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BMC Bioinformatics, Volume 13
Volume 13, 2012
- Rebecca F. Halperin, Phillip Stafford, Jack S. Emery, Krupa Navalkar
, Stephen A. Johnston:
GuiTope: an application for mapping random-sequence peptides to protein sequences. 1 - Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jingchu Luo, Ge Gao:
ABrowse - a customizable next-generation genome browser framework. 2 - Leonid L. Chepelev, Janna Hastings
, Marcus Ennis, Christoph Steinbeck
, Michel Dumontier
:
Self-organizing ontology of biochemically relevant small molecules. 3 - Yanglan Gan, Jihong Guan, Shuigeng Zhou:
A comparison study on feature selection of DNA structural properties for promoter prediction. 4 - David Rosenkranz, Hans Zischler
:
proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis. 5 - Akhil Kumar
, Patrick F. Suthers
, Costas D. Maranas
:
MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. 6 - Bin Li, Daisuke Kihara:
Protein docking prediction using predicted protein-protein interface. 7 - Danny Challis, Jin Yu
, Uday S. Evani, Andrew R. Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A. Gibbs, Fuli Yu:
An integrative variant analysis suite for whole exome next-generation sequencing data. 8 - Ana Brândusa Pavel, Cristian Ioan Vasile
:
PyElph - a software tool for gel images analysis and phylogenetics. 9 - Shannon M. Bell, Lyle D. Burgoon
, Robert L. Last
:
MIPHENO: data normalization for high throughput metabolite analysis. 10 - Kentaro Tomii
, Yoshito Sawada
, Shinya Honda
:
Convergent evolution in structural elements of proteins investigated using cross profile analysis. 11 - Ruoting Yang, Bernie J. Daigle Jr., Linda R. Petzold, Francis J. Doyle III:
Core module biomarker identification with network exploration for breast cancer metastasis. 12 - Douglas Londono, Steven Buyske
, Stephen J. Finch, Swarkar Sharma
, Carol A. Wise
, Derek Gordon
:
TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data. 13 - Muneef Ayyash, Hashem Tamimi
, Yaqoub Ashhab
:
Developing a powerful In Silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome. 14 - Thomas Triplet, Gregory Butler:
The EnzymeTracker: an open-source laboratory information management system for sample tracking. 15 - Ruihua Fang, Gary Schindelman, Kimberly Van Auken, Jolene Fernandes, Wen J. Chen, Xiaodong Wang, Paul Davis
, Mary Ann Tuli
, Steven J. Marygold
, Gillian H. Millburn, Beverley Matthews, Haiyan Zhang, Nick Brown
, William M. Gelbart, Paul W. Sternberg
:
Automatic categorization of diverse experimental information in the bioscience literature. 16 - Ning Kang, Erik M. van Mulligen
, Jan A. Kors:
Training text chunkers on a silver standard corpus: can silver replace gold? 17 - Marvin Schulz, Edda Klipp, Wolfram Liebermeister
:
Propagating semantic information in biochemical network models. 18 - Cyrille Lepoivre, Aurélie Bergon, Fabrice Lopez, Narayanan Perumal, Catherine Nguyen, Jean Imbert
, Denis Puthier
:
TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. 19 - Gabriele Sales
, Enrica Calura
, Duccio Cavalieri
, Chiara Romualdi
:
graphite - a Bioconductor package to convert pathway topology to gene network. 20 - Ching-Wei Wang
:
Fast automatic quantitative cell replication with fluorescent live cell imaging. 21 - Monir Hajiaghayi, Anne Condon, Holger H. Hoos
:
Analysis of energy-based algorithms for RNA secondary structure prediction. 22 - H. Robert Frost, Alexa T. McCray:
Markov Chain Ontology Analysis (MCOA). 23 - Fangzhou Yao, Jeff Coquery, Kim-Anh Lê Cao
:
Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets. 24 - Hani Z. Girgis, Ivan Ovcharenko:
Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs. 25 - Satish Viswanath
, Anant Madabhushi
:
Consensus embedding: theory, algorithms and application to segmentation and classification of biomedical data. 26 - Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim, Changyu Shen:
Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry. 27 - Alejandro Cáceres
, Suzanne S. Sindi, Benjamin J. Raphael, Mario Cáceres
, Juan R. González:
Identification of polymorphic inversions from genotypes. 28 - Richard J. Giuly, Maryann E. Martone
, Mark H. Ellisman:
Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets. 29 - Itziar Irigoien
, Basilio Sierra
, Concepción Arenas
:
ICGE: an R package for detecting relevant clusters and atypical units in gene expression. 30 - Andre P. Masella, Andrea K. Bartram, Jakub Truszkowski
, Daniel Gregory Brown, Josh D. Neufeld:
PANDAseq: paired-end assembler for illumina sequences. 31 - Yang Ding, William Andrew Lorenz, Jeffrey H. Chuang
:
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences. 32 - Matti Kankainen
, Teija Ojala
, Liisa Holm
:
BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins. 33 - Chris Bauer, Frank Kleinjung, Dorothea Rutishauser
, Christian Panse, Alexandra Chadt, Tanja Dreja, Hadi Al-Hasani
, Knut Reinert
, Ralph Schlapbach
, Johannes Schuchhardt:
PPINGUIN: Peptide Profiling Guided Identification of Proteins improves quantitation of iTRAQ ratios. 34 - Leonid Chindelevitch
, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek:
Assessing statistical significance in causal graphs. 35 - Cedric Laczny
, Petra Leidinger, Jan Haas, Nicole Ludwig
, Christina Backes, Andreas Gerasch, Michael Kaufmann, Britta Vogel, Hugo A. Katus, Benjamin Meder, Cord Stähler, Eckart Meese, Hans-Peter Lenhof, Andreas Keller
:
miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases. 36 - Bhakti Dwivedi
, Robert Schmieder, Dawn B. Goldsmith, Robert A. Edwards
, Mya Breitbart
:
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity. 37 - Sandra Ortega-Martorell
, Paulo J. G. Lisboa, Alfredo Vellido
, Margarida Julià-Sapé
, Carles Arús
:
Non-negative matrix factorisation methods for the spectral decomposition of MRS data from human brain tumours. 38 - Paul Ashford
, David S. Moss, Alexander Alex, Siew K. Yeap, Alice Povia, Irene Nobeli
, Mark A. Williams
:
Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets. 39 - Chun-Wei Tung
:
PupDB: a database of pupylated proteins. 40 - Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs
, Vasant G. Honavar
:
Predicting protein-protein interface residues using local surface structural similarity. 41 - Konstantinos Krampis, Tim Booth, Brad Chapman
, Bela Tiwari, Mesude Bicak, Dawn Field, Karen E. Nelson:
Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community. 42 - Zhang Zhang
, Jun Li
, Peng Cui, Feng Ding
, Ang Li, Jeffrey P. Townsend
, Jun Yu:
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. 43 - Jianguo Liu, Xianjiang Kang:
Grading amino acid properties increased accuracies of single point mutation on protein stability prediction. 44 - Maria Secrier
, Georgios A. Pavlopoulos
, Jan Aerts
, Reinhard Schneider
:
Arena3D: visualizing time-driven phenotypic differences in biological systems. 45 - Chia-Ling Huang, John Lamb, Leonid Chindelevitch
, Jarek Kostrowicki, Justin Guinney
, Charles DeLisi, Daniel Ziemek:
Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. 46 - John P. Archer
, Greg Baillie
, Simon J. Watson
, Paul Kellam
, Andrew Rambaut
, David L. Robertson
:
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. 47 - Pierre Peterlongo
, Rayan Chikhi:
Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. 48 - Yanglan Gan, Jihong Guan, Shuigeng Zhou, Weixiong Zhang
:
Structural features based genome-wide characterization and prediction of nucleosome organization. 49 - Tudor Groza
, Jane Hunter
, Andreas Zankl
:
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain. 50 - Zhenhua Li
, Ying He
, Limsoon Wong
, Jinyan Li:
Progressive dry-core-wet-rim hydration trend in a nested-ring topology of protein binding interfaces. 51 - Xingbin Wang, Yan Lin, Chi Song, Etienne Sibille, George C. Tseng:
Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder. 52 - Benjamin A. Logsdon, Gabriel E. Hoffman, Jason G. Mezey:
Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control. 53 - Alain B. Tchagang, Sieu Phan, Fazel Famili, Heather Shearer, Pierre R. Fobert, Yi Huang
, Jitao Zou, Daiqing Huang, Adrian Cutler, Ziying Liu, Youlian Pan
:
Mining biological information from 3D short time-series gene expression data: the OPTricluster algorithm. 54 - Jan-Oliver Janda, Markus Busch
, Fabian Kück, Mikhail Porfenenko, Rainer Merkl
:
CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure. 55 - Michael Dannemann, Michael Lachmann, Anna Lorenc
:
'maskBAD' - a package to detect and remove Affymetrix probes with binding affinity differences. 56 - Abdelhalim Larhlimi
, László Dávid, Joachim Selbig, Alexander Bockmayr
:
F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks. 57 - John Boyle
, Richard Kreisberg, Ryan Bressler, Sarah A. Killcoyne
:
Methods for visual mining of genomic and proteomic data atlases. 58 - Joanna Zhuang, Martin Widschwendter
, Andrew E. Teschendorff:
A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform. 59 - Neetika Nath
, John B. O. Mitchell
:
Is EC class predictable from reaction mechanism? 60 - Luna De Ferrari
, Stuart Aitken, Jano I. van Hemert
, Igor Goryanin
:
EnzML: multi-label prediction of enzyme classes using InterPro signatures. 61 - Adam Hilterbrand, Joseph Saelens, Catherine Putonti
:
CBDB: The codon bias database. 62 - Teerasak E.-komon, Richard J. Burchmore
, Pawel Herzyk, Robert Davies:
Predicting the outer membrane proteome of Pasteurella multocida based on consensus prediction enhanced by results integration and manual confirmation. 63 - Ilya Plyusnin
, Liisa Holm
:
Comprehensive comparison of graph based multiple protein sequence alignment strategies. 64 - Jianlin Cheng
, Jilong Li, Zheng Wang, Jesse Eickholt, Xin Deng:
The MULTICOM toolbox for protein structure prediction. 65 - Yejun Wang, He Huang, Ming-an Sun
, Qing Zhang, Dianjing Guo:
T3DB: an integrated database for bacterial type III secretion system. 66 - Nicolas Terrapon
, Olivier Gascuel, Eric Maréchal
, Laurent Bréhélin:
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. 67 - Bernie J. Daigle Jr., Min K. Roh
, Linda R. Petzold, Jarad Niemi
:
Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. 68 - Yupeng Cun
, Holger Fröhlich
:
Prognostic gene signatures for patient stratification in breast cancer - accuracy, stability and interpretability of gene selection approaches using prior knowledge on protein-protein interactions. 69 - Xian-Wen Ren, Yong Wang, Jiguang Wang
, Xiang-Sun Zhang:
A unified computational model for revealing and predicting subtle subtypes of cancers. 70 - Duojiao Wu, Catherine M. Rice, Xiangdong Wang:
Cancer bioinformatics: A new approach to systems clinical medicine. 71 - Masao Ueki, Gen Tamiya
:
Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis. 72 - Axel Skarman, Mohammad Shariati
, Luc Jans, Li Jiang, Peter Sørensen:
A Bayesian variable selection procedure to rank overlapping gene sets. 73 - Joseph E. Lucas, J. Will Thompson, Laura G. Dubois, Jeanette McCarthy, Hans Tillmann, Alexander Thompson, Norah Shire, Ron Hendrickson, Francisco Dieguez, Phyllis Goldman, Kathleen Schwarz, Keyur Patel, John McHutchison, M. Arthur Moseley:
Metaprotein expression modeling for label-free quantitative proteomics. 74 - Tianlei Xu, Ruixin Zhu
, Qi Liu, Zhi-Wei Cao:
Quantitatively integrating molecular structure and bioactivity profile evidence into drug-target relationship analysis. 75 - Thomas Hladish
, Eugene Melamud, Luis Barrera, Alison P. Galvani, Lauren Ancel Meyers
:
EpiFire: An open source C++ library and application for contact network epidemiology. 76 - Mohamed Abouelhoda
, Shadi Issa
, Moustafa Ghanem
:
Tavaxy: Integrating Taverna and Galaxy workflows with cloud computing support. 77 - James W. J. Anderson, Paula Tataru
, Joe Staines, Jotun Hein, Rune B. Lyngsø:
Evolving stochastic context-free grammars for RNA secondary structure prediction. 78 - Xueping Yu, Anders Wallqvist
, Jaques Reifman:
Inferring high-confidence human protein-protein interactions. 79 - Wessel N. van Wieringen
, Kristian Unger
, Gwenaël G. R. Leday
, Oscar Krijgsman, Renée X. de Menezes, Bauke Ylstra
, Mark A. van de Wiel
:
Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses. 80 - Sonja Zehetmayer
, Martin Posch
:
False discovery rate control in two-stage designs. 81 - Giorgio Gonnella
, Stefan Kurtz:
Readjoiner: a fast and memory efficient string graph-based sequence assembler. 82 - Eric Audemard
, Thomas Schiex, Thomas Faraut:
Detecting long tandem duplications in genomic sequences. 83 - Douglas B. Craig, Sujatha Kannan
, Alan A. Dombkowski
:
Augmented annotation and orthologue analysis for Oryctolagus cuniculus: Better Bunny. 84 - Felix Dreher, Thomas Kreitler, Christopher Hardt
, Atanas Kamburov
, Reha Yildirimman, Karl Schellander, Hans Lehrach, Bodo M. H. Lange, Ralf Herwig
:
DIPSBC - data integration platform for systems biology collaborations. 85 - Eugene Andres Houseman
, William P. Accomando, Devin C. Koestler
, Brock C. Christensen, Carmen J. Marsit
, Heather H. Nelson
, John K. Wiencke, Karl T. Kelsey:
DNA methylation arrays as surrogate measures of cell mixture distribution. 86 - Alexandre P. Francisco
, Cátia Vaz
, Pedro T. Monteiro
, José Melo-Cristino
, Mário Ramirez, João A. Carriço:
PHYLOViZ: phylogenetic inference and data visualization for sequence based typing methods. 87 - Gad Abraham
, Adam Kowalczyk, Justin Zobel, Michael Inouye
:
SparSNP: Fast and memory-efficient analysis of all SNPs for phenotype prediction. 88 - Rasna R. Walia
, Cornelia Caragea
, Benjamin A. Lewis, Fadi Towfic, Michael Terribilini, Yasser El-Manzalawy, Drena Dobbs
, Vasant G. Honavar
:
Protein-RNA interface residue prediction using machine learning: an assessment of the state of the art. 89 - Antoni Miró, Carlos Pozo
, Gonzalo Guillén-Gosálbez
, Jose A. Egea
, Laureano Jiménez
:
Deterministic global optimization algorithm based on outer approximation for the parameter estimation of nonlinear dynamic biological systems. 90 - Jacek Blazewicz
, Marcin Borowski, Wahiba Chaara, Pawel Kedziora, David Klatzmann
, Piotr Lukasiak
, Adrien Six
, Pawel Wojciechowski
:
GeVaDSs - decision support system for novel Genetic Vaccine development process. 91 - Adam L. Bazinet, Michael P. Cummings:
A comparative evaluation of sequence classification programs. 92 - Sunisa Chatsurachai, Chikara Furusawa
, Hiroshi Shimizu:
An in silico platform for the design of heterologous pathways in nonnative metabolite production. 93 - Steven M. Hill
, Richard M. Neve, Nora Bayani, Wen-Lin Kuo, Safiyyah Ziyad, Paul T. Spellman, Joe W. Gray, Sach Mukherjee:
Integrating biological knowledge into variable selection: an empirical Bayes approach with an application in cancer biology. 94 - Yu-Shen Liu, Meng Wang, Jean-Claude Paul, Karthik Ramani:
3DMolNavi: A web-based retrieval and navigation tool for flexible molecular shape comparison. 95 - Zanoni Dias, Ulisses Dias
, João C. Setubal
:
SIS: a program to generate draft genome sequence scaffolds for prokaryotes. 96 - Tahir Mehmood
, Jon Bohlin
, Anja Bråthen Kristoffersen, Solve Sæbø, Jonas Warringer
, Lars Snipen:
Exploration of multivariate analysis in microbial coding sequence modeling. 97 - Weiliang Shi, Grace Wahba, Rafael A. Irizarry, Héctor Corrada Bravo
, Stephen J. Wright:
The partitioned LASSO-patternsearch algorithm with application to gene expression data. 98 - Dinesh K. Barupal
, Pradeep Kumar Haldiya, Gert Wohlgemuth, Tobias Kind
, Shanker L. Kothari, Kent E. Pinkerton, Oliver Fiehn:
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity. 99 - Dandi Qiao, Wai-Ki Yip, Christoph Lange:
Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data. 100 - Marine Dumousseau, Nicolas Rodriguez
, Nick S. Juty
, Nicolas Le Novère:
MELTING, a flexible platform to predict the melting temperatures of nucleic acids. 101 - Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda:
Workflows for microarray data processing in the Kepler environment. 102 - András Bodor, István Csabai
, Michael W. Mahoney, Norbert Solymosi
:
rCUR: an R package for CUR matrix decomposition. 103 - Niall J. Haslam
, Denis C. Shields:
Profile-based short linear protein motif discovery. 104 - Paul Shealy, Homayoun Valafar
:
Multiple structure alignment with msTALI. 105 - Kalai Vanii
, Pablo A. Moreno
, Andreas Truszkowski, Peter Ertl
, Christoph Steinbeck
:
Natural product-likeness score revisited: an open-source, open-data implementation. 106 - Lei Yuan, Alexander Woodard, Shuiwang Ji
, Yuan Jiang, Zhi-Hua Zhou, Sudhir Kumar
, Jieping Ye:
Learning Sparse Representations for Fruit-Fly Gene Expression Pattern Image Annotation and Retrieval. 107 - Makoto Miwa, Paul Thompson, John McNaught, Douglas B. Kell
, Sophia Ananiadou:
Extracting semantically enriched events from biomedical literature. 108 - Min Li, Xuehong Wu
, Jianxin Wang, Yi Pan
:
Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data. 109 - Thomas Laubach, Arndt von Haeseler, Martin J. Lercher
:
TreeSnatcher plus: capturing phylogenetic trees from images. 110 - Lukasz Pawel Kozlowski
, Janusz M. Bujnicki:
MetaDisorder: a meta-server for the prediction of intrinsic disorder in proteins. 111 - Suleiman A. Khan, Ali Faisal
, John Mpindi, Juuso A. Parkkinen, Tuomo Kalliokoski
, Antti Poso
, Olli-P. Kallioniemi
, Krister Wennerberg
, Samuel Kaski:
Comprehensive data-driven analysis of the impact of chemoinformatic structure on the genome-wide biological response profiles of cancer cells to 1159 drugs. 112