniel Alonso-Alemany, Aurélien Barré, Stefano Beretta
, Paola Bonizzoni
, Macha Nikolski, Gabriel Valiente
:
Further Steps in TANGO: improved taxonomic assignment in metagenomics. 17-23 - Lilian Janin, Giovanna Rosone
, Anthony J. Cox
:
Adaptive reference-free compression of sequence quality scores. 24-30 - Rayan Chikhi, Paul Medvedev:
Informed and automated k-mer size selection for genome assembly. 31-37 - Daniel H. Huson, Chao Xie:
A poor man's BLASTX - high-throughput metagenomic protein database search using PAUDA. 38-39
- David Hernández, Ryan Tewhey, Jean-Baptiste Veyrieras, Laurent Farinelli, Magne Østerås, Patrice François
, Jacques Schrenzel
:
De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads. 40-49 - Noemi Andor, Julie V. Harness, Sabine Müller, Hans-Werner Mewes
, Claudia Petritsch:
EXPANDS: expanding ploidy and allele frequency on nested subpopulations. 50-60
- Paulo Vieira Milreu, Cecilia Coimbra Klein, Ludovic Cottret
, Vicente Acuña, Etienne Birmelé, Michele Borassi, Christophe Junot, Alberto Marchetti-Spaccamela, Andrea Marino
, Leen Stougie, Fabien Jourdan
, Pierluigi Crescenzi
, Vincent Lacroix, Marie-France Sagot:
Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. 61-70 - Mingjun Wang, Xing-Ming Zhao, Hao Tan, Tatsuya Akutsu
, James C. Whisstock
, Jiangning Song
:
Cascleave 2.0, a new approach for predicting caspase and granzyme cleavage targets. 71-80
- Yijie Wang, Xiaoning Qian
:
Functional module identification in protein interaction networks by interaction patterns. 81-93 - Yungang Xu
, Maozu Guo, Xiaoyan Liu, Chun-yu Wang, Yang Liu:
Inferring the soybean (Glycine max) microRNA functional network based on target gene network. 94-103
- Songhua Xu, Hong-Jun Yoon, Georgia D. Tourassi
:
A user-oriented web crawler for selectively acquiring online content in e-health research. 104-114
- Sebastian Bartschat, Stephanie Kehr
, Hakim Tafer
, Peter F. Stadler
, Jana Hertel
:
snoStrip: a snoRNA annotation pipeline. 115-116
- Armando J. Pinho
, Diogo Pratas
:
MFCompress: a compression tool for FASTA and multi-FASTA data. 117-118 - André Schumacher, Luca Pireddu
, Matti Niemenmaa, Aleksi Kallio, Eija Korpelainen
, Gianluigi Zanetti
, Keijo Heljanko
:
SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop. 119-120 - Christoph Gille, Birgit Weyand, Andreas Gille
:
Sequence alignment visualization in HTML5 without Java. 121-122
- Michael J. Landis
, Trevor Bedford:
Phylowood: interactive web-based animations of biogeographic and phylogeographic histories. 123-124
- Shannon L. N. Mayne, Hugh-George Patterton
:
AnchorMS: a bioinformatics tool to derive structural information from the mass spectra of cross-linked protein complexes. 125-126
- Thomas Sandmann, Sarah K. Kummerfeld
, Robert Gentleman, Richard Bourgon
:
gCMAP: user-friendly connectivity mapping with R. 127-128
- Maxwell Lewis Neal, Michal Galdzicki
, J. T. Gallimore, Herbert M. Sauro:
A C library for retrieving specific reactions from the BioModels database. 129-130 - Matthias Bock
, Till Scharp, Chaitanya Talnikar, Edda Klipp:
BooleSim: an interactive Boolean network simulator. 131-132 - Grant Hughes, Charmion Cruickshank-Quinn
, Richard Reisdorph, Sharon Lutz, Irina Petrache, Nichole Reisdorph, Russell Bowler, Katerina J. Kechris
:
MSPrep - Summarization, normalization and diagnostics for processing of mass spectrometry-based metabolomic data. 133-134 - Minji Jeon, Sunwon Lee, Kyubum Lee
, Aik Choon Tan
, Jaewoo Kang:
BEReX: Biomedical Entity-Relationship eXplorer. 135-136 - Tomasz Jetka
, Agata Charzynska
, Anna Gambin
, Michael P. H. Stumpf, Michal Komorowski:
StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems. 137-138
- Özgün Babur
, Bülent Arman Aksoy, Igor V. Rodchenkov, Selçuk Onur Sümer, Chris Sander, Emek Demir:
Pattern search in BioPAX models. 139-140 - Jianfei Hu
, Hee-Sool Rho, Robert H. Newman, Jin Zhang, Heng Zhu, Jiang Qian:
PhosphoNetworks: a database for human phosphorylation networks. 141-142
- Burkhard Rost
:
ISCB: past-present perspective for the International Society for Computational Biology. 143-145 - Andreas W. M. Dress, Michal Linial
, Olga G. Troyanskaya, Martin Vingron:
ISCB/SPRINGER series in computational biology. 146-147 - Jim Cavalcoli, Lonnie R. Welch, Bruce J. Aronow, Sorin Draghici
, Daisuke Kihara:
The International Society of Computational Biology presents: the Great Lakes Bioinformatics Conference, May 16-18, 2014, Cincinnati, Ohio. 148-149
Volume 30, Number 2, January 2014
- Laurence O. W. Wilson, Andrew Spriggs, Jennifer M. Taylor, Aude M. Fahrer
:
A novel splicing outcome reveals more than 2000 new mammalian protein isoforms. 151-156 - Dandi Qiao, Michael H. Cho, Heide Loehlein Fier, Per S. Bakke, Amund Gulsvik, Edwin K. Silverman, Christoph Lange:
On the simultaneous association analysis of large genomic regions: a massive multi-locus association test. 157-164 - Sebastian M. Waszak
, Helena Kilpinen
, Andreas R. Gschwind
, Andrea Orioli, Sunil K. Raghav, Robert M. Witwicki, Eugenia Migliavacca, Alisa Yurovsky, Tuuli Lappalainen
, Nouria Hernandez
, Alexandre Reymond
, Emmanouil T. Dermitzakis, Bart Deplancke
:
Identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data. 165-171 - Longjie Cheng, Yu Zhu:
A classification approach for DNA methylation profiling with bisulfite next-generation sequencing data. 172-179
- Ernest Turro
, William J. Astle
, Simon Tavaré:
Flexible analysis of RNA-seq data using mixed effects models. 180-188 - Kevin Lim, Limsoon Wong
:
Finding consistent disease subnetworks using PFSNet. 189-196 - Yaqing Si, Peng Liu, Pinghua Li, Thomas P. Brutnell
:
Model-based clustering for RNA-seq data. 197-205
- Buhm Han, Eun Yong Kang, Soumya Raychaudhuri
, Paul I. W. de Bakker, Eleazar Eskin:
Fast pairwise IBD association testing in genome-wide association studies. 206-213
- Simina M. Boca
, Rashmi Sinha, Amanda J. Cross, Steven C. Moore
, Joshua N. Sampson:
Testing multiple biological mediators simultaneously. 214-220 - Mikael Sunnåker, Elías Zamora-Sillero, Adrián López García de Lomana, Florian Rudroff
, Uwe Sauer, Jörg Stelling, Andreas Wagner:
Topological augmentation to infer hidden processes in biological systems. 221-227 - Marianna De Santis
, Francesco Rinaldi
, Emmanuela Falcone, Stefano Lucidi
, Giulia Piaggio
, Aymone Gurtner
, Lorenzo Farina
:
Combining optimization and machine learning techniques for genome-wide prediction of human cell cycle-regulated genes. 228-233
- Attila Kertész-Farkas, Beáta Reiz, Roberto Vera
, Michael P. Myers, Sándor Pongor:
PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. 234-241 - Mohammad Shahrokh Esfahani
, Edward R. Dougherty:
Effect of separate sampling on classification accuracy. 242-250
- Mandy L. Wilson, Sakiko Okumoto, Laura Adam, Jean Peccoud
:
Development of a domain-specific genetic language to design Chlamydomonas reinhardtii expression vectors. 251-257 - Álvaro Sebastián, Bruno Contreras-Moreira
:
footprintDB: a database of transcription factors with annotated cis elements and binding interfaces. 258-265
- Lei Yuan, Cheng Pan, Shuiwang Ji
, Michael McCutchan, Zhi-Hua Zhou, Stuart J. Newfeld, Sudhir Kumar
, Jieping Ye:
Automated annotation of developmental stages of Drosophila embryos in images containing spatial patterns of expression. 266-273
- Nicolas Terrapon
, January 3rd Weiner, Sonja Grath
, Andrew D. Moore, Erich Bornberg-Bauer
:
Rapid similarity search of proteins using alignments of domain arrangements. 274-281
- Andrew D. Moore, Andreas Held, Nicolas Terrapon
, January 3rd Weiner, Erich Bornberg-Bauer
:
DoMosaics: software for domain arrangement visualization and domain-centric analysis of proteins. 282-283 - Matthias Lienhard, Christina Grimm
, Markus Morkel
, Ralf Herwig
, Lukas Chavez
:
MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments. 284-286 - João F. Matias Rodrigues
, Christian von Mering
:
HPC-CLUST: distributed hierarchical clustering for large sets of nucleotide sequences. 287-288
- Toma Tebaldi
, Erik Dassi
, Galena Kostoska
, Gabriella Viero
, Alessandro Quattrone
:
tRanslatome: an R/Bioconductor package to portray translational control. 289-291
- Michael L. Blinov
, James C. Schaff, Oliver Ruebenacker, Xintao Wei, Dan Vasilescu, Fei Gao, Frank Morgan, Li Ye, Anuradha Lakshminarayana, Ion I. Moraru
, Leslie M. Loew
:
Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling. 292-294
- Luke E. Ulrich, Igor B. Zhulin
:
SeqDepot: streamlined database of biological sequences and precomputed features. 295-297 - Rodrigo Ochoa
, Mark Davies
, George Papadatos
, Francis Atkinson
, John P. Overington
:
myChEMBL: a virtual machine implementation of open data and cheminformatics tools. 298-300
Volume 30, Number 3, February 2014
- Yuwen Liu, Jie Zhou, Kevin P. White:
RNA-seq differential expression studies: more sequence or more replication? 301-304
- Min Xiong, Bin Li, Qiang Zhu, Yun-Xing Wang, Hong-yu Zhang:
Identification of transcription factors for drug-associated gene modules and biomedical implications. 305-309
- Dror Hibsh, Hadas Schori, Sol Efroni, Orit Shefi:
Spatial regulation dominates gene function in the ganglia chain. 310-316
- Kazunori D. Yamada, Kentaro Tomii
:
Revisiting amino acid substitution matrices for identifying distantly related proteins. 317-325
- Ali May, René Pool
, Erik van Dijk
, Jochem Bijlard, Sanne Abeln
, Jaap Heringa, K. Anton Feenstra
:
Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins. 326-334 - Douglas E. V. Pires
, David B. Ascher
, Tom L. Blundell:
mCSM: predicting the effects of mutations in proteins using graph-based signatures. 335-342 - Luke Day, Ouala Abdelhadi Ep Souki, Andreas Alexander Albrecht, Kathleen Steinhöfel:
Accessibility of microRNA binding sites in metastable RNA secondary structures in the presence of SNPs. 343-352 - Hamidreza Khataee, Alan Wee-Chung Liew
:
A mathematical model describing the mechanical kinetics of kinesin stepping. 353-359
- Yasir Rahmatallah
, Frank Emmert-Streib
, Galina V. Glazko:
Gene Sets Net Correlations Analysis (GSNCA): a multivariate differential coexpression test for gene sets. 360-368 - Chuan Gao, Nicole L. Tignor, Jacqueline Salit, Yael Strulovici-Barel, Neil R. Hackett, Ronald G. Crystal, Jason G. Mezey:
HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. 369-376 - Hari Krishna Yalamanchili, Bin Yan, Mulin Jun Li, Jing Qin
, Zhongying Zhao
, Francis Y. L. Chin, Junwen Wang
:
DDGni: Dynamic delay gene-network inference from high-temporal data using gapped local alignment. 377-383
- Barbara Di Camillo, Francesco Sambo, Gianna Toffolo, Claudio Cobelli:
ABACUS: an entropy-based cumulative bivariate statistic robust to rare variants and different direction of genotype effect. 384-391
- Søren Mørk, Sune Pletscher-Frankild
, Albert Pallejà Caro
, Jan Gorodkin
, Lars Juhl Jensen
:
Protein-driven inference of miRNA-disease associations. 392-397 - Jianlong Peng, Jing Lu, Qiancheng Shen, Mingyue Zheng
, Xiaomin Luo
, Weiliang Zhu, Hualiang Jiang, Kaixian Chen:
In silico site of metabolism prediction for human UGT-catalyzed reactions. 398-405 - Matan Bodaker, Eran Meshorer
, Eduardo Mitrani, Yoram Louzoun:
Genes related to differentiation are correlated with the gene regulatory network structure. 406-413 - Sebastian Dümcke, Johannes Bräuer, Benedict Anchang, Rainer Spang
, Niko Beerenwinkel, Achim Tresch:
Exact likelihood computation in Boolean networks with probabilistic time delays, and its application in signal network reconstruction. 414-419
- Violeta N. Kovacheva, Adnan Mujahid Khan, Michael Khan
, David B. A. Epstein, Nasir M. Rajpoot
:
DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data. 420-427
- Tiffany J. Morris, Lee M. Butcher, Andrew Feber
, Andrew E. Teschendorff, Ankur R. Chakravarthy, Tomasz K. Wojdacz
, Stephan Beck:
ChAMP: 450k Chip Analysis Methylation Pipeline. 428-430 - Bai Zhang, Xuchu Hou, Xiguo Yuan, Ie-Ming Shih, Zhen Zhang, Robert Clarke
, Roger R. Wang, Yi Fu, Subha Madhavan, Yue Joseph Wang, Guoqiang Yu:
AISAIC: a software suite for accurate identification of significant aberrations in cancers. 431-433
- Guan-Zheng Luo, Wei Yang, Ying-Ke Ma, Xiu-Jie Wang:
ISRNA: an integrative online toolkit for short reads from high-throughput sequencing data. 434-436
- Esteban López-Camacho
, María Jesús García-Godoy
, Antonio J. Nebro
, José Francisco Aldana Montes
:
jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework. 437-438 - Mohammad Mehdi Ghahremanpour, Seyed Shahriar Arab
, Saman Biook Aghazadeh, Jin Zhang
, David van der Spoel:
MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program. 439-441
- Biao Li, Gao T. Wang, Suzanne M. Leal:
PhenoMan: phenotypic data exploration, selection, management and quality control for association studies of rare and common variants. 442-444
- Zeliha Görmez, Burcu Bakir-Gungor
, Mahmut Samil Sagiroglu:
HomSI: a homozygous stretch identifier from next-generation sequencing data. 445-447
Volume 30, Number 4, February 2014
- Olga Tanaseichuk, James Borneman, Tao Jiang
:
Phylogeny-based classification of microbial communities. 449-456 - Ruslan A. Soldatov, Svetlana V. Vinogradova, Andrey A. Mironov:
RNASurface: fast and accurate detection of locally optimal potentially structured RNA segments. 457-463 - Francisco Fernandes
, Ana T. Freitas
:
slaMEM: efficient retrieval of maximal exact matches using a sampled LCP array. 464-471 - Bin Liu, Deyuan Zhang, Ruifeng Xu, Jinghao Xu, Xiaolong Wang, Qingcai Chen, Qiwen Dong, Kuo-Chen Chou:
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection. 472-479 - Song Yan, Yun Li:
BETASEQ: a powerful novel method to control type-I error inflation in partially sequenced data for rare variant association testing. 480-487
- Nicolas Lartillot:
A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data. 488-496
- Hua Zhang, Lukasz A. Kurgan
:
Sequence-based Gaussian network model for protein dynamics. 497-505
- Chen Suo, Stefano Calza
, Agus Salim
, Yudi Pawitan:
Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data. 506-513 - Hongjie Zhu
, Man Luo:
Chemical structure informing statistical hypothesis testing in metabolomics. 514-522
- Andreas Krämer
, Jeff Green, Jack Pollard Jr., Stuart Tugendreich:
Causal analysis approaches in Ingenuity Pathway Analysis. 523-530 - Ferhat Alkan
, Cesim Erten
:
BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks. 531-539 - Jialu Hu
, Birte Kehr, Knut Reinert
:
NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks. 540-548 - Cong Zhou, Michael J. Walker, Andrew J. K. Williamson, Andrew Pierce
, Carlo Berzuini
, Caroline Dive
, Anthony D. Whetton
:
A hierarchical statistical modeling approach to analyze proteomic isobaric tag for relative and absolute quantitation data. 549-558
- Tomaz Hocevar
, Janez Demsar:
A combinatorial approach to graphlet counting. 559-565
- Richard M. Leggett
, Bernardo J. Clavijo
, Leah Clissold, Matthew D. Clark, Mario Cáccamo:
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries. 566-568
- José Colmenares, Jesús Ortiz
, Walter Rocchia
:
GPU linear and non-linear Poisson-Boltzmann solver module for DelPhi. 569-570
- Nicolas Jung, Frédéric Bertrand
, Seiamak Bahram
, Laurent Vallat, Myriam Maumy-Bertrand:
Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network. 571-573 - Raghavendra Hosur, Suzanne Szak, Alice Thai, Norm Allaire, Jadwiga R. Bienkowska:
ProbeSelect: selecting differentially expressed probes in transcriptional profile data. 574-575
- Darren Kessner, John Novembre:
forqs: forward-in-time simulation of recombination, quantitative traits and selection. 576-577 - Michel Petitjean
, Anne Vanet
:
VIRAPOPS: a forward simulator dedicated to rapidly evolved viral populations. 578-580
- Jiarui Zhou, Ralf J. M. Weber, James William Allwood
, Robert Mistrik, Zexuan Zhu, Zhen Ji, Siping Chen, Warwick B. Dunn
, Shan He, Mark R. Viant
:
HAMMER: automated operation of mass frontier to construct in silico mass spectral fragmentation libraries. 581-583 - Longfei Mao
, Wynand S. Verwoerd
:
ORCA: a COBRA toolbox extension for model-driven discovery and analysis. 584-585 - Cheng Chang
, Jiyang Zhang, Mingfei Han, Jie Ma, Wei Zhang, Songfeng Wu, Kehui Liu, Hongwei Xie, Fuchu He, Yunping Zhu:
SILVER: an efficient tool for stable isotope labeling LC-MS data quantitative analysis with quality control methods. 586-587
- Denis Fourches
, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha:
HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data. 588-589
- Muhammad A. Shah, Emily Denton, Lihua Liu, Matthieu Schapira:
ChromoHub V2: cancer genomics. 590-592 - Dennis Bromley, Steven J. Rysavy, Robert Su, Rudesh D. Toofanny, Tom Schmidlin, Valerie Daggett:
DIVE: a data intensive visualization engine. 593-595
- Sarah Sheppard, Nathan D. Lawson
, Lihua Julie Zhu:
Accurate identification of polyadenylation sites from 3′ end deep sequencing using a naïve Bayes classifier. 596
Volume 30, Number 5, March 2014
- Balamurugan Palanisamy, Rajasekaran Ekambaram
, Klaus Heese
:
Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite Plasmodium falciparum 3D7. 597-600
- Douglas D. Baumann, Rebecca W. Doerge:
Robust adjustment of sequence tag abundance. 601-605 - Franziska Zickmann, Martin S. Lindner, Bernhard Y. Renard
:
GIIRA - RNA-Seq driven gene finding incorporating ambiguous reads. 606-613