Volume 8, Number S-1, 2007

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  Rita Casadio, Manuela Helmer-Citterich, Graziano Pesole: Bioinformatics in Italy: BITS2006, the third annual meeting of the Italian Society of Bioinformatics.
• 
  Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Lorenzo Scortichini: BioWMS: a web-based Workflow Management System for bioinformatics.
• 
  Lisa Bartoli, Remo Calabrese, Piero Fariselli, Damiano G. Mita, Rita Casadio: A computational approach for detecting peptidases and their specific inhibitors at the genome level.
• 
  Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti, Gianni Cesareni: ProtNet: a tool for stochastic simulations of protein interaction networks dynamics.
• 
  Roberta Bosotti, Giuseppe Locatelli, Sandra Healy, Emanuela Scacheri, Luca Sartori, Ciro Mercurio, Raffaele Calogero, Antonella Isacchi: Cross platform microarray analysis for robust identification of differentially expressed genes.
• 
  Tiziana Castrignanò, Paolo D'Onorio De Meo, Danilo Carrabino, Massimiliano Orsini, Matteo Floris, Anna Tramontano: The MEPS server for identifying protein conformational epitopes.
• 
  Ivan Porro, Livia Torterolo, Luca Corradi, Marco Fato, Adam Papadimitropoulos, Silvia Scaglione, Andrea Schenone, Federica Viti: A Grid-based solution for management and analysis of microarrays in distributed experiments.
• 
  Claudio Corsi, Paolo Ferragina, Roberto Marangoni: The BioPrompt-box: an ontology-based clustering tool for searching in biological databases.
• 
  Nunzio D'Agostino, Alessandra Traini, Luigi Frusciante, Maria Luisa Chiusano: Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome.
• 
  Barbara Di Camillo, Gianna Toffolo, Sreekumaran K. Nair, Laura J. Greenlund, Claudio Cobelli: Significance analysis of microarray transcript levels in time series experiments.
• 
  Pasqualina D'Ursi, Francesca Marino, Andrea Caprera, Luciano Milanesi, Elena M. Faioni, Ermanna Rovida: ProCMD: a database and 3D web resource for protein C mutants.
• 
  Marco Fondi, Matteo Brilli, Renato Fani: On the origin and evolution of biosynthetic pathways: integrating microarray data with structure and organization of the Common Pathway genes.
• 
  Barbara Lazzari, Andrea Caprera, Cristian Cosentino, Alessandra Stella, Luciano Milanesi, Angelo Viotti: ESTuber db: an online database for Tuber borchii EST sequences.
• 
  Marco Masseroli, Elisa Bellistri, Andrea Franceschini, Francesco Pinciroli: Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists.
• 
  K. Mizuguchi, M. Sele, Maria Vittoria Cubellis: Environment specific substitution tables for thermophilic proteins.
• 
  Nicola Neretti, Daniel Remondini, Marc Tatar, John M. Sedivy, Michela Pierini, Dawn Mazzatti, Jonathan Powell, Claudio Franceschi, Gastone C. Castellani: Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation.
• 
  Davide Rambaldi, Barbara Felice, Viviane Praz, Philipp Bucher, Davide Cittaro, Alessandro Guffanti: Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data.
• 
  Dietrich Rebholz-Schuhmann, Graham Cameron, Dominic Clark, Erik M. van Mulligen, Jean-Louis Coatrieux, Eva del Hoyo-Barbolla, Fernando Martín-Sánchez, Luciano Milanesi, Ivan Porro, Francesco Beltrame, Ioannis G. Tollis, Johan van der Lei: SYMBIOmatics: Synergies in Medical Informatics and Bioinformatics - exploring current scientific literature for emerging topics.
• 
  Paolo Romano, Ezio Bartocci, Guglielmo Bertolini, Flavio De Paoli, Domenico Marra, Giancarlo Mauri, Emanuela Merelli, Luciano Milanesi: Biowep: a workflow enactment portal for bioinformatics applications.
• 
  Elisabetta Sbisà, Domenico Catalano, Giorgio Grillo, Flavio Licciulli, Antonio Turi, Sabino Liuni, Graziano Pesole, Anna De Grassi, Mariano Francesco Caratozzolo, Anna Maria D'Erchia, Beatriz Navarro, Apollonia Tullo, Cecilia Saccone, Andreas Gisel: p53FamTaG: a database resource of human p53, p63 and p73 direct target genes combining in silico prediction and microarray data.
• 
  Andrea Splendiani, Marco Brandizi, Gael Even, Ottavio Beretta, Norman Pavelka, Mattia Pelizzola, Manuel Mayhaus, Maria Foti, Giancarlo Mauri, Paola Ricciardi-Castagnoli: The Genopolis Microarray Database.
• 
  Gabriele Antonio Trombetti, Raoul J. P. Bonnal, Ermanno Rizzi, Gianluca De Bellis, Luciano Milanesi: Data handling strategies for high throughput pyrosequencers.
• 
  Nicola Vitulo, Alessandro Vezzi, Chiara Romualdi, Stefano Campanaro, Giorgio Valle: A global gene evolution analysis on Vibrionaceae family using phylogenetic profile.
• 
  Gabriele Ausiello, Daniele Peluso, Allegra Via, Manuela Helmer-Citterich: Local comparison of protein structures highlights cases of convergent evolution in analogous functional sites.

Volume 8, Number S-2, 2007

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  Samuel Kaski, Juho Rousu, Esko Ukkonen: Probabilistic modeling and machine learning in structural and systems biology.
• 
  Simon Rogers, Raya Khanin, Mark Girolami: Bayesian model-based inference of transcription factor activity.
• 
  Rainer Opgen-Rhein, Korbinian Strimmer: Learning causal networks from systems biology time course data: an effective model selection procedure for the vector autoregressive process.
• 
  Pierre Geurts, Nizar Touleimat, Marie Dutreix, Florence d'Alché-Buc: Inferring biological networks with output kernel trees.
• 
  Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal, Yves Van de Peer: Validating module network learning algorithms using simulated data.
• 
  Dankyu Yoon, Eun-Kyung Lee, Taesung Park: Robust imputation method for missing values in microarray data.
• 
  Alberto Bertoni, Giorgio Valentini: Model order selection for bio-molecular data clustering.
• 
  Aki Vehtari, Ville-Petteri Mäkinen, Pasi Soininen, Petri Ingman, Sanna M. Mäkelä, Markku J. Savolainen, Minna L. Hannuksela, Kimmo Kaski, Mika Ala-Korpela: A novel Bayesian approach to quantify clinical variables and to determine their spectroscopic counterparts in ¹H NMR metabonomic data.
• 
  Niels Landwehr, Taneli Mielikäinen, Lauri Eronen, Hannu Toivonen, Heikki Mannila: Constrained hidden Markov models for population-based haplotyping.
• 
  Trevor I. Dix, David R. Powell, Lloyd Allison, Julie Bernal, Samira Jaeger, Linda Stern: Comparative analysis of long DNA sequences by per element information content using different contexts.
• 
  Merja Oja, Jaakko Peltonen, Jonas Blomberg, Samuel Kaski: Methods for estimating human endogenous retrovirus activities from EST databases.
• 
  Volker Roth, Bernd Fischer: Improved functional prediction of proteins by learning kernel combinations in multilabel settings.

Volume 8, Number S-3, 2007

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  Huajun Chen, Yimin Wang, Zhaohui Wu: Introduction to semantic e-Science in biomedicine.
• 
  Alan Ruttenberg, Tim Clark, William J. Bug, Matthias Samwald, Olivier Bodenreider, Helen Chen, Donald Doherty, Kerstin Forsberg, Yong Gao, Vipul Kashyap, June Kinoshita, Joanne Luciano, M. Scott Marshall, Chimezie Ogbuji, Jonathan Rees, Susie Stephens, Gwendolyn T. Wong, Elizabeth Wu, Davide Zaccagnini, Tonya Hongsermeier, Eric Neumann, Ivan Herman, Kei-Hoi Cheung: Advancing translational research with the Semantic Web.
• 
  Joanne S. Luciano, Robert D. Stevens: e-Science and biological pathway semantics.
• 
  Hugo Y. K. Lam, Luis N. Marenco, Tim Clark, Yong Gao, June Kinoshita, Gordon M. Shepherd, Perry L. Miller, Elizabeth Wu, Gwendolyn T. Wong, Nian Liu, Chiquito J. Crasto, Thomas M. Morse, Susie Stephens, Kei-Hoi Cheung: AlzPharm: integration of neurodegeneration data using RDF.
• 
  Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Martin H. Schultz, Mark Gerstein: LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics.
• 
  Huajun Chen, Yuxin Mao, Xiaoqing Zheng, Meng Cui, Yi Feng, ShuiGuang Deng, Aining Yin, Chunying Zhou, Jingming Tang, Xiaohong Jiang, Zhaohui Wu: Towards Semantic e-Science for Traditional Chinese Medicine.
• 
  James L. Chen, Yang Liu, Lee T. Sam, Jianrong Li, Yves A. Lussier: Evaluation of high-throughput functional categorization of human disease genes.

Volume 8, Number S-4, 2007

• 
  Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg: The 2006 Automated Function Prediction Meeting.
• 
  Iain Melvin, Eugene Ie, Rui Kuang, Jason Weston, William Stafford Noble, Christina S. Leslie: SVM-Fold: a tool for discriminative multi-class protein fold and superfamily recognition.
• 
  Benjamin Audit, Emmanuel D. Levy, Walter R. Gilks, Leon Goldovsky, Christos A. Ouzounis: CORRIE: enzyme sequence annotation with confidence estimates.
• 
  Marc A. Martí-Renom, Andrea Rossi, Fátima Al-Shahrour, Fred P. Davis, Ursula Pieper, Joaquín Dopazo, Andrej Sali: The AnnoLite and AnnoLyze programs for comparative annotation of protein structures.
• 
  Andreas Henschel, Christof Winter, Wan Kyu Kim, Michael Schroeder: Using structural motif descriptors for sequence-based binding site prediction.
• 
  Jason Li, Saman K. Halgamuge, Christopher I. Kells, Sen-Lin Tang: Gene function prediction based on genomic context clustering and discriminative learning: an application to bacteriophages.
• 
  Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini: An improved method for identifying functionally linked proteins using phylogenetic profiles.
• 
  Hon Nian Chua, Wing-Kin Sung, Limsoon Wong: Using indirect protein interactions for the prediction of Gene Ontology functions.
• 
  Lei Xie, Philip E. Bourne: A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites.
• 
  Sungroh Yoon, Jessica C. Ebert, Eui-Young Chung, Giovanni De Micheli, Russ B. Altman: Clustering protein environments for function prediction: finding PROSITE motifs in 3D.

Volume 8, Number S-5, 2007

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  Alberto Apostolico, Raffaele Giancarlo, Concettina Guerra, Giuseppe Lancia: Articles selected from posters presented at the Tenth Annual International Conference on Research in Computational Biology - Preface.
• 
  Fulvia Ferrazzi, Paola Sebastiani, Marco Ramoni, Riccardo Bellazzi: Bayesian approaches to reverse engineer cellular systems: a simulation study on nonlinear Gaussian networks.
• 
  Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, Srinivas Devadas: Learning biophysically-motivated parameters for alpha helix prediction.
• 
  Adriana Climescu-Haulica, Michelle D. Quirk: A stochastic differential equation model for transcriptional regulatory networks.
• 
  Janusz Dutkowski, Anna Gambin: On consensus biomarker selection.
• 
  Milana Frenkel-Morgenstern, Rachel Magid, Eran Eyal, Shmuel Pietrokovski: Refining intra-protein contact prediction by graph analysis.
• 
  Jürgen Kleffe, Friedrich Möller, Burghardt Wittig: Simultaneous identification of long similar substrings in large sets of sequences.
• 
  Chen-Ming Hsu, Chien-Yu Chen, Baw-Jhiune Liu, Chih-Chang Huang, Min-Hung Laio, Chien-Chieh Lin, Tzung-Lin Wu: Identification of hot regions in protein-protein interactions by sequential pattern mining.
• 
  Timo Lassmann, Erik L. L. Sonnhammer: Automatic extraction of reliable regions from multiple sequence alignments.

Volume 8, Number S-6, 2007

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  Peter F. Arndt, Martin Vingron: The Otto Warburg International Summer School and Workshop on Networks and Regulation.
• 
  Silke Sperling: Transcriptional regulation at a glance.
• 
  Michael Q. Zhang: Computational analyses of eukaryotic promoters.
• 
  Erik van Nimwegen: Finding regulatory elements and regulatory motifs: a general probabilistic framework.
• 
  Florian Markowetz, Rainer Spang: Inferring cellular networks - a review.
• 
  Harmen J. Bussemaker, Lucas D. Ward, André Boorsma: Dissecting complex transcriptional responses using pathway-level scores based on prior information.
• 
  Michael Lässig: From biophysics to evolutionary genetics: statistical aspects of gene regulation.
• 
  Wolfgang Huber, Vincent J. Carey, Li Long, Seth Falcon, Robert Gentleman: Graphs in molecular biology.
• 
  Thomas Schlitt, Alvis Brazma: Current approaches to gene regulatory network modelling.

Volume 8, Number S-7, 2007

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  Dawn Wilkins, Yuriy Gusev, Raja Loganantharaj, Susan Bridges, Stephen Winters-Hilt, Jonathan D. Wren: Proceedings of the Fourth Annual Conference of the MidSouth Computational Biology and Bioinformatics Society.
• 
  Mikhail G. Dozmorov, Kimberly D. Kyker, Ricardo Saban, Nathan Shankar, Arto S. Baghdayan, Michael Centola, Robert E. Hurst: Systems biology approach for mapping the response of human urothelial cells to infection by Enterococcus faecalis.
• 
  Laura K. Schnackenberg, Jinchun Sun, Parvaneh Espandiari, Ricky D. Holland, Joseph Hanig, Richard D. Beger: Metabonomics evaluations of age-related changes in the urinary compositions of male Sprague Dawley rats and effects of data normalization methods on statistical and quantitative analysis.
• 
  Nan Mei, Lei Guo, Ruqing Liu, James C. Fuscoe, Tao Chen: Gene expression changes induced by the tumorigenic pyrrolizidine alkaloid riddelliine in liver of Big Blue rats.
• 
  Vijayaraj Nagarajan, Mohamed O. Elasri: Structure and function predictions of the Msa protein in Staphylococcus aureus.
• 
  Joshua S. Yuan, Jason N. Burris, Nathan R. Stewart, Ayalew Mentewab, C. Neal Stewart Jr.: Statistical tools for transgene copy number estimation based on real-time PCR.
• 
  Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S. Inouye, Kuan Yang, Edward J. Perkins, Youping Deng: Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida.
• 
  Yuanyuan Ding, Xin Dang, Hanxiang Peng, Dawn Wilkins: Robust clustering in high dimensional data using statistical depths.
• 
  Stephen Winters-Hilt: The alpha-Hemolysin nanopore transduction detector - single-molecule binding studies and immunological screening of antibodies and aptamers.
• 
  Stephen Winters-Hilt, Amanda Davis, Iftekhar Amin, Eric Morales: Nanopore current transduction analysis of protein binding to non-terminal and terminal DNA regions: analysis of transcription factor binding, retroviral DNA terminus dynamics, and retroviral integrase-DNA binding.
• 
  Karen Thomson, Iftekhar Amin, Eric Morales, Stephen Winters-Hilt: Preliminary nanopore cheminformatics analysis of aptamer-target binding strength.
• 
  Matthew Landry, Stephen Winters-Hilt: Analysis of nanopore detector measurements using Machine-Learning methods, with application to single-molecule kinetic analysis.
• 
  Peng Li, Chaoyang Zhang, Edward J. Perkins, Ping Gong, Youping Deng: Comparison of probabilistic Boolean network and dynamic Bayesian network approaches for inferring gene regulatory networks.
• 
  Alexander G. Churbanov, Carl Baribault, Stephen Winters-Hilt: Duration learning for analysis of nanopore ionic current blockades.
• 
  Andrey A. Ptitsyn, Jeffrey M. Gimble: Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway.
• 
  Yuriy Gusev, Thomas D. Schmittgen, Megan Lerner, Russell Postier, Daniel Brackett: Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer.
• 
  Mutlu Mete, Xiaowei Xu, Chun-Yang Fan, Gal Shafirstein: Automatic delineation of malignancy in histopathological head and neck slides.
• 
  Stephen Winters-Hilt, Sam Merat: SVM clustering.
• 
  Stephen Winters-Hilt, Carl Baribault: A novel, fast, HMM-with-Duration implementation - for application with a new, pattern recognition informed, nanopore detector.
• 
  Stephen Winters-Hilt, Eric Morales, Iftekhar Amin, Alexander Stoyanov: Nanopore-based kinetics analysis of individual antibody-channel and antibody-antigen interactions.
• 
  Modan K. Das, Ho-Kwok Dai: A survey of DNA motif finding algorithms.
• 
  Lei Guo, Nan Mei, Stacey L. Dial, James C. Fuscoe, Tao Chen: Comparison of gene expression profiles altered by comfrey and riddelliine in rat liver.
• 
  William S. Sanders, Susan M. Bridges, Fiona M. McCarthy, Bindu Nanduri, Shane C. Burgess: Prediction of peptides observable by mass spectrometry applied at the experimental set level.
• 
  Susan M. Bridges, G. Bryce Magee, Nan Wang, W. Paul Williams, Shane C. Burgess, Bindu Nanduri: ProtQuant: a tool for the label-free quantification of MudPIT proteomics data.
• 
  Raja Loganantharaj, Mazen Atwi: Towards validating the hypothesis of phylogenetic profiling.

Volume 8, Number S-8, 2007

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  Nils Gehlenborg, Manuel Corpas, Sarath Chandra Janga: Highlights from the Third International Society for Computational Biology Student Council Symposium at the Fifteenth Annual International Conference on Intelligent Systems for Molecular Biology.
• 
  Adrien Fauré, Claudine Chaouiya, Andrea Ciliberto, Denis Thieffry: Logical modelling and analysis of the budding yeast cell cycle.
• 
  Alexander Goncearenco, Yasmin Karimi-Nejad, Konrad Koehler: Homology modeling of a voltage-gated potassium channel (human K_v7.1).
• 
  Axel Rasche, Ralf Herwig: T2DM-GeneMiner a web resource for meta-analysis and marker identification for type 2 diabetes mellitus.
• 
  Fiona G. G. Nielsen, Stefan Gräf, Xinmin Zhang, Stefan Kurtz, Sergei Denissov, Roland Green, Ewan Birney, Paul Flicek, Martijn A. Huynen, Henk Stunnenberg: Optimising oligonucleotide array design for ChIP-on-chip.
• 
  Maital Ashkenazi, Menachem Moshelion: Shared transcriptional correlations in seed formation and in plants response to drought.
• 
  Nicola Barbarini, Paolo Magni, Riccardo Bellazzi: A procedure to decompose high resolution mass spectra.
• 
  Paul Fisher, Cornelia Hedeler, Katherine Wolstencroft, Helen Hulme, Harry Noyes, Stephen Kemp, Robert D. Stevens, Andy Brass: A systematic strategy for the discovery of candidate genes responsible for phenotypic variation.
• 
  Stinus Lindgreen, Paul P. Gardner, Anders Krogh: Multiple alignment and structure prediction of non-coding RNA sequences.
• 
  Abdullah Kahraman, Richard J. Morris, Roman A. Laskowski, Janet M. Thornton: Variation of geometrical and physicochemical properties in protein binding pockets and their ligands.
• 
  Adam A. Margolin, Teresa Palomero, Adolfo A. Ferrando, Andrea Califano, Gustavo Stolovitzky: ChIP-on-chip significance analysis reveals ubiquitous transcription factor binding.
• 
  Ángela Blanco, Manuel Martín-Merino, Javier De Las Rivas: Combining dissimilarity based classifiers for cancer prediction using gene expression profiles.
• 
  Elisabeth Georgii, Sabine Dietmann, Takeaki Uno, Philipp Pagel, Koji Tsuda: Mining expression-dependent modules in the human interaction network.
• 
  Lucia Peixoto, David S. Roos: Genomic scale analysis of lateral gene transfer in Apicomplexan parasites: insights into early eukaryotic evolution, host-pathogen interaction and drug target development.
• 
  Israel Steinfeld, Roy Navon, Diego Ardigò, Ivana Zavaroni, Zohar Yakhini: Semi-supervised class discovery using quantitative phenotypes - CVD as a case study.

Volume 8, Number S-9, 2007

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  Darren A. Natale, Cecilia N. Arighi, Winona C. Barker, Judith A. Blake, Ti-Cheng Chang, Zhang-Zhi Hu, Hongfang Liu, Barry Smith, Cathy H. Wu: Framework for a Protein Ontology.
• 
  Doheon Lee, Sangwoo Kim, Younghoon Kim: BioCAD: an information fusion platform for bio-network inference and analysis.
• 
  Padmini Srinivasan, Xin Ying Qiu: GO for gene documents.
• 
  Illhoi Yoo, Xiaohua Hu, Il-Yeol Song: A coherent graph-based semantic clustering and summarization approach for biomedical literature and a new summarization evaluation method.
• 
  Manabu Torii, Zhang-Zhi Hu, Min Song, Cathy H. Wu, Hongfang Liu: A comparison study on algorithms of detecting long forms for short forms in biomedical text.
• 
  Hyunsoo Kim, Haesun Park, Barry L. Drake: Extracting unrecognized gene relationships from the biomedical literature via matrix factorizations.

Volume 8, Number S-10, 2007

• 
  Gal Chechik, Christina S. Leslie, William Stafford Noble, Gunnar Rätsch, Quaid Morris, Koji Tsuda: NIPS workshop on New Problems and Methods in Computational Biology.
• 
  Xiaoyu Chen, Mathieu Blanchette: Prediction of tissue-specific cis-regulatory modules using Bayesian networks and regression trees.
• 
  Ivan G. Costa, Roland Krause, Lennart Opitz, Alexander Schliep: Semi-supervised learning for the identification of syn-expressed genes from fused microarray and in situ image data.
• 
  Bernd Fischer, Volker Roth, Joachim M. Buhmann: Time-series alignment by non-negative multiple generalized canonical correlation analysis.
• 
  Manjunatha Jagalur, Chris Pal, Erik G. Learned-Miller, R. Thomas Zoeller, David Kulp: Analyzing in situ gene expression in the mouse brain with image registration, feature extraction and block clustering.
• 
  Yanjun Qi, Judith Klein-Seetharaman, Ziv Bar-Joseph: A mixture of feature experts approach for protein-protein interaction prediction.
• 
  Sören Sonnenburg, Gabriele Schweikert, Petra Philips, Jonas Behr, Gunnar Rätsch: Accurate splice site prediction using support vector machines.
• 
  Jean-Philippe Vert, Jian Qiu, William Stafford Noble: A new pairwise kernel for biological network inference with support vector machines.

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