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ORCIDBMC Bioinformatics, Volume 9 - Supplements
Volume 9, Number S-1, 2008
- Shoba Ranganathan
, Michael Gribskov, Tin Wee Tan:
Bioinformatics research in the Asia Pacific: a 2007 update.
- Byoung-Chul Kim, Woo-Yeon Kim, Daeui Park, Won-Hyong Chung, Kwang-Sik Shin, Jong Bhak:
SNP@Promoter: a database of human SNPs (Single Nucleotide Polymorphisms) within the putative promoter regions. - Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin, Wen-Lian Hsu:
Exploiting likely-positive and unlabeled data to improve the identification of protein-protein interaction articles. - Madhavi Ganapathiraju, Narayanaswamy Balakrishnan, Raj Reddy, Judith Klein-Seetharaman:
Transmembrane helix prediction using amino acid property features and latent semantic analysis. - Christopher J. O. Baker, Kanagasabai Rajaraman, Wee Tiong Ang, Anitha Veeramani, Hong Sang Low, Markus R. Wenk:
Towards ontology-driven navigation of the lipid bibliosphere. - Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qing-ming Luo, Yixue Li:
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. - Olivo Miotto, Tin Wee Tan, Vladimir Brusic:
Rule-based knowledge aggregation for large-scale protein sequence analysis of influenza A viruses. - Shu-Hwa Chen, Chen-Zen Lo, Ming-Chi Tsai, Chao A. Hsiung, Chung-Yen Lin:
The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays. - Hongya Zhao, Kwok-Leung Chan, Lee-Ming Cheng, Hong Yan:
Multivariate hierarchical Bayesian model for differential gene expression analysis in microarray experiments. - Shivashankar H. Nagaraj, Robin B. Gasser, Alasdair J. Nisbet, Shoba Ranganathan:
In silico analysis of expressed sequence tags from Trichostrongylus vitrinus (Nematoda): comparison of the automated ESTExplorer workflow platform with conventional database searches. - Rafael Ördög, Zoltan Szabadka, Vince Grolmusz:
Analyzing the simplicial decomposition of spatial protein structures. - Paul D. Yoo, Abdur R. Sikder, Bing Bing Zhou, Albert Y. Zomaya:
Improved general regression network for protein domain boundary prediction. - Vijayalakshmi Chelliah, William R. Taylor:
Functional site prediction selects correct protein models. - Siavoush Dastmalchi, W. Bret Church, Michael B. Morris:
Modelling the structures of G protein-coupled receptors aided by three-dimensional validation. - Khar Heng Choo, Joo Chuan Tong, Shoba Ranganathan:
Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage. - Naveena Yanamala, Kalyan C. Tirupula, Judith Klein-Seetharaman:
Preferential binding of allosteric modulators to active and inactive conformational states of metabotropic glutamate receptors. - Arumugam Madhumalar, Derek John Smith, Chandra Verma:
Stability of the core domain of p53: insights from computer simulations. - Olivo Miotto, A. T. Heiny, Tin Wee Tan, J. Thomas August, Vladimir Brusic:
Identification of human-to-human transmissibility factors in PB2 proteins of influenza A by large-scale mutual information analysis. - Guanglan Zhang, Asif M. Khan, Kellathur N. Srinivasan, A. T. Heiny, Kenneth X. Lee, Chee Keong Kwoh, J. Thomas August, Vladimir Brusic:
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes. - Woo-Yeon Kim, Sungsoo Kang, Byoung-Chul Kim, Jeehyun Oh, Seong-Woong Cho, Jong Bhak, Jong-Soon Choi:
SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. - Chen Wang, Jianhua Xuan, Li Chen, Po Zhao, Yue Joseph Wang, Robert Clarke, Eric P. Hoffman:
Motif-directed network component analysis for regulatory network inference. - Lesheng Kong, Shoba Ranganathan:
Tandem duplication, circular permutation, molecular adaptation: how Solanaceae resist pests via inhibitors. - Dadabhai T. Singh, Rahul Trehan, Bertil Schmidt, Timo Bretschneider:
Comparative phyloinformatics of virus genes at micro and macro levels in a distributed computing environment.
Volume 9, Number S-2, 2008
- Graziano Pesole, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS2007, the fourth annual meeting of the Italian Society of Bioinformatics. - Gabriele Ausiello, Pier Federico Gherardini, Paolo Marcatili, Anna Tramontano, Allegra Via, Manuela Helmer-Citterich:
FunClust: a web server for the identification of structural motifs in a set of non-homologous protein structures. - Ezio Bartocci, Flavio Corradini, Emilia Entcheva, Radu Grosu, Scott A. Smolka:
CellExcite: an efficient simulation environment for excitable cells. - Alberto Bertoni, Giorgio Valentini:
Discovering multi-level structures in bio-molecular data through the Bernstein inequality. - Luigi Buonaguro, Alessandro Monaco, Eleonora Aricò, Ena Wang, Maria Lina Tornesello, George K. Lewis, Francesco M. Marincola, Franco M. Buonaguro:
Gene expression profile of peripheral blood mononuclear cells in response to HIV-VLPs stimulation. - Emidio Capriotti, Piero Fariselli, Ivan Rossi, Rita Casadio:
A three-state prediction of single point mutations on protein stability changes. - Maria Luisa Chiusano, Nunzio D'Agostino, Alessandra Traini, Concetta Licciardello, Enrico Raimondo, Mario Aversano, Luigi Frusciante, Luigi Monti:
ISOL@: an Italian SOLAnaceae genomics resource. - Bernard Degryse, Juan Fernández-Recio, Valentina Citro, Francescol Blasi, Maria Vittoria Cubellis:
In silico docking of urokinase plasminogen activator and integrins. - Barbara Lazzari, Andrea Caprera, Alberto Vecchietti, Ivan Merelli, Francesca Barale, Luciano Milanesi, Alessandra Stella, Carlo Pozzi:
Version VI of the ESTree db: an improved tool for peach transcriptome analysis. - Svetlin Manavski, Giorgio Valle:
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. - Paolo Marcatili, Giovanni Bussotti, Anna Tramontano:
The MoVIN server for the analysis of protein interaction networks. - Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì M. V. Grober, Maria Ravo, Angelo M. Facchiano, Claudia Angelini, Alessandro Weisz:
Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells. - Alessandro Orro, Guia Guffanti, Erika Salvi, Fabio Macciardi, Luciano Milanesi:
SNPLims: a data management system for genome wide association studies. - Ernesto Picardi, Carla Quagliariello:
Is plant mitochondrial RNA editing a source of phylogenetic incongruence? An answer from in silico and in vivo data sets. - Paolo Romano, Domenico Marra:
SWS: accessing SRS sites contents through Web Services.
Volume 9, Number S-3, 2008
- Jian Su, Christopher J. O. Baker:
The Second International Symposium on Languages in Biology and Medicine (LBM) 2007. - Yoshimasa Tsuruoka, John McNaught, Sophia Ananiadou:
Normalizing biomedical terms by minimizing ambiguity and variability. - Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Vivian Lee, Sylvain Gaudan, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann:
Assessment of disease named entity recognition on a corpus of annotated sentences. - Hongning Wang, Minlie Huang, Shilin Ding, Xiaoyan Zhu:
Exploiting and integrating rich features for biological literature classification. - Kanae Oda, Jin-Dong Kim, Tomoko Ohta, Daisuke Okanohara, Takuya Matsuzaki, Yuka Tateisi, Jun'ichi Tsujii:
New challenges for text mining: mapping between text and manually curated pathways. - Sampo Pyysalo, Antti Airola, Juho Heimonen, Jari Björne, Filip Ginter, Tapio Salakoski:
Comparative analysis of five protein-protein interaction corpora. - Jong C. Park, Tak-Eun Kim, Jinah Park:
Monitoring the evolutionary aspect of the Gene Ontology to enhance predictability and usability. - Ai Kawazoe, Hutchatai Chanlekha, Mika Shigematsu, Nigel Collier:
Structuring an event ontology for disease outbreak detection. - Julien Gobeill, Imad Tbahriti, Frédéric Ehrler, Anaïs Mottaz, Anne-Lise Veuthey, Patrick Ruch:
Gene Ontology density estimation and discourse analysis for automatic GeneRiF extraction. - Richárd Farkas, György Szarvas:
Automatic construction of rule-based ICD-9-CM coding systems. - Hui Yang, Goran Nenadic, John A. Keane:
Identification of transcription factor contexts in literature using machine learning approaches.
Volume 9, Number S-4, 2008
- Nicola Cannata, Michael Schroeder, Roberto Marangoni, Paolo Romano:
A Semantic Web for bioinformatics: goals, tools, systems, applications. - Dimitra Alexopoulou, Thomas Wächter, Laura Pickersgill, Cecilia Eyre, Michael Schroeder:
Terminologies for text-mining; an experiment in the lipoprotein metabolism domain. - Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli, Marie-Dominique Devignes:
Ontology-guided data preparation for discovering genotype-phenotype relationships. - Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella, Luciano Milanesi:
Ontology-based, Tissue MicroArray oriented, image centered tissue bank. - Ismael Navas-Delgado, Raúl Montañez, Almudena Pino-Ángeles, Aurelio A. Moya-García, José Luis Urdiales, Francisca Sánchez-Jiménez, José Francisco Aldana Montes:
AMMO-Prot: amine system project 3D-model finder. - Andrea Splendiani:
RDFScape: Semantic Web meets Systems Biology. - Andrea Bracciali, Marcello Brunelli, Enrico Cataldo, Pierpaolo Degano:
Stochastic models for the in silico simulation of synaptic processes. - Chiara Bodei, Andrea Bracciali, Davide Chiarugi:
On deducing causality in metabolic networks. - Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M. Sedivy, Leon N. Cooper, Ettore Verondini, Luciano Milanesi, Gastone C. Castellani:
Reconstructing networks of pathways via significance analysis of their intersections. - Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dmitry Skripin, Dennis E. Shasha:
GraphFind: enhancing graph searching by low support data mining techniques. - Sara Brunetti, Elena Lodi, Elisa Mori, Maria Stella:
PARPST: a PARallel algorithm to find peptide sequence tags. - Tiziana Margaria, Christian Kubczak, Bernhard Steffen:
Bio-jETI: a service integration, design, and provisioning platform for orchestrated bioinformatics processes. - Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier, Robert Giegerich:
GeneFisher-P: variations of GeneFisher as processes in Bio-jETI.
Volume 9, Number S-5, 2008
- Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens:
Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. - David P. Hill, Barry Smith, Monica S. McAndrews-Hill, Judith A. Blake:
Gene Ontology annotations: what they mean and where they come from. - Anaïs Mottaz, Yum Lina Yip, Patrick Ruch, Anne-Lise Veuthey:
Mapping proteins to disease terminologies: from UniProt to MeSH. - Catia Pesquita, Daniel Faria, Hugo P. Bastos, António E. N. Ferreira, André O. Falcão, Francisco M. Couto:
Metrics for GO based protein semantic similarity: a systematic evaluation. - Irena Spasic, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B. Kell, Norman W. Paton:
Facilitating the development of controlled vocabularies for metabolomics technologies with text mining.
Volume 9, Number S-6, 2008
- Guoqing Lu, Jun Ni:
Highlighting computations in bioscience and bioinformatics: review of the Symposium of Computations in Bioinformatics and Bioscience (SCBB07). - Manika Govil, Alberto M. Segre, Veronica J. Vieland:
MLIP: using multiple processors to compute the posterior probability of linkage. - Yao-Lin Chang, Huai-Kuang Tsai, Cheng-Yan Kao, Yung-Chiang Chen, Yuh-Jyh Hu, Jinn-Moon Yang:
Evolutionary conservation of DNA-contact residues in DNA-binding domains. - Maozu Guo, Jian-Fu Li, Yang Liu:
A topological transformation in evolutionary tree search methods based on maximum likelihood combining p-ECR and neighbor joining. - Fei Gu, Hang Chen, Jun Ni:
Protein structural class prediction based on an improved statistical strategy. - George Chin Jr., Daniel G. Chavarría-Miranda, Grant C. Nakamura, Heidi J. Sofia:
BioGraphE: high-performance bionetwork analysis using the Biological Graph Environment. - Guo-Zheng Li, Hao-Hua Meng, Wen-Cong Lu, Jack Y. Yang, Mary Qu Yang:
Asymmetric bagging and feature selection for activities prediction of drug molecules. - Xue-Qiang Zeng, Guo-Zheng Li, Jack Y. Yang, Mary Qu Yang, Gengfeng Wu:
Dimension reduction with redundant gene elimination for tumor classification. - Mary Qu Yang, James Taylor, Laura Elnitski:
Comparative analyses of bidirectional promoters in vertebrates. - Hiroyuki Mishima, Andrew C. Lidral, Jun Ni:
Application of the Linux cluster for exhaustive window haplotype analysis using the FBAT and Unphased programs. - Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura, Akihiko Konagaya:
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation. - Fang-Xiang Wu:
Genetic weighted k-means algorithm for clustering large-scale gene expression data. - Fang-Xiang Wu, Pierre Gagné, Arnaud Droit, Guy G. Poirier:
Quality assessment of peptide tandem mass spectra. - Xutao Deng, Jun Xu, Charles Wang:
Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists. - Guoqing Lu, Shunpu Zhang, Xiang Fang:
An improved string composition method for sequence comparison. - Lily R. Liang, Vinay Mandal, Yi Lu, Deepak Kumar:
MCM-test: a fuzzy-set-theory-based approach to differential analysis of gene pathways. - Chang F. Quo, May D. Wang:
Quantitative analysis of numerical solvers for oscillatory biomolecular system models. - Todd H. Stokes, J. T. Torrance, Henry Li, May D. Wang:
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. - Gregory A. Wilkin, Xiuzhen Huang:
A practical comparison of two K-Means clustering algorithms.
Volume 9, Number S-7, 2008
- Eric C. Rouchka, Julia Krushkal, Daniel Goldowitz:
Proceedings of the Seventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2008. - Elina Tjioe, Michael W. Berry, Ramin Homayouni, Kevin Heinrich:
Using a literature-based NMF model for discovering gene functional relationships. - Weikuan Gu, Ivan Gerling, Yan Jiao, Peng Gao, Qing Xiong:
Candidate genes within known QTL of type 1 diabetes from mouse models. - Zachary S. Ware, Lisbeth A. Selby, Jerzy W. Jaromczyk:
MedSurv: a software application for creating, conducting and managing medical surveys and questionnaires. - Brandon Barker, Jim Lund:
Genomic analysis of gene regulation complexity. - Chanchai McDonald, Anand Kulkarni, Teeradache Viangteeravat:
Scientific Laboratory Information Management System: Tissue Bank. - Nourtan Abdeltawab, Rita Kansal, Sarah Rowe, Lidia Gardner, Charity Brannen, Mohammed Nooh, Santhosh Mukundan, Hossam Abdelsamed, Ramy Attia, William Taylor, Lu Lu, Robert W. Williams, Malak Kotb:
Bioinformatics analysis of immune response to group A streptococcal sepsis integrating quantitative trait loci mapping with genome-wide expression studies. - Sham S. Kakar, Siva K. Panguluri, Sabine J. Waigel:
Global profile of genes regulated by securin. - Rami N. Mahdi, Eric C. Rouchka:
Buffered codons in human transcriptional units. - Ronald M. Adkins, Julia Krushkal, Chad Klauser, Everett F. Magann, Grant Somes, John Fain, John Morrison:
Haplotypes of the imprinted insulin gene are associated with size for gestational age and umbilical cord IGF-II levels. - Dana Marshall, Jeremy Peirce, Fang Zhou, Lu Lu, Robert W. Williams, Kenneth F. Manly, John Stuart:
QTL mapping arthritis traits in CXB mice. - Siddharth Pratap, Scott M. Williams, Shawn E. Levy:
Evaluation of pooled allelotyping versus individual genotyping for genome-wide association analysis of complex disease. - Stan Pounds, Cheng Cheng, Wenjian Yang, Arzu Onar, Christine Hartford, Susana C. Raimondi, Mary Relling:
A permutation-based method to identify loss-of-heterozygosity using paired genotype microarray data. - Christy M. Bogard, Eric C. Rouchka, Benjamin Arazi:
Random number generation for DNA-based security circuitry. - Mariofanna G. Milanova:
Model of visual attention for video sequences. - Julie B. Schuck, Michael E. Smith, Xiaohong Li, Nigel G. F. Cooper:
Microarray analysis of gene expression during auditory hair cell regeneration in zebrafish (Danio rerio). - Dorothy N. Kakoola, Nataliya Lenchik, Anita Curcio-Brint, Ivan Gerling:
Analysis of the transcriptome of CD4 T-Lymphocytes from young Non-Obese Diabetic (NOD) mice suggests a key role for cytokines and apoptosis. - Jim Lund:
Identifying regulatory elements and gene boundaries with comparative genomic sequence analysis. - Jonathan Quiton, Claire Rinehart, Joseph Chavarria-Smith, Nancy Rice:
Gene classification for microarray data with multiple time measurements. - Shesh N. Rai, Stanley Pounds:
Robust detection method for differential expression studies. - Mohammed Yeasin, Bhanu Vanteru, Jahangheer S. Shaik, Faruk Ahmed:
i-SEGOPubmed: a web interface for semantic enabled browsing of PubMed using Gene Ontology. - Erik S. Gough, Cheolhwan Oh, Jing He, Catherine P. Riley, Charles R. Buck, Xiang Zhang:
Proteome discovery pipeline for mass spectrometry-based proteomics. - Xinnan Niu, K. Jill McAfee, Dexter T. Duncan, Michael Assink, Andrew J. Link:
A computational and analysis tool for proteomics research. - Pongsathorn Chotikasemsri, Claire Rinehart:
Modeling mis-folded lysozyme aggregates. - Victor X. Jin, Alina Rabinovich, Henny O'Geen, Sushma Iyengar, Peggy J. Farnham:
De novo identification of in vivo binding sites from ChIP-chip data. - Joseph Morris, Eric C. Rouchka, David Schultz:
Techniques for the analysis of trichome Pelagonium xhortorum expressed sequence tags.
Volume 9, Number S-8, 2008
- Amos Bairoch, Sarah Cohen Boulakia, Christine Froidevaux:
Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008. - Samira Jaeger, Sylvain Gaudan, Ulf Leser, Dietrich Rebholz-Schuhmann:
Integrating protein-protein interactions and text mining for protein function prediction. - Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg,