


Остановите войну!
for scientists:


default search action
BMC Bioinformatics, Volume 12
Volume 12, 2011
- Wen Huang, Naoki Takebayashi, Yan Qi, Michael J. Hickerson:
MTML-msBayes: Approximate Bayesian comparative phylogeographic inference from multiple taxa and multiple loci with rate heterogeneity. 1 - Ariel E. Bayá
, Pablo M. Granitto
:
Clustering gene expression data with a penalized graph-based metric. 2 - Zasha Weinberg
, Ronald R. Breaker
:
R2R - software to speed the depiction of aesthetic consensus RNA secondary structures. 3 - Geert Vandeweyer
, Edwin Reyniers, Wim Wuyts
, Liesbeth Rooms, R. Frank Kooy
:
CNV-WebStore: Online CNV Analysis, Storage and Interpretation. 4 - Mattia C. F. Prosperi, Luciano Prosperi, Alessandro Bruselles
, Isabella Abbate, Gabriella Rozera
, Donatella Vincenti, Maria Carmela Solmone, Maria Rosaria Capobianchi
, Giovanni Ulivi:
Combinatorial analysis and algorithms for quasispecies reconstruction using next-generation sequencing. 5 - Terrence F. Meehan
, Anna Maria Masci
, Amina Abdulla, Lindsay G. Cowell, Judith A. Blake
, Christopher J. Mungall
, Alexander D. Diehl
:
Logical Development of the Cell Ontology. 6 - Kyle C. Chipman, Ambuj K. Singh:
Using Stochastic Causal Trees to Augment Bayesian Networks for Modeling eQTL Datasets. 7 - José Carlos Clemente, Jesper Jansson
, Gabriel Valiente
:
Flexible taxonomic assignment of ambiguous sequencing reads. 8 - Dong-Dong Pan, Qizhai Li, Ningning Jiang, Aiyi Liu
, Kai F. Yu:
Robust joint analysis allowing for model uncertainty in two-stage genetic association studies. 9 - Robert K. Luecking
, Brendan P. Hodkinson, Alexandros Stamatakis, Reed A. Cartwright:
PICS-Ord: Unlimited Coding of Ambiguous Regions by Pairwise Identity and Cost Scores Ordination. 10 - Benjamin Linard, Julie Dawn Thompson, Olivier Poch, Odile Lecompte
:
OrthoInspector: comprehensive orthology analysis and visual exploration. 11 - Hatice U. Osmanbeyoglu
, Madhavi Ganapathiraju
:
N-gram analysis of 970 microbial organisms reveals presence of biological language models. 12 - Anshu Sinha, Marianthi Markatou:
A Platform for Processing Expression of Short Time Series (PESTS). 13 - Yizhou Li, Zhining Wen, Jiamin Xiao, Hui Yin, Lezheng Yu, Li Yang, Menglong Li:
Predicting disease-associated substitution of a single amino acid by analyzing residue interactions. 14 - Valerie Hower, Steven N. Evans, Lior Pachter
:
Shape-based peak identification for ChIP-Seq. 15 - Raphaël Mourad, Christine Sinoquet, Philippe Leray
:
A hierarchical Bayesian network approach for linkage disequilibrium modeling and data-dimensionality reduction prior to genome-wide association studies. 16 - Jingyuan Zhao, Simone Gupta, Mark Seielstad
, Jianjun Liu, Anbupalam Thalamuthu
:
Pathway-based analysis using reduced gene subsets in genome-wide association studies. 17 - Jialiang Yang
, Jun Li
, Liuhuan Dong, Stefan Grünewald:
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states. 18 - Sohyun Hwang, Sangwoo Kim
, Heesung Shin, Doheon Lee
:
Context-dependent transcriptional regulations between signal transduction pathways. 19 - Non G. Yok, Gail L. Rosen
:
Combining gene prediction methods to improve metagenomic gene annotation. 20 - Daniel Restrepo-Montoya
, Camilo Pino, Luis F. Niño, Manuel-Elkin Patarroyo
, Manuel A. Patarroyo
:
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins. 21 - Andrew K. Miller, Tommy Yu, Randall Britten, Mike T. Cooling
, James R. Lawson
, Dougal Cowan, Alan Garny, Matt D. B. Halstead, Peter J. Hunter
, David P. Nickerson
, Geoff Nunns, Sarala M. Wimalaratne
, Poul M. F. Nielsen:
Revision history aware repositories of computational models of biological systems. 22 - Bernat Gel
, Andrew M. Jenkinson
, Rafael C. Jiménez
, Xavier Messeguer Peypoch
, Henning Hermjakob
:
easyDAS: Automatic creation of DAS servers. 23 - Oleksii Kuchaiev, Aleksandar Stevanovic, Wayne B. Hayes
, Natasa Przulj
:
GraphCruch 2: Software tool for network modeling, alignment and clustering. 24 - Plamen Dragiev, Robert Nadon, Vladimir Makarenkov:
Systematic error detection in experimental high-throughput screening. 25 - Mark A. Levenstien, Robert J. Klein:
Predicting functionally important SNP classes based on negative selection. 26 - Franck Gauthier, Olivier C. Martin
, Matthieu Falque
:
CODA (CrossOver Distribution Analyzer): quantitative characterization of crossover position patterns along chromosomes. 27 - Andreas Hoppe
, Sabrina Hoffmann, Andreas Gerasch, Christoph Gille, Hermann-Georg Holzhütter
:
FASIMU: flexible software for flux-balance computation series in large metabolic networks. 28 - Andre J. Faure, Cathal Seoighe, Nicola J. Mulder
:
Investigating the effect of paralogs on microarray gene-set analysis. 29 - Martin O. Jones, Georgios D. Koutsovoulos
, Mark L. Blaxter:
iPhy: an integrated phylogenetic workbench for supermatrix analyses. 30 - Daniel Glez-Peña
, Gonzalo Gómez-López
, Miguel Reboiro-Jato
, Florentino Fdez-Riverola
, David G. Pisano
:
PileLine: a toolbox to handle genome position information in next-generation sequencing studies. 31 - Gary Schindelman, Jolene Fernandes, Carol Bastiani, Karen Yook
, Paul W. Sternberg
:
Worm Phenotype Ontology: integrating phenotype data within and beyond the C. elegans community. 32 - Elon Santos Correa
, Royston Goodacre
:
A genetic algorithm-Bayesian network approach for the analysis of metabolomics and spectroscopic data: application to the rapid detection of Bacillus spores and identification of Bacillus species. 33 - Tania Dottorini
, Nicola Senin
, Giorgio Mazzoleni, Kalle Magnusson, Andrea Crisanti
:
Gepoclu: a software tool for identifying and analyzing gene positional clusters in large-scale gene expression analysis. 34 - Hanbo Chen, Paul C. Boutros
:
VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R. 35 - Lin Li, Dachuan Guo, Yangyu Huang, Shiyong Liu
, Yi Xiao:
ASPDock: protein-protein docking algorithm using atomic solvation parameters model. 36 - John J. Heine, Walker H. Land Jr., Kathleen M. Egan:
Statistical learning techniques applied to epidemiology: a simulated case-control comparison study with logistic regression. 37 - Christopher Quince
, Anders Lanzén
, Russell J. Davenport
, Peter J. Turnbaugh
:
Removing Noise From Pyrosequenced Amplicons. 38 - Peter Humburg
, Chris A. Helliwell
, David W. Bulger
, Glenn Stone:
ChIPseqR: Analysis of ChIP-seq Experiments. 39 - Alexander Herbig
, Kay Nieselt
:
nocoRNAc: Characterization of non-coding RNAs in prokaryotes. 40 - Özkan U. Nalbantoglu, Samuel F. Way, Steven H. Hinrichs, Khalid Sayood:
RAIphy: Phylogenetic classification of metagenomics samples using iterative refinement of relative abundance index profiles. 41 - Harri T. Kiiveri:
Multivariate analysis of microarray data: differential expression and differential connection. 42 - Jesse Eickholt, Xin Deng, Jianlin Cheng
:
DoBo: Protein domain boundary prediction by integrating evolutionary signals and machine learning. 43 - Suyu Mei, Wang Fei, Shuigeng Zhou:
Gene ontology based transfer learning for protein subcellular localization. 44 - Nathan W. Lemons, Bin Hu, William S. Hlavacek
:
Hierarchical graphs for rule-based modeling of biochemical systems. 45 - Fenglong Liu, Joseph White, Corina Antonescu, John Quackenbush
:
GCOD - GeneChip Oncology Database. 46 - Stefan Wolfsheimer, Inke Herms, Sven Rahmann
, Alexander K. Hartmann:
Accurate statistics for local sequence alignment with position-dependent scoring by rare-event sampling. 47 - Eric di Luccio
, Patrice Koehl
:
A quality metric for homology modeling: the H-factor. 48 - Riccardo De Bin
, Davide Risso
:
A novel approach to the clustering of microarray data via nonparametric density estimation. 49 - Nobuyoshi Sugaya, Toshio Furuya:
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. 50 - Mohan Krishnamoorthy, Pragneshkumar Patel, Mira Dimitrijevic, Jonathan Dietrich, Margaret Green, Catherine Macken:
Tree Pruner: An efficient tool for selecting data from a biased genetic database. 51 - Barry Zeeberg, Hongfang Liu, Ari B. Kahn, Martin Ehler, Vinodh N. Rajapakse
, Robert F. Bonner, Jacob D. Brown, Brian P. Brooks, Vladimir L. Larionov, William C. Reinhold
, John N. Weinstein
, Yves Pommier:
RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. 52 - Bo Zhang
, Beibei Chen, Tao Wu
, Zhenyu Xuan, Xiaopeng Zhu
, Runsheng Chen
:
Estimating developmental states of tumors and normal tissues using a linear time-ordered model. 53 - Shuying Sun, Zhengyi Chen, Pearlly Yan, Yi-Wen Huang, Tim Hui-Ming Huang, Shili Lin:
Identifying hypermethylated CpG islands using a quantile regression model. 54 - Johannes Eichner, Georg Zeller
, Sascha Laubinger
, Gunnar Rätsch
:
Support vector machines-based identification of alternative splicing in Arabidopsis thaliana from whole-genome tiling arrays. 55 - José Santos Reyes, Ángel Monteagudo
:
Simulated evolution applied to study the genetic code optimality using a model of codon reassignments. 56 - Alexander Karpikov, Joel S. Rozowsky
, Mark Gerstein:
Tiling array data analysis: a multiscale approach using wavelets. 57 - Francesco Cerutti
, Luigi Bertolotti
, Tony L. Goldberg, Mario Giacobini
:
Taxon ordering in phylogenetic trees: a workbench test. 58 - Elizabeth Tapia
, Leonardo Ornella, Pilar Bulacio, Laura Angelone:
Multiclass classification of microarray data samples with a reduced number of genes. 59 - Richard Tzong-Han Tsai
, Po-Ting Lai:
Dynamic programming re-ranking for PPI interactor and pair extraction in full-text articles. 60 - Marcin Cieslik, Cameron Mura
:
A lightweight, flow-based toolkit for parallel and distributed bioinformatics pipelines. 61 - Jonathon T. Hill
, Keith R. Anderson, Teresa L. Mastracci, Klaus H. Kaestner, Lori Sussel:
Novel computational analysis of protein binding microarray data identifies direct targets of Nkx2.2 in the pancreas. 62 - Rutger A. Vos
, Jason Caravas, Klaas Hartmann, Mark A. Jensen
, Chase A. Miller:
Bio: : Phylo - phyloinformatic analysis using Perl. 63 - W. Andrew Lancaster, Jeremy L. Praissman, Farris L. Poole II, Aleksandar Cvetkovic, Angeli L. Menon, Joseph W. Scott, Francis E. Jenney Jr., Michael P. Thorgersen
, Ewa Kalisiak, Junefredo V. Apon, Sunia A. Trauger, Gary Siuzdak
, John A. Tainer
, Michael W. W. Adams:
A Computational Framework for Proteome-Wide Pursuit and Prediction of Metalloproteins using ICP-MS and MS/MS Data. 64 - Raphael Cohen, Avitan Gefen, Michael Elhadad
, Ohad S. Birk
:
Clinical Synopsis Search in OMIM. 65 - Gordana Pavlovic-Lazetic, Nenad S. Mitic, Jovana J. Kovacevic, Zoran Obradovic, Sasa N. Malkov, Milos V. Beljanski:
Bioinformatics analysis of disordered proteins in prokaryotes. 66 - Antony Le Béchec
, Elodie Portales-Casamar
, Guillaume Vetter, Michèle Moes, Pierre-Joachim Zindy, Anne Saumet, David J. Arenillas, Charles Theillet
, Wyeth W. Wasserman
, Charles-Henri Lecellier, Evelyne Friederich:
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. 67 - Matthew E. Ritchie
, Ruijie Liu
, Benilton S. Carvalho
, Rafael A. Irizarry:
Comparing genotyping algorithms for Illumina's Infinium whole-genome SNP BeadChips. 68 - Yufan Guo, Anna Korhonen, Maria Liakata
, Ilona Silins, Johan Högberg, Ulla Stenius:
A comparison and user-based evaluation of models of textual information structure in the context of cancer risk assessment. 69 - Harald Barsnes
, Marc Vaudel
, Niklaas Colaert, Kenny Helsens
, Albert Sickmann
, Frode S. Berven, Lennart Martens
:
compomics-utilities: an open-source Java library for computational proteomics. 70 - Elizabeth K. Nelson, Britt Piehler, Josh Eckels, Adam Rauch, Matthew Bellew, Peter Hussey, Sarah Ramsay, Cory Nathe, Karl Lum, Kevin Krouse, David Stearns, Brian Connolly, Tom Skillman, Mark Igra:
LabKey Server: An open source platform for scientific data integration, analysis and collaboration. 71 - Samir B. Amin
, Parantu K. Shah, Aimin Yan, Sophia Adamia, Stéphane Minvielle
, Herve Avet-Loiseau
, Nikhil C. Munshi, Cheng Li:
The dChip survival analysis module for microarray data. 72 - Peter Sykacek, David P. Kreil, Lisa A. Meadows, Richard P. Auburn, Bettina Fischer, Steven Russell
, Gos Micklem
:
The impact of quantitative optimization of hybridization conditions on gene expression analysis. 73 - William H. Haskins, Konstantinos Petritis
, Jianqiu Zhang:
MRCQuant- an accurate LC/MS relative isotopic quantification algorithm on TOF instruments. 74 - Jihoon Kim, Kiltesh Patel, Hyunchul Jung, Winston Patrick Kuo, Lucila Ohno-Machado
:
AnyExpress: Integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. 75 - Ren-Xiang Yan, Zhen Chen
, Ziding Zhang
:
Outer membrane proteins can be simply identified using secondary structure element alignment. 76 - Xavier Robin
, Natacha Turck, Alexandre Hainard, Natalia Tiberti
, Frédérique Lisacek, Jean-Charles Sanchez, Markus Müller
:
pROC: an open-source package for R and S+ to analyze and compare ROC curves. 77 - Mi-Youn K. Brusniak, Sung-Tat Kwok, Mark Christiansen, David S. Campbell, Lukas Reiter, Paola Picotti, Ulrike Kusebauch, Hector Ramos, Eric W. Deutsch, Jingchun Chen, Robert L. Moritz, Ruedi Aebersold:
ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. 78 - Bin Cai, Xiaohan Yang
, Gerald A. Tuskan
, (Max) Zong-Ming Cheng:
MicroSyn: A user friendly tool for detection of microsynteny in a gene family. 79 - Deepali Jhamb, Nandini Rao, Derek J. Milner, Fengyu Song, Jo Ann Cameron, David L. Stocum, Mathew J. Palakal:
Network based transcription factor analysis of regenerating axolotl limbs. 80 - Jun Ma, Maureen A. Sartor, H. V. Jagadish:
Appearance frequency modulated gene set enrichment testing. 81 - Ting Gong, Jianhua Xuan, Li Chen, Rebecca B. Riggins
, Huai Li, Eric P. Hoffman
, Robert Clarke
, Yue Joseph Wang:
Motif-guided sparse decomposition of gene expression data for regulatory module identification. 82 - Juliana S. Bernardes, Alessandra Carbone
, Gerson Zaverucha:
A discriminative method for family-based protein remote homology detection that combines inductive logic programming and propositional models. 83 - Fan Shi, Gad Abraham
, Christopher Leckie
, Izhak Haviv, Adam Kowalczyk:
Meta-analysis of gene expression microarrays with missing replicates. 84 - Yongchao Liu
, Bertil Schmidt
, Douglas L. Maskell:
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI. 85 - Raffaele Fronza, Michele Tramonti, William R. Atchley, Christine Nardini
:
Joint Analysis of Transcriptional and post- Transcriptional Data: Searching Emergent Properties in Brain Tumor Samples. 86 - Benjamin Roche
, John M. Drake
, Pejman Rohani
:
An Agent-Based Model to study the epidemiological and evolutionary dynamics of Influenza viruses. 87 - Richard Newton, Jason Hinds
, Lorenz Wernisch:
Empirical Bayesian models for analysing molecular serotyping microarrays. 88 - Xia Jiang, Richard E. Neapolitan, M. Michael Barmada
, Shyam Visweswaran:
Learning genetic epistasis using Bayesian network scoring criteria. 89 - Alejandro Ochoa
, Manuel Llinás, Mona Singh
:
Using context to improve protein domain identification. 90 - Jinlian Wang, Manabu Torii
, Hongfang Liu, Gerald W. Hart
, Zhang-Zhi Hu:
dbOGAP - An Integrated Bioinformatics Resource for Protein O-GlcNAcylation. 91 - Paolo G. V. Martini
, Davide Risso
, Gabriele Sales
, Chiara Romualdi
, Gerolamo Lanfranchi, Stefano Cagnin
:
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. 92 - Thomas Unterthiner
, Anne-Kathrin Schultz
, Jan Bulla, Burkhard Morgenstern
, Mario Stanke, Ingo Bulla:
Detection of viral sequence fragments of HIV-1 subfamilies yet unknown. 93 - Joost C. M. Uitdehaag, Guido J. R. Zaman:
A theoretical entropy score as a single value to express inhibitor selectivity. 94 - Joshua L. Wetzel, Carl Kingsford, Mihai Pop
:
Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies. 95 - Se-Eun Bae, Hyeon Seok Son:
Classification of viral zoonosis through receptor pattern analysis. 96 - Andrew T. Milnthorpe, Mikhail Soloviev
:
Errors in CGAP xProfiler and cDNA DGED: the importance of library parsing and gene selection algorithms. 97 - Brandon Chisham, Ben Wright, Trung Le, Tran Cao Son, Enrico Pontelli
:
CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis. 98 - Lingjie Weng, Fabio Macciardi
, Aravind Subramanian, Guia Guffanti, Steven G. Potkin
, Zhaoxia Yu, Xiaohui Xie:
SNP-based pathway enrichment analysis for genome-wide association studies. 99 - Hsin-Chou Yang
, Hsin-Chi Lin, Meijyh Kang, Chun-Houh Chen
, Chien-Wei Lin
, Ling-Hui Li, Jer-Yuarn Wu, Yuan-Tsong Chen, Wen-Harn Pan:
SAQC: SNP array quality control. 100 - Wolfram Stacklies, Christian Seifert, Frauke Graeter:
Implementation of Force Distribution Analysis for Molecular Dynamics simulations. 101 - Haibao Tang
, Eric Lyons, Brent S. Pedersen, James C. Schnable
, Andrew H. Paterson, Michael Freeling:
Screening synteny blocks in pairwise genome comparisons through integer programming. 102 - Zsuzsanna Sükösd, Bjarne Knudsen, Morten Vaerum, Jørgen Kjems
, Ebbe Sloth Andersen:
Multithreaded comparative RNA secondary structure prediction using stochastic context-free grammars. 103 - Botond Sipos
, Tim Massingham, Gregory E. Jordan
, Nick Goldman
:
PhyloSim - Monte Carlo simulation of sequence evolution in the R statistical computing environment. 104 - Jorge Amigo
, Antonio Salas
, Christopher Phillips
:
ENGINES: exploring single nucleotide variation in entire human genomes. 105 - Franziska Hufsky
, Léon Kuchenbecker, Katharina Jahn, Jens Stoye
, Sebastian Böcker
:
Swiftly Computing Center Strings. 106 - Yonggan Wu, Bo Wei, Haizhou Liu, Tianxian Li, Simon Rayner
:
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences. 107 - Arif Ozgun Harmanci, Gaurav Sharma, David H. Mathews:
TurboFold: Iterative probabilistic estimation of secondary structures for multiple RNA sequences. 108 - Wenling E. Chang, Keri Sarver, Brandon W. Higgs
, Timothy D. Read
, Nichole M. E. Nolan, Carol E. Chapman, Kimberly A. Bishop-Lilly
, Shanmuga Sozhamannan
:
PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data. 109 - Shannon Zhang, Yaping Zong:
Was the Scanner Calibration Slide Used for Its Intended Purpose? 110 - Shu-Chuan Chen, Michael S. Rosenberg
, Bruce G. Lindsay:
MixtureTree: a program for constructing phylogeny. 111 - Frank P. Y. Lin, Stephen Anthony, Thomas M. Polasek, Guy Tsafnat
, Matthew P. Doogue:
BICEPP: an example-based statistical text mining method for predicting the binary characteristics of drugs. 112 - Luis Rueda, Iman Rezaeian:
A Fully Automatic Gridding Method for cDNA Microarray Images. 113 - Anna M. Ritz
, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael:
Detection of recurrent rearrangement breakpoints from copy number data. 114