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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 - Anna M. Ritz, Pamela L. Paris, Michael Ittmann, Colin C. Collins, Benjamin J. Raphael:
Detection of recurrent rearrangement breakpoints from copy number data. 114 - William S. Sanders, Nan Wang, Susan M. Bridges, Brandon M. Malone, Yoginder S. Dandass, Fiona M. McCarthy, Bindu Nanduri, Mark L. Lawrence, Shane C. Burgess:
The Proteogenomic Mapping Tool. 115 - Vincent Miele, Simon Penel, Laurent Duret:
Ultra-fast sequence clustering from similarity networks with SiLiX. 116 - A. J. Agopian, Laura E. Mitchell:
MI-GWAS: a SAS platform for the analysis of inherited and maternal genetic effects in genome-wide association studies using log-linear models. 117 - Qin Chang, Yihui Luan, Fengzhu Sun:
Variance adjusted weighted UniFrac: a powerful beta diversity measure for comparing communities based on phylogeny. 118 - Osvaldo Zagordi, Arnab Bhattacharya, Nicholas Eriksson, Niko Beerenwinkel:
ShoRAH: estimating the genetic diversity of a mixed sample from next-generation sequencing data. 119 - Zohar Yakhini, Igor Jurisica:
Cancer Computational Biology. 120 - Jarno Mäkelä, Jason Lloyd-Price, Olli Yli-Harja, Andre S. Ribeiro:
Stochastic sequence-level model of coupled transcription and translation in prokaryotes. 121 - Alvaro Olivera-Nappa, Barbara A. Andrews, Juan A. Asenjo:
Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins. 122 - Cristian Andrés Gallo, Jessica Andrea Carballido, Ignacio Ponzoni:
Discovering Time-Lagged Rules from Microarray Data using Gene Profile Classifiers. 123 - Marcus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F. Stadler, Sonja J. Prohaska:
Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis. 124 - Jan Hasenauer, Steffen Waldherr, Malgorzata Doszczak, Nicole Radde, Peter Scheurich, Frank Allgöwer:
Identification of models of heterogeneous cell populations from population snapshot data. 125 - Szymon Stoma, Martina Fröhlich, Susanne Gerber, Edda Klipp:
STSE: Spatio-Temporal Simulation Environment Dedicated to Biology. 126 - Andreas Leha, Tim Beißbarth, Klaus Jung:
Sequential Interim Analyses of Survival Data in DNA Microarray Experiments. 127 - Bailing Zhang, Tuan D. Pham:
Phenotype Recognition with Combined Features and Random Subspace Classifier Ensemble. 128 - Hugues Sicotte, David N. Rider, Gregory A. Poland, Neelam Dhiman, Jean-Pierre A. Kocher:
SNPPicker: High quality tag SNP selection across multiple populations. 129 - Ryan C. Kennedy, Maria F. Unger, Scott Christley, Frank H. Collins, Gregory R. Madey:
An automated homology-based approach for identifying transposable elements. 130 - Hiroshi Tsugawa, Yuki Tsujimot, Masanori Arita, Takeshi Bamba, Eiichiro Fukusaki:
GC/MS Based Metabolomics: Development of a Data Mining System for Metabolite Identification by using Soft Independent Modeling of Class Analogy (SIMCA). 131 - Wanding Zhou, Luay Nakhleh:
Properties of Metabolic Graphs: Biological Organization or Representation Artifacts? 132 - Sharon I. Greenblum, Sol Efroni, Carl F. Schaefer, Kenneth H. Buetow:
The PathOlogist: An Automated Tool for Pathway-Centric Analysis. 133 - Alexis Dereeper, Stéphane Nicolas, Loic Le Cunff, Roberto Bacilieri, Agnes Doligez, Jean-Pierre Peros, Manuel Ruiz, Patrice This:
SNiPlay: a web-based tool for detection, management and analysis of SNPs. Application to grapevine diversity projects. 134 - Damien Paulet, Mireille Claustres, Christophe Béroud:
Hydrophobic pulses predict transmembrane helix irregularities and channel transmembrane units. 135 - Christopher C. Overall, D. Andrew Carr, Ehsan S. Tabari, Kevin J. Thompson, Jennifer W. Weller:
ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs. 136 - Matthew N. McCall, Peter N. Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry:
Assessments of Affymetrix GeneChip Microarray Quality for Laboratories and Single Samples. 137 - Natalia Becker, Grischa Toedt, Peter Lichter, Axel Benner:
Elastic SCAD as a novel penalization method for SVM classification tasks in high-dimensional data. 138 - Xin Feng, Robert Grossman, Lincoln Stein:
PeakRanger: A cloud-enabled peak caller for ChIP-seq data. 139 - Chris Bauer, Frank Kleinjung, Celia J. Smith, Mark W. Towers, Ali Tiss, Alexandra Chadt, Tanja Dreja, Dieter Beule, Hadi Al-Hasani, Knut Reinert, Johannes Schuchhardt, Rainer Cramer:
Biomarker Discovery and Redundancy Reduction towards Classification using a Multi-factorial MALDI-TOF MS T2DM Mouse Model Dataset. 140 - Sebastian G. A. Konietzny, Laura Dietz, Alice Carolyn McHardy:
Inferring functional modules of protein families with probabilistic topic models. 141 - Costas P. Exarchos, Themis P. Exarchos, Georgios Rigas, Costas Papaloukas, Dimitrios I. Fotiadis:
Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment. 142 - Gustavo A. Salazar, Rafael C. Jiménez, Alexander García Castro, Henning Hermjakob, Nicola J. Mulder, Edwin H. Blake:
DAS Writeback: A Collaborative Annotation System. 143 - Krishna M. Roskin, Benedict Paten, David Haussler:
Meta-Alignment with Crumble and Prune: Partitioning very large alignment problems for performance and parallelization. 144 - Shareef Dabdoub, William C. Ray, Sheryl S. Justice:
FIND: A new software tool and development platform for enhanced multicolor flow analysis. 145 - Youngmi Hur, Hyunju Lee:
Wavelet-based identification of DNA focal genomic aberrations from single nucleotide polymorphism arrays. 146 - Alejandro Cáceres, Lluís Armengol, Sergi Villatoro, Juan R. González:
MLPAstats: An R GUI package for the integrated analysis of copy number alterations using MLPA data. 147 - Anja Hartmann, Tobias Czauderna, Roberto Hoffmann, Nils Stein, Falk Schreiber:
HTPheno: An Image Analysis Pipeline for High-Throughput Plant Phenotyping. 148 - Zhiao Shi, Bing Zhang:
Fast network centrality analysis using GPUs. 149 - Josep Rius, Fernando Cores, Francesc Solsona, Jano I. van Hemert, Jos Koetsier, Cédric Notredame:
A user-friendly web portal for T-Coffee on supercomputers. 150 - Yves Dehouck, Jean Marc Kwasigroch, Dimitri Gilis, Marianne Rooman:
PoPMuSiC 2.1 : a web server for the estimation of protein stability changes upon mutation and sequence optimality. 151 - Thomas J. Cradick, Giovanna Ambrosini, Christian Iseli, Philipp Bucher, Anton P. McCaffrey:
ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites. 152 - Cheng-Jian Xu, Huub C. J. Hoefsloot, Age K. Smilde:
To aggregate or not to aggregate high-dimensional classifiers. 153 - Zafer Aydin, Ajit P. Singh, Jeff A. Bilmes, William Stafford Noble:
Learning sparse models for a dynamic Bayesian network classifier of protein secondary structure. 154 - Zhihua Zhang, Michael Q. Zhang:
Histone modification profiles are predictive for tissue/cell-type specific expression of both protein-coding and microRNA genes. 155 - Can Yang, Xiang Wan, Qiang Yang, Hong Xue, Nelson L. S. Tang, Weichuan Yu:
A hidden two-locus disease association pattern in genome-wide association studies. 156 - Kailin Tang, Ruixin Zhu, Yixue Li, Zhi-Wei Cao:
Discrimination of Approved Drugs from Experimental Drugs by Learning Methods. 157 - Domenico Fraccalvieri, Alessandro Pandini, Fabio Stella, Laura Bonati:
Conformational and functional analysis of molecular dynamics trajectories by Self-Organising Maps. 158 - Yuzhen Ye, Jeong-Hyeon Choi, Haixu Tang:
RAPSearch: a Fast Protein Similarity Search Tool for Short Reads. 159 - Daniel B. Roche, Stuart J. Tetchner, Liam J. McGuffin:
FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins. 160 - Haibin Gu, Pengcheng Zhu, Yinming Jiao, Yijun Meng, Ming Chen:
PRIN, a predicted rice interactome network. 161 - Zheng Xia, Jianguo Wen, Chung-Che Chang, Xiaobo Zhou:
NSMAP: A Method for Spliced Isoforms Identification and Quantification from RNA-Seq. 162 - Francisco Fernandes, Paulo G. S. da Fonseca, Luís M. S. Russo, Arlindo L. Oliveira, Ana T. Freitas:
Efficient alignment of pyrosequencing reads for re-sequencing applications. 163 - Kai Wang, Fuyan Hu, Kejia Xu, Hua Cheng, Meng Jiang, Ruili Feng, Jing Li, Tieqiao Wen:
CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method. 164 - Jiamin Xiao, Xiaojing Tang, Yizhou Li, Zheng Fang, Daichuan Ma, Yangzhige He, Menglong Li:
Identification of microRNA precursors based on random forest with network-level representation method of stem-loop structure. 165 - Juan R. González, Benjamin Rodriguez-Santiago, Alejandro Cáceres, Roger Pique-Regi, Nathaniel Rothman, Stephen J. Chanock, Lluís Armengol, Luis A. Pérez-Jurado:
A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data. 166 - Augustin Luna, Evrim I. Karac, Margot Sunshine, Lucas Chang, Ruth Nussinov, Mirit I. Aladjem, Kurt W. Kohn:
A Formal MIM Specification and Tools for the Common Exchange of MIM Diagrams: an XML-Based Format, an API, and a Validation Method. 167 - Jakub Truszkowski, Daniel Gregory Brown:
More accurate recombination prediction in HIV-1 using a robust decoding algorithm for HMMs. 168 - Edouard Pauwels, Véronique Stoven, Yoshihiro Yamanishi:
Predicting drug side-effect profiles: a chemical fragment-based approach. 169 - Donata K. Kirchner, Peter Güntert:
Objective identification of residue ranges for the superposition of protein structures. 170 - Mitja I. Kurki, Jussi Paananen, Markus Storvik, Seppo Ylä-Herttuala, Juha E. Jääskeläinen, Mikael von und zu Fraunberg, Garry Wong, Petri Pehkonen:
TAFFEL: Independent Enrichment Analysis of gene sets. 171 - Roeland E. Voorrips, Gerrit Gort, Ben Vosman:
Genotype calling in tetraploid species from bi-allelic marker data using mixture models. 172 - Pawel P. Labaj, Peter Sykacek, David P. Kreil:
An analysis of single amino acid repeats as use case for application specific background models. 173 - Roberto Blanco, Elvira Mayordomo, Julio Montoya, Eduardo Ruiz-Pesini:
Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge. 174 - Arun Rangarajan, Tim Schedl, Karen Yook, Juancarlos Chan, Stephen Haenel, Lolly Otis, Sharon Faelten, Tracey DePellegrin-Connelly, Ruth Isaacson, Marek S. Skrzypek, J. Michael Cherry, Paul W. Sternberg, Hans-Michael Müller:
Toward an interactive article: integrating journals and biological databases. 175 - Mario Latendresse, Peter D. Karp:
Web-Based Metabolic Network Visualization with a Zooming User Interface. 176 - Florian Martin:
An application of kernel methods to variety identification based on SSR markers genetic fingerprinting. 177 - Joseph Hughes:
TreeRipper web application: towards a fully automated optical tree recognition software. 178 - Jonathan Alvarsson, Claes R. Andersson, Ola Spjuth, Rolf Larsson, Jarl E. S. Wikberg:
Brunn: An open source laboratory information system for microplates with a graphical plate layout design process. 179 - Alfredo A. Kalaitzis, Neil D. Lawrence:
A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression. 180 - Jacek Blazewicz, Wojciech Frohmberg, Michal Kierzynka, Erwin Pesch, Pawel Wojciechowski:
Protein alignment algorithms with an efficient backtracking routine on multiple GPUs. 181 - Surendra Kumar, Tor Carlsen, Bjørn-Helge Mevik, Pål Enger, Rakel Blaalid, Kamran Shalchian-Tabrizi, Havard Kauserud:
CLOTU: An online pipeline for processing and clustering of 454 amplicon reads into OTUs followed by taxonomic annotation. 182 - Brian J. Darby, Kenneth L. Jones, David Wheeler, Michael A. Herman:
Normalization and centering of array-based heterologous genome hybridization between species of unknown or unequal divergence. 183 - Catherine L. Anderson, Cory L. Strope, Etsuko N. Moriyama:
SuiteMSA: Visual Tools for Multiple Sequence Alignment Comparison and Molecular Sequence Simulation. 184 - Catherine L. Worth, Annika Kreuchwig, Gunnar Kleinau, Gerd Krause:
GPCR-SSFE: A comprehensive database of G-protein-coupled receptor template predictions and homology models. 185 - David Habier, Rohan L. Fernando, Kadir Kizilkaya, Dorian Garrick:
Extension of the Bayesian Alphabet for Genomic Selection. 186 - Roderic D. M. Page:
Extracting scientific articles from a large digital archive: BioStor and the Biodiversity Heritage Library. 187 - Rashmi Prasad, Susan McRoy, Nadya Frid, Aravind K. Joshi, Hong Yu:
The Biomedical Discourse Relation Bank. 188 - Daijin Ko, Brad Windle:
Enriching for Correct Prediction of Biological Processes Using a Combination of Diverse Classifiers. 189 - Eduard Schreiner, Leonardo G. Trabuco, Peter L. Freddolino, Klaus Schulten:
Stereochemical errors and their implications to molecular dynamics simulations. 190 - Liqing Zhang, Layne T. Watson, Lenwood S. Heath:
A Network of SCOP Hidden Markov Models and Its Analysis. 191 - Kahn Rhrissorrakrai, Kristin C. Gunsalus:
MINE: Module Identification in NEtworks. 192 - Yves-Pol Deniélou, Marie-France Sagot, Frédéric Boyer, Alain Viari:
Bacterial syntenies: an exact approach with gene quorum. 193 - Yao-Ting Huang, Min-Han Wu:
Inference of Chromosome-Specific Copy Numbers Using Population Haplotypes. 194 - Sankar Basu, Dhananjay Bhattacharyya, Rahul Banerjee:
Mapping the distribution of packing topologies within protein interiors shows predominant preference for specific packing motifs. 195 - Jacek Sroka, Lukasz Bieniasz-Krzywiec, Szymon Gwozdz, Dariusz Leniowski, Jakub Lacki, Mateusz Markowski, Claudio Avignone-Rossa, Michael E. Bushell, Johnjoe McFadden, Andrzej M. Kierzek:
Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. 196 - Hiroko K. Solvang, Ole Christian Lingjærde, Arnoldo Frigessi, Anne-Lise Børresen-Dale, Vessela N. Kristensen:
Linear and non-linear dependencies between copy number aberrations and mRNA expression reveal distinct molecular pathways in Breast Cancer. 197 - Yuan Zhang, Yanni Sun:
HMM-FRAME: accurate protein domain classification for metagenomic sequences in the presence of frameshift errors. 198 - Wen Han Chen, Ping Ping Sun, Yang Lu, William W. Guo, Yan Xin Huang, Zhi Qiang Ma:
MimoPro: a more efficient Web-based tool for epitope prediction using phage display libraries. 199 - Anna Lesniewska, Michal J. Okoniewski:
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration. 200 - Ren-Hua Chung, Michael A. Schmidt, Eden R. Martin:
CAPL: an efficient association software package using family and case-control data and accounting for population stratification. 201 - Miguel Pérez-Enciso, Ignacy Misztal:
Qxpak.5: Old mixed model solutions for new genomics problems. 202 - Artem Lysenko, Michael Defoin-Platel, Keywan Hassani-Pak, Jan Taubert, Charlie Hodgman, Christopher J. Rawlings, Mansoor A. S. Saqi:
Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. 203 - Jakub Koperwas, Krzysztof Walczak:
Tree Edit Distance for Leaf-labelled trees on free leafset and its comparison with Frequent Subsplit dissimilarity and popular distance measures. 204 - Takeshi Nishiyama, Kunihiko Takahashi, Toshiro Tango, Dalila Pinto, Stephen W. Scherer, Satoshi Takami, Hirohisa Kishino:
A Scan Statistic to Extract Causal Gene Clusters from Case-Control Genome-wide Rare CNV Data. 205 - Hongyun Gao, Yongchao Dou, Jialiang Yang, Jun Wang:
New methods to measure residues coevolution in proteins. 206 - Rong Liu, Jianjun Hu:
HemeBIND: a novel method for heme binding residue prediction by combining structural and sequence information. 207 - Liqing Tian, Aiping Wu, Yang Cao, Xiaoxi Dong, Yun Hu, Taijiao Jiang:
NCACO-score: An effective main-chain dependent scoring function for structure modeling. 208 - Insuk Sohn, Kouros Owzar, Johan Lim, Stephen L. George, Stephanie MacKey Cushman, Sin-Ho Jung:
Multiple Testing for Gene Sets from Microarray Experiments. 209 - Manuel Holtgrewe, Anne-Katrin Emde, David Weese, Knut Reinert:
A Novel And Well-Defined Benchmarking Method For Second Generation Read Mapping. 210 - Xiaodong Cai, Anhui Huang, Shizhong Xu:
Fast Empirical Bayesian LASSO for Multiple Quantitative Trait Locus Mapping. 211 - Thomas Lippincott, Diarmuid Ó Séaghdha, Anna Korhonen:
Exploring subdomain variation in biomedical language. 212 - Roger S. Day, Kevin K. McDade, Uma R. Chandran, Alex Lisovich, Thomas P. Conrads, Brian L. Hood, Vs Kumar Kolli, David Kirchner, Tracy Litzi, G. Larry Maxwell:
Identifier mapping performance for integrating transcriptomics and proteomics experimental results. 213 - Fernando Meyer, Stefan Kurtz, Rolf Backofen, Sebastian Will, Michael Beckstette:
Structator: fast index-based search for RNA sequence-structure patterns. 214 - Kirsti Laurila, Bodil Oster, Claus L. Andersen, Philippe Lamy, Torben F. Ørntoft, Olli Yli-Harja, Carsten Wiuf:
A Beta-Mixture Model for Dimensionality Reduction, Sample Classification and Analysis. 215 - Jiandong Ding, Shuigeng Zhou, Jihong Guan:
miRFam: an effective automatic miRNA classification method based on n-grams and a multiclass SVM. 216 - Nazar Zaki, Stefan Wolfsheimer, Grégory Nuel, Sawsan Khuri:
Conotoxin Protein Classification Using Free Scores of Words and Support Vector Machines. 217 - Tomasz Adamusiak, Tony Burdett, Natalja Kurbatova, K. Joeri van der Velde, Niran Abeygunawardena, Despoina Antonakaki, Misha Kapushesky, Helen E. Parkinson, Morris A. Swertz:
OntoCAT - simple ontology search and integration in Java, R and REST/JavaScript. 218 - Joseph A. Izzo, Namhee Kim, Shereef Elmetwaly, Tamar Schlick:
RAG: An Update to the RNA-As-Graphs Resource. 219 - Jeanette E. Eckel-Passow, Elizabeth J. Atkinson, Sooraj Maharjan, Sharon L. R. Kardia, Mariza de Andrade:
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform. 220 - Torbjørn Rognes:
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation. 221 - Wen-Ping Hsieh, Tzu-Ming Chu, Yu-Min Lin, Russell D. Wolfinger:
Kernel density weighted loess normalization improves the performance of detection within asymmetrical data. 222 - Antonio José Jimeno-Yepes, Bridget T. McInnes, Alan R. Aronson:
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation. 223 - Claudio Borile, Mathieu Labarre, Silvio Franz, Christophe Sola, Guislaine Refregier:
Using affinity propagation for identifying subspecies among clonal organisms: lessons from M. tuberculosis. 224 - Adam Amos-Binks, Catalin Patulea, Sylvain Pitre, Andrew Schoenrock, Yuan Gui, James R. Green, Ashkan Golshani, Frank K. H. A. Dehne:
Binding Site Prediction for Protein-Protein Interactions and Novel Motif Discovery using Re-occurring Polypeptide Sequences. 225 - Adam T. Zemla, Dorothy M. Lang, Tanya Kostova, Raul Andino, Carol L. Ecale Zhou:
StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase. 226 - Koji Kadota, Kentaro Shimizu:
Evaluating methods for ranking differentially expressed genes applied to MicroArray Quality Control data. 227 - Tracy L. Bergemann, Jason Wilson:
Proportion statistics to detect differentially expressed genes: a comparison with log-ratio statistics. 228 - Nophar Geifman, Eitan Rubin:
Towards an Age-Phenome Knowledge-base. 229 - Shinn-Ying Ho, Chih-Yuan Chao, Hui-Ling Huang, Tzai-Wen Chiu, Phasit Charoenkwan, Eric Hwang:
NeurphologyJ: an automatic neuronal morphology quantification method and its application in pharmacological discovery. 230 - Su Yeon Kim, Kirk E. Lohmueller, Anders Albrechtsen, Yingrui Li, Thorfinn Korneliussen, Geng Tian, Niels Grarup, Tao Jiang, Gitte Andersen, Daniel Witte, Torben Jørgensen, Torben Hansen, Oluf Pedersen, Jun Wang, Rasmus Nielsen:
Estimation of allele frequency and association mapping using next-generation sequencing data. 231 - Janos Kriston-Vizi, Ng Wee Thong, Cheok Leong Poh, Kwo Chia Yee, Joan Sim Poh Ling, Rachel Kraut, Martin Wasser:
Gebiss: An ImageJ Plugin for the Specification of Ground Truth and the Performance Evaluation of 3D Segmentation Algorithms. 232 - Yao Fu, Laura R. Jarboe, Julie A. Dickerson:
Reconstructing genome-wide regulatory network of E. coli using transcriptome data and predicted transcription factor activities. 233 - Yantao Qiao, Hong Zhang, Dongbo Bu, Shiwei Sun:
PI: An open-source software package for validation of the SEQUEST result and visualization of mass spectrum. 234 - Seongho Kim, Imhoi Koo, Aiqin Fang, Xiang Zhang:
Smith-Waterman Peak Alignment for Comprehensive Two-dimensional Gas Chromatography Mass Spectrometry. 235 - László Dávid, Sayed-Amir Marashi, Abdelhalim Larhlimi, Bettina Mieth, Alexander Bockmayr:
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks. 236 - Leila Baghdadi, Mojdeh Zamyadi, John G. Sled, Jürgen E. Schneider, Shuomo Bhattacharya, R. Mark Henkelman, Jason P. Lerch:
Semi-Automatic Segmentation of Multiple Mouse Embryos in MR Images. 237 - Shaoqiang Zhang, Shan Li, Meng Niu, Phuc T. Pham, Zhengchang Su:
MotifClick: prediction of cis-regulatory binding sites via merging cliques. 238 - George D. Kritikos, Charalampos N. Moschopoulos, Michalis Vazirgiannis, Sophia Kossida:
Noise reduction in protein-protein interaction graphs by the implementation of a novel weighting scheme. 239 - Clinton Torres, Elizabeth A. Vitalis, Brian R. Baker, Shea N. Gardner, Marisa W. Torres, John M. Dzenitis:
LAVA: An Open-Source Approach To Designing LAMP (Loop-Mediated Isothermal Amplification) DNA Signatures. 240 - Bernhard Knapp, Verena Giczi, Reiner Ribarics, Wolfgang Schreiner:
PeptX: Using Genetic Algorithms to optimize peptides for MHC binding. 241 - Nicolas Philippe, Mikaël Salson, Thierry Lecroq, Martine Léonard, Therese Commes, Eric Rivals:
Querying large read collections in main memory: a versatile data structure. 242 - Angel Alvarez, Peter J. Woolf:
RegNetB: Predicting Relevant Regulator-Gene Relationships in Localized Prostate Tumor Samples. 243 - Li C. Xue, Drena Dobbs, Vasant G. Honavar:
HomPPI: A Class of Sequence Homology Based Protein-Protein Interface Prediction Methods. 244 - Marcin J. Mizianty, Tuo Zhang, Bin Xue, Yaoqi Zhou, A. Keith Dunker, Vladimir N. Uversky, Lukasz A. Kurgan:
In-silico prediction of disorder content using hybrid sequence representation. 245 - David H. Alexander, Kenneth Lange:
Enhancements to the ADMIXTURE Algorithm for Individual Ancestry Estimation. 246 - Leslie Regad, Juliette Martin, Anne-Claude Camproux:
Dissecting protein loops with a statistical scalpel suggests a functional implication of some structural motifs. 247 - Jiajie Zhang, Amir Madany Mamlouk, Thomas Martinetz, Suhua Chang, Jing Wang, Rolf Hilgenfeld:
PhyloMap: an algorithm for visualizing relationships of large sequence data sets and its application to the influenza A virus genome. 248 - Ewa Szczurek, Florian Markowetz, Irit Gat-Viks, Przemyslaw Biecek, Jerzy Tiuryn, Martin Vingron:
Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. 249 - Lars-Henrik Heckmann, Peter B. Sørensen, Paul Henning Krogh, Jesper G. Sorensen:
NORMA-Gene: A simple and robust method for qPCR normalization based on target gene data. 250 - Yulong Wang, Wenjun Wu, Nicolas N. Negre, Kevin P. White, Cheng Li, Parantu K. Shah:
Determinants of Antigenicity and Specificity in immune response for Protein Sequences. 251 - Jukka Intosalmi, Tiina Manninen, Keijo Ruohonen, Marja-Leena Linne:
Computational study of noise in a large signal transduction network. 252 - Kim-Anh Lê Cao, Simon Boitard, Philippe Besse:
Sparse PLS Discriminant Analysis: biologically relevant feature selection and graphical displays for multiclass problems. 253 - Lionel Blanchet, Agnieszka Smolinska, Amos Attali, Marcel P. Stoop, Kirsten A. M. Ampt, Hans van Aken, Ernst Suidgeest, Tinka Tuinstra, Sybren S. Wijmenga, Theo Luider, Lutgarde M. C. Buydens:
Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis. 254 - Tulaya Limpiti, Apichart Intarapanich, Anunchai Assawamakin, Philip James Shaw, Pongsakorn Wangkumhang, Jittima Piriyapongsa, Chumpol Ngamphiw, Sissades Tongsima:
Study of large and highly stratified population datasets by combining iterative pruning principal component analysis and STRUCTURE. 255 - Qian Zhu, Yuyin Sun, Sashikiran Challa, Ying Ding, Michael S. Lajiness, David J. Wild:
Semantic Inference using Chemogenomics Data for Drug Discovery. 256 - Ubbo Visser, Saminda Abeyruwan, Uma Vempati, Robin P. Smith, Vance P. Lemmon, Stephan C. Schürer:
BioAssay Ontology (BAO): A Semantic Description of Bioassays and High-Throughput Screening Results. 257 - Christopher R. Bolen, Mohamed Uduman, Steven H. Kleinstein:
Cell Subset Prediction for Blood Genomic Studies. 258 - Hiroki Takahashi, Takuya Morimoto, Naotake Ogasawara, Shigehiko Kanaya:
AMDORAP: Non-targeted metabolic profiling based on high-resolution LC-MS. 259 - Jaturon Harnsomburana, Jason M. Green, Adrian S. Barb, Mary L. Schaeffer, Leszek Vincent, Chi-Ren Shyu:
Computable visually observed phenotype ontological framework for plants. 260 - Tzong-Yi Lee, Neil Arvin Bretaña, Cheng-Tsung Lu:
PlantPhos: using Maximal Dependence Decomposition to Identify Plant Phosphorylation Sites with Substrate Site Specificity. 261 - Changqing Zhang, Jin Wang, Xu Hua, Jinggui Fang, Huaiqiu Zhu, Xiang Gao:
A mutation degree model for the identification of transcriptional regulatory elements. 262 - Akio Onogi, Masanobu Nurimoto, Mitsuo Morita:
Characterization of a Bayesian genetic clustering algorithm based on a Dirichlet process prior and comparison among Bayesian clustering methods. 263 - Michael T. Zimmermann, Andrzej Kloczkowski, Robert L. Jernigan:
MAVEN: Motion Analysis and Visualization of Elastic Networks and Structural Ensembles. 264 - Torsten Gunther, Inka Gawenda, Karl J. Schmid:
phenosim - A software to simulate phenotypes for testing in genome-wide association studies. 265 - Jiang Li, Bingsheng Gong, Xi Chen, Tao Liu, Chao Wu, Fan Zhang, Chunquan Li, Xiang Li, Shaoqi Rao, Xia Li:
DOSim: An R package for similarity between diseases based on Disease Ontology. 266 - Xutao Deng:
SeqGene: a comprehensive software solution for mining exome- and transcriptome- sequencing data. 267 - Alexander Y. Panchin, Sergey I. Mitrofanov, Andrei Alexeevski, Sergei A. Spirin, Yuri V. Panchin:
New Words in Human Mutagenesis. 268 - Weichen Wang, Xuegong Zhang:
Network-based group variable selection for detecting expression quantitative trait loci (eQTL). 269 - Holger Pillmann, Klas Hatje, Florian Odronitz, Björn Hammesfahr, Martin Kollmar:
Predicting mutually exclusive spliced exons based on exon length, splice site and reading frame conservation, and exon sequence homology. 270 - Mohammadreza Ghodsi, Bo Liu, Mihai Pop:
DNACLUST: accurate and efficient clustering of phylogenetic marker genes. 271 - Samuel V. Angiuoli, Julie C. Dunning Hotopp, Steven L. Salzberg, Hervé Tettelin:
Improving pan-genome annotation using whole genome multiple alignment. 272 - Ke Zhang, Haiyan Wang, Arne C. Bathke, Solomon W. Harrar, Hans-Peter Piepho, Youping Deng:
Gene set analysis for longitudinal gene expression data. 273 - Mihaela Pertea, Geo Pertea, Steven L. Salzberg:
Detection of Lineage-Specific Evolutionary Changes among Primate Species. 274 - Oruganty Krishnadev, Narayanaswamy Srinivasan:
AlignHUSH : Alignment of HMMs Using Structure and Hydrophobicity information. 275 - Patrick W. Sheppard, Xiaoyun Sun, John F. Emery, Rona G. Giffard, Mustafa Khammash:
Quantitative characterization and analysis of the dynamic NF-kappaB response in microglia. 276 - Eugenia G. Giannopoulou, Olivier Elemento:
An integrated ChIP-seq analysis platform with customizable workflows. 277 - P. Alexander Rolfe, David K. Gifford:
ReadDB Provides Efficient Storage for Mapped Short Reads. 278 - Hannah M. W. Salim, Amanda M. Koire, Nicholas A. Stover, Andre R. O. Cavalcanti:
Detection of Fused Genes in Eukaryotic Genomes using Gene deFuser: Analysis of the Tetrahymena thermophila genome. 279 - Shiyong Liu, Ilya A. Vakser:
DECK: Distance and environment-dependent, coarse-grained, knowledge-based potentials for protein-protein docking. 280 - Jeh-Ting Hsu, Chien Hua Peng, Wen-Ping Hsieh, Chung-Yu Lan, Chuan Yi Tang:
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. 281 - David López, David Casero, Shawn Cokus, Sabeeha S. Merchant, Matteo Pellegrini:
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data. 282 - Zehui Tang, Tonghua Li, Rida Liu, Wenwei Xiong, Jiangming Sun, Yaojuan Zhu, Guanyan Chen:
Improving the performance of beta-turn prediction using predicted shape strings and a two-layer support vector machine model. 283 - Cyril Rakovski, Daniel J. Weisenberger, Paul Marjoram, Peter W. Laird, Kimberly D. Siegmund:
Modeling measurement error in tumor characterization studies. 284 - Helena F. Deus, Miria C. Correa, Romesh Stanislaus, Maria Miragaia, Wolfgang Maass, Hermínia de Lencastre, Ronan Fox, Jonas S. Almeida:
S3QL: A distributed domain specific language for controlled semantic integration of life sciences data. 285 - Jeff Skinner, Yuri Kotliarov, Sudhir Varma, Karina L. Mine, Anatoly Yambartsev, Richard Simon, Yentram Huyen, Andrey Morgun:
Construct and Compare Gene Coexpression Networks with DAPfinder and DAPview. 286 - Victor Missirian, Luca Comai, Vladimir Filkov:
Statistical Mutation Calling from Sequenced Overlapping DNA Pools in TILLING Experiments. 287 - Klaus Jung, Tim Friede, Tim Beißbarth:
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes. 288 - Giuseppe Gallone, T. Ian Simpson, J. Douglas Armstrong, Andrew P. Jarman:
Bio: : Homology: : InterologWalk - A Perl module to build putative protein-protein interaction networks through interolog mapping. 289 - Wei Zheng, Lisa M. Chung, Hongyu Zhao:
Bias Detection and Correction in RNA-Sequencing Data. 290 - Christian Bender, Silvia von der Heyde, Frauke Henjes, Stefan Wiemann, Ulrike Korf, Tim Beißbarth:
Inferring signalling networks from longitudinal data using sampling based approaches in the R-package 'ddepn'. 291 - Sabrina Hempel, Aneta Koseska, Zoran Nikoloski, Jürgen Kurths:
Unraveling gene regulatory networks from time-resolved gene expression data - a measures comparison study. 292 - Fredrik Lysholm, Björn Andersson, Bengt Persson:
FAAST: Flow-space Assisted Alignment Search Tool. 293 - Qi Liu, Han Zhou, Lin Liu, Xi Chen, Ruixin Zhu, Zhi-Wei Cao:
Multi-target QSAR Modelling in the Analysis and Design of HIV-HCV Co-Inhibitors : An In-silico Study. 294 - Franziska Hinkelmann, Madison Brandon, Bonny Guang, Rustin McNeill, Grigoriy Blekherman, Alan Veliz-Cuba, Reinhard C. Laubenbacher:
ADAM: Analysis of Discrete Models of Biological Systems Using Computer Algebra. 295 - Gokmen Altay, Mohammad Asim, Florian Markowetz, David E. Neal:
Differential C3NET reveals disease networks of direct physical interactions. 296 - Christian Loyek, Nasir M. Rajpoot, Michael Khan, Tim W. Nattkemper:
BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data. 297 - Marie E. Fahey, Melanie J. Bennett, Cathal Mahon, Stefanie Jäger, Lars Pache, Dhiraj Kumar, Alex Shapiro, Kanury Rao, Sumit K. Chanda, Charles S. Craik, Alan D. Frankel, Nevan J. Krogan:
GPS-Prot: a web-based visualization platform for integrating host-pathogen interaction data. 298 - Amin Zia, Alan M. Moses:
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. 299 - Justin Bo-Kai Hsu, Chih-Min Chiu, Sheng-Da Hsu, Wei-Yun Huang, Chia-Hung Chien, Tzong-Yi Lee, Hsien-Da Huang:
miRTar: an integrated system for identifying miRNA-target interactions in Human. 300 - Michail Stamatakis, Kyriacos Zygourakis:
Deterministic and stochastic population-level simulations of an artificial lac operon genetic network. 301 - Lu Cheng, Thomas R. Connor, David M. Aanensen, Brian G. Spratt, Jukka Corander:
Bayesian semi-supervised classification of bacterial samples using MLST databases. 302 - Leonid L. Chepelev, Alexandre Riazanov, Alexandre Kouznetsov, Hong Sang Low, Michel Dumontier, Christopher J. O. Baker:
Prototype Semantic Infrastructure for Automated Small Molecule Classification and Annotation in Lipidomics. 303 - Ivo D. Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul R. Eggert, Jonathan Pierce, Alex Genco, James A. Knowles, Andrew P. Clark, John D. Van Horn, Joseph Ames, Carl Kesselman, Arthur W. Toga:
Applications of the Pipeline Environment for Visual Informatics and Genomics Computations. 304 - Hyunsoo Kim, Yingtao Bi, Sharmistha Pal, Ravi Gupta, Ramana V. Davuluri:
IsoformEx: Isoform level gene expression estimation using weighted non-negative least squares from mRNA-Seq data. 305 - Henry Wirth, Markus Löffler, Martin von Bergen, Hans Binder:
Expression cartography of human tissues using self organizing maps. 306 - Magnus Fontes, Charlotte Soneson:
The projection score - an evaluation criterion for variable subset selection in PCA visualization. 307 - Eugenia G. Giannopoulou, George Lepouras, Elias S. Manolakos:
Visualizing Meta-Features in Proteomic Maps. 308 - Jonathan L. Lustgarten, Shyam Visweswaran, Vanathi Gopalakrishnan, Gregory F. Cooper:
Application of an efficient Bayesian discretization method to biomedical data. 309 - Qiyuan Li, Aron C. Eklund, Nicolai J. Birkbak, Christine Desmedt, Benjamin Haibe-Kains, Christos P. Sotiriou, W. Fraser Symmans, Lajos Pusztai, Søren Brunak, Andrea L. Richardson, Zoltan Szallasi:
Consistent metagenes from cancer expression profiles yield agent specific predictors of chemotherapy response. 310 - Ruoying Chen, Wenjing Chen, Sixiao Yang, Di Wu, Yong Wang, Yingjie Tian, Yong Shi:
Rigorous assessment and integration of the sequence and structure based features to predict hot spots. 311 - Hui Wang, Mark J. van der Laan:
Dimension Reduction with Gene Expression Data Using Targeted Variable Importance Measurement. 312 - George R. Bickerton, Alicia P. Higueruelo, Tom L. Blundell:
Comprehensive, atomic-level characterization of structurally characterized protein-protein interactions: the PICCOLO database. 313 - Mojdeh Mohtashemi, David K. Walburger, Matthew W. Peterson, Felicia N. Sutton, Haley B. Skaer, James C. Diggans:
Open-Target Sparse Sensing of Biological Agents using DNA Microarray. 314 - Hui Yu, Bao-Hong Liu, Zhi-Qiang Ye, Chun Li, Yi-Xue Li, Yuan-Yuan Li:
Link-based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs. 315 - Kashi Vishwanath Revanna, Chi-Chen Chiu, Ezekiel Bierschank, Qunfeng Dong:
GSV: A Web-based Genome Synteny Viewer for Customized Data. 316 - Michelle S. Scott, Peter V. Troshin, Geoffrey J. Barton:
NoD: a Nucleolar localization sequence detector for eukaryotic and viral proteins. 317 - Tahir Mehmood, Harald Martens, Solve Saebo, Jonas Warringer, Lars Snipen:
Mining for Genotype-Phenotype Relations in Saccharomyces using Partial Least Squares. 318 - Assaf Avihoo, Alexander Churkin, Danny Barash:
RNAexinv: An Extended Inverse RNA Folding from Shape and Physical Attributes to Sequences. 319 - Ekaterina M. Myasnikova, Svetlana Surkova, Grigory Stein, Andrei Pisarev, Maria Samsonova:
A regression system for estimation of errors introduced by confocal imaging into gene expression data in situ. 320 - Kirsten Skogerson, Gert Wohlgemuth, Dinesh Kumar Barupal, Oliver Fiehn:
The volatile compound BinBase mass spectral database. 321 - Jeremy A. Miller, Chaochao Cai, Peter Langfelder, Daniel H. Geschwind, Sunil M. Kurian, Daniel R. Salomon, Steve Horvath:
Strategies for aggregating gene expression data: The collapseRows R function. 322 - Bo Li, Colin N. Dewey:
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. 323 - Bernhard Y. Renard, Martin Löwer, Yvonne Kuhne, Ulf Reimer, Andree Rothermel, Özlem Türeci, John C. Castle, Ugur Sahin:
rapmad: Robust Analysis of Peptide Microarray Data. 324 - Sabina Leonelli, Alexander D. Diehl, Karen R. Christie, Midori A. Harris, Jane Lomax:
How the Gene Ontology Evolves. 325 - Kristoffer Forslund, Isabella Pekkari, Erik L. L. Sonnhammer:
Domain architecture conservation in orthologs. 326 - Vinay Jethava, Chiranjib Bhattacharyya, Devdatt P. Dubhashi, Goutham N. Vemuri:
NETGEM: Network Embedded Temporal GEnerative Model for gene expression data. 327 - Donovan H. Parks, Norman J. MacDonald, Robert G. Beiko:
Classifying short genomic fragments from novel lineages using composition and homology. 328 - Carola Söhngen, Antje Chang, Dietmar Schomburg:
Development of an automatic Classification Scheme for Disease-related Enzyme Information. 329 - Aleksi Kallio, Niko Vuokko, Markus Ojala, Niina Haiminen, Heikki Mannila:
Randomization techniques for assessing the significance of gene periodicity results. 330 - Yaji Xu, Bo Peng, Yunxin Fu, Christopher I. Amos:
Genome-wide algorithm for detecting CNV associations with diseases. 331 - Marijn P. A. Sanders, Wilco W. M. Fleuren, Stefan Verhoeven, Sven van den Beld, Wynand Alkema, Jacob de Vlieg, Jan P. G. Klomp:
ss-TEA: Entropy based identification of receptor specific ligand binding residues from a multiple sequence alignment of class A GPCRs. 332 - Páll Melsted, Jonathan K. Pritchard:
Efficient counting of k-mers in DNA sequences using a Bloom Filter. 333 - Rudesh D. Toofanny, Andrew M. Simms, David A. C. Beck, Valerie Daggett:
Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection. 334 - Cheng-Wei Yao, Ban-Dar Hsu, Bor-Sen Chen:
Constructing gene regulatory networks for long term photosynthetic light acclimation in Arabidopsis thaliana. 335 - Ernesto Iacucci, Fabian Ojeda, Bart De Moor, Yves Moreau:
Predicting Receptor-Ligand Pairs through Kernel Learning. 336 - Xu Song, Bo-Li Zhang, Hongmin Liu, Bo-Yang Yu, Xiu-Mei Gao, Li-Yuan Kang:
IQMNMR: Open source software using time-domain NMR data for automated identification and quantification of metabolites in batches. 337 - Vackar Afzal, Jeffrey T.-J. Huang, Abdel Atrih, Daniel J. Crowther:
PChopper: High Throughput Peptide Prediction For MRM/SRM Transition Design. 338 - Xiwei Tang, Jianxin Wang, Binbin Liu, Min Li, Gang Chen, Yi Pan:
A comparison of the functional modules identified from time course and static PPI network data. 339 - Sang-Kyu Jung, Karen McDonald:
Visual Gene Developer: a fully programmable bioinformatics software for synthetic gene optimization. 340 - Wen Zhang, Yi Xiong, Meng Zhao, Hua Zou, Xinghuo Ye, Juan Liu:
Prediction of conformational B-cell epitopes from 3D structures by random forest with a distance-based feature. 341 - Elin Axelsson, Thomas Sandmann, Thomas Horn, Michael Boutros, Wolfgang Huber, Bernd Fischer:
Extracting quantitative genetic interaction phenotypes from matrix combinatorial RNAi. 342 - Sangaalofa T. Clark, Wynand S. Verwoerd:
A systems approach to identifying correlated gene targets for the loss of colour pigmentation in plants. 343 - Pawel Daniluk, Bogdan Lesyng:
A novel method to compare protein structures using local descriptors. 344 - Krishna Kumar Kandaswamy, Ganesan Pugalenthi, Mehrnaz Khodam Hazrati, Kai-Uwe Kalies, Thomas Martinetz:
BLProt: Prediction of bioluminescent proteins based on Support Vector Machine and ReliefF feature selection. 345 - Shenghui Zhang, Yaojun Wang, Dongbo Bu, Hong Zhang, Shiwei Sun:
ProbPS: A new model for peak selection based on quantifying the dependence of the existence of derivative peaks on primary ion intensity. 346 - Yuan Yuan, Yi-Ping Phoebe Chen, Shengyu Ni, Augix Guohua Xu, Lin Tang, Martin Vingron, Mehmet Somel, Philipp Khaitovich:
Development and application of a modified dynamic time warping algorithm (DTW-S) to analyses of primate brain expression time series. 347 - Irina Tuszynska, Janusz M. Bujnicki:
DARS-RNP and QUASI-RNP: New statistical potentials for protein-RNA docking. 348 - Justin R. Brown, Phillip Stafford, Stephen A. Johnston, Valentin Dinu:
Statistical Methods for Analyzing Immunosignatures. 349 - Feng Cheng, Xianglong Zhang, Yinan Zhang, Chaohua Li, Changqing Zeng:
Haplo2Ped: a tool using haplotypes as markers for linkage analysis. 350 - Thomas A. Russ, Cartic Ramakrishnan, Eduard H. Hovy, Mihail Bota, Gully A. P. C. Burns:
Knowledge Engineering Tools for Reasoning with Scientific Observations and Interpretations: a Neural Connectivity Use Case. 351 - Joan Segura, Pamela F. Jones, Narcis Fernandez-Fuentes:
Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi Diagrams. 352 - Farhana Naznin, Ruhul A. Sarker, Daryl Essam:
Vertical Decomposition with Genetic Algorithm for Multiple Sequence Alignment. 353 - Yongchao Liu, Bertil Schmidt, Douglas L. Maskell:
Parallelized short read assembly of large genomes using de Bruijn graphs. 354 - Laura Plaza, Antonio José Jimeno-Yepes, Alberto Díaz, Alan R. Aronson:
Studying the correlation between different word sense disambiguation methods and summarization effectiveness in biomedical texts. 355 - Samuel V. Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R. Riley, Cesar Arze, James Robert White, Owen White, W. Florian Fricke:
CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing. 356 - Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon, Stephanie E. Mohr:
An Integrative Approach to Ortholog Prediction for Disease-Focused and Other Functional Studies. 357 - Rudolf Frühwirth, Deepak R. Mani, Saumyadipta Pyne:
Clustering with position-specific constraints on variance: Applying redescending M-estimators to label-free LC-MS data analysis. 358 - Shouguo Gao, Xujing Wang:
Quantitative utilization of prior biological knowledge in the Bayesian network modeling of gene expression data. 359 - Norberto Díaz-Díaz, Jesús S. Aguilar-Ruiz:
GO-based Functional Dissimilarity of Gene Sets. 360 - Gen-Tao Chiang, Peter Clapham, Guoying Qi, Kevin Sale, Guy Coates:
Implementing a genomic data management system using iRODS in Wellcome Trust Sanger Institute. 361 - Bas Vroling, David Thorne, Philip McDermott, Teresa K. Attwood, Gert Vriend, Steve Pettifer:
Integrating GPCR-specific information with full text articles. 362 - Dorota Herman, David Ochoa, David de Juan, Daniel Lopez, Alfonso Valencia, Florencio Pazos:
Selection of organisms for the co-evolution-based study of protein interactions. 363 - Ting Hu, Nicholas A. Sinnott-Armstrong, Jeff Kiralis, Angeline S. Andrew, Margaret R. Karagas, Jason H. Moore:
Characterizing Genetic Interactions in Human Disease Association Studies Using Statistical Epistasis Networks. 364 - Jeremy Gruel, Michel Le Borgne, Nolwenn LeMeur, Nathalie Théret:
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. 365 - Christian Ludwig, Ulrich L. Günther:
MetaboLab - advanced NMR data processing and analysis for metabolomics. 366 - Angela P. Presson, Namshin Kim, Xiaofei Yan, Irvin S. Y. Chen, Sanggu Kim:
Methodology and software to detect viral integration site hot-spots. 367 - Stewart E. Moughon, Ram Samudrala:
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. 368 - Matthew N. McCall, Rafael A. Irizarry:
Thawing Frozen Robust Multi-array Analysis (fRMA). 369 - Olga Domanova, Stefan Borbe, Stefanie Muhlfeld, Martin Becker, Ralf Kubitz, Dieter Häussinger, Thomas Berlage:
Toponomics method for the automated quantification of membrane protein translocation. 370 - Carol J. Bult, Harold J. Drabkin, Alexei V. Evsikov, Darren A. Natale, Cecilia N. Arighi, Natalia V. Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A. Blake, Cathy H. Wu:
The Representation of Protein Complexes in the Protein Ontology (PRO). 371 - Erika Cule, Paolo Vineis, Maria De Iorio:
Significance testing in ridge regression for genetic data. 372 - Meghana Chitale, Shriphani Palakodety, Daisuke Kihara:
Quantification of Protein Group Coherence and Pathway Assignment Using Functional Association. 373 - Mark Needham, Rui Hu, Sandhya Dwarkadas, Xing Qiu:
Hierarchical Parallelization of Gene Differential Association Analysis. 374 - Ping Shi, Surajit Ray, Qifu Zhu, Mark A. Kon:
Top Scoring Pairs for Feature Selection in Machine Learning and Applications to Cancer Outcome Prediction. 375 - Susanne Quester, Dietmar Schomburg:
EnzymeDetector: an integrated enzyme function prediction tool and database. 376 - Seungyeoun Lee, Jinheum Kim, Sunho Lee:
A comparative study on gene-set analysis methods for assessing differential expression associated with the survival phenotype. 377 - Carles Pons, Fabian Glaser, Juan Fernández-Recio:
Prediction of protein-binding areas by small-world residue networks and application to docking. 378 - Franklin Bristow, Runtao He, Gary H. Van Domselaar:
GOmotif: A web server for investigating the biological role of protein sequence motifs. 379 - Lili Wang, Pouya Khankhanian, Sergio Baranzini, Parvin Mousavi:
iCTNet: A Cytoscape plugin to produce and analyze integrative complex traits networks. 380 - Adam C. Gower, Avrum Spira, Marc E. Lenburg:
Discovering biological connections between experimental conditions based on common patterns of differential gene expression. 381 - Claudio Isella, Tommaso Renzulli, Davide Corà, Enzo Medico:
Mulcom: a multiple comparison statistical test for microarray data in Bioconductor. 382 - Richard A. Moffitt, Qiqin Yin-Goen, Todd H. Stokes, R. Mitchell Parry, James H. Torrance, John H. Phan, Andrew N. Young, May D. Wang:
caCORRECT2: Improving the accuracy and reliability of microarray data in the presence of artifacts. 383 - Zhe Liu, Yuanyuan Shen, Jurg Ott:
Multilocus association mapping using generalized ridge logistic regression. 384 - Brian D. Ondov, Nicholas H. Bergman, Adam M. Phillippy:
Interactive metagenomic visualization in a Web browser. 385 - Koen Van der Borght, Elke Van Craenenbroeck, Pierre Lecocq, Margriet Van Houtte, Barbara Van Kerckhove, Lee Bacheler, Geert Verbeke, Herman van Vlijmen:
Cross-validated stepwise regression for identification of novel non-nucleoside reverse transcriptase inhibitor resistance associated mutations. 386 - Anabel Usie, Hiren Karathia, Ivan Teixido, Joan Valls, Xavier Faus, Rui Alves, Francesc Solsona:
Biblio-MetReS: A bibliometric network reconstruction application and server. 387 - Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie, Ian M. Donaldson:
iRefScape. A Cytoscape plug-in for visualization and data mining of protein interaction data from iRefIndex. 388 - Fantine Mordelet, Jean-Philippe Vert:
ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples. 389 - Jenny Önskog, Eva Freyhult, Mattias Landfors, Patrik Rydén, Torgeir R. Hvidsten:
Classification of microarrays; synergistic effects between normalization, gene selection and machine learning. 390 - Xiaosheng Wang, Richard Simon:
Microarray-based Cancer Prediction Using Single Genes. 391 - Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim, Changyu Shen:
An empirical Bayes model using a competition score for metabolite identification in gas chromatography mass spectrometry. 392 - Paul Thompson, Raheel Nawaz, John McNaught, Sophia Ananiadou:
Enriching a biomedical event corpus with meta-knowledge annotation. 393 - Paul M. Ruegger, Gianluca Della Vedova, Tao Jiang, James Borneman:
Improving Probe Set Selection for Microbial Community Analysis by Leveraging Taxonomic Information of Training Sequences. 394 - Steven G. Cresawn, Matt Bogel, Nathan Day, Deborah Jacobs-Sera, Roger W. Hendrix, Graham F. Hatfull:
Phamerator: a bioinformatic tool for comparative bacteriophage genomics. 395 - John A. Fozard, Glen R. Kirkham, Lee D. K. Buttery, John R. King, Oliver E. Jensen, Helen M. Byrne:
Techniques for analysing pattern formation in populations of stem cells and their progeny. 396 - Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo Del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, C. J. Rupp, Yutaka Sasaki, Giulia Venturi, Dietrich Rebholz-Schuhmann, Sophia Ananiadou:
The BioLexicon: a large-scale terminological resource for biomedical text mining. 397 - Joan Teyra, Sergey A. Samsonov, Sven Schreiber, M. Teresa Pisabarro:
SCOWLP update: 3D classification of protein-protein, -peptide, -saccharide and -nucleic acid interactions, and structure-based binding inferences across folds. 398 - Emma J. Cooke, Richard S. Savage, Paul D. W. Kirk, Robert Darkins, David L. Wild:
Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements. 399 - Dan C. Tulpan, Serge Léger, Luc Belliveau, Adrian Culf, Miroslava Cuperlovic-Culf:
MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures. 400 - Miquel Salicru, Jordi Ocana, Alex Sánchez-Pla:
Comparison of lists of genes based on functional profiles. 401 - Hongbo M. Xie, Juan C. Perin, Theodore G. Schurr, Matthew C. Dulik, Sergey I. Zhadanov, Joseph A. Baur, Michael P. King, Emily Place, Colleen Clarke, Michael Grauer, Jonathan Schug, Avni Santani, Anthony Albano, Cecilia Kim, Vincent Procaccio, Hakon Hakonarson, Xiaowu Gai, Marni J. Falk:
Mitochondrial Genome Sequence Analysis: A custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy. 402 - Yan Jiao, Katherine Lawler, Gargi S. Patel, Arnie Purushotham, Annete F. Jones, Anita Grigoriadis, Andrew Tutt, Tony C. Ng, Andrew E. Teschendorff:
DART: Denoising Algorithm based on Relevance network Topology improves molecular pathway activity inference. 403 - Izaskun Mallona, Julia Weiss, Marcos Egea-Cortines:
pcrEfficiency: a Web tool for PCR amplification efficiency prediction. 404 - Trung-Nghia Vu, Dirk Valkenborg, Koen Smets, Kim A. Verwaest, Roger Dommisse, Filip Lemière, Alain Verschoren, Bart Goethals, Kris Laukens:
An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data. 405 - Julien Gagneur, Markus C. Elze, Achim Tresch:
Selective Phenotyping, Entropy Reduction and the Mastermind Game. 406 - Vasanth R. Singan, Thouis R. Jones, Kathleen M. Curran, Jeremy C. Simpson:
Dual channel rank-based intensity weighting for quantitative co-localization of microscopy images. 407 - Luca Pinello, Giosuè Lo Bosco, Bret M. Hanlon, Guo-Cheng Yuan:
A motif-independent metric for DNA sequence specificity. 408 - Xian-Wen Ren, Yong-Cui Wang, Yong Wang, Xiang-Sun Zhang, Nai-Yang Deng:
Improving accuracy of protein-protein interaction prediction by considering the converse problem for sequence representation. 409 - Hieu Dinh, Sanguthevar Rajasekaran, Vamsi Kundeti:
PMS5: an efficient exact algorithm for the (l, d)-motif finding problem. 410 - Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich:
EPEPT: A web service for enhanced P-value estimation in permutation tests. 411 - Ozgur Demir-Kavuk, Mayumi Kamada, Tatsuya Akutsu, Ernst-Walter Knapp:
Prediction using step-wise L1, L2 regularization and feature selection for small data sets with large number of features. 412 - Jérôme Ambroise, Bertrand Bearzatto, Annie Robert, Bernadette Govaerts, Benoît Macq, Jean-Luc Gala:
Impact of the spotted microarray preprocessing method on fold-change compression and variance stability. 413 - Mathieu Rousseau, James Fraser, Maria A. Ferraiuolo, Josee Dostie, Mathieu Blanchette:
Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling. 414 - Orion J. Buske, Michael M. Hoffman, Nadia Ponts, Karine G. Le Roch, William Stafford Noble:
Exploratory analysis of genomic segmentations with Segtools. 415 - Vid Podpecan, Nada Lavrac, Igor Mozetic, Petra Kralj Novak, Igor Trajkovski, Laura Langohr, Kimmo Kulovesi, Hannu Toivonen, Marko Petek, Helena Motaln, Kristina Gruden:
SegMine workflows for semantic microarray data analysis in Orange4WS. 416 - Samuel Flores, Mark B. Gerstein:
Predicting protein ligand binding motions with the Conformation Explorer. 417 - Sebastian Köhler, Sebastian Bauer, Chris Mungall, Gabriele Carletti, Cynthia L. Smith, Paul N. Schofield, Georgios V. Gkoutos, Peter N. Robinson:
Improving ontologies by automatic reasoning and evaluation of logical definitions. 418 - Sergio Ramírez, Tor Johan Mikael Karlsson, Oswaldo Trelles:
MAPI: towards the integrated exploitation of bioinformatics Web Services. 419 - Shashank Agarwal, Hong Yu, Isaac S. Kohane:
BioNOT: A searchable database of biomedical negated sentences. 420 - Michael Bieri, Paul R. Gooley:
Automated NMR relaxation dispersion data analysis using NESSY. 421 - Askar Obulkasim, Gerrit Meijer, Mark A. van de Wiel:
Stepwise classification of cancer samples using clinical and molecular Data. 422 - Seungmook Lee, Min-Seok Kwon, Hyoung-Joo Lee, Young-Ki Paik, Haixu Tang, Jae K. Lee, Taesung Park:
Enhanced peptide quantification using spectral count clustering and cluster abundance. 423 - Scott Doyle, James Monaco, Michael D. Feldman, John Tomaszewski, Anant Madabhushi:
An Active Learning Based Classification Strategy for the Minority Class Problem: Application to Histopathology Annotation. 424 - Cong V. C. Truong, Linn F. Groeneveld, Burkhard Morgenstern, Eildert Groeneveld:
MolabIS - An Integrated Information System for Storing and Managing Molecular Genetics Data. 425 - Liang Liu, Lili Yu, Venugopal Kalavacharla, Zhanji Liu:
A Bayesian model for gene family evolution. 426 - Jie Yang, Geroge Casella, Lauren M. McIntyre:
Generalized shrinkage F-like statistics for testing an interaction term in gene expression analysis in the presence of heteroscedasticity. 427 - Md Pavel Mahmud, Alexander Schliep:
Fast MCMC Sampling for Hidden Markov Models to Determine Copy Number Variations. 428 - Stefan Janssen, Christian Schudoma, Gerhard Steger, Robert Giegerich:
Lost in folding space? Comparing four variants of the thermodynamic model for RNA secondary structure prediction. 429 - Omid Abbasi, Ali Rostami, Ghader Karimian:
Identification of exonic regions in DNA sequences using cross-correlation and noise suppression by discrete wavelet transform. 430 - Michael Defoin-Platel, Matthew Morritt Hindle, Artem Lysenko, Stephen J. Powers, Dimah Z. Habash, Christopher J. Rawlings, Mansoor A. S. Saqi:
AIGO: Towards a unified framework for the Analysis and the Inter-comparison of GO functional annotations. 431 - Alexey V. Nefedov, Rovshan G. Sadygov:
A parallel method for enumerating amino acid compositions and masses of all theoretical peptides. 432 - Feng Li, Françoise Seillier-Moiseiwitsch:
Analyzing 2D Gel Images using a Two-Component Empirical Bayes Model. 433 - Malay Kumar Basu, Jeremy D. Selengut, Daniel H. Haft:
ProPhylo: Partial Phylogenetic Profiling to guide protein family construction and assignment of biological process. 434 - Adriano Barbosa-Silva, Jean-Fred Fontaine, Elisa R. Donnard, Fernanda Stussi, José Miguel Ortega, Miguel A. Andrade-Navarro:
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. 435 - John H. Morris, Leonard Apeltsin, Aaron M. Newman, Jan Baumbach, Tobias Wittkop, Gang Su, Gary D. Bader, Thomas E. Ferrin:
clusterMaker: a multi-algorithm clustering plugin for Cytoscape. 436 - Xiaoxiao Chi, Jingyu Hou:
An Iterative Approach of Protein Function Prediction. 437 - Lam C. Tsoi, Tingting Qin, Elizabeth H. Slate, W. Jim Zheng:
Consistent Differential Expression Pattern (CDEP) on microarray to identify genes related to metastatic behavior. 438 - Jian Cui, Xuepo Ma, Long Chen, Jianqiu Zhang:
SCFIA: A Statistical Corresponding Feature Identification Algorithm for LC/MS. 439 - Matthew C. Schmidt, Andrea M. Rocha, Kanchana Padmanabhan, Zhengzhang Chen, Kathleen Scott, James R. Mihelcic, Nagiza F. Samatova:
Efficient alpha, beta-motif Finder for Identification of Phenotype-related Functional Modules. 440 - Marcel H. Schulz, Sebastian Köhler, Sebastian Bauer, Peter N. Robinson:
Exact score distribution computation for ontological similarity searches. 441 - Yoshiharu Sato, Akiko Takaya, Tomoko Yamamoto:
Meta-analytic approach to the accurate prediction of secreted virulence effectors in Gram-negative bacteria. 442 - Jeffrey T. Chang, Michael L. Gatza, Joseph E. Lucas, William T. Barry, Peyton Vaughn, Joseph Nevins:
SIGNATURE: A workbench for gene expression signature analysis. 443 - Janrdanan Sreekumar, Cajo J. F. ter Braak, Roeland C. H. J. van Ham, Aalt D. J. van Dijk:
Correlated mutations via regularized multinomial regression. 444 - Joshua L. Phillips, Michael E. Colvin, Shawn D. Newsam:
Validating Clustering of Molecular Dynamics Simulations Using Polymer Models. 445 - Chun-Wei Tung, Matthias Ziehm, Andreas Kämper, Oliver Kohlbacher, Shinn-Ying Ho:
POPISK: T-cell reactivity prediction using support vector machines and string kernels. 446 - John Antoniw, Andrew M. Beacham, Thomas K. Baldwin, Martin Urban, Jason J. Rudd, Kim E. Hammond-Kosack:
OmniMapFree: A unified tool to visualise and explore sequenced genomes. 447 - Katrijn Van Deun, Tom F. Wilderjans, Robert A. van den Berg, Anestis Antoniadis, Iven Van Mechelen:
A flexible framework for sparse simultaneous component based data integration. 448 - Alyssa C. Frazee, Ben Langmead, Jeffrey T. Leek:
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets. 449 - Shengqiao Li, E. James Harner, Donald A. Adjeroh:
Random KNN feature selection - a fast and stable alternative to Random Forests. 450 - Frazer Meacham, Dario Boffelli, Joseph Dhahbi, David I. K. Martin, Meromit Singer, Lior Pachter:
Identification and correction of systematic error in high-throughput sequence data. 451 - Amit U. Sinha, Emily Merrill, Scott A. Armstrong, Timothy W. Clark, Sudeshna Das:
eXframe: reusable framework for storage, analysis and visualization of genomics experiments. 452 - Yi Zheng, Liangjun Zhao, Junping Gao, Zhangjun Fei:
iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. 453 - Paula Helena Reyes-Herrera, Elisa Ficarra, Andrea Acquaviva, Enrico Macii:
miREE: miRNA Recognition Elements Ensemble. 454 - Antonio Mora, Ian M. Donaldson:
iRefR: an R package to manipulate the iRefIndex consolidated protein interaction database. 455 - Martin Boeker, Ilinca Tudose, Janna Hastings, Daniel Schober, Stefan Schulz:
Unintended consequences of existential quantifications in biomedical ontologies. 456 - Claire Lemaitre, Aurélien Barré, Christine Citti, Florence Tardy, Francois Thiaucourt, Pascal Sirand-Pugnet, Patricia Thébault:
A novel substitution matrix fitted to the compositional bias in Mollicutes improves the prediction of homologous relationships. 457 - Gianluca Bontempi, Benjamin Haibe-Kains, Christine Desmedt, Christos P. Sotiriou, John Quackenbush:
Multiple-input multiple-output causal strategies for gene selection. 458 - Laila M. Poisson, Jeremy M. G. Taylor, Debashis Ghosh:
Integrative set enrichment testing for multiple omics platforms. 459 - Rafael Carreira, Sónia Carneiro, Rui Pereira, Miguel Rocha, Isabel Rocha, Eugénio C. Ferreira, Anália Lourenço:
Semantic annotation of biological concepts interplaying microbial cellular responses. 460 - Satya Sanket Sahoo, Vinh Nguyen, Olivier Bodenreider, Priti Parikh, Todd Minning, Amit P. Sheth:
A unified framework for managing provenance information in translational research. 461 - Yan Yang, Phillip Stafford, YoonJoo Kim:
Segmentation and intensity estimation for microarray images with saturated pixels. 462 - Kenneth R. Hess, Caimiao Wei, Yuan Qi, Takayuki Iwamoto, W. Fraser Symmans, Lajos Pusztai:
Lack of sufficiently strong informative features limits the potential of gene expression analysis as predictive tool for many clinical classification problems. 463 - Fabrice Berger, Enrico Carlon:
From hybridization theory to microarray data analysis: performance evaluation. 464 - Paula Tataru, Asger Hobolth:
Comparison of methods for calculating conditional expectations of sufficient statistics for continuous time Markov chains. 465 - Scott Lloyd, Quinn O. Snell:
Accelerated large-scale multiple sequence alignment. 466 - Jason Rudy, Faramarz Valafar:
Empirical comparison of cross-platform normalization methods for gene expression data. 467 - Angela Bauch, Izabela Adamczyk, Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Manuel Kohler, Tomasz Pylak, Andreas Quandt, Chandrasekhar Ramakrishnan, Christian Beisel, Lars Malmström, Ruedi Aebersold, Bernd Rinn:
openBIS: a flexible framework for managing and analyzing complex data in biology research. 468 - Makiko Yoshida, Asako Koike:
SNPInterForest: A new method for detecting epistatic interactions. 469 - Fernando Izquierdo-Carrasco, Stephen A. Smith, Alexandros Stamatakis:
Algorithms, data structures, and numerics for likelihood-based phylogenetic inference of huge trees. 470 - Yu-Ching Fang, Po-Ting Lai, Hong-Jie Dai, Wen-Lian Hsu:
MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature. 471 - Xin Deng, Jianlin Cheng:
MSACompro: protein multiple sequence alignment using predicted secondary structure, solvent accessibility, and residue-residue contacts. 472 - Jorge Barriuso, José R. Valverde, Rafael P. Mellado:
Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows. 473 - Qiyuan Li, Nicolai J. Birkbak, Balazs Györffy, Zoltan Szallasi, Aron C. Eklund:
Jetset: selecting the optimal microarray probe set to represent a gene. 474 - Junliang Shang, Junying Zhang, Yan Sun, Dan Liu, Daojun Ye, Yaling Yin:
Performance analysis of novel methods for detecting epistasis. 475 - Jike Cui, Todd F. DeLuca, Jae-Yoon Jung, Dennis P. Wall:
Phylogenetically informed logic relationships improve detection of biological network organization. 476 - Kathleen M. Doherty, Priyanka Nakka, Bracken M. King, Soo-Yon Rhee, Susan P. Holmes, Robert W. Shafer, Mala L. Radhakrishnan:
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. 477 - Kai Kammers, Michel Lang, Jan G. Hengstler, Marcus Schmidt, Jörg Rahnenführer:
Survival models with preclustered gene groups as covariates. 478 - Christopher D. Brumbaugh, Hyunsung John Kim, Mario Giovacchini, Nader Pourmand:
NanoStriDE: normalization and differential expression analysis of NanoString nCounter data. 479 - Davide Risso, Katja Schwartz, Gavin Sherlock, Sandrine Dudoit:
GC-Content Normalization for RNA-Seq Data. 480 - Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E. Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana L. Neves, Alberto D. Pascual-Montano, Arzucan Özgür, Dragomir R. Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta, Jun'ichi Tsujii:
U-Compare bio-event meta-service: compatible BioNLP event extraction services. 481 - Emily Seymour, Rohini Damle, Alessandro Sette, Bjoern Peters:
Cost sensitive hierarchical document classification to triage PubMed abstracts for manual curation. 482 - Abhishek Golugula, George Lee, Stephen R. Master, Michael D. Feldman, John Tomaszewski, David W. Speicher, Anant Madabhushi:
Supervised Regularized Canonical Correlation Analysis: integrating histologic and proteomic measurements for predicting biochemical recurrence following prostate surgery. 483 - Hang Chang, Gerald Fontenay, Ju Han, Ge Cong, Frederick L. Baehner, Joe W. Gray, Paul T. Spellman, Bahram Parvin:
Morphometic analysis of TCGA glioblastoma multiforme. 484 - Bettina Knapp, Ilka Rebhan, Anil Kumar, Petr Matula, Narsis Aftab Kiani, Marco Binder, Holger Erfle, Karl Rohr, Roland Eils, Ralf Bartenschlager, Lars Kaderali:
Normalizing for individual cell population context in the analysis of high-content cellular screens. 485 - Halil Kilicoglu, Graciela Rosemblat, Marcelo Fiszman, Thomas C. Rindflesch:
Constructing a semantic predication gold standard from the biomedical literature. 486 - Anne L. Plant, John T. Elliott, Talapady N. Bhat:
New concepts for building vocabulary for cell image ontologies. 487 - Stephan Gade, Christine Porzelius, Maria Fälth, Jan C. Brase, Daniela Wuttig, Ruprecht Kuner, Harald Binder, Holger Sültmann, Tim Beißbarth:
Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer. 488 - Usha Muppirala, Vasant G. Honavar, Drena Dobbs:
Predicting RNA-Protein Interactions Using Only Sequence Information. 489 - Gustavo Arellano, Julián Argil, Eugenio Azpeitia, Mariana Benítez, Miguel Carrillo, Pedro Arturo Góngora, David A. Rosenblueth, Elena R. Álvarez-Buylla:
"Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis. 490 - Carson Holt, Mark Yandell:
MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects. 491 - Laurin A. J. Mueller, Karl G. Kugler, Armin Graber, Frank Emmert-Streib, Matthias Dehmer:
Structural Measures for Network Biology Using QuACN. 492 - Yan Ji, Yixiang Shi, Guohui Ding, Yixue Li:
A new strategy for better genome assembly from very short reads. 493 - Sveinung Gundersen, Matús Kalas, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Kjetil Sandve:
Identifying elemental genomic track types and representing them uniformly. 494 - Kenneth Daily, Vishal R. Patel, Paul Rigor, Xiaohui Xie, Pierre Baldi:
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. 495 - Ivica Kopriva, Marko Filipovic:
A mixture model with a reference-based automatic selection of components for disease classification from protein and/or gene expression levels. 496 - Rosemary Braun, Gregory Leibon, Scott D. Pauls, Daniel N. Rockmore:
Partition decoupling for multi-gene analysis of gene expression profiling data. 497
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