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ORCIDBMC 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