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Bioinformatics, Volume 28
Volume 28, Number 1, January 2012
- Yang Chen, Jin Gu
, Dan Li, Shao Li
:
Time-course network analysis reveals TNF-α can promote G1/S transition of cell cycle in vascular endothelial cells. 1-4
- Minzhu Xie, Jing Li
, Tao Jiang
:
Detecting genome-wide epistases based on the clustering of relatively frequent items. 5-12
- Guohui Yao, Liang Ye, Hongyu Gao, Patrick Minx, Wesley C. Warren, George M. Weinstock
:
Graph accordance of next-generation sequence assemblies. 13-16 - David Langenberger
, Sachin Pundhir
, Claus Thorn Ekstrøm
, Peter F. Stadler
, Steve Hoffmann, Jan Gorodkin
:
deepBlockAlign: a tool for aligning RNA-seq profiles of read block patterns. 17-24 - Natsuhiro Ichinose, Tetsushi Yada, Osamu Gotoh:
Large-scale motif discovery using DNA Gray code and equiprobable oligomers. 25-31 - Dapeng Li, Tonghua Li, Peisheng Cong, Wenwei Xiong
, Jiangming Sun:
A novel structural position-specific scoring matrix for the prediction of protein secondary structures. 32-39 - Arief Gusnanto, Henry M. Wood
, Yudi Pawitan, Pamela Rabbitts, Stefano Berri
:
Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data. 40-47
- Ryan M. Ames, Daniel Money, Vikramsinh P. Ghatge, Simon Whelan, Simon C. Lovell
:
Determining the evolutionary history of gene families. 48-55
- Gabriel Cuéllar-Partida
, Fabian A. Buske, Robert C. McLeay, Tom Whitington, William Stafford Noble, Timothy L. Bailey:
Epigenetic priors for identifying active transcription factor binding sites. 56-62 - Ming Hu
, Yu Zhu, Jeremy M. G. Taylor, Jun S. Liu, Zhaohui S. Qin
:
Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. 63-68
- Stefan Maetschke, Martin Simonsen, Melissa J. Davis
, Mark A. Ragan
:
Gene Ontology-driven inference of protein-protein interactions using inducers. 69-75 - Nicola Soranzo, Fahimeh Ramezani, Giovanni Iacono, Claudio Altafini:
Decompositions of large-scale biological systems based on dynamical properties. 76-83 - Emmanuelle Becker
, Benoît Robisson, Charles E. Chapple, Alain Guénoche, Marie-Christine Brun
:
Multifunctional proteins revealed by overlapping clustering in protein interaction network. 84-90 - Muhammad Tahir
, Asifullah Khan
, Abdul Majid:
Protein subcellular localization of fluorescence imagery using spatial and transform domain features. 91-97 - Xiujun Zhang
, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao
, Zhi-Ping Liu, Luonan Chen:
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. 98-104 - Edward Y. Chen, Huilei Xu, Simon Gordonov, Maribel P. Lim, Matthew H. Perkins, Avi Ma'ayan
:
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers. 105-111
- Daniel J. Stekhoven, Peter Bühlmann
:
MissForest - non-parametric missing value imputation for mixed-type data. 112-118
- Xavier Rafael Palou
, Michael P. Schroeder
, Núria López-Bigas
:
SVGMap: configurable image browser for experimental data. 119-120 - Kun Liang, Sündüz Keles:
Detecting differential binding of transcription factors with ChIP-seq. 121-122 - Francesco Vezzi, Cristian Del Fabbro
, Alexandru I. Tomescu
, Alberto Policriti:
rNA: a fast and accurate short reads numerical aligner. 123-124
- Yongan Zhao, Haixu Tang, Yuzhen Ye:
RAPSearch2: a fast and memory-efficient protein similarity search tool for next-generation sequencing data. 125-126 - Manal Kalkatawi
, Farania Rangkuti, Michael Schramm, Boris R. Jankovic, Allan Kamau
, Rajesh Chowdhary, John A. C. Archer, Vladimir B. Bajic
:
Dragon PolyA Spotter: predictor of poly(A) motifs within human genomic DNA sequences. 127-129 - Marc Torrent
, Paolo Di Tommaso
, David Pulido
, Victòria M. Nogués, Cédric Notredame
, Ester Boix
, David Andreu:
AMPA: an automated web server for prediction of protein antimicrobial regions. 130-131 - Mattia C. F. Prosperi, Marco Salemi:
QuRe: software for viral quasispecies reconstruction from next-generation sequencing data. 132-133
- Céline Bellenguez
, Amy Strange, Colin Freeman, Peter Donnelly
, Chris C. A. Spencer:
A robust clustering algorithm for identifying problematic samples in genome-wide association studies. 134-135
- Brian Pratt, J. Jeffry Howbert, Natalie I. Tasman, Erik J. Nilsson:
MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services. 136-137 - Walter Georgescu, John P. Wikswo, Vito Quaranta:
CellAnimation: an open source MATLAB framework for microscopy assays. 138-139
- Stephanie A. Canny, Yasel Cruz, Mark R. Southern, Patrick R. Griffin:
PubChem promiscuity: a web resource for gathering compound promiscuity data from PubChem. 140-141
- Erik Dassi
, A. Malossini, Angela Re
, Tommaso Mazza
, Toma Tebaldi
, Luigi Caputi
, Alessandro Quattrone
:
AURA: Atlas of UTR Regulatory Activity. 142-144
- Xiang Wan, Can Yang, Weichuan Yu
:
Comments on 'An empirical comparison of several recent epistatic interaction detection methods'. 145-146
- Yue Wang, Guimei Liu
, Mengling Feng, Limsoon Wong
:
Response: an empirical comparison of several recent epistatic interaction detection methods. 147-148
- Marie Brown, David C. Wedge
, Royston Goodacre
, Douglas B. Kell
, Philip N. Baker, Louise C. Kenny, Mamas A. Mamas
, Ludwig Neyses, Warwick B. Dunn
:
Automated workflows for accurate mass-based putative metabolite identification in LC/MS-derived metabolomic datasets. 149 - Farhad Hormozdiari, Faraz Hach
, Süleyman Cenk Sahinalp, Evan E. Eichler, Can Alkan:
Sensitive and fast mapping of di-base encoded reads. 150
Volume 28, Number 2, January 2012
- Gerard Wong, Christopher Leckie
, Adam Kowalczyk:
FSR: feature set reduction for scalable and accurate multi-class cancer subtype classification based on copy number. 151-159 - David R. Riley, Samuel V. Angiuoli
, Jonathan Crabtree, Julie C. Dunning Hotopp, Hervé Tettelin:
Using Sybil for interactive comparative genomics of microbes on the web. 160-166
- Jiarui Ding, Ali Bashashati, Andrew Roth, Arusha Oloumi, Kane Tse, Thomas Zeng, Gholamreza Haffari, Martin Hirst, Marco A. Marra, Anne Condon, Sam Aparicio
, Sohrab P. Shah:
Feature-based classifiers for somatic mutation detection in tumour-normal paired sequencing data. 167-175 - Yi-Fei Huang
, Geoffrey Brian Golding:
Inferring sequence regions under functional divergence in duplicate genes. 176-183 - David T. Jones, Daniel W. A. Buchan, Domenico Cozzetto
, Massimiliano Pontil:
PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments. 184-190
- Benjamin Albrecht, Céline Scornavacca, Alberto Cenci
, Daniel H. Huson:
Fast computation of minimum hybridization networks. 191-197
- Anna Philips
, Kaja Milanowska
, Grzegorz Lach
, Michal J. Boniecki
, Kristian Rother, Janusz M. Bujnicki:
MetalionRNA: computational predictor of metal-binding sites in RNA structures. 198-205
- Mark Maienschein-Cline, Jie Zhou, Kevin P. White, Roger Sciammas, Aaron R. Dinner:
Discovering transcription factor regulatory targets using gene expression and binding data. 206-213 - Geert Geeven
, Ronald E. van Kesteren
, August B. Smit, Mathisca C. M. de Gunst:
Identification of context-specific gene regulatory networks with GEMULA - gene expression modeling using LAsso. 214-221 - Bettina Grün
, Theresa Scharl
, Friedrich Leisch
:
Modelling time course gene expression data with finite mixtures of linear additive models. 222-228
- Hua Wang, Feiping Nie, Heng Huang, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin
, Li Shen
:
Identifying quantitative trait loci via group-sparse multitask regression and feature selection: an imaging genetics study of the ADNI cohort. 229-237
- Jose L. Rubio-Guivernau, Vasily Gurchenkov, Miguel A. Luengo-Oroz
, Louise Duloquin, Paul Bourgine, Andrés Santos
, Nadine Peyriéras
, María J. Ledesma-Carbayo
:
Wavelet-based image fusion in multi-view three-dimensional microscopy. 238-245
- José Caldas, Nils Gehlenborg
, Eeva Kettunen, Ali Faisal
, Mikko Rönty, Andrew G. Nicholson, Sakari Knuutila, Alvis Brazma
, Samuel Kaski:
Data-driven information retrieval in heterogeneous collections of transcriptomics data links SIM2s to malignant pleural mesothelioma. 246-253 - Nathan Harmston
, Wendy Filsell, Michael P. H. Stumpf:
Which species is it? Species-driven gene name disambiguation using random walks over a mixture of adjacency matrices. 254-260 - Jean-Philippe Carralot, Arnaud Ogier, Annette Boese, Auguste Genovesio
, Priscille Brodin
, Peter Sommer, Thierry Dorval:
A novel specific edge effect correction method for RNA interference screenings. 261-268
- Fidel Ramírez, Glenn Lawyer, Mario Albrecht:
Novel search method for the discovery of functional relationships. 269-276
- Yan W. Asmann, Sumit Middha
, Asif Hossain, Saurabh Baheti, Ying Li, High-Seng Chai, Zhifu Sun
, Patrick H. Duffy, Ahmed A. Hadad, Asha A. Nair, Xiaoyu Liu, Yuji Zhang
, Eric W. Klee, Krishna R. Kalari
, Jean-Pierre A. Kocher:
TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data. 277-278 - Pablo Librado
, Filipe G. Vieira
, Julio Rozas
:
BadiRate: estimating family turnover rates by likelihood-based methods. 279-281 - Aristotelis Tsirigos
, Niina Haiminen
, Erhan Bilal, Filippo Utro
:
GenomicTools: a computational platform for developing high-throughput analytics in genomics. 282-283
- R. W. W. Brouwer, M. C. G. N. van den Hout, Frank G. Grosveld, Wilfred F. J. van IJcken
:
NARWHAL, a primary analysis pipeline for NGS data. 284-285
- Chi-Ho Ngan, David R. Hall, Brandon S. Zerbe, Laurie E. Grove
, Dima Kozakov
, Sandor Vajda:
FTSite: high accuracy detection of ligand binding sites on unbound protein structures. 286-287
- Laurent Gatto
, Kathryn S. Lilley:
MSnbase-an R/Bioconductor package for isobaric tagged mass spectrometry data visualization, processing and quantitation. 288-289
- Christopher W. Whelan
, M. Kemal Sönmez:
Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter. 290-291 - Dominique F. Chu, Nicolae Radu Zabet
, Tobias von der Haar
:
A novel and versatile computational tool to model translation. 292-293 - Lu Zhang, Shengchang Gu, Yuan Liu, Bingqiang Wang, Francisco Azuaje:
Gene set analysis in the cloud. 294-295
- Nigel F. Reuel, Peter Bojo, Jingqing Zhang, Ardemis A. Boghossian, Jin-Ho Ahn, Jong-Ho Kim, Michael S. Strano:
NoRSE: noise reduction and state evaluator for high-frequency single event traces. 296-297 - Heidi E. L. Lischer, Laurent Excoffier
:
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs. 298-299
- Christian M. Reidys, Fenix W. D. Huang, Jørgen E. Andersen
, Robert C. Penner, Peter F. Stadler
, Markus E. Nebel:
Addendum: topology and prediction of RNA pseudoknots. 300
Volume 28, Number 3, February 2012
- Xin Wei, Ann F. Hoffman, Shannon M. Hamilton, Qing Xiang, Yang He, W. Venus So, Sung-Sau So, David Mark:
A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens. 301-305
- Olga Shevchuk, Louisa Roselius, Gabriele Günther, Johannes Klein, Dieter Jahn
, Michael Steinert, Richard Münch:
InFiRe - a novel computational method for the identification of insertion sites in transposon mutagenized bacterial genomes. 306-310
- David E. Larson, Christopher C. Harris, Ken Chen
, Daniel C. Koboldt, Travis E. Abbott, David J. Dooling, Timothy J. Ley, Elaine R. Mardis, Richard K. Wilson, Li Ding:
SomaticSniper: identification of somatic point mutations in whole genome sequencing data. 311-317 - Antonio Marco
, Sam Griffiths-Jones
:
Detection of microRNAs in color space. 318-323
- Ryotaro Koike, Motonori Ota:
SCPC: a method to structurally compare protein complexes. 324-330 - Ke Chen
, Marcin J. Mizianty, Lukasz A. Kurgan
:
Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors. 331-341 - Valdete M. Gonçalves-Almeida, Douglas E. V. Pires
, Raquel Cardoso de Melo Minardi
, Carlos Henrique da Silveira
, Wagner Meira Jr., Marcelo M. Santoro:
HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids. 342-349 - J. W. Heal, J. E. Jimenez-Roldan, Stephen A. Wells
, R. B. Freedman, Rudolf A. Römer
:
Inhibition of HIV-1 protease: the rigidity perspective. 350-357
- Gengxin Li, Joel Gelernter
, Henry R. Kranzler, Hongyu Zhao:
M3: an improved SNP calling algorithm for Illumina BeadArray data. 358-365
- Wei Liu, Mahesan Niranjan
:
Gaussian process modelling for bicoid mRNA regulation in spatio-temporal Bicoid profile. 366-372 - Alla Karnovsky, Terry E. Weymouth, Tim Hull, V. Glenn Tarcea, Giovanni Scardoni, Carlo Laudanna, Maureen A. Sartor, Kathleen A. Stringer
, H. V. Jagadish, Charles F. Burant
, Brian D. Athey
, Gilbert S. Omenn
:
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data. 373-380 - Kathrin Ballerstein, Axel von Kamp, Steffen Klamt
, Utz-Uwe Haus:
Minimal cut sets in a metabolic network are elementary modes in a dual network. 381-387 - Mario Latendresse, Markus Krummenacker, Miles Trupp, Peter D. Karp
:
Construction and completion of flux balance models from pathway databases. 388-396
- Natalia Jiménez-Lozano, Joan Segura
, José Ramón Macías
, Juanjo Vega, José María Carazo:
Integrating human and murine anatomical gene expression data for improved comparisons. 397-402 - Yupeng Wang
, Sandeep J. Joseph
, Xinyu Liu, Michael Kelley, Romdhane Rekaya:
SNPxGE2: a database for human SNP-coexpression associations. 403-410 - Nestor Milyaev, David Osumi-Sutherland
, Simon Reeve, Nicholas Burton, Richard A. Baldock
, J. Douglas Armstrong
:
The Virtual Fly Brain browser and query interface. 411-415
- Yongbing Zhao, Jiayan Wu
, Junhui Yang, Shixiang Sun
, Jing-Fa Xiao, Jun Yu:
PGAP: pan-genomes analysis pipeline. 416-418 - Mikhail G. Dozmorov
, Lukas R. Cara, Cory B. Giles, Jonathan D. Wren
:
GenomeRunner: automating genome exploration. 419-420 - F. Anthony San Lucas, Gao T. Wang, Paul Scheet, Bo Peng:
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. 421-422 - Valentina Boeva
, Tatiana G. Popova, Kevin Bleakley, Pierre Chiche, Julie Cappo, Gudrun Schleiermacher, Isabelle Janoueix-Lerosey
, Olivier Delattre
, Emmanuel Barillot
:
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. 423-425
- Carlos Prieto
, Carlos García-Estrada
, Diego Lorenzana, Juan Francisco Martín:
NRPSsp: non-ribosomal peptide synthase substrate predictor. 426-427 - Benjamin Kreck, George Marnellos, Julia Richter, Felix Krueger
, Reiner Siebert, Andre Franke:
B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data. 428-429 - Yuanxin Xi, Christoph Bock
, Fabian Müller, Deqiang Sun
, Alexander Meissner, Wei Li:
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing. 430-432 - Robert Schmieder, Yan Wei Lim, Robert A. Edwards
:
Identification and removal of ribosomal RNA sequences from metatranscriptomes. 433-435 - Antonio Gonzalez, Jesse Stombaugh
, Christian L. Lauber, Noah Fierer, Rob Knight
:
SitePainter: a tool for exploring biogeographical patterns. 436-438
- Conan K. Wang, Saroja K. Weeratunga
, Chris M. Pacheco, Andreas Hofmann
:
DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments. 439-440 - Julia T. Philip, Charles H. Pence
, Holly V. Goodson
:
MTBindingSim: simulate protein binding to microtubules. 441-443
- Christian Fuchsberger
, Daniel Taliun, Peter P. Pramstaller
, Cristian Pattaro:
GWAtoolbox: an R package for fast quality control and handling of genome-wide association studies meta-analysis data. 444-445
- Enrico Glaab
, Reinhard Schneider
:
PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data. 446-447
- Sarala M. Wimalaratne
, Pierre Grenon
, Robert Hoehndorf
, Georgios V. Gkoutos
, Bernard de Bono
:
An infrastructure for ontology-based information systems in biomedicine: RICORDO case study. 448-450 - Kai Xia
, Andrey A. Shabalin
, Shunping Huang, Vered Madar
, Yi-Hui Zhou, Wei Wang
, Fei Zou, Wei Sun, Patrick F. Sullivan, Fred A. Wright:
seeQTL: a searchable database for human eQTLs. 451-452
Volume 28, Number 4, February 2012
- Wilson Wen Bin Goh
, Hirotaka Oikawa
, Judy Chia Ghee Sng, Marek J. Sergot, Limsoon Wong
:
The role of miRNAs in complex formation and control. 453-456
- Thomas J. Hardcastle
, Krystyna A. Kelly, David C. Baulcombe
:
Identifying small interfering RNA loci from high-throughput sequencing data. 457-463 - Tim Carver, Simon R. Harris
, Matthew Berriman
, Julian Parkhill
, Jacqueline A. McQuillan
:
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. 464-469 - Alberto Magi
, Lorenzo Tattini
, Tommaso Pippucci, Francesca Torricelli, Matteo Benelli
:
Read count approach for DNA copy number variants detection. 470-478
- Yanju Zhang, Eric-Wubbo Lameijer, Peter A. C. 't Hoen
, Zemin Ning
, P. Eline Slagboom
, Kai Ye
:
PASSion: a pattern growth algorithm-based pipeline for splice junction detection in paired-end RNA-Seq data. 479-486 - Phil Arnold, Ionas Erb
, Mikhail Pachkov, Nacho Molina
, Erik van Nimwegen
:
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences. 487-494 - Benjamin P. Blackburne
, Simon Whelan:
Measuring the distance between multiple sequence alignments. 495-502
- Ian Walsh
, Alberto J. M. Martin
, Tomás Di Domenico
, Silvio C. E. Tosatto
:
ESpritz: accurate and fast prediction of protein disorder. 503-509 - Tim Harder, Mikael Borg
, Wouter Boomsma
, Peter Røgen
, Thomas Hamelryck
:
Fast large-scale clustering of protein structures using Gauss integrals. 510-515 - Sikander Hayat
, Arne Elofsson
:
BOCTOPUS: improved topology prediction of transmembrane β barrel proteins. 516-522 - Sudhakar Sahoo, Andreas Alexander Albrecht:
Approximating the set of local minima in partial RNA folding landscapes. 523-530
- Tiejun Tong
, Liang Chen, Hongyu Zhao:
Improved mean estimation and its application to diagonal discriminant analysis. 531-537 - Isaac S. Kohane, Vladimir I. Valtchinov:
Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. 538-545
- Lipi R. Acharya, Thair Judeh, Guangdi Wang, Dongxiao Zhu:
Optimal structural inference of signaling pathways from unordered and overlapping gene sets. 546-556 - Thomas Handorf,