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ORCIDBMC Bioinformatics, Volume 9
Volume 9, 2008
- Ana Carolina Fierro, Raphael Thuret
, Kristof Engelen, Gilles Bernot, Kathleen Marchal, Nicolas Pollet:
Evaluation of time profile reconstruction from complex two-color microarray designs. - Cuong To, Jiri Vohradsky:
Supervised inference of gene-regulatory networks. - Florian Hahne, Alexander Mehrle, Dorit Arlt, Annemarie Poustka, Stefan Wiemann, Tim Beißbarth:
Extending pathways based on gene lists using InterPro domain signatures. - Romesh Stanislaus, John M. Arthur, Balaji Rajagopalan, Rick Moerschell, Brian McGlothlen, Jonas S. Almeida:
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis. - Javier Forment, Francisco Gilabert Villamón, Antonio Robles, Vicente Conejero, Fernando Nuez, Jose M. Blanca:
EST2uni: an open, parallel tool for automated EST analysis and database creation, with a data mining web interface and microarray expression data integration. - Jean-François Taly, Antoine Marin, Jean-François Gibrat:
Can molecular dynamics simulations help in discriminating correct from erroneous protein 3D models? - Michelle N. Knowlton, Tongbin Li, Yongliang Ren, Brent R. Bill, Lynda B. M. Ellis, Stephen C. Ekker:
A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information. - Jialin Xu, Yun He, Boqin Qiang, Jiangang Yuan, Xiaozhong Peng, Xian-Ming Pan:
A novel method for high accuracy sumoylation site prediction from protein sequences. - Joan Teyra, Maciej Paszkowski-Rogacz, Gerd Anders, M. Teresa Pisabarro:
SCOWLP classification: Structural comparison and analysis of protein binding regions. - Jin-Dong Kim, Tomoko Ohta, Jun'ichi Tsujii:
Corpus annotation for mining biomedical events from literature. - Andreas Döring, David Weese, Tobias Rausch, Knut Reinert:
SeqAn An efficient, generic C++ library for sequence analysis. - Guy N. Brock, John R. Shaffer, Richard E. Blakesley, Meredith J. Lotz, George C. Tseng:
Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes. - Paolo Verderio, Sara Pizzamiglio, Fabio Gallo, Simon C. Ramsden:
FCI: an R-based algorithm for evaluating uncertainty of absolute real-time PCR quantification. - Harald Binder, Martin Schumacher:
Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models. - Scott Christley, Neil F. Lobo, Gregory R. Madey:
Multiple organism algorithm for finding ultraconserved elements. - Thierry Rème, Dirk Hose, John De Vos, Aurélien Vassal, Pierre-Olivier Poulain, Véronique Pantesco, Hartmut Goldschmidt, Bernard Klein:
A new method for class prediction based on signed-rank algorithms applied to Affymetrix® microarray experiments. - David M. Kristensen, R. Matthew Ward, Andreas Martin Lisewski, Serkan Erdin, Brian Y. Chen, Viacheslav Fofanov, Marek Kimmel, Lydia E. Kavraki, Olivier Lichtarge:
Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. - David Ellinghaus, Stefan Kurtz, Ute Willhoeft:
LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. - Mutlu Dogruel, Thomas A. Down, Tim J. P. Hubbard:
NestedMICA as an ab initio protein motif discovery tool. - Marc Vincent, Andrea Passerini, Matthieu Labbé, Paolo Frasconi:
A simplified approach to disulfide connectivity prediction from protein sequences. - Céline Noirot, Christine Gaspin, Thomas Schiex, Jérôme Gouzy:
LeARN: a platform for detecting, clustering and annotating non-coding RNAs. - Yu-Ching Fang, Hsuan-Cheng Huang, Hsueh-Fen Juan:
MeInfoText: associated gene methylation and cancer information from text mining. - Shuhei Kimura, Katsuki Sonoda, Soichiro Yamane, Hideki Maeda, Koki Matsumura, Mariko Hatakeyama:
Function approximation approach to the inference of reduced NGnet models of genetic networks. - Jonathan G. Lees, Robert W. Janes:
Combining sequence-based prediction methods and circular dichroism and infrared spectroscopic data to improve protein secondary structure determinations. - Huiling Xiong, Dapeng Zhang, Christopher J. Martyniuk, Vance L. Trudeau, Xuhua Xia:
Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data. - Alexandre Kuhn, Ruth Luthi-Carter, Mauro Delorenzi:
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. - Botond Sipos, Kálmán Somogyi, István Andó, Zsolt Pénzes:
t2prhd: a tool to study the patterns of repeat evolution. - Donald Maier, Farrell Wymore, Gavin Sherlock, Catherine A. Ball:
The XBabelPhish MAGE-ML and XML Translator. - Jiyang Zhang, Jianqi Li, Xin Liu, Hongwei Xie, Yunping Zhu, Fuchu He:
A nonparametric model for quality control of database search results in shotgun proteomics. - Ramón Díaz-Uriarte:
SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data. - Andrey M. Leontovich, Konstantin Y. Tokmachev, Hans C. van Houwelingen:
The comparative analysis of statistics, based on the likelihood ratio criterion, in the automated annotation problem. - Ho-Joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron:
Prioritization of gene regulatory interactions from large-scale modules in yeast. - Yasuo Tabei, Hisanori Kiryu, Taishin Kin, Kiyoshi Asai:
A fast structural multiple alignment method for long RNA sequences. - Patrick D. Schloss, Jo Handelsman:
A statistical toolbox for metagenomics: assessing functional diversity in microbial communities. - José M. G. Izarzugaza, David de Juan, Carles Pons, Florencio Pazos, Alfonso Valencia:
Enhancing the prediction of protein pairings between interacting families using orthology information. - Leming Zhou, Jonathan Stanton, Liliana Florea:
Universal seeds for cDNA-to-genome comparison. - Rekin's Janky, Jacques van Helden:
Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution. - Samiran Ghosh, David F. Grant, Dipak K. Dey, Dennis W. Hill:
A semiparametric modeling framework for potential biomarker discovery and the development of metabonomic profiles. - Shay Artzi, Adam Kiezun, Noam Shomron:
miRNAminer: A tool for homologous microRNA gene search. - Yang Zhang:
I-TASSER server for protein 3D structure prediction. - Jeong-Gu Kim, Daeui Park, Byoung-Chul Kim, Seong-Woong Cho, Yeong Tae Kim, Young-Jin Park, Hee Jung Cho, Hyunseok Park, Ki-Bong Kim, Kyong-Oh Yoon, Soo-Jun Park, Byoung-Moo Lee, Jong Bhak:
Predicting the Interactome of Xanthomonas oryzae pathovar oryzae for target selection and DB service. - Irina Gana Dresen, Tanja Boes, Johannes Hüsing, Markus Neuhäuser, Karl-Heinz Jöckel:
New resampling method for evaluating stability of clusters. - Erwin P. Gianchandani, Matthew A. Oberhardt, Anthony P. Burgard, Costas D. Maranas, Jason A. Papin:
Predicting biological system objectives de novo from internal state measurements. - Jing Li, Yixuan Chen:
Generating samples for association studies based on HapMap data. - Loris Nanni, Alessandra Lumini:
A genetic approach for building different alphabets for peptide and protein classification. - Yuerong Zhu, Yuelin Zhu, Wei Xu:
EzArray: A web-based highly automated Affymetrix expression array data management and analysis system. - Changhui Yan, Jing Hu, Yingfeng Wang:
Discrimination of outer membrane proteins with improved performance. - Mark Bauer, Sheldon M. Schuster, Khalid Sayood:
The Average Mutual Information Profile as a Genomic Signature. - Xin-Qiu Yao, Huaiqiu Zhu, Zhen-Su She:
A dynamic Bayesian network approach to protein secondary structure prediction. - Angela del Pozo, Florencio Pazos, Alfonso Valencia:
Defining functional distances over Gene Ontology. - Jonathan R. Manning, Emily R. Jefferson, Geoffrey J. Barton:
The contrasting properties of conservation and correlated phylogeny in protein functional residue prediction. - Chenggang Yu, Nela Zavaljevski, Valmik Desai, Seth Johnson, Fred J. Stevens, Jaques Reifman:
The development of PIPA: an integrated and automated pipeline for genome-wide protein function annotation. - Paul J. Rushton, Marta T. Bokowiec, Thomas W. Laudeman, Jennifer F. Brannock, Xianfeng Chen, Michael P. Timko:
TOBFAC: the database of tobacco transcription factors. - Cornelia Frömke, Ludwig A. Hothorn, Siegfried Kropf:
Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes. - Hamed Shateri Najafabadi, Noorossadat Torabi, Mahmood Chamankhah:
Designing multiple degenerate primers via consecutive pairwise alignments. - Chang Sik Kim, Cheol Soo Bae, Hong Joon Tcha:
A phase synchronization clustering algorithm for identifying interesting groups of genes from cell cycle expression data. - Xing-Ming Zhao, Yong Wang, Luonan Chen, Kazuyuki Aihara:
Gene function prediction using labeled and unlabeled data. - Chih-Hung Jen, Tsun-Po Yang, Chien-Yi Tung, Shu-Han Su, Chi-Hung Lin, Ming-Ta Hsu, Hsei-Wei Wang:
Signature Evaluation Tool (SET): a Java-based tool to evaluate and visualize the sample discrimination abilities of gene expression signatures. - Irene Kouskoumvekaki, Zhiyong Yang, Svava Ósk Jónsdóttir, Lisbeth Olsson, Gianni Panagiotou:
Identification of biomarkers for genotyping Aspergilli using non-linear methods for clustering and classification. - Hans-Georg Müller, Jeng-Min Chiou, Xiaoyan Leng:
Inferring gene expression dynamics via functional regression analysis. - Usman Roshan, Satish Chikkagoudar, Dennis R. Livesay:
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. - Aarti Garg, Dinesh Gupta:
VirulentPred: a SVM based prediction method for virulent proteins in bacterial pathogens. - David D. Smith, Pål Sætrom, Ola R. Snøve Jr., Cathryn Lundberg, Guillermo E. Rivas, Carlotta Glackin, Garrett P. Larson:
Meta-analysis of breast cancer microarray studies in conjunction with conserved cis-elements suggest patterns for coordinate regulation. - Woochang Hwang, Young-Rae Cho, Aidong Zhang, Murali Ramanathan:
CASCADE: a novel quasi all paths-based network analysis algorithm for clustering biological interactions. - Pere Puigbò, Ignacio G. Bravo, Santiago Garcia-Vallvé:
E-CAI: a novel server to estimate an expected value of Codon Adaptation Index (eCAI). - Paolo Mereghetti, Maria Luisa Ganadu, Elena Papaleo, Piercarlo Fantucci, Luca De Gioia:
Validation of protein models by a neural network approach. - Hans A. Kestler, André Müller, Johann M. Kraus, Malte Buchholz, Thomas M. Gress, Hongfang Liu, David W. Kane, Barry Zeeberg, John N. Weinstein:
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays. - Bruno F. Bettencourt, Margarida R. Santos, Raquel N. Fialho, Ana R. Couto, Maria J. Peixoto, João P. Pinheiro, Hélder Spínola, Marian G. Mora, Cristina Santos, António Brehm, Jácome Bruges-Armas:
Evaluation of two methods for computational HLA haplotypes inference using a real dataset. - Richárd Farkas:
The strength of co-authorship in gene name disambiguation. - Tijana Milenkovic, Jason Lai, Natasa Przulj:
GraphCrunch: A tool for large network analyses. - Violaine Moreau, Cécile Fleury, Dominique Piquer, Christophe Nguyen, Nicolas Novali, Sylvie Villard, Daniel Laune, Claude Granier, Franck Molina:
PEPOP: Computational design of immunogenic peptides. - John K. Vries, Xiong Liu:
Subfamily specific conservation profiles for proteins based on n-gram patterns. - Fabrice Touzain, Sophie Schbath, Isabelle Debled-Rennesson, Bertrand Aigle, Gregory Kucherov, Pierre Leblond:
SIGffRid: A tool to search for sigma factor binding sites in bacterial genomes using comparative approach and biologically driven statistics. - Vichetra Sam, Chin-Hsien Tai, Jean Garnier, Jean-François Gibrat, Byungkook Lee, Peter J. Munson:
Towards an automatic classification of protein structural domains based on structural similarity. - Guanrao Chen, Peter E. Larsen, Eyad Almasri, Yang Dai:
Rank-based edge reconstruction for scale-free genetic regulatory networks. - Sung-Gon Yi, Taesung Park, Jae K. Lee:
Response projected clustering for direct association with physiological and clinical response data. - Xiaoyi Gao, Joshua D. Starmer:
AWclust: point-and-click software for non-parametric population structure analysis. - Lawrence Hunter, Zhiyong Lu, James Firby, William A. Baumgartner Jr., Helen L. Johnson, Philip V. Ogren, K. Bretonnel Cohen:
OpenDMAP: An open source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-type-specific gene expression. - Feng Gao, Chun-Ting Zhang:
Ori-Finder: A web-based system for finding oriCs in unannotated bacterial genomes. - Wen-Lin Huang, Chun-Wei Tung, Shih-Wen Ho, Shiow-Fen Hwang, Shinn-Ying Ho:
ProLoc-GO: Utilizing informative Gene Ontology terms for sequence-based prediction of protein subcellular localization. - Nicholas A. Hamilton, Rohan D. Teasdale:
Visualizing and clustering high throughput sub-cellular localization imaging. - Mathieu Fourment, Michael R. Gillings:
A comparison of common programming languages used in bioinformatics. - Mathieu Fourment, Mark J. Gibbs:
The VirusBanker database uses a Java program to allow flexible searching through Bunyaviridae sequences. - Laura Inés Furlong, Holger Dach, Martin Hofmann-Apitius, Ferran Sanz:
OSIRISv1.2: A named entity recognition system for sequence variants of genes in biomedical literature. - Mark J. Dunning, Nuno L. Barbosa-Morais, Andy G. Lynch, Simon Tavaré, Matthew E. Ritchie:
Statistical issues in the analysis of Illumina data. - Frédéric Chalmel, Michael Primig:
The Annotation, Mapping, Expression and Network (AMEN) suite of tools for molecular systems biology. - Herbert Pang, Hongyu Zhao:
Building pathway clusters from Random Forests classification using class votes. - Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Jos H. Beijnen, Marcel J. T. Reinders, Lodewyk F. A. Wessels:
Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data. - Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arlindo L. Oliveira:
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance. - Eva Grafahrend-Belau, Falk Schreiber, Monika Heiner, Andrea Sackmann, Björn H. Junker, Stefanie Grunwald, Astrid Speer, Katja Winder, Ina Koch:
Modularization of biochemical networks based on classification of Petri net t-invariants. - Cédric Auliac, Vincent Frouin, Xavier Gidrol, Florence d'Alché-Buc:
Evolutionary approaches for the reverse-engineering of gene regulatory networks: A study on a biologically realistic dataset. - Pankaj Chopra, Jaewoo Kang, Jiong Yang, HyungJun Cho, Heenam Stanley Kim, Min-Goo Lee:
Microarray data mining using landmark gene-guided clustering. - Sacha A. F. T. van Hijum, Richard J. S. Baerends, Aldert L. Zomer, Harma A. Karsens, Victoria Martin-Requena, Oswaldo Trelles, Jan Kok, Oscar P. Kuipers:
Supervised Lowess normalization of comparative genome hybridization data - application to lactococcal strain comparisons. - Ching-Wai Tan, David T. Jones:
Using neural networks and evolutionary information in decoy discrimination for protein tertiary structure prediction. - Anke Batsch, Andrea Noetel, Christian Fork, Anita Urban, Daliborka Lazic, Tina Lucas, Julia Pietsch, Andreas Lazar, Edgar Schömig, Dirk Gründemann:
Simultaneous fitting of real-time PCR data with efficiency of amplification modeled as Gaussian function of target fluorescence. - Mark W. E. J. Fiers, Ate van der Burgt, Erwin Datema, Joost C. W. de Groot, Roeland C. H. J. van Ham:
High-throughput bioinformatics with the Cyrille2 pipeline system. - Ken E. Whelan, Ross D. King:
Using a logical model to predict the growth of yeast. - Tristan Mary-Huard, Julie Aubert, Nadera Mansouri-Attia, Olivier Sandra, Jean-Jacques Daudin:
Statistical methodology for the analysis of dye-switch microarray experiments. - John Drakos, Marina Karakantza, Nicholas C. Zoumbos, John Lakoumentas, George Nikiforidis, George Sakellaropoulos:
A perspective for biomedical data integration: Design of databases for flow cytometry. - Dominik Lutter, Peter Ugocsai, Margot Grandl, Evelyn Orso, Fabian J. Theis, Elmar Wolfgang Lang, Gerd Schmitz:
Analyzing M-CSF dependent monocyte/macrophage differentiation: Expression modes and meta-modes derived from an independent component analysis. - Yong-Zi Chen, Yu-Rong Tang, Zhi-Ya Sheng, Ziding Zhang:
Prediction of mucin-type O-glycosylation sites in mammalian proteins using the composition of k-spaced amino acid pairs. - Alvaro J. González, Li Liao:
Clustering exact matches of pairwise sequence alignments by weighted linear regression. - Indra Neil Sarkar, Mary G. Egan, Gloria M. Coruzzi, Ernest K. Lee, Robert DeSalle:
Automated simultaneous analysis phylogenetics (ASAP): an enabling tool for phlyogenomics. - Zhenting Gao, Honglin Li, Hailei Zhang, Xiaofeng Liu, Ling Kang, Xiaomin Luo, Weiliang Zhu, Kaixian Chen, Xicheng Wang, Hualiang Jiang:
PDTD: a web-accessible protein database for drug target identification. - Mattias Rantalainen, Olivier Cloarec, Timothy M. D. Ebbels, Torbjörn Lundstedt, Jeremy K. Nicholson, Elaine Holmes, Johan Trygg:
Piecewise multivariate modelling of sequential metabolic profiling data. - Max Bylesjö, Mattias Rantalainen, Jeremy K. Nicholson, Elaine Holmes, Johan Trygg:
K-OPLS package: Kernel-based orthogonal projections to latent structures for prediction and interpretation in feature space. - Francisco-Javier Lopez, Armando Blanco, Fernando García-Alcalde, Carlos Cano, Antonio Marín:
Fuzzy association rules for biological data analysis: A case study on yeast. - Graham L. Poulter, Daniel L. Rubin, Russ B. Altman, Cathal Seoighe:
MScanner: a classifier for retrieving Medline citations. - Wolfram Gronwald, Tim Hohm, Daniel Hoffmann:
Evolutionary Pareto-optimization of stably folding peptides. - Ran Elkon, Rita Vesterman, Nira Amit, Igor Ulitsky, Idan Zohar, Mali Weisz, Gilad Mass, Nir Orlev, Giora Sternberg, Ran Blekhman, Jackie Assa, Yosef Shiloh, Ron Shamir:
SPIKE - a database, visualization and analysis tool of cellular signaling pathways. - Abhishek Tripathi, Arto Klami, Samuel Kaski:
Simple integrative preprocessing preserves what is shared in data sources. - Hisakazu Iwama, Yukio Hori, Kensuke Matsumoto, Koji Murao, Toshihiko Ishida:
ReAlignerV: Web-based genomic alignment tool with high specificity and robustness estimated by species-specific insertion sequences. - Jianyi Yang, Yu Zhou, Zu-Guo Yu, Vo Anh, Li-Qian Zhou:
Human Pol II promoter recognition based on primary sequences and free energy of dinucleotides.