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ORCIDBMC Bioinformatics, Volume 10
Volume 10, 2009
- Shuangge Ma, Jian Huang
:
Regularized gene selection in cancer microarray meta-analysis. - Steffen Durinck, James H. Bullard, Paul T. Spellman, Sandrine Dudoit:
GenomeGraphs: integrated genomic data visualization with R. - Alessandro Ferrantini, Joke Allemeersch, Paul van Hummelen, Enrico Carlon:
Thermodynamic scaling behavior in genechips. - Chao Yang, Zengyou He, Weichuan Yu:
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis. - Jing Cao, Xian-Jin Xie, Song Zhang, Angelique Whitehurst, Michael A. White:
Bayesian optimal discovery procedure for simultaneous significance testing. - Jaume Bacardit, Michael Stout, Jonathan D. Hirst, Alfonso Valencia, Robert Elliott Smith, Natalio Krasnogor:
Automated Alphabet Reduction for Protein Datasets. - Michael Hackenberg, Gorka Lasso, Rune Matthiesen:
ContDist: a tool for the analysis of quantitative gene and promoter properties. - Pengfei Han, Xiuzhen Zhang, Raymond S. Norton, Zhi-Ping Feng:
Large-scale prediction of long disordered regions in proteins using random forests. - Takashi Yoneya, Reina Nishida:
TCP: a tool for designing chimera proteins based on the tertiary structure information. - Paola M. V. Rancoita, Marcus Hutter, Francesco Bertoni, Ivo Kwee:
Bayesian DNA copy number analysis. - Amber J. Hackstadt, Ann M. Hess:
Filtering for increased power for microarray data analysis. - Kai Wang, Jian Li, Shengting Li, Lars Bolund, Carsten Wiuf:
Estimation of tumor heterogeneity using CGH array data. - Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L. S. Tang, Weichuan Yu:
MegaSNPHunter: a learning approach to detect disease predisposition SNPs and high level interactions in genome wide association study. - Yun Xu, ZhiHao Wang, YiMing Lei, YuZhong Zhao, Yu Xue:
MBA: a literature mining system for extracting biomedical abbreviations. - Kuo-ching Liang, Xiaodong Wang, Ta-Hsin Li:
Robust discovery of periodically expressed genes using the laplace periodogram. - Victoria Martin-Requena, Antonio Muñoz-Merida, M. Gonzalo Claros, Oswaldo Trelles:
PreP+07: improvements of a user friendly tool to preprocess and analyse microarray data. - Kyle C. Chipman, Ambuj K. Singh:
Predicting genetic interactions with random walks on biological networks. - Harald Binder, Martin Schumacher:
Incorporating pathway information into boosting estimation of high-dimensional risk prediction models. - Tatsunori B. Hashimoto, Masao Nagasaki, Kaname Kojima, Satoru Miyano:
BFL: a node and edge betweenness based fast layout algorithm for large scale networks. - Rui Hu, Xing Qiu, Galina V. Glazko, Lev Klebanov, Andrei Yakovlev:
Detecting intergene correlation changes in microarray analysis: a new approach to gene selection. - Christian Frech, Michael Kommenda, Viktoria Dorfer, Thomas Kern, Helmut Hintner, Johann W. Bauer, Kamil Önder:
Improved homology-driven computational validation of protein-protein interactions motivated by the evolutionary gene duplication and divergence hypothesis. - Manish Kumar, Gajendra P. S. Raghava:
Prediction of nuclear proteins using SVM and HMM models. - Debayan Datta, Hongyu Zhao:
Effect of false positive and false negative rates on inference of binding target conservation across different conditions and species from ChIP-chip data. - Tsong Yueh Chen, Joshua Wing Kei Ho, Huai Liu, Xiaoyuan Xie:
An innovative approach for testing bioinformatics programs using metamorphic testing. - J. B. Brown, Tatsuya Akutsu:
Identification of novel DNA repair proteins via primary sequence, secondary structure, and homology. - Sonia H. Shah, Jacqueline A. Pallas:
Identifying differential exon splicing using linear models and correlation coefficients. - Ujjwal Maulik, Anirban Mukhopadhyay, Sanghamitra Bandyopadhyay:
Combining Pareto-optimal clusters using supervised learning for identifying co-expressed genes. - Dimitra Alexopoulou, Bill Andreopoulos, Heiko Dietze, Andreas Doms, Fabien Gandon, Jörg Hakenberg, Khaled Khelif, Michael Schroeder, Thomas Wächter:
Biomedical word sense disambiguation with ontologies and metadata: automation meets accuracy. - Yu-Shen Liu, Yi Fang, Karthik Ramani:
Using least median of squares for structural superposition of flexible proteins. - Bart H. J. van den Berg, Jay H. Konieczka, Fiona M. McCarthy, Shane C. Burgess:
ArrayIDer: automated structural re-annotation pipeline for DNA microarrays. - Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita:
Genome Projector: zoomable genome map with multiple views. - Georg Steinkellner, Robert Rader, Gerhard G. Thallinger, Christoph Kratky, Karl Gruber:
VASCo: computation and visualization of annotated protein surface contacts. - Nils Arrigo, Jarek W. Tuszynski, Dorothee Ehrich, Tommy Gerdes, Nadir Alvarez:
Evaluating the impact of scoring parameters on the structure of intra-specific genetic variation using RawGeno, an R package for automating AFLP scoring. - Kim-Anh Lê Cao, Pascal G. P. Martin, Christèle Robert-Granié, Philippe Besse:
Sparse canonical methods for biological data integration: application to a cross-platform study. - Andrew S. Warren, João Carlos Setubal:
The Genome Reverse Compiler: an explorative annotation tool. - Sung-Hee Park, José A. Reyes, David R. Gilbert, Ji Woong Kim, Sangsoo Kim:
Prediction of protein-protein interaction types using association rule based classification. - Daniel Glez-Peña, Rodrigo Álvarez, Fernando Díaz, Florentino Fdez-Riverola:
DFP: a Bioconductor package for fuzzy profile identification and gene reduction of microarray data. - Roland Nilsson, Johan Björkegren, Jesper Tegnér:
On reliable discovery of molecular signatures. - Sarah K. Kummerfeld, Sarah A. Teichmann:
Protein domain organisation: adding order. - Sudhakar Jonnalagadda, Rajagopalan Srinivasan:
NIFTI: An evolutionary approach for finding number of clusters in microarray data. - Lars Kraemer, Bánk Beszteri, Steffi Gäbler-Schwarz, Christoph Held, Florian Leese, Christoph Mayer, Kevin Pöhlmann, Stephan Frickenhaus:
STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design. - Vlad Popovici, Darlene R. Goldstein, Janine Antonov, Rolf Jaggi, Mauro Delorenzi, Pratyaksha Wirapati:
Selecting control genes for RT-QPCR using public microarray data. - Qingbo Li, Bryan A. P. Roxas:
An assessment of false discovery rates and statistical significance in label-free quantitative proteomics with combined filters. - Pei-Chun Chen, Su-Yun Huang, Wei J. Chen, Chuhsing Kate Hsiao:
A new regularized least squares support vector regression for gene selection. - Carl Murie, Owen Z. Woody, Anna Y. Lee, Robert Nadon:
Comparison of small n statistical tests of differential expression applied to microarrays. - Jimmy Lin:
Is searching full text more effective than searching abstracts? - Marit Ackermann, Korbinian Strimmer:
A general modular framework for gene set enrichment analysis. - Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini:
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. - Sergio Barlati, Sergio Chiesa, Chiara Magri:
"GenotypeColourTM": colour visualisation of SNPs and CNVs. - Michael Dondrup, Stefan P. Albaum, Thasso Griebel, Kolja Henckel, Sebastian Jünemann, Tim Kahlke, Christiane K. Kleindt, Helge Küster, Burkhard Linke, Dominik Mertens, Virginie Mittard-Runte, Heiko Neuweger, Kai J. Runte, Andreas Tauch, Felix Tille, Alfred Pühler, Alexander Goesmann:
EMMA 2 - A MAGE-compliant system for the collaborative analysis and integration of microarray data. - José Carlos Clemente, Kazuho Ikeo, Gabriel Valiente, Takashi Gojobori:
Optimized ancestral state reconstruction using Sankoff parsimony. - Uwe Thissen, Suzan Wopereis, Sjoerd A. A. van den Berg, Ivana Bobeldijk, Robert Kleemann, Teake Kooistra, Ko Willems van Dijk, Ben van Ommen, Age K. Smilde:
Improving the analysis of designed studies by combining statistical modelling with study design information. - Michalis E. Zervakis, Michalis E. Blazadonakis, Georgia Tsiliki, Vasiliki Danilatou, Manolis Tsiknakis, Dimitris Kafetzopoulos:
Outcome prediction based on microarray analysis: a critical perspective on methods. - André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner, Rainer Merkl:
TransCent: Computational enzyme design by transferring active sites and considering constraints relevant for catalysis. - Eric Yang, Ioannis P. Androulakis:
Assessing and selecting gene expression signals based upon the quality of the measured dynamics. - Naryttza N. Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus, Tim W. Nattkemper:
TACOA - Taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. - Ivan Erill, Michael C. O'Neill:
A reexamination of information theory-based methods for DNA-binding site identification. - Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang, Hualiang Jiang:
An effective docking strategy for virtual screening based on multi-objective optimization algorithm. - Sandra N. Loevenich, Erich Brunner, Nichole L. King, Eric W. Deutsch, Stephen E. Stein, Ruedi Aebersold, Ernst Hafen:
The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. - David P. Leader, E. James Milner-White:
Motivated Proteins: A web application for studying small three-dimensional protein motifs. - Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi:
A comparison on effects of normalisations in the detection of differentially expressed genes. - Vasyl Pihur, Susmita Datta, Somnath Datta:
RankAggreg, an R package for weighted rank aggregation. - Zhaoxia Yu, Chad Garner, Argyrios Ziogas, Hoda Anton-Culver, Daniel J. Schaid:
Genotype determination for polymorphisms in linkage disequilibrium. - Geert C. W. M. Mulders, Gerard T. Barkema, Enrico Carlon:
Inverse Langmuir method for oligonucleotide microarray analysis. - Leng Han, Zhongming Zhao:
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? - Shaleen K. Botting, Jerome P. Trzeciakowski, Michelle F. Benoit, Salama A. Salama, Concepcion R. Diaz-Arrastia:
Sample entropy analysis of cervical neoplasia gene-expression signatures. - Karen Eilbeck, Barry Moore, Carson Holt, Mark Yandell:
Quantitative measures for the management and comparison of annotated genomes. - Joshua N. Sampson, Hongyu Zhao:
Genotyping and inflated type I error rate in genome-wide association case/control studies. - Douglas W. Bryant Jr., Weng-Keen Wong, Todd C. Mockler:
QSRA - a quality-value guided de novo short read assembler. - Anna Maria Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, Lindsay G. Cowell:
An improved ontological representation of dendritic cells as a paradigm for all cell types. - Atsushi Niida, Andrew D. Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q. Zhang, Tetsu Akiyama:
Gene set-based module discovery in the breast cancer transcriptome. - Amalia Annest, Roger Eugene Bumgarner, Adrian E. Raftery, Ka Yee Yeung:
Iterative Bayesian Model Averaging: a method for the application of survival analysis to high-dimensional microarray data. - Jing Chen, Bruce J. Aronow, Anil G. Jegga:
Disease candidate gene identification and prioritization using protein interaction networks. - Ilhami Visne, Erkan Dilaveroglu, Klemens Vierlinger, Martin Lauss, Ahmet Yildiz, Andreas Weinhäusel, Christa Noehammer, Friedrich Leisch, Albert Kriegner:
RGG: A general GUI Framework for R scripts. - Tobias Gebäck, Petros Koumoutsakos:
Edge detection in microscopy images using curvelets. - Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson, Ron Unger:
RNAslider: a faster engine for consecutive windows folding and its application to the analysis of genomic folding asymmetry. - Donna M. Toleno, Gabriel Renaud, Tyra G. Wolfsberg, Munirul Islam, Derek E. Wildman, Kimberly D. Siegmund, Joseph G. Hacia:
Development and evaluation of new mask protocols for gene expression profiling in humans and chimpanzees. - Yan A. Meng, Yi Yu, L. Adrienne Cupples, Lindsay A. Farrer, Kathryn L. Lunetta:
Performance of random forest when SNPs are in linkage disequilibrium. - John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich:
Adaptable data management for systems biology investigations. - Chao Xie, Martti T. Tammi:
CNV-seq, a new method to detect copy number variation using high-throughput sequencing. - Markus Teuber, Michael H. Wenz, Stefan Schreiber, Andre Franke:
GMFilter and SXTestPlate: software tools for improving the SNPlexTM genotyping system. - Bartek Wilczynski, Norbert Dojer, Mateusz Patelak, Jerzy Tiuryn:
Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs. - Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin, Bin Xia:
Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis. - Mickaël Guedj, Stéphane Robin, Alain Celisse, Grégory Nuel:
Kerfdr: a semi-parametric kernel-based approach to local false discovery rate estimation. - Li-Yu Daisy Liu, Chien-Yu Chen, Mei-Ju May Chen, Ming-Shian Tsai, Cho-Han S. Lee, Tzu L. Phang, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Huang-Chun Lien, Shih-Ming Jung, Yi-Shing Lin, King-Jen Chang, Fon-Jou Hsieh:
Statistical identification of gene association by CID in application of constructing ER regulatory network. - Frank P. Y. Lin, Enrico W. Coiera, Ruiting Lan, Vitali Sintchenko:
In silico prioritisation of candidate genes for prokaryotic gene function discovery: an application of phylogenetic profiles. - Navdeep Jaitly, Anoop M. Mayampurath, Kyle Littlefield, Joshua N. Adkins, Gordon A. Anderson, Richard D. Smith:
Decon2LS: An open-source software package for automated processing and visualization of high resolution mass spectrometry data. - Qi Liu, Jinling Huang, Huiqing Liu, Ping Wan, Xiuzi Ye, Ying Xu:
Analyses of domains and domain fusions in human proto-oncogenes. - Michael Knoll, Thomas M. Hamm, Florian Wagner, Virginia Martinez, Jürgen Pleiss:
The PHA Depolymerase Engineering Database: A systematic analysis tool for the diverse family of polyhydroxyalkanoate (PHA) depolymerases. - Pekka Marttinen, Samuel Myllykangas, Jukka Corander:
Bayesian clustering and feature selection for cancer tissue samples. - Lars Snipen, Otto L. Nyquist, Margrete Solheim, Ågot Aakra, Ingolf F. Nes:
Improved analysis of bacterial CGH data beyond the log-ratio paradigm. - Alexander Kaever, Thomas Lingner, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Peter Meinicke:
MarVis: a tool for clustering and visualization of metabolic biomarkers. - Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdi Sadeghi, Abbas Nowzari-Dalini, Bahram Goliaei:
New scoring schema for finding motifs in DNA Sequences. - Nicholas A. Hamilton, Jack T. H. Wang, Markus C. Kerr, Rohan D. Teasdale:
Statistical and visual differentiation of subcellular imaging. - Jamie I. MacPherson, John W. Pinney, David L. Robertson:
JNets: Exploring networks by integrating annotation. - Stephen C. Billups, Margaret C. Neville, Michael Rudolph, Weston Porter, Pepper Schedin:
Identifying significant temporal variation in time course microarray data without replicates. - Norbert Busch, Gero Wedemann:
Modeling genomic data with type attributes, balancing stability and maintainability. - Annie Glatigny, Hervé Delacroix, Thomas Tang, Nicolas François, Lawrence Aggerbeck, Marie-Hélène Mucchielli-Giorgi:
Characterisation and correction of signal fluctuations in successive acquisitions of microarray images. - James Vlasblom, Shoshana J. Wodak:
Markov clustering versus affinity propagation for the partitioning of protein interaction graphs. - Jonas S. Almeida, Susana Vinga:
Biological sequences as pictures - a generic two dimensional solution for iterated maps. - Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li, Hualiang Jiang:
Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. - High-Seng Chai, Hugues Sicotte, Kent R. Bailey, Stephen T. Turner, Yan W. Asmann, Jean-Pierre A. Kocher:
GLOSSI: a method to assess the association of genetic loci-sets with complex diseases. - Arumay Pal, Ranjit Prasad Bahadur, Partha Sarathi Ray, Pinak Chakrabarti:
Accessibility and partner number of protein residues, their relationship and a webserver, ContPlot for their display. - Jorge Estrada, Pau Bernadó, Martin Blackledge, Javier Sancho:
ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble. - Firoz Ahmed, Hifzur Rahman Ansari, Gajendra P. S. Raghava:
Prediction of guide strand of microRNAs from its sequence and secondary structure. - Florian Hahne, Nolwenn LeMeur, Ryan Remy Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain, Robert Gentleman:
flowCore: a Bioconductor package for high throughput flow cytometry. - Adrian K. Arakaki, Ying Huang, Jeffrey Skolnick:
EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. - Manoj Hariharan, Vinod Scaria, Samir K. Brahmachari:
dbSMR: a novel resource of genome-wide SNPs affecting microRNA mediated regulation. - Sung-Bum Cho, Jihun Kim, Ju Han Kim:
Identifying set-wise differential co-expression in gene expression microarray data. - Jessica Cara Mar, Yasumasa Kimura, Kate Schroder, Katharine M. Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David A. Hume, John Quackenbush:
Data-driven normalization strategies for high-throughput quantitative RT-PCR. - Todd Riley, Xin Yu, Eduardo D. Sontag, Arnold Levine:
The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes. - Aleksandar Poleksic:
Island method for estimating the statistical significance of profile-profile alignment scores. - Costas P. Exarchos, Themis P. Exarchos, Costas Papaloukas, Anastassios N. Troganis, Dimitrios I. Fotiadis:
Detection of discriminative sequence patterns in the neighborhood of proline cis peptide bonds and their functional annotation. - Sheng-An Lee, Chen-hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao, Chi-Ying F. Huang:
POINeT: protein interactome with sub-network analysis and hub prioritization. - Zhipeng Cai, Hadi Sabaa, Yining Wang, Randy Goebel, Zhiquan Wang, Jiaofen Xu, Paul Stothard, Guohui Lin:
Most parsimonious haplotype allele sharing determination. - Christopher Previti, Oscar Harari, Igor Zwir, Coral del Val:
Profile analysis and prediction of tissue-specific CpG island methylation classes. - Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig, Dirk Walther:
Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins. - Michael J. Joss, Jeremy E. Koenig, Maurizio Labbate, Martin F. Polz, Michael R. Gillings, Harold W. Stokes, W. Ford Doolittle, Yan Boucher:
ACID: annotation of cassette and integron data. - Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar, Jieping Ye:
A bag-of-words approach for Drosophila gene expression pattern annotation. - Eric Tannier, Chunfang Zheng, David Sankoff:
Multichromosomal median and halving problems under different genomic distances. - Yoko Fukuda, Yasuo Nakahara, Hidetoshi Date, Yuji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, Shoji Tsuji:
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data. - Cunlu Zou, Jianfeng Feng:
Granger causality vs. dynamic Bayesian network inference: a comparative study. - Jinyu Wu, Xiang Xu, Jian Xiao, Long Xu, Huiguang Yi, Shengjie Gao, Jing Liu, Qiyu Bao, Fangqing Zhao, Xiaokun Li:
FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families. - Carlos Oscar Sánchez Sorzano, Cédric Messaoudi, Matthias Eibauer, Jose-Roman Bilbao-Castro, Reiner Hegerl, S. Nickell, Sergio Marco, José María Carazo:
Marker-free image registration of electron tomography tilt-series. - Daniel Schober, Barry Smith, Suzanna E. Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F. Taylor, Philippe Rocca-Serra, Susanna-Assunta Sansone:
Survey-based naming conventions for use in OBO Foundry ontology development. - Philippe Lemey, Martin Lott, Darren P. Martin, Vincent Moulton:
Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning. - Simone Scalabrin, Michele Morgante, Alberto Policriti:
Automated FingerPrint Background removal: FPB. - Taeyoung Hwang, Taesung Park:
Identification of differentially expressed subnetworks based on multivariate ANOVA. - Antonis Koussounadis, Oliver Redfern, David T. Jones:
Improving classification in protein structure databases using text mining. - Heping Zhang, Minghui Wang, Xiang Chen:
Willows: a memory efficient tree and forest construction package. - Hironori Fujisawa, Youko Horiuchi, Yoshiaki Harushima, Toyoyuki Takada, Shinto Eguchi, Takako Mochizuki, Takayuki Sakaguchi, Toshihiko Shiroishi, Nori Kurata:
SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip. - James Anderson, Antonis Papachristodoulou:
On validation and invalidation of biological models. - Hideya Kawaji, Yoshihide Hayashizaki, Carsten O. Daub:
SDRF2GRAPH - a visualization tool of a spreadsheet-based description of experimental processes. - Daniel Restrepo-Montoya, Carolina Vizcaíno, Luis F. Niño, Marisol Ocampo, Manuel-Elkin Patarroyo, Manuel A. Patarroyo:
Validating subcellular localization prediction tools with mycobacterial proteins. - Pufeng Du, Liyan Jia, Yanda Li:
CURE-Chloroplast: A chloroplast C-to-U RNA editing predictor for seed plants. - Eric Jain, Amos Bairoch, Severine Duvaud, Isabelle Phan, Nicole Redaschi, Baris E. Suzek, Maria Jesus Martin, Peter B. McGarvey, Elisabeth Gasteiger:
Infrastructure for the life sciences: design and implementation of the UniProt website. - Armando J. Pinho, Paulo Jorge S. G. Ferreira, Sara P. Garcia, João M. O. S. Rodrigues:
On finding minimal absent words. - Mario Huerta, Juan Cedano, Dario Peña, Antonio Rodriguez, Enrique Querol:
PCOPGene-Net: Holistic Characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships. - Sebastian Schönherr, Hansi Weißensteiner, Stefan Coassin, Günther Specht, Florian Kronenberg, Anita Brandstätter:
eCOMPAGT - efficient Combination and Management of Phenotypes and Genotypes for Genetic Epidemiology. - Chih-Lung Ko, Eberhard O. Voit, Feng-Sheng Wang:
Estimating parameters for generalized mass action models with connectivity information. - Claus A. Andersen, Stefano Gotta, Letizia Magnoni, Roberto Raggiaschi, Andreas Kremer, Georg C. Terstappen:
Robust MS quantification method for phospho-peptides using 18O/16O labeling. - Gaurav Pandey, Chad L. Myers, Vipin Kumar:
Incorporating functional inter-relationships into protein function prediction algorithms. - Robert Kofler, Tatiana Teixeira Torres, Tamas Lelley, Christian Schlötterer:
PanGEA: Identification of allele specific gene expression using the 454 technology. - Niclas Chiang Tan, Wayne G. Fisher, Kevin P. Rosenblatt, Harold R. Garner:
Application of multiple statistical tests to enhance mass spectrometry-based biomarker discovery. - Kenneth Lo, Florian Hahne, Ryan Remy Brinkman, Raphael Gottardo:
flowClust: a Bioconductor package for automated gating of flow cytometry data. - Tianqing Liu, Nan Lin, Ningzhong Shi, Baoxue Zhang:
Information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. - Seon-Young Kim:
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature. - Szymon Kaczanowski, Pawel Siedlecki, Piotr Zielenkiewicz:
The High Throughput Sequence Annotation Service (HT-SAS) - the shortcut from sequence to true Medline words. - Thorsteinn S. Rögnvaldsson, Terence A. Etchells, Liwen You, Daniel Garwicz, Ian H. Jarman, Paulo J. G. Lisboa:
How to find simple and accurate rules for viral protease cleavage specificities. - Nazar Zaki, Sanja Lazarova-Molnar, Wassim El-Hajj, Piers Campbell:
Protein-protein interaction based on pairwise similarity. - Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont, Michael Primig:
MIMAS 3.0 is a Multiomics Information Management and Annotation System. - Alexandre P. Francisco, Miguel M. F. Bugalho, Mário Ramirez, João A. Carriço:
Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach. - Alex D. Stivala, Anthony Wirth, Peter J. Stuckey:
Tableau-based protein substructure search using quadratic programming. - Jochen Blom, Stefan P. Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski, Alexander Goesmann:
EDGAR: A software framework for the comparative analysis of prokaryotic genomes. - Iftach Nachman, Aviv Regev:
BRNI: Modular analysis of transcriptional regulatory programs. - Mark D. Robinson, Terence P. Speed:
Differential splicing using whole-transcript microarrays. - Yu-Shen Liu, Yi Fang, Karthik Ramani:
IDSS: deformation invariant signatures for molecular shape comparison. - Jaume Mercadé, Antonio Espinosa, José-Enrique Adsuara, Rosa Adrados, Jordi Segura, Tamara Maes:
Orymold: ontology based gene expression data integration and analysis tool applied to rice. - Timothy Nugent, David T. Jones:
Transmembrane protein topology prediction using support vector machines. - Tzong-Yuan Wu, Chi-Chun Hsieh, Jun-Jie Hong, Chung-Yung Chen, Yuh-Show Tsai:
IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico. - Weijun Luo, Michael S. Friedman, Kerby Shedden, Kurt D. Hankenson, Peter J. Woolf:
GAGE: generally applicable gene set enrichment for pathway analysis. - Gordon W. Slysz, Charles A. H. Baker, Benjamin M. Bozsa, Anthony Dang, Andrew J. Percy, Melissa Bennett, David C. Schriemer:
Hydra: software for tailored processing of H/D exchange data from MS or tandem MS analyses. - Sanghamitra Bandyopadhyay, Malay Bhattacharyya:
Analyzing miRNA co-expression networks to explore TF-miRNA regulation. - Sin-Ho Jung, Insuk Sohn, Stephen L. George, Liping Feng, Phyllis C. Leppert:
Sample size calculation for microarray experiments with blocked one-way design. - Xiaofeng Dai, Timo Erkkilä, Olli Yli-Harja, Harri Lähdesmäki:
A joint finite mixture model for clustering genes from independent Gaussian and beta distributed data. - Kosuke M. Teshima, Hideki Innan:
mbs: modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection. - Haruo Suzuki, Rintaro Saito, Masaru Tomita:
Measure of synonymous codon usage diversity among genes in bacteria. - Vincent Le Guilloux, Peter Schmidtke, Pierre Tufféry:
Fpocket: An open source platform for ligand pocket detection. - Min Wu, Xiaoli Li, Chee Keong Kwoh, See-Kiong Ng:
A core-attachment based method to detect protein complexes in PPI networks. - Daniel Guariz Pinheiro, Pedro A. F. Galante, Sandro J. de Souza, Marco A. Zago, Wilson A. Silva Jr.:
A score system for quality evaluation of RNA sequence tags: an improvement for gene expression profiling. - Steven W. Culman, Robert Bukowski, Hugh G. Gauch, Hinsby Cadillo-Quiroz, Daniel H. Buckley:
T-REX: software for the processing and analysis of T-RFLP data. - Juan R. González, Isaac Subirana, Geòrgia Escaramís, Solymar Peraza, Alejandro Cáceres, Xavier Estivill, Lluís Armengol:
Accounting for uncertainty when assessing association between copy number and disease: a latent class model. - Wei Sun, Michael J. Buck, Mukund Patel, Ian J. Davis:
Improved ChIP-chip analysis by a mixture model approach. - Olga V. Kalinina, Mikhail S. Gelfand, Robert B. Russell:
Combining specificity determining and conserved residues improves functional site prediction. - Nils Homer, Barry Merriman, Stanley F. Nelson:
Local alignment of two-base encoded DNA sequence. - Ursula K. Frei, Bernd Wollenweber, Thomas Lübberstedt:
"PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation. - Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M. Greene, Nicole T. Perna, Jeremy D. Glasner, Guy Plunkett III, Matthew Shaker, David Pot:
Text-mining of PubMed abstracts by natural language processing to create a public knowledge base on molecular mechanisms of bacterial enteropathogens. - José-Jesús Fernández:
TOMOBFLOW: feature-preserving noise filtering for electron tomography. - Lau Sennels, Jimi-Carlo Bukowski-Wills, Juri Rappsilber:
Improved results in proteomics by use of local and peptide-class specific false discovery rates. - Helen I. Field, Serena A. Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M. Dunning, Douglas F. Easton, Paul D. P. Pharoah:
Seq4SNPs: new software for retrieval of multiple, accurately annotated DNA sequences, ready formatted for SNP assay design. - Steffen Klamt, Axel von Kamp:
Computing paths and cycles in biological interaction graphs. - Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani, Manuela Helmer-Citterich:
Structural motifs recurring in different folds recognize the same ligand fragments. - Karin Verspoor, K. Bretonnel Cohen, Lawrence Hunter:
The textual characteristics of traditional and Open Access scientific journals are similar. - Yu Qian, Olga Tchuvatkina, Josef Spidlen, Peter Wilkinson, Maura Gasparetto, Andrew R. Jones, Frank J. Manion, Richard H. Scheuermann, Rafick-Pierre Sekaly, Ryan Remy Brinkman:
FuGEFlow: data model and markup language for flow cytometry. - Michael H. T. Li, Peter M. U. Ung, James Zajkowski, Sylvie Garneau-Tsodikova, David H. Sherman:
Automated genome mining for natural products. - Daniela Eggle, Svenja Debey-Pascher, Marc Beyer, Joachim L. Schultze:
The development of a comparison approach for Illumina bead chips unravels unexpected challenges applying newest generation microarrays. - Daniel Glez-Peña, Fernando Díaz, Jesús M. Hernández, Juan M. Corchado, Florentino Fdez-Riverola:
geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research. - Yang Li, Morris A. Swertz, Gonzalo Vera, Jingyuan Fu, Rainer Breitling, Ritsert C. Jansen:
designGG: an R-package and web tool for the optimal design of genetical genomics experiments. - Rose Du, Kelan Tantisira, Vincent J. Carey, Soumyaroop Bhattacharya, Stephanie Metje, Alvin T. Kho, Barbara J. Klanderman, Roger Gaedigk, Ross Lazarus, Thomas J. Mariani, J. Steven Leeder, Scott T. Weiss:
Platform dependence of inference on gene-wise and gene-set involvement in human lung development. - Tingzhe Sun, Chun Chen, Yuanyuan Wu, Shuai Zhang, Jun Cui, Pingping Shen:
Modeling the role of p53 pulses in DNA damage- induced cell death decision. - Brian E. Howard, Beate Sick, Steffen Heber:
Unsupervised assessment of microarray data quality using a Gaussian mixture model. - Man-Ping Ng, Ismael A. Vergara, Christian Frech, Qingkang Chen, Xinghuo Zeng, Jian Pei, Nansheng Chen:
OrthoClusterDB: an online platform for synteny blocks. - David Tritchler, Elena Parkhomenko, Joseph Beyene:
Filtering Genes for Cluster and Network Analysis. - Otávio J. B. Brustolini, Luciano G. Fietto, Cosme D. Cruz, Flávia M. L. Passos:
Computational analysis of the interaction between transcription factors and the predicted secreted proteome of the yeast Kluyveromyces lactis. - Ian Walsh, Alberto J. M. Martin, Catherine Mooney, Enrico Rubagotti, Alessandro Vullo, Gianluca Pollastri:
Ab initio and homology based prediction of protein domains by recursive neural networks. - Bill Andreopoulos, Christof Winter, Dirk Labudde, Michael Schroeder:
Triangle network motifs predict complexes by complementing high-error interactomes with structural information. - Ron Alterovitz, Aaron Arvey, Sriram Sankararaman, Carolina Dallett, Yoav Freund, Kimmen Sjölander:
ResBoost: characterizing and predicting catalytic residues in enzymes. - Shane T. Jensen, Sameer Soi, Li-San Wang:
A Bayesian approach to efficient differential allocation for resampling-based significance testing. - Tomás Hirmajer, Eva Balsa-Canto, Julio R. Banga:
DOTcvpSB, a software toolbox for dynamic optimization in systems biology. - Ming Yi, Uma Mudunuri, Anney Che, Robert M. Stephens:
Seeking unique and common biological themes in multiple gene lists or datasets: pathway pattern extraction pipeline for pathway-level comparative analysis. - Andrea Bisognin, Alessandro Coppe, Francesco Ferrari, Davide Risso, Chiara Romualdi, Silvio Bicciato, Stefania Bortoluzzi:
A-MADMAN: Annotation-based microarray data meta-analysis tool. - Alex N. Nguyen Ba, Anastassia Pogoutse, Nicholas Provart, Alan M. Moses:
NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction. - Renée X. de Menezes, Marten Boetzer, Melle Sieswerda, Gert-Jan B. van Ommen, Judith M. Boer:
Integrated analysis of DNA copy number and gene expression microarray data using gene sets. - Ho-Ryun Chung, Martin Vingron:
Comparison of sequence-dependent tiling array normalization approaches. - Tsutomu Matsunaga, Chikara Yonemori, Etsuji Tomita, Masaaki Muramatsu:
Clique-based data mining for related genes in a biomedical database. - Jia Zeng, Reda Alhajj, Douglas J. Demetrick:
Representative transcript sets for evaluating a translational initiation sites predictor. - Saikat Chakrabarti, Anna R. Panchenko:
Ensemble approach to predict specificity determinants: benchmarking and validation. - Amar Drawid, Nupur Gupta, Vijayalakshmi H. Nagaraj, Céline Gélinas, Anirvan M. Sengupta:
OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. - Antonio Carvajal-Rodríguez, Jacobo de Uña-Álvarez, Emilio Rolán-Alvarez:
A new multitest correction (SGoF) that increases its statistical power when increasing the number of tests. - Changhoon Kim, Chin-Hsien Tai, Byungkook Lee:
Iterative refinement of structure-based sequence alignments by Seed Extension. - Richard D. Pearson, Xuejun Liu, Guido Sanguinetti, Marta Milo, Neil D. Lawrence, Magnus Rattray:
puma: a Bioconductor package for propagating uncertainty in microarray analysis. - Lee Aaron Newberg:
Error statistics of hidden Markov model and hidden Boltzmann model results. - Bjoern H. Menze, B. Michael Kelm, Ralf Masuch, Uwe Himmelreich, Peter Bachert, Wolfgang Petrich, Fred A. Hamprecht:
A comparison of random forest and its Gini importance with standard chemometric methods for the feature selection and classification of spectral data. - Jérôme Hennetin, Petri Pehkonen, Michel Bellis:
Construction and use of gene expression covariation matrix. - Sivakumar Gowrisankar, Anil G. Jegga:
Regression based predictor for p53 transactivation. - Lusheng Wang, Zhanyong Wang, Wanling Yang:
Linked region detection using high-density SNP genotype data via the minimum recombinant model of pedigree haplotype inference. - Serdar Bozdag, Timothy J. Close, Stefano Lonardi:
A compartmentalized approach to the assembly of physical maps. - John E. Reid, Sascha Ott, Lorenz Wernisch:
Transcriptional programs: Modelling higher order structure in transcriptional control. - Fabian Schreiber, Kerstin Pick, Dirk Erpenbeck, Gert Wörheide, Burkhard Morgenstern:
OrthoSelect: a protocol for selecting orthologous groups in phylogenomics. - Alexander C. J. Roth, Gaston H. Gonnet, Christophe Dessimoz:
Algorithm of OMA for large-scale orthology inference. - Jan Aerts, Andy Law:
An introduction to scripting in Ruby for biologists. - James R. Green, Michael J. Korenberg, Mohammed O. Aboul-Magd:
PCI-SS: MISO dynamic nonlinear protein secondary structure prediction. - Yanpeng Li, Hongfei Lin, Zhihao Yang:
Incorporating rich background knowledge for gene named entity classification and recognition. - Fernando García-Alcalde, Francisco-Javier Lopez, Carlos Cano, Armando Blanco:
FISim: A new similarity measure between transcription factor binding sites based on the fuzzy integral. - Wei Zhao, Kirk E. Hevener, Stephen W. White, Richard E. Lee, James M. Boyett:
A statistical framework to evaluate virtual screening. - Daniel Jameson, David A. Turner, John Ankers, Stephnie Kennedy, Sheila Ryan, Neil Swainston, Tony Griffiths, David G. Spiller, Stephen G. Oliver, Michael R. H. White, Douglas B. Kell, Norman W. Paton:
Information management for high content live cell imaging. - John Draper, David P. Enot, David Parker, Manfred Beckmann, Stuart Snowdon, Wanchang Lin, Hassan Zubair:
Metabolite signal identification in accurate mass metabolomics data with MZedDB, an interactive m/z annotation tool utilising predicted ionisation behaviour 'rules'. - Kimberly Van Auken, Joshua Jaffery, Juancarlos Chan, Hans-Michael Müller, Paul W. Sternberg:
Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. - Bernhard Thielen, Stephanie Heinen, Dietmar Schomburg:
mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics. - Francisco Fernandes, Luísa Pereira, Ana T. Freitas:
CSA: An efficient algorithm to improve circular DNA multiple alignment. - Daniel Faria, António E. N. Ferreira, André O. Falcão:
Enzyme classification with peptide programs: a comparative study. - Yuanxin Xi, Wei Li:
BSMAP: whole genome bisulfite sequence MAPping program. - Renata Kabiljo, Andrew B. Clegg, Adrian J. Shepherd:
A realistic assessment of methods for extracting gene/protein interactions from free text. - Johannes M. Freudenberg, Vineet K. Joshi, Zhen Hu, Mario Medvedovic:
CLEAN: CLustering Enrichment ANalysis. - Christian Schwager, Amir Abdollahi, Ute Wirkner, Peter Huber:
TableButler - A tool for combining, handling and processing of huge data tables. - Shu-Dong Zhang, Timothy W. Gant:
sscMap: An extensible Java application for connecting small-molecule drugs using gene-expression signatures. - Yiyuan She, Earl Hubbell, Hui Wang:
Resolving deconvolution ambiguity in gene alternative splicing. - Feng Qi, Ranjan K. Dash, Yu Han, Daniel A. Beard:
Generating rate equations for complex enzyme systems by a computer-assisted systematic method. - Roberto T. Arrial, Roberto C. Togawa, Marcelo M. Brigido:
Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. - Tao Xu, Jianlei Gu, Yan Zhou, LinFang Du:
Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology. - Kevin Y. Yip, Philip M. Kim, Drew McDermott, Mark Gerstein:
Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels. - Richard S. Savage, Katherine A. Heller, Yang Xu, Zoubin Ghahramani, William M. Truman, Murray Grant, Katherine J. Denby, David L. Wild:
R/BHC: fast Bayesian hierarchical clustering for microarray data. - Chris Thachuk, Jose Crossa, Jorge Franco, Susanne Dreisigacker, Marilyn Warburton, Guy F. Davenport:
Core Hunter: an algorithm for sampling genetic resources based on multiple genetic measures. - Jason W. H. Wong, Alexander B. Schwahn, Kevin M. Downard:
ETISEQ - an algorithm for automated elution time ion sequencing of concurrently fragmented peptides for mass spectrometry-based proteomics. - Flavien Quintus, Olivier Sperandio, Julien Grynberg, Michel Petitjean, Pierre Tufféry:
Ligand scaffold hopping combining 3D maximal substructure search and molecular similarity. - Katrijn Van Deun, Age K. Smilde, Mariët J. van der Werf, Henk A. L. Kiers, Iven Van Mechelen:
A structured overview of simultaneous component based data integration. - Bjarne Knudsen, Michael M. Miyamoto:
Accurate and fast methods to estimate the population mutation rate from error prone sequences. - David J. Jeffries, Neil Abernethy, Bouke C. de Jong:
Supervised learning for the automated transcription of spacer classification from spoligotype films. - Wenjie Shu, Ming Ni, Xiaochen Bo, Zhiqiang Zheng, Shengqi Wang:
EvoRSR: an integrated system for exploring evolution of RNA structural robustness. - Michael Hartung, Toralf Kirsten, Anika Groß, Erhard Rahm:
OnEX: Exploring changes in life science ontologies. - Igor A. Sidorov, Denis A. Reshetov, Alexander E. Gorbalenya:
SNAD: Sequence Name Annotation-based Designer. - Trevor Paterson, Andy Law:
An XML transfer schema for exchange of genomic and genetic mapping data: implementation as a web service in a Taverna workflow. - Dejan Stokic, Rudolf Hanel, Stefan Thurner:
A fast and efficient gene-network reconstruction method from multiple over-expression experiments. - Christopher W. Maier, Jeffrey G. Long, Bradley M. Hemminger, Morgan C. Giddings:
Ultra-Structure database design methodology for managing systems biology data and analyses. - Alain B. Tchagang, Kevin V. Bui, Thomas McGinnis, Panayiotis V. Benos:
Extracting biologically significant patterns from short time series gene expression data. - Xue Lin, Bahman Afsari, Luigi Marchionni, Leslie Cope, Giovanni Parmigiani, Daniel Q. Naiman, Donald Geman:
The ordering of expression among a few genes can provide simple cancer biomarkers and signal BRCA1 mutations. - Tao Xu, Lujia Zhang, Xuedong Wang, Dongzhi Wei, Tianbi Li:
Structure-based substrate screening for an enzyme. - Christian Fufezan, Michael Specht:
p3d - Python module for structural bioinformatics. 258 - Wei Guan, Manshui Zhou, Christina Y. Hampton, Benedict B. Benigno, L. DeEtte Walker, Alexander G. Gray, John F. McDonald, Facundo M. Fernández:
Ovarian cancer detection from metabolomic liquid chromatography/mass spectrometry data by support vector machines. 259 - Eun-Youn Kim, Seon-Young Kim, Daniel A. Ashlock, Dougu Nam:
MULTI-K: accurate classification of microarray subtypes using ensemble k-means clustering. 260 - Derek Gordon, Andrew R. Zinn:
Computing power of quantitative trait locus association mapping for haploid loci. 261 - Michael Hecker, Robert Hermann Goertsches, Robby Engelmann, Hans-Jürgen Thiesen, Reinhard Guthke:
Integrative modeling of transcriptional regulation in response to antirheumatic therapy. 262 - Nobuyoshi Sugaya, Kazuyoshi Ikeda:
Assessing the druggability of protein-protein interactions by a supervised machine-learning method. 263 - Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li:
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. 264 - Gregor Rot, Anup Parikh, Tomaz Curk, Adam Kuspa, Gad Shaulsky, Blaz Zupan:
dictyExpress: a Dictyostelium discoideum gene expression database with an explorative data analysis web-based interface. 265 - Gregg A. Helt, John W. Nicol, Ed Erwin, Eric Blossom, Steven G. Blanchard Jr., Stephen A. Chervitz, Cyrus L. Harmon, Ann E. Loraine:
Genoviz Software Development Kit: Java tool kit for building genomics visualization applications. 266 - Yiming Ying, Kaizhu Huang, Colin Campbell:
Enhanced protein fold recognition through a novel data integration approach. 267 - Stephan Pabinger, Gerhard G. Thallinger, René Snajder, Heiko Eichhorn, Robert Rader, Zlatko Trajanoski:
QPCR: Application for real-time PCR data management and analysis. 268 - Ali Katanforoush, Mehdi Sadeghi, Hamid Pezeshk, Elahe Elahi:
Global haplotype partitioning for maximal associated SNP pairs. 269 - Mônica G. Campiteli, Frederico M. Soriani, Iran Malavazi, Osame Kinouchi, Carlos A. de B. Pereira, Gustavo H. Goldman:
A reliable measure of similarity based on dependency for short time series: an application to gene expression networks. 270 - Ronna R. Mallios, David M. Ojcius, David H. Ardell:
An iterative strategy combining biophysical criteria and duration hidden Markov models for structural predictions of Chlamydia trachomatis sigma66 promoters. 271 - Chuen Seng Tan, Agus Salim, Alexander Ploner, Janne Lehtiö, Kee Seng Chia, Yudi Pawitan:
Correlating gene and protein expression data using Correlated Factor Analysis. 272 - Riccardo Percudani, Alessio Peracchi:
The B6 database: a tool for the description and classification of vitamin B6-dependent enzymatic activities and of the corresponding protein families. 273 - Torsten Blum, Sebastian Briesemeister, Oliver Kohlbacher:
MultiLoc2: integrating phylogeny and Gene Ontology terms improves subcellular protein localization prediction. 274 - Luca Abatangelo, Rosalia Maglietta, Angela Distaso, Annarita D'Addabbo, Teresa Maria Creanza, Sayan Mukherjee, Nicola Ancona:
Comparative study of gene set enrichment methods. 275 - Joachim Giard, Jérôme Ambroise, Jean-Luc Gala, Benoît Macq:
Regression applied to protein binding site prediction and comparison with classification. 276 - Wenhui Wang, Juan Nunez-Iglesias, Yihui Luan, Fengzhu Sun:
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. 277 - Angelo Nuzzo, Alberto Riva:
Genephony: a knowledge management tool for genome-wide research. 278 - Johannes Wagener, Ola Spjuth, Egon L. Willighagen, Jarl E. S. Wikberg:
XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services. 279 - Aaron L. Vollrath, Adam A. Smith, Mark Craven, Christopher A. Bradfield:
EDGE3: A web-based solution for management and analysis of Agilent two color microarray experiments. 280 - Guy Tsafnat, Enrico W. Coiera, Sally R. Partridge, Jaron Schaeffer, Jonathan R. Iredell:
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. 281 - Matteo Re, Graziano Pesole, David Stephen Horner:
Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics. 282 - Kathy Macropol, Tolga Can, Ambuj K. Singh:
RRW: repeated random walks on genome-scale protein networks for local cluster discovery. 283 - Virginie Lopez Rascol, Anthony Levasseur, Olivier Chabrol, Simona Grusea, Philippe Gouret, Etienne G. J. Danchin, Pierre Pontarotti:
CASSIOPE: An expert system for conserved regions searches. 284 - Fabrício Martins Lopes, David Correa Martins Jr., Roberto Marcondes Cesar Junior:
Feature selection environment for genomic applications. 285 - Chao Li, Yuhua Li, Xiangmin Zhang, Phillip Stafford, Valentin Dinu:
ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites. 286 - Nimrod D. Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko:
Epitopia: a web-server for predicting B-cell epitopes. 287 - Theresa Scharl, Ingo Voglhuber, Friedrich Leisch:
Exploratory and inferential analysis of gene cluster neighborhood graphs. 288 - Claus Desler, Prashanth Suravajhala, May Sanderhoff, Merete Rasmussen, Lene Juel Rasmussen:
In Silico screening for functional candidates amongst hypothetical proteins. 289 - Marcio Luis Acencio, Ney Lemke:
Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information. 290 - Jonathan R. Manning, Ann Hedley, John J. Mullins, Donald R. Dunbar:
Automated seeding of specialised wiki knowledgebases with BioKb. 291 - Robert A. Rubin:
A first principles approach to differential expression in microarray data analysis. 292 - Adam M. Phillippy, Xiangyu Deng, Wei Zhang, Steven L. Salzberg:
Efficient oligonucleotide probe selection for pan-genomic tiling arrays. 293 - Waranyu Wongseree, Anunchai Assawamakin, Theera Piroonratana, Saravudh Sinsomros, Chanin Limwongse, Nachol Chaiyaratana:
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses. 294 - Manolis Maragkakis, Panagiotis Alexiou, Giorgos L. Papadopoulos, Martin Reczko, Theodore Dalamagas, Giorgos Giannopoulos, George I. Goumas, Evangelos Koukis, Kornilios Kourtis, Victor A. Simossis, Praveen Sethupathy, Thanasis Vergoulis, Nectarios Koziris, Timos K. Sellis, Panayotis Tsanakas, Artemis G. Hatzigeorgiou:
Accurate microRNA target prediction correlates with protein repression levels. 295 - Morten Nielsen, Ole Lund:
NN-align. An artificial neural network-based alignment algorithm for MHC class II peptide binding prediction. 296 - Konstantin Voevodski, Shang-Hua Teng, Yu Xia:
Finding local communities in protein networks. 297 - Philippe Gouret, Julie Dawn Thompson, Pierre Pontarotti:
PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. 298 - Christiana Spyrou, Rory Stark, Andy G. Lynch, Simon Tavaré:
BayesPeak: Bayesian analysis of ChIP-seq data. 299 - Phillip D. Yates, Mark A. Reimers:
RCMAT: a regularized covariance matrix approach to testing gene sets. 300 - Scott Bringans, James K. Hane, Tammy Casey, Kar-Chun Tan, Richard Lipscombe, Peter S. Solomon, Richard P. Oliver:
Deep proteogenomics; high throughput gene validation by multidimensional liquid chromatography and mass spectrometry of proteins from the fungal wheat pathogen Stagonospora nodorum. 301 - Shide Liang, Dandan Zheng, Chi Zhang, Martin Zacharias:
Prediction of antigenic epitopes on protein surfaces by consensus scoring. 302 - Anna Korhonen, Ilona Silins, Lin Sun, Ulla Stenius:
The first step in the development of text mining technology for cancer risk assessment: identifying and organizing scientific evidence in risk assessment literature. 303 - Ahmet Sacan, Nilgun Ferhatosmanoglu, Hakan Ferhatosmanoglu:
MicroarrayDesigner: an online search tool and repository for near-optimal microarray experimental designs. 304 - Simon R. V. Knott, Christopher J. Viggiani, Oscar M. Aparicio, Simon Tavaré:
Strategies for analyzing highly enriched IP-chip datasets. 305 - Jesse A. Gillis, Paul Pavlidis:
A methodology for the analysis of differential coexpression across the human lifespan. 306 - Petri Törönen, Pauli J. Ojala, Pekka Marttinen, Liisa Holm:
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. 307 - Oscar M. Rueda, Ramón Díaz-Uriarte:
Detection of recurrent copy number alterations in the genome: taking among-subject heterogeneity seriously. 308 - Damian Gessler, Gary S. Schiltz, Gregory D. May, Shulamit Avraham, Christopher D. Town, David M. Grant, Rex T. Nelson:
SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services. 309 - Peter Tiño:
Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays. 310 - Tara McIntosh, James R. Curran:
Challenges for automatically extracting molecular interactions from full-text articles. 311 - Andrew J. Bordner:
Predicting protein-protein binding sites in membrane proteins. 312 - Benjamin M. Good, Joseph T. Tennis, Mark D. Wilkinson:
Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics. 313 - Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. L. Sonnhammer:
MetaTM - a consensus method for transmembrane protein topology prediction. 314 - Sandra Waaijenborg, Aeilko H. Zwinderman:
Sparse canonical correlation analysis for identifying, connecting and completing gene-expression networks. 315 - Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff, Joshua S. Weitz:
Unsupervised statistical clustering of environmental shotgun sequences. 316 - Timo Duchrow, Timur Shtatland, Daniel Guettler, Misha Pivovarov, Stefan Kramer, Ralph Weissleder:
Enhancing navigation in biomedical databases by community voting and database-driven text classification. 317 - Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz Saberi Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber, Ali Masoudi-Nejad:
Kavosh: a new algorithm for finding network motifs. 318 - Petri Törönen, Petri Pehkonen, Liisa Holm:
Generation of Gene Ontology benchmark datasets with various types of positive signal. 319 - Guillermo de la Calle, Miguel García-Remesal, Stefano Chiesa, Diana de la Iglesia, Victor Maojo:
BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature. 320 - Tak-Ming Chan, Gang Li, Kwong-Sak Leung, Kin-Hong Lee:
Discovering multiple realistic TFBS motifs based on a generalized model. 321 - Holger Fröhlich, Özgür Sahin, Dorit Arlt, Christian Bender, Tim Beißbarth:
Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions. 322 - Witold Dyrka, Jean-Christophe Nebel:
A stochastic context free grammar based framework for analysis of protein sequences. 323 - Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis, Fragiskos N. Kolisis:
KEGGconverter: a tool for the in-silico modelling of metabolic networks of the KEGG Pathways database. 324 - Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, A. Krishnamachari, Supratim Sengupta:
Riboswitch Detection Using Profile Hidden Markov Models. 325 - Thomas C. Wiegers, Allan Peter Davis, K. Bretonnel Cohen, Lynette Hirschman, Carolyn J. Mattingly:
Text mining and manual curation of chemical-gene-disease networks for the Comparative Toxicogenomics Database (CTD). 326 - Steffen Brasch, Lars Linsen, Georg Fuellen:
VANLO - Interactive visual exploration of aligned biological networks. 327 - Wei-Chi Wang, Feng-Mao Lin, Wen-Chi Chang, Kuan-Yu Lin, Hsien-Da Huang, Na-Sheng Lin:
miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression. 328 - Van Hoa Nguyen, Dominique Lavenier:
PLAST: parallel local alignment search tool for database comparison. 329 - Johan Vallon-Christersson, Nicklas Nordborg, Martin Svensson, Jari Häkkinen:
BASE - 2nd generation software for microarray data management and analysis. 330 - Frank M. You, Naxin Huo, Yong Qiang Gu, Gerard R. Lazo, Jan Dvorak, Olin D. Anderson:
ConservedPrimers 2.0: A high-throughput pipeline for comparative genome referenced intron-flanking PCR primer design and its application in wheat SNP discovery. 331 - Daniel Jupiter, Hailin Chen, Vincent VanBuren:
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. 332 - Sinan Erten, Xin Li, Gürkan Bebek, Jing Li, Mehmet Koyutürk:
Phylogenetic analysis of modularity in protein interaction networks. 333 - Javier Ríos, Tor Johan Mikael Karlsson, Oswaldo Trelles:
Magallanes: a web services discovery and automatic workflow composition tool. 334 - Pavle Goldstein, Jurica Zucko, Dusica Vujaklija, Anita Krisko, Daslav Hranueli, Paul F. Long, Catherine Etchebest, Bojan Basrak, John Cullum:
Clustering of protein domains for functional and evolutionary studies. 335 - Insuk Sohn, Kouros Owzar, Stephen L. George, Sujong Kim, Sin-Ho Jung:
A permutation-based multiple testing method for time-course microarray experiments. 336 - Malik Yousef, Mohamed Ketany, Larry M. Manevitz, Louise C. Showe, Michael K. Showe:
Classification and biomarker identification using gene network modules and support vector machines. 337 - Glennie Helles, Rasmus Fonseca:
Predicting dihedral angle probability distributions for protein coil residues from primary sequence using neural networks. 338 - Andrija Tomovic, Michael B. Stadler, Edward J. Oakeley:
Transcription factor site dependencies in human, mouse and rat genomes. 339 - Robert A. van den Berg, Iven Van Mechelen, Tom F. Wilderjans, Katrijn Van Deun, Henk A. L. Kiers, Age K. Smilde:
Integrating functional genomics data using maximum likelihood based simultaneous component analysis. 340 - Stefan Maetschke, Zheng Yuan:
Exploiting structural and topological information to improve prediction of RNA-protein binding sites. 341 - John Schwacke, Elizabeth G. Hill, Edward L. Krug, Susana Comte-Walters, Kevin L. Schey:
iQuantitator: A tool for protein expression inference using iTRAQ. 342 - Michal Komorowski, Bärbel Finkenstädt, Claire V. Harper, David A. Rand:
Bayesian inference of biochemical kinetic parameters using the linear noise approximation. 343 - Marvin Schulz, Barbara M. Bakker, Edda Klipp:
TIde: a software for the systematic scanning of drug targets in kinetic network models. 344 - Junbai Wang, Morigen:
BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors. 345 - Linyong Mao, John L. Van Hemert, Sudhansu Dash, Julie A. Dickerson:
Arabidopsis gene co-expression network and its functional modules. 346 - Hui-Hsien Chou, Arunee Trisiriroj, Sunyoung Park, Yue-Ie C. Hsing, Pamela C. Ronald, Patrick S. Schnable:
Direct calibration of PICKY-designed microarrays. 347 - Arye Harel, Aron Inger, Gil Stelzer, Liora Strichman-Almashanu, Irina Dalah, Marilyn Safran, Doron Lancet:
GIFtS: annotation landscape analysis with GeneCards. 348 - Paul Thompson, Syed A. Iqbal, John McNaught, Sophia Ananiadou:
Construction of an annotated corpus to support biomedical information extraction. 349 - Jing Su, Pedro J. Zapata, Chien-Chiang Chen, J. Carson Meredith:
Local cell metrics: a novel method for analysis of cell-cell interactions. 350 - Allegra Via, Cathryn M. Gould, Christine Gemünd, Toby J. Gibson, Manuela Helmer-Citterich:
A structure filter for the Eukaryotic Linear Motif Resource. 351 - Mingqi Wu, Faming Liang, Yanan Tian:
Bayesian modeling of ChIP-chip data using latent variables. 352 - Yury Goltsev, Dmitri A. Papatsenko:
Time warping of evolutionary distant temporal gene expression data based on noise suppression. 353 - Aristotelis Chatziioannou, Panagiotis Moulos, Fragiskos N. Kolisis:
Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB. 354 - Shiri Freilich, Leon Goldovsky, Assaf Gottlieb, Eric Blanc, Sophia Tsoka, Christos A. Ouzounis:
Stratification of co-evolving genomic groups using ranked phylogenetic profiles. 355 - Mira V. Han, Christian M. Zmasek:
phyloXML: XML for evolutionary biology and comparative genomics. 356 - Surendra Kumar, Åsmund Skjæveland, Russell J. S. Orr, Pål Enger, Torgeir Ruden, Bjørn-Helge Mevik, Fabien Burki, Andreas Botnen, Kamran Shalchian-Tabrizi:
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. 357 - Enrico Glaab, Jonathan M. Garibaldi, Natalio Krasnogor:
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. 358 - Weizhong Li:
Analysis and comparison of very large metagenomes with fast clustering and functional annotation. 359 - Naoki Hasegawa, Wataru Sugiura, Junko Shibata, Masakazu Matsuda, Fengrong Ren, Hiroshi Tanaka:
Inferring within-patient HIV-1 evolutionary dynamics under anti-HIV therapy using serial virus samples with vSPA. 360 - Zheng Rong Yang:
Predicting sulfotyrosine sites using the random forest algorithm with significantly improved prediction accuracy. 361 - Daniel N. Frank:
BARCRAWL and BARTAB: software tools for the design and implementation of barcoded primers for highly multiplexed DNA sequencing. 362 - Jose L. Izquierdo-García, Ignacio Rodríguez, Angelos Kyriazis, Palmira Villa, Pilar Barreiro, Manuel Desco, Jesús Ruiz-Cabello:
A novel R-package graphic user interface for the analysis of metabonomic profiles. 363 - Jignesh R. Parikh, Manor Askenazi, Scott B. Ficarro, Tanya Cashorali, James T. Webber, Nathaniel C. Blank, Yi Zhang, Jarrod A. Marto:
multiplierz: an extensible API based desktop environment for proteomics data analysis. 364 - Stefano Lise, Cédric Archambeau, Massimiliano Pontil, David T. Jones:
Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods. 365 - Chih-Chieh Chen, Jenn-Kang Hwang, Jinn-Moon Yang:
(PS)2-v2: template-based protein structure prediction server. 366 - Robert Lawrence, Aaron G. Day-Williams, Richard Mott, John Broxholme, Lon R. Cardon, Eleftheria Zeggini:
GLIDERS - A web-based search engine for genome-wide linkage disequilibrium between HapMap SNPs. 367 - Elisa Drelie Gelasca, Boguslaw Obara, Dmitry V. Fedorov, Kristian Kvilekval, B. S. Manjunath:
A biosegmentation benchmark for evaluation of bioimage analysis methods. 368 - Joel Gillespie, Martin Mayne, Minghui Jiang:
RNA folding on the 3D triangular lattice. 369 - Adaoha E. C. Ihekwaba, Phuong T. Nguyen, Corrado Priami:
Elucidation of functional consequences of signalling pathway interactions. 370 - David J. Klinke II:
An empirical Bayesian approach for model-based inference of cellular signaling networks. 371 - Wei Shi, Ashish Banerjee, Matthew E. Ritchie, Steve Gerondakis, Gordon K. Smyth:
Illumina WG-6 BeadChip strips should be normalized separately. 372 - Marc Torrent, Victòria M. Nogués, Ester Boix:
A theoretical approach to spot active regions in antimicrobial proteins. 373 - Timur Fayruzov, Martine De Cock, Chris Cornelis, Véronique Hoste:
Linguistic feature analysis for protein interaction extraction. 374 - Falk Schreiber, Tim Dwyer, Kim Marriott, Michael Wybrow:
A generic algorithm for layout of biological networks. 375 - Ugur Dogrusöz, Ahmet Cetintas, Emek Demir, Ozgun Babur:
Algorithms for effective querying of compound graph-based pathway databases. 376 - Robert Hoehndorf, Janet Kelso, Heinrich Herre:
The ontology of biological sequences. 377 - Byonghyo Shim, Hyeyoung Min, Sungroh Yoon:
Nonlinear preprocessing method for detecting peaks from gas chromatograms. 378 - Tracey Bray, Pedro Chan, Salim Bougouffa, Richard B. Greaves, Andrew J. Doig, Jim Warwicker:
SitesIdentify: a protein functional site prediction tool. 379 - Joke Allemeersch, Steven Van Vooren, Femke Hannes, Bart De Moor, Joris Robert Vermeesch, Yves Moreau:
An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH. 380 - Bin Liu, Xiaolong Wang, Lei Lin, Buzhou Tang, Qiwen Dong, Xuan Wang:
Prediction of protein binding sites in protein structures using hidden Markov support vector machine. 381 - Apichart Intarapanich, Philip James Shaw, Anunchai Assawamakin, Pongsakorn Wangkumhang, Chumpol Ngamphiw, Kridsadakorn Chaichoompu, Jittima Piriyapongsa, Sissades Tongsima:
Iterative pruning PCA improves resolution of highly structured populations. 382 - Valentín Ruano-Rubio, Olivier Poch, Julie Dawn Thompson:
Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. 383 - Nicole Krämer, Juliane Schäfer, Anne-Laure Boulesteix:
Regularized estimation of large-scale gene association networks using graphical Gaussian models. 384 - Mikaela Keller, Clark C. Freifeld, John S. Brownstein:
Automated vocabulary discovery for geo-parsing online epidemic intelligence. 385 - Gonzalo Guillén-Gosálbez, Albert Sorribas:
Identifying quantitative operation principles in metabolic pathways: a systematic method for searching feasible enzyme activity patterns leading to cellular adaptive responses. 386 - Valentina Baldazzi, Paola Paci, Massimo Bernaschi, Filippo Castiglione:
Modeling lymphocyte homing and encounters in lymph nodes. 387 - Isabelle da Piedade, Man-Hung Eric Tang, Olivier Elemento:
DISPARE: DIScriminative PAttern REfinement for Position Weight Matrices. 388 - Herman M. J. Sontrop, Perry D. Moerland, René van den Ham, Marcel J. T. Reinders, Wim F. J. Verhaegh:
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability. 389 - Gernot Stocker, Maria Fischer, Dietmar Rieder, Gabriela Bindea, Simon Kainz, Michael Oberstolz, James G. McNally, Zlatko Trajanoski:
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis. 390 - Chunguang Liang, Alexander Schmid, María José López-Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar:
JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes. 391 - Yuki Naito, Jun Yoshimura, Shinichi Morishita, Kumiko Ui-Tei:
siDirect 2.0: updated software for designing functional siRNA with reduced seed-dependent off-target effect. 392 - Janusz Dutkowski, Jerzy Tiuryn:
Phylogeny-guided interaction mapping in seven eukaryotes. 393 - Yohan Kim, John Sidney, Clemencia Pinilla, Alessandro Sette, Björn Peters:
Derivation of an amino acid similarity matrix for peptide: MHC binding and its application as a Bayesian prior. 394 - Song Zhang, Hu Chen, Ke Liu, Zhirong Sun:
Inferring protein function by domain context similarities in protein-protein interaction networks. 395 - Robert C. Edgar:
Optimizing substitution matrix choice and gap parameters for sequence alignment. 396 - Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain M. Torrance, Johannes Wagener, Egon L. Willighagen, Christoph Steinbeck, Jarl E. S. Wikberg:
Bioclipse 2: A scriptable integration platform for the life sciences. 397 - Ying Chih Lin, Chun-Yuan Lin, Chunhung Richard Lin:
Sorting by reversals and block-interchanges with various weight assignments. 398 - Ruslan Sadreyev, Yong Wang, Nick V. Grishin:
Considering scores between unrelated proteins in the search database improves profile comparison. 399 - Cheng-Long Chuang, Kenneth Hung, Chung-Ming Chen, Grace S. Shieh:
Uncovering transcriptional interactions via an adaptive fuzzy logic approach. 400 - Cunlu Zou, Katherine J. Denby, Jianfeng Feng:
Granger causality vs. dynamic Bayesian network inference: a comparative study. 401 - Song Zhang, Jing Cao:
A close examination of double filtering with fold change and t test in microarray analysis. 402 - Yue Wang, Jin-Dong Kim, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii:
Investigating heterogeneous protein annotations toward cross-corpora utilization. 403 - Shuying Sun, Pearlly Yan, Tim Hui-Ming Huang, Shili Lin:
Identifying differentially methylated genes using mixed effect and generalized least square models. 404 - Shweta Bansal, Shashank Khandelwal, Lauren Ancel Meyers:
Exploring biological network structure with clustered random networks. 405 - Jing Chen, Bruce J. Aronow, Anil G. Jegga:
Correction: Disease candidate gene identification and prioritization using protein interaction networks. 406 - Vishwesh Venkatraman, Yifeng D. Yang, Lee Sael, Daisuke Kihara:
Protein-protein docking using region-based 3D Zernike descriptors. 407 - Bing Liu, Jiuyong Li, Anna Tsykin, Lin Liu, Arti B. Gaur, Gregory J. Goodall:
Exploring complex miRNA-mRNA interactions with Bayesian networks by splitting-averaging strategy. 408 - Martin J. Aryee, José A. Gutiérrez-Pabello, Igor Kramnik, Tapabrata Maiti, John Quackenbush:
An improved empirical bayes approach to estimating differential gene expression in microarray time-course data: BETR (Bayesian Estimation of Temporal Regulation). 409 - Amira Djebbari, Aurélie Labbe:
Refining gene signatures: a Bayesian approach. 410 - Erdem Arslan, Ian J. Laurenzi:
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays. 411 - André Fujita, Alexandre Galvão Patriota, João Ricardo Sato, Satoru Miyano:
The impact of measurement errors in the identification of regulatory networks. 412 - Hege M. Bøvelstad, Ståle Nygård, Ørnulf Borgan:
Survival prediction from clinico-genomic models - a comparative study. 413 - Marcin J. Mizianty, Lukasz A. Kurgan:
Modular prediction of protein structural classes from sequences of twilight-zone identity with predicting sequences. 414 - Liang Goh, Von Bing Yap:
Effects of normalization on quantitative traits in association test. 415 - Ren-Xiang Yan, Jing-Na Si, Chuan Wang, Ziding Zhang:
DescFold: A web server for protein fold recognition. 416 - Curtis Huttenhower, Sajid O. Mehmood, Olga G. Troyanskaya:
Graphle: Interactive exploration of large, dense graphs. 417 - Haiquan Li, Vagner A. Benedito, Michael K. Udvardi, Patrick Xuechun Zhao:
TransportTP: A two-phase classification approach for membrane transporter prediction and characterization. 418 - Yungki Park:
Critical assessment of sequence-based protein-protein interaction prediction methods that do not require homologous protein sequences. 419 - Jun Wu, Qingchao Qiu, Lu Xie, Joseph Fullerton, Jian Yu, Yu Shyr, Alfred L. George Jr., Yajun Yi:
Web-based interrogation of gene expression signatures using EXALT. 420 - Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason S. Papadopoulos, Kevin Bealer, Thomas L. Madden:
BLAST+: architecture and applications. 421 - Hans-Ulrich Klein, Christian Ruckert, Alexander Kohlmann, Lars Bullinger, Christian Thiede, Torsten Haferlach, Martin Dugas:
Quantitative comparison of microarray experiments with published leukemia related gene expression signatures. 422 - Kwangbom Choi, Shawn M. Gomez:
Comparison of phylogenetic trees through alignment of embedded evolutionary distances. 423 - Mikyung Lee, Yangseok Kim:
CHESS (CgHExpreSS): A comprehensive analysis tool for the analysis of genomic alterations and their effects on the expression profile of the genome. 424 - Jeroen J. Jansen, Nicole M. van Dam, Huub C. J. Hoefsloot, Age K. Smilde:
Crossfit analysis: a novel method to characterize the dynamics of induced plant responses. 425 - Lei Deng, Jihong Guan, Qiwen Dong, Shuigeng Zhou:
Prediction of protein-protein interaction sites using an ensemble method. 426 - Jiamin Xiao, Yizhou Li, Kelong Wang, Zhining Wen, Menglong Li, Lifang Zhang, Xuanmin Guang:
In silico method for systematic analysis of feature importance in microRNA-mRNA interactions. 427 - Álvaro Cuadros-Inostroza, Camila Caldana, Henning Redestig, Miyako Kusano, Jan Lisec, Hugo Peña-Cortés, Lothar Willmitzer, Matthew A. Hannah:
TargetSearch - a Bioconductor package for the efficient preprocessing of GC-MS metabolite profiling data. 428 - Yan-Fang Guo, Jian Li, Yuan Chen, Li-Shu Zhang, Hong-Wen Deng:
A new permutation strategy of pathway-based approach for genome-wide association study. 429 - Wolfgang Gerlach, Sebastian Jünemann, Felix Tille, Alexander Goesmann, Jens Stoye:
WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. 430 - Clark D. Jeffries, William O. Ward, Diana O. Perkins, Fred A. Wright:
Discovering collectively informative descriptors from high-throughput experiments. 431 - Huei-Hun Elizabeth Tseng, Martin Tompa:
Algorithms for locating extremely conserved elements in multiple sequence alignments. 432 - Abhik Shah, Toyoaki Tenzen, Andrew P. McMahon, Peter J. Woolf:
Using mechanistic Bayesian networks to identify downstream targets of the Sonic Hedgehog pathway. 433 - Jagat Singh Chauhan, Nitish K. Mishra, Gajendra P. S. Raghava:
Identification of ATP binding residues of a protein from its primary sequence. 434 - Damion Nero, Manpreet S. Katari, Jonathan Kelfer, Daniel Tranchina, Gloria M. Coruzzi:
In Silico Evaluation of Predicted Regulatory Interactions in Arabidopsis thaliana. 435 - Xin Deng, Jesse Eickholt, Jianlin Cheng:
PreDisorder: ab initio sequence-based prediction of protein disordered regions. 436 - Petros Kountouris, Jonathan D. Hirst:
Prediction of backbone dihedral angles and protein secondary structure using support vector machines. 437 - Shyamal D. Peddada, David M. Umbach, Shawn F. Harris:
A response to information criterion-based clustering with order-restricted candidate profiles in short time-course microarray experiments. 438 - Huzefa Rangwala, Christopher Kauffman, George Karypis:
svmPRAT: SVM-based Protein Residue Annotation Toolkit. 439 - Marian Thieme, Claudio Lottaz, Harald Niederstätter, Walther Parson, Rainer Spang, Peter J. Oefner:
ReseqChip: Automated integration of multiple local context probe data from the MitoChip array in mitochondrial DNA sequence assembly. 440 - Ji He, Vagner A. Benedito, Mingyi Wang, Jeremy D. Murray, Patrick Xuechun Zhao, Yuhong Tang, Michael K. Udvardi:
The Medicago truncatula gene expression atlas web server. 441 - Desiree Tillo, Timothy R. Hughes:
G+C content dominates intrinsic nucleosome occupancy. 442 - Thierry De Meeûs, Jean-François Guégan, Anatoly T. Teriokhin:
MultiTest V.1.2, a program to binomially combine independent tests and performance comparison with other related methods on proportional data. 443 - Sandro Morganella, Pietro Zoppoli, Michele Ceccarelli:
IRIS: a method for reverse engineering of regulatory relations in gene networks. 444 - Jayashree Ramana, Dinesh Gupta:
LipocalinPred: a SVM-based method for prediction of lipocalins. 445 - Uri Weingart, Yair Lavi, David Horn:
Data mining of enzymes using specific peptides. 446 - Alexie Papanicolaou, Remo Stierli, Richard H. ffrench-Constant, David G. Heckel:
Next generation transcriptomes for next generation genomes using est2assembly. 447 - Johanna Mazur, Daniel Ritter, Gerhard Reinelt, Lars Kaderali:
Reconstructing nonlinear dynamic models of gene regulation using stochastic sampling. 448 - Kevin J. Thompson, Hrishikesh Deshmukh, Jeffrey L. Solka, Jennifer W. Weller:
A white-box approach to microarray probe response characterization: the BaFL pipeline. 449 - Pedro T. Monteiro, Estelle Dumas, Bruno Besson, Radu Mateescu, Michel Page, Ana T. Freitas, Hidde de Jong:
A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks. 450 - Selpi, Christopher H. Bryant, Graham J. L. Kemp, Janeli Sarv, Erik Kristiansson, Per Sunnerhagen:
Predicting functional upstream open reading frames in Saccharomyces cerevisiae. 451 - Josiah D. Seaman, John C. Sanford:
Skittle: A 2-Dimensional Genome Visualization Tool. 452 - Andreas Buness, Markus Ruschhaupt, Ruprecht Kuner, Achim Tresch:
Classification across gene expression microarray studies. 453 - Marcelo M. Brandão, Luiza L. Dantas, Marcio C. Silva-Filho:
AtPIN: Arabidopsis thaliana Protein Interaction Network. 454 - Seokha Ko, Hyunju Lee:
Integrative approaches to the prediction of protein functions based on the feature selection. 455
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