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ORCIDBMC Bioinformatics, Volume 8
Volume 8, 2007
- Gilles Didier
, Laurent Debomy, Maude Pupin, Ming Zhang, Alexander Grossmann, Claudine Devauchelle, Ivan Laprevotte:
Comparing sequences without using alignments: application to HIV/SIV subtyping.
- Manjunatha R. Karpenahalli, Andrei N. Lupas, Johannes Söding:
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. - Limin Fu, Enzo Medico:
FLAME, a novel fuzzy clustering method for the analysis of DNA microarray data. - Irini A. Doytchinova, Darren R. Flower:
VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. - Nikhil R. Pal, Kripamoy Aguan, Animesh Sharma, Shun-ichi Amari:
Discovering biomarkers from gene expression data for predicting cancer subgroups using neural networks and relational fuzzy clustering. - Roger A. Craig, Li Liao:
Phylogenetic tree information aids supervised learning for predicting protein-protein interaction based on distance matrices. - Wei Zou, David L. Aylor, Zhao-Bang Zeng:
eQTL Viewer: visualizing how sequence variation affects genome-wide transcription. - Jongrae Kim, Declan G. Bates, Ian Postlethwaite, Pat Heslop-Harrison, Kwang-Hyun Cho:
Least-squares methods for identifying biochemical regulatory networks from noisy measurements. - Andreu Alibés, Patricio Yankilevich, Andrés Cañada, Ramón Díaz-Uriarte:
IDconverter and IDClight: Conversion and annotation of gene and protein IDs. - Eric Yang, Timothy Maguire, Martin L. Yarmush, Francois Berthiaume, Ioannis P. Androulakis:
Bioinformatics analysis of the early inflammatory response in a rat thermal injury model. - Yukiko Yagi, Kotaro Terada, Takahisa Noma, Kazunori Ikebukuro, Koji Sode:
In silico panning for a non-competitive peptide inhibitor. - Lars Kuepfer, Uwe Sauer, Pablo A. Parrilo:
Efficient classification of complete parameter regions based on semidefinite programming. - Maria A. Stalteri, Andrew P. Harrison:
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. - Rob Jelier, Guido Jenster, Lambert C. J. Dorssers, Bas J. Wouters, Peter J. M. Hendriksen, Barend Mons, Ruud Delwel, Jan A. Kors:
Text-derived concept profiles support assessment of DNA microarray data for acute myeloid leukemia and for androgen receptor stimulation. - Ayumu Saito, Masao Nagasaki, Masaaki Oyama, Hiroko Kozuka-Hata, Kentaro Semba, Sumio Sugano, Tadashi Yamamoto, Satoru Miyano:
AYUMS: an algorithm for completely automatic quantitation based on LC-MS/MS proteome data and its application to the analysis of signal transduction. - Mark C. Emerick, Giovanni Parmigiani, William S. Agnew:
Multivariate Analysis and Visualization of Splicing Correlations in Single-Gene Transcriptomes. - Michael R. Seringhaus, Mark B. Gerstein:
Publishing perishing? Towards tomorrow's information architecture. - Robert C. Edgar:
PILER-CR: Fast and accurate identification of CRISPR repeats. - Dustin E. Schones, Andrew D. Smith, Michael Q. Zhang:
Statistical significance of cis-regulatory modules. - Abdallah Sayyed-Ahmad, Kagan Tuncay, Peter J. Ortoleva:
Transcriptional regulatory network refinement and quantification through kinetic modeling, gene expression microarray data and information theory. - Jamie M. Thomas, Daniel Horspool, Gordon Brown, Vasily Tcherepanov, Chris Upton:
GraphDNA: a Java program for graphical display of DNA composition analyses. - Andy M. Yip, Steve Horvath:
Gene network interconnectedness and the generalized topological overlap measure. - Tony Håndstad, Arne J. H. Hestnes, Pål Sætrom:
Motif kernel generated by genetic programming improves remote homology and fold detection. - Andrew B. Clegg, Adrian J. Shepherd:
Benchmarking natural-language parsers for biological applications using dependency graphs. - Carolin Strobl, Anne-Laure Boulesteix, Achim Zeileis, Torsten Hothorn:
Bias in random forest variable importance measures: Illustrations, sources and a solution. - Andy G. Lynch, David E. Neal, John D. Kelly, Glyn J. Burtt, Natalie P. Thorne:
Missing channels in two-colour microarray experiments: Combining single-channel and two-channel data. - Chrysi Konstantinou-Kirtay, John B. O. Mitchell, James A. Lumley:
Scoring functions and enrichment: a case study on Hsp90. - Elena Perelman, Alexander Ploner, Stefano Calza, Yudi Pawitan:
Detecting differential expression in microarray data: comparison of optimal procedures. - Kyungpil Kim, Shibo Zhang, Keni Jiang, Li Cai, In-Beum Lee, Lewis J. Feldman, Haiyan Huang:
Measuring similarities between gene expression profiles through new data transformations. - Ana P. Teixeira, Carlos Alves, Paula M. Alves, Manuel J. T. Carrondo, Rui Oliveira:
Hybrid elementary flux analysis/nonparametric modeling: application for bioprocess control. - Kacy K. Verdi, Heidi J. C. Ellis, Michael R. Gryk:
Conceptual-level workflow modeling of scientific experiments using NMR as a case study. - Meng Wang, Xiaobo Zhou, Randy W. King, Stephen T. C. Wong:
Context based mixture model for cell phase identification in automated fluorescence microscopy. - Tomas Babak, Benjamin J. Blencowe, Timothy R. Hughes:
Considerations in the identification of functional RNA structural elements in genomic alignments. - Rosalía Aguirre-Hernández, Holger H. Hoos, Anne Condon:
Computational RNA secondary structure design: empirical complexity and improved methods. - Franck Rapaport, Andrei Yu. Zinovyev, Marie Dutreix, Emmanuel Barillot, Jean-Philippe Vert:
Classification of microarray data using gene networks. - Ofir Davidovich, Gad Kimmel, Ron Shamir:
GEVALT: An integrated software tool for genotype analysis. - Haseong Kim, Jae K. Lee, Taesung Park:
Boolean networks using the chi-square test for inferring large-scale gene regulatory networks. - Zailong Wang, Pearlly Yan, Dustin P. Potter, Charis Eng, Tim Hui-Ming Huang, Shili Lin:
Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data. - Andrea Passerini, Claudia Andreini, Sauro Menchetti, Antonio Rosato, Paolo Frasconi:
Predicting zinc binding at the proteome level. - Carl Gustafson, William J. Bug, Jonathan Nissanov:
NeuroTerrain - a client-server system for browsing 3D biomedical image data sets. - Kay Prüfer, Bjoern Muetzel, Hong Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Pääbo, Michael Lachmann, Wolfgang Enard:
FUNC: a package for detecting significant associations between gene sets and ontological annotations. - Diego Mauricio Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer, Bernd Mueller-Roeber:
PlnTFDB: an integrative plant transcription factor database. - Guoli Ji, Jianti Zheng, Yingjia Shen, Xiaohui Wu, Ronghan Jiang, Yun Lin, Johnny C. Loke, Kimberly M. Davis, Greg J. Reese, Qingshun Quinn Li:
Predictive modeling of plant messenger RNA polyadenylation sites. - Francisco R. Pinto, João A. Carriço, Mário Ramirez, Jonas S. Almeida:
Ranked Adjusted Rand: integrating distance and partition information in a measure of clustering agreement. - Jenny Gu, Philip E. Bourne:
Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2. - Giulio Pavesi, Federico Zambelli, Graziano Pesole:
WeederH: an algorithm for finding conserved regulatory motifs and regions in homologous sequences. - Yuko Makita, Michiel J. L. de Hoon, Antoine Danchin:
Hon-yaku: a biology-driven Bayesian methodology for identifying translation initiation sites in prokaryotes. - Rickard Sandberg, Ola Larsson:
Improved precision and accuracy for microarrays using updated probe set definitions. - Jean-Baptiste Veyrieras, Bruno Goffinet, Alain Charcosset:
MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments. - Sampo Pyysalo, Filip Ginter, Juho Heimonen, Jari Björne, Jorma Boberg, Jouni Järvinen, Tapio Salakoski:
BioInfer: a corpus for information extraction in the biomedical domain. - Jason W. H. Wong, Matthew J. Sullivan, Hugh M. Cartwright, Gerard Cagney:
msmsEval: tandem mass spectral quality assignment for high-throughput proteomics. - Juris Viksna, Edgars Celms, Martins Opmanis, Karlis Podnieks, Peteris Rucevskis, Andris Zarins, Amy Barrett, Sudeshna Guha Neogi, Maria Krestyaninova, Mark I. McCarthy, Alvis Brazma, Ugis Sarkans:
PASSIM - an open source software system for managing information in biomedical studies. - Ji He, Xinbin Dai, Xuechun Zhao:
PLAN: a web platform for automating high-throughput BLAST searches and for managing and mining results. - Brian Fristensky:
BIRCH: A user-oriented, locally-customizable, bioinformatics system. - Najib Naamane, Jacques van Helden, Decio L. Eizirik:
In silico identification of NF-kappaB-regulated genes in pancreatic beta-cells. - Elena A. Ananko, Yury V. Kondrakhin, Tatyana I. Merkulova, Nikolay A. Kolchanov:
Recognition of interferon-inducible sites, promoters, and enhancers. - Mikel Egaña Aranguren, Sean Bechhofer, Phillip W. Lord, Ulrike Sattler, Robert D. Stevens:
Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL. - Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Cinzia Di Pietro, Michele Purrello, Marco Ragusa:
Sequence similarity is more relevant than species specificity in probabilistic backtranslation. - Ola Spjuth, Tobias Helmus, Egon L. Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E. S. Wikberg:
Bioclipse: an open source workbench for chemo- and bioinformatics. - Shuangge Ma, Xiao Song, Jian Huang:
Supervised group Lasso with applications to microarray data analysis. - Iosifina Pournara, Lorenz Wernisch:
Factor analysis for gene regulatory networks and transcription factor activity profiles. - Anne Friedrich, Raymond Ripp, Nicolas B. Garnier, Emmanuel Bettler, Gilbert Deléage, Olivier Poch, Luc Moulinier:
Blast sampling for structural and functional analyses. - Arthur Chun-Chieh Shih, D. T. Lee, Chin-Lin Peng, Yu-Wei Wu:
Phylo-mLogo: an interactive and hierarchical multiple-logo visualization tool for alignment of many sequences. - Daniel D. Sommer, Arthur L. Delcher, Steven L. Salzberg, Mihai Pop:
Minimus: a fast, lightweight genome assembler. - Oscar Conchillo-Solé, Natalia Sanchez de Groot, Francesc X. Avilés, Josep Vendrell, Xavier Daura, Salvador Ventura:
AGGRESCAN: a server for the prediction and evaluation of "hot spots" of aggregation in polypeptides. - Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, D. T. Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao, Chi-Ying F. Huang:
Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online). - Xin Zhao, Leo Wang-Kit Cheung:
Kernel-imbedded Gaussian processes for disease classification using microarray gene expression data. - Allegra Via, Pier Federico Gherardini, Enrico Ferraro, Gabriele Ausiello, Gianpaolo Scalia Tomba, Manuela Helmer-Citterich:
False occurrences of functional motifs in protein sequences highlight evolutionary constraints. - Dimos Gaidatzis, Erik van Nimwegen, Jean Hausser, Mihaela Zavolan:
Inference of miRNA targets using evolutionary conservation and pathway analysis. - John Moriarty, Julian R. Marchesi, Anthony Metcalfe:
Bounds on the distribution of the number of gaps when circles and lines are covered by fragments: Theory and practical application to genomic and metagenomic projects. - Kenneth Evans, Sascha Ott, Annika Hansen, Georgy Koentges, Lorenz Wernisch:
A comparative study of S/MAR prediction tools. - Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita:
Visualization of three-way comparisons of omics data. - Karolina L. Tkaczuk, Stanislaw Dunin-Horkawicz, Elzbieta Purta, Janusz M. Bujnicki:
Structural and evolutionary bioinformatics of the SPOUT superfamily of methyltransferases. - James J. Chen, Chen-An Tsai, ShengLi Tzeng, Chun-Houh Chen:
Gene selection with multiple ordering criteria. - Ari B. Kahn, Michael C. Ryan, Hongfang Liu, Barry Zeeberg, D. Curtis Jamison, John N. Weinstein:
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. - Kaname Kojima, Masao Nagasaki, Euna Jeong, Mitsuru Kato, Satoru Miyano:
An efficient grid layout algorithm for biological networks utilizing various biological attributes. - Sourangshu Bhattacharya, Chiranjib Bhattacharyya, Nagasuma R. Chandra:
Comparison of protein structures by growing neighborhood alignments. - Kana Shimizu, Yoichi Muraoka, Shuichi Hirose, Kentaro Tomii, Tamotsu Noguchi:
Predicting mostly disordered proteins by using structure-unknown protein data. - Nicolas Rodriguez, Marco Donizelli, Nicolas Le Novère:
SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML). - Erin M. Conlon, Joon J. Song, Anna Liu:
Bayesian meta-analysis models for microarray data: a comparative study. - Gerhard G. Thallinger, Kerstin Baumgartner, Martin Pirklbauer, Martina Uray, Elke Pauritsch, Gabor Mehes, Charles R. Buck, Kurt Zatloukal, Zlatko Trajanoski:
TAMEE: data management and analysis for tissue microarrays. - Amit U. Sinha, Jaroslaw Meller:
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms. - René T. J. M. van der Heijden, Berend Snel, Vera van Noort, Martijn A. Huynen:
Orthology prediction at scalable resolution by phylogenetic tree analysis. - Stéphane Robin, Sophie Schbath, Vincent Vandewalle:
Statistical tests to compare motif count exceptionalities. - Mariano J. Alvarez, Guillermo J. Vila-Ortiz, Mariano C. Salibe, Osvaldo L. Podhajcer, Fernando J. Pitossi:
Model based analysis of real-time PCR data from DNA binding dye protocols. - Russell L. Marsden, Tony A. Lewis, Christine A. Orengo:
Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. - Nicolas Goffard, Georg Weiller:
GeneBins: a database for classifying gene expression data, with application to plant genome arrays. - Alex Gutteridge, Minoru Kanehisa, Susumu Goto:
Regulation of metabolic networks by small molecule metabolites. - Isaac Elias, Jens Lagergren:
Fast computation of distance estimators. - Caroline Truntzer, Catherine Mercier, Jacques Estève, Christian Gautier, Pascal Roy:
Importance of data structure in comparing two dimension reduction methods for classification of microarray gene expression data. - Jung-Hsien Chiang, Shih-Yi Chao:
Modeling human cancer-related regulatory modules by GA-RNN hybrid algorithms. - Jeppe Emmersen, Anna M. Heidenblut, Annabeth Laursen Høgh, Stephan A. Hahn, Karen G. Welinder, Kåre L. Nielsen:
Discarding duplicate ditags in LongSAGE analysis may introduce significant error. - Marko Sysi-Aho, Mikko Katajamaa, Laxman Yetukuri, Matej Oresic:
Normalization method for metabolomics data using optimal selection of multiple internal standards. - Sung Tae Doh, Yunyu Zhang, Matthew H. Temple, Li Cai:
Non-coding sequence retrieval system for comparative genomic analysis of gene regulatory elements. - Robert P. Hanzlik, Yakov M. Koen, Bhargav Theertham, Yinghua Dong, Jianwen Fang:
The reactive metabolite target protein database (TPDB) - a web-accessible resource. - César L. Avila, Viviana A. Rapisarda, Ricardo N. Farías, Javier De Las Rivas, Rosana Chehín:
Linear array of conserved sequence motifs to discriminate protein subfamilies: study on pyridine nucleotide-disulfide reductases. - Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, Zhen-Su She:
MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes. - Xuejun Liu, Kevin K. Lin, Bogi Andersen, Magnus Rattray:
Including probe-level uncertainty in model-based gene expression clustering. - Aurélia Boissin-Quillon, Didier Piau, Caroline Leroux:
In silico segmentations of lentivirus envelope sequences. - Mamoru Kato, Tatsuhiko Tsunoda:
MotifCombinator: a web-based tool to search for combinations of cis-regulatory motifs. - Dante Mantini, Francesca Petrucci, Damiana Pieragostino, Piero Del Boccio, Marta Di Nicola, Carmine Di Ilio, Giorgio Federici, Paolo Sacchetta, Silvia Comani, Andrea Urbani:
LIMPIC: a computational method for the separation of protein MALDI-TOF-MS signals from noise. - Hans-Michael Kaltenbach, Andreas Wilke, Sebastian Böcker:
SAMPI: Protein Identification with Mass Spectra Alignments. - Johannes J. Mandel, Hendrik Fuß, Niall M. Palfreyman, Werner Dubitzky:
Modeling biochemical transformation processes and information processing with Narrator. - Prashant K. Srivastava, Dhwani K. Desai, Soumyadeep Nandi, Andrew M. Lynn:
HMM-ModE - Improved classification using profile hidden Markov models by optimising the discrimination threshold and modifying emission probabilities with negative training sequences. - Tobias Kind, Oliver Fiehn:
Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. - Minko Dudev, Carmay Lim:
Discovering structural motifs using a structural alphabet: Application to magnesium-binding sites. - John P. Rasmussen, Christopher P. Saint, Paul T. Monis:
Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes. - Jun Lu, Joseph C. Lee, Marc L. Salit, Margaret C. Cam:
Transcript-based redefinition of grouped oligonucleotide probe sets using AceView: High-resolution annotation for microarrays. - Rebecka Jörnsten, Ming Ouyang, Hui-Yu Wang:
A meta-data based method for DNA microarray imputation. - Nicholas A. Hamilton, Radosav S. Pantelic, Kelly Hanson, Rohan D. Teasdale:
Fast automated cell phenotype image classification. - Ido Priness, Oded Maimon, Irad E. Ben-Gal:
Evaluation of gene-expression clustering via mutual information distance measure. - Michael C. Riley, Amanda Clare, Ross D. King:
Locational distribution of gene functional classes in Arabidopsis thaliana. - Jianlin Cheng, Pierre Baldi:
Improved residue contact prediction using support vector machines and a large feature set. - Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquín Dopazo:
From genes to functional classes in the study of biological systems. - Thomas L. York, Richard Durrett, Rasmus Nielsen:
Dependence of paracentric inversion rate on tract length. - Daron M. Standley, Hiroyuki Toh, Haruki Nakamura:
ASH structure alignment package: Sensitivity and selectivity in domain classification.