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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.