Journal: BMC Bioinformatics

Volume 10, Issue S-9

0 -- 0Yves A. Lussier, Indra Neil Sarkar. Selected proceedings of the 2009 Summit on Translational Bioinformatics
1 -- 0Hsun-Hsien Chang, Marco Ramoni. Transcriptional network classifiers
2 -- 0Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong Won Kim, Doheon Lee. Analysis of AML genes in dysregulated molecular networks
3 -- 0Suresh K. Bhavnani, Felix Eichinger, Sebastian Martini, Paul Saxman, H. V. Jagadish, Matthias Kretzler. Network analysis of genes regulated in renal diseases: implications for a molecular-based classification
4 -- 0Adam D. Grossman, Mitchell J. Cohen, Geoffrey T. Manley, Atul J. Butte. Infection in the intensive care unit alters physiological networks
5 -- 0Angela K. Dean, Stephen E. Harris, Ivo Kalajzic, Jianhua Ruan. A systems biology approach to the identification and analysis of transcriptional regulatory networks in osteocytes
6 -- 0Xinan Yang, Yong Huang, James L. Chen, Jianming Xie, Xiao Sun, Yves A. Lussier. Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia
7 -- 0Angel Janevski, Sitharthan Kamalakaran, Nilanjana Banerjee, Vinay Varadan, Nevenka Dimitrova. PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment
8 -- 0Casey Lynnette Overby, Peter Tarczy-Hornoch, Dina Demner-Fushman. The potential for automated question answering in the context of genomic medicine: an assessment of existing resources and properties of answers
9 -- 0Erik Pitzer, Ronilda Lacson, Christian Hinske, Jihoon Kim, Pedro A. F. Galante, Lucila Ohno-Machado. Towards large-scale sample annotation in gene expression repositories
10 -- 0Ronilda Lacson, Erik Pitzer, Christian Hinske, Pedro A. F. Galante, Lucila Ohno-Machado. Evaluation of a large-scale biomedical data annotation initiative
11 -- 0Terry H. Shen, Christopher S. Carlson, Peter Tarczy-Hornoch. Evaluating the accuracy of a functional SNP annotation system
12 -- 0Brett R. South, Shuying Shen, Makoto Jones, Jennifer Garvin, Matthew H. Samore, Wendy Webber Chapman, Adi V. Gundlapalli. Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease
13 -- 0Xiaoyan Wang, George Hripcsak, Carol Friedman. Characterizing environmental and phenotypic associations using information theory and electronic health records
14 -- 0Nigam H. Shah, Nipun Bhatia, Clement Jonquet, Daniel L. Rubin, Annie P. Chiang, Mark A. Musen. Comparison of concept recognizers for building the Open Biomedical Annotator
15 -- 0Bo Jin, Alvin Strasburger, Steven J. Laken, F. Andrew Kozel, Kevin A. Johnson, Mark S. George, Xinghua Lu. Feature selection for fMRI-based deception detection
16 -- 0Jonathan L. Lustgarten, Shyam Visweswaran, Robert P. Bowser, William R. Hogan, Vanathi Gopalakrishnan. Knowledge-based variable selection for learning rules from proteomic data
17 -- 0Pavithra Shivakumar, Michael Krauthammer. Structural similarity assessment for drug sensitivity prediction in cancer

Volume 10, Issue S-8

0 -- 0Christopher J. O. Baker, Dietrich Rebholz-Schuhmann. Between proteins and phenotypes: annotation and interpretation of mutations
1 -- 0Martin Krallinger, José M. G. Izarzugaza, Carlos Rodríguez Penagos, Alfonso Valencia. Extraction of human kinase mutations from literature, databases and genotyping studies
2 -- 0Süveyda Yeniterzi, Osman Ugur Sezerman. EnzyMiner: automatic identification of protein level mutations and their impact on target enzymes from PubMed abstracts
3 -- 0Rainer Winnenburg, Conrad Plake, Michael Schroeder. Improved mutation tagging with gene identifiers applied to membrane protein stability prediction
4 -- 0Kevin Nagel, Antonio Jimeno-Yepes, Dietrich Rebholz-Schuhmann. Annotation of protein residues based on a literature analysis: cross-validation against UniProtKb
5 -- 0José M. G. Izarzugaza, Anja Baresic, Lisa E. M. McMillan, Corin Yeats, Andrew B. Clegg, Christine A. Orengo, Andrew C. R. Martin, Alfonso Valencia. An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D
6 -- 0Anna Bauer-Mehren, Laura Inés Furlong, Michael Rautschka, Ferran Sanz. From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways
7 -- 0Anshu Bhardwaj, Mitali Mukerji, Shipra Sharma, Jinny Paul, Chaitanya S. Gokhale, Achal K. Srivastava, Shrish Tiwari. MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease
8 -- 0Yana Bromberg, Burkhard Rost. Correlating protein function and stability through the analysis of single amino acid substitutions
9 -- 0Joke Reumers, Joost Schymkowitz, Frederic Rousseau. Using structural bioinformatics to investigate the impact of non synonymous SNPs and disease mutations: scope and limitations
10 -- 0Omar Haq, Ronald M. Levy, Alexandre V. Morozov, Michael Andrec. Pairwise and higher-order correlations among drug-resistance mutations in HIV-1 subtype B protease

Volume 10, Issue S-7

0 -- 0Sirshendu Majumdar, I. Maria Johnson, Gipsy Majumdar, William J. Valentine, Rajendra Raghow. Molecular dissection of cardiac hypertrophy induced by interleukin-18
0 -- 0Teeradache Viangteeravat, Ian Brooks, Somchan Vuthipadadon, Eunice Huang, Ebony Smith, Ramin Homayouni, Chanchai McDonald. Slim-Prim: an integrated data system for clinical and translational research
0 -- 0Dorothy N. Kakoola, Nataliya Lenchik, Anita Curcio-Brint, Ivan Gerling. Transcriptional profiling of CD4 T-lymphocytes reveals abnormal gene expression in young prediabetic NOD mice
0 -- 0Mohammed Yeasin, Haritha Malempati, Ramin Homayouni, Mohammad S. Sorower. A systematic study on latent semantic analysis model parameters for mining biomedical literature
0 -- 0Ronald M. Adkins, Julia Krushkal, Grant Somes, John Fain, John Morrison, Chad Klauser, Everett F. Magann. Extensive parent-of-origin genetic effects on fetal growth
0 -- 0Heba M. Amin, Abdel-Gawad M. Hashem, Ramy K. Aziz. Bioinformatics determination of ETEC signature genes as potential targets for molecular diagnosis and reverse vaccinology
0 -- 0Sungbo Jung. Parallelized pairwise sequence alignment using CUDA on multiple GPUs
0 -- 0Ramy K. Aziz, Leslie Klis McNeil. Reconstructing the virulome of the human pathogen ::::Streptococcus pyogenes ::::using NMPDR subsystems-based annotation
0 -- 0Julie B. Schuck, Chia-Hui Lin, William T. Penberthy, Xiaohong Li, Nigel G. F. Cooper, Michael E. Smith. Microarray analysis and quantitative real-time PCR validation of gene expression during auditory hair cell regeneration in zebrafish (::::Danio rerio::::)
0 -- 0Elissaveta G. Arnaoudova, Philip J. Bowens, Roger G. Chui, Randy D. Dinkins, Uljana Hesse, Jerzy W. Jaromczyk, Mitchell Martin, Paul Maynard, Neil Moore, Chris L. Schardl. Visualizing and sharing results in bioinformatics projects: GBrowse and GenBank exports
0 -- 0ReddySailaja Marpuri, Claire A. Rinehart. E. coli K12 databases
0 -- 0Sujoy Roy, Lijing Xu, Ramin Homayouni. LSI based framework to predict gene regulatory information
0 -- 0Nishchal K. Verma, Pooja Agrawal, Yan Cui. Fuzzy rule based unsupervised approach for gene saliency
0 -- 0Vinhthuy Phan. Motif Tool Manager: a web-based platform for motif discovery
0 -- 0Bing Wang, Steve Valentine, Sriram Raghuraman, Manolo Plasencia, Xiang Zhang. Prediction of peptide drift time in ion mobility-mass spectrometry
0 -- 0Jarret Glasscock, Ryan Richt, Matthew T. Hickenbotham. Flipping NextGen: using biological systems to characterize NextGen sequencing technologies
0 -- 0Julia Krushkal, Yanhua Qu, Peter Brown, Sreedhar Sontineni, Toshiyuki Ueki, Katy Juarez, Ching Leang, Enrique Merino, Jeanette Peeples, Jose F. Barbe, Ronald M. Adkins, Derek R. Lovley. Bioinformatic analysis of gene regulation in ::::Geobacter sulfurreducens::::
0 -- 0Eric C. Rouchka, Julia Krushkal. Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009
0 -- 0Antony T. Athippozhy, Liping Huang, Tianyong Zhao, Clavia Ruth Wooton-Kee, Paiboon Jungsuwadee, Arnold J. Stromberg, Mary Vore. Utilizing a mixed model approach to compare the lactating rat transcriptome against age-matched control virgins

Volume 10, Issue S-6

0 -- 0Roberto Barbera, Giacinto Donvito, Alberto Falzone, Giuseppe La Rocca, Luciano Milanesi, Giorgio Pietro Maggi, Saverio Vicario. The GENIUS Grid Portal and robot certificates: a new tool for e-Science
0 -- 0Göran O. Sperber, Anders Lövgren, Nils-Einar Eriksson, Farid Benachenhou, Jonas Blomberg. RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences
0 -- 0Simon Penel, Anne-Muriel Arigon, Jean-François Dufayard, Anne-Sophie Sertier, Vincent Daubin, Laurent Duret, Manolo Gouy, Guy Perrière. Databases of homologous gene families for comparative genomics
0 -- 0Antonio Turi, Corrado Loglisci, Eliana Salvemini, Giorgio Grillo, Donato Malerba, Domenica D Elia. Computational annotation of UTR cis-regulatory modules through Frequent Pattern Mining
0 -- 0Zhe Li, He Zhang, Song Ge, Xiaocheng Gu, Ge Gao, Jingchu Luo. Expression pattern divergence of duplicated genes in rice
0 -- 0Teresa Maria Creanza, David S. Horner, Annarita D Addabbo, Rosalia Maglietta, Flavio Mignone, Nicola Ancona, Graziano Pesole. Statistical assessment of discriminative features for protein-coding and non coding cross-species conserved sequence elements
0 -- 0Ziomara P. Gerdtzen, J. Cristian Salgado, Axel Osses, Juan A. Asenjo, Ivan Rapaport, Barbara A. Andrews. Modeling heterocyst pattern formation in cyanobacteria
0 -- 0Dimosthenis Tsagkrasoulis, Panagiotis Zerefos, George Loudos, Antonia Vlahou, Marc Baumann, Sophia Kossida. Brukin2D : a 2D visualization and comparison tool for LC-MS data
0 -- 0Gregory A. C. Singer, Mehrdad Hajibabaei. iBarcode.org: web-based molecular biodiversity analysis
0 -- 0Vincenzo Lagani, Alberto Montesanto, Fausta Di Cianni, Victor Moreno, Stefano Landi, Domenico Conforti, Giuseppina Rose, Giuseppe Passarino. A novel similarity-measure for the analysis of genetic data in complex phenotypes
0 -- 0Franck Picard, Vincent Miele, Jean-Jacques Daudin, Ludovic Cottret, Stéphane Robin. Deciphering the connectivity structure of biological networks using MixNet
0 -- 0Giovanni Minervini, Giuseppe Evangelista, Laura Villanova, Debora Slanzi, Davide De Lucrezia, Irene Poli, Pier Luigi Luisi, Fabio Polticelli. Massive non-natural proteins structure prediction using grid technologies
0 -- 0Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B. Kell, Teresa K. Attwood. Visualising biological data: a semantic approach to tool and database integration
0 -- 0María José Nueda, Patricia Sebastián, Sonia Tarazona, Francisco García-García, Joaquín Dopazo, Alberto Ferrer, Ana Conesa. Functional assessment of time course microarray data
0 -- 0Monica Santamaria, Saverio Vicario, Graziano Pappadà, Gaetano Scioscia, Claudio Scazzocchio, Cecilia Saccone. Towards barcode markers in Fungi: an intron map of Ascomycota mitochondria
0 -- 0Alvaro Martinez Barrio, Erik Lagercrantz, Göran O. Sperber, Jonas Blomberg, Erik Bongcam-Rudloff. Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX
0 -- 0Domenica D Elia, Andreas Gisel, Nils-Einar Eriksson, Sophia Kossida, Kimmo Mattila, Lubos Klucar, Erik Bongcam-Rudloff. The 20:::th::: anniversary of EMBnet: 20 years of bioinformatics for the Life Sciences community
0 -- 0Endre Sebestyén, Tibor Nagy, Sándor Suhai, Endre Barta. DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes
0 -- 0Marcello Castellano, Giuseppe Mastronardi, Roberto Bellotti, Gianfranco Tarricone. A bioinformatics knowledge discovery in text application for grid computing
0 -- 0Maria G. Roubelakis, Pantelis Zotos, Georgios Papachristoudis, Ioannis Michalopoulos, Kalliopi I. Pappa, Nicholas P. Anagnou, Sophia Kossida. Human microRNA target analysis and gene ontology clustering by GOmir, a novel stand-alone application
0 -- 0Francesco Rubino, Marcella Attimonelli. RegExpBlasting (REB), a Regular Expression Blasting algorithm based on multiply aligned sequences
0 -- 0Charalampos N. Moschopoulos, Georgios A. Pavlopoulos, Reinhard Schneider, Spiridon D. Likothanassis, Sophia Kossida. GIBA: a clustering tool for detecting protein complexes
0 -- 0Helena Strömbergsson, Gerard J. Kleywegt. A chemogenomics view on protein-ligand spaces
0 -- 0Ernesto Picardi, Flavio Mignone, Graziano Pesole. EasyCluster: a fast and efficient gene-oriented clustering tool for large-scale transcriptome data
0 -- 0Sandra P. Calderon-Copete, George Wigger, Christof Wunderlin, Tobias Schmidheini, Joachim Frey, Michael A. Quail, Laurent Falquet. The ::::Mycoplasma conjunctivae ::::genome sequencing, annotation and analysis

Volume 10, Issue S-5

0 -- 0Xiaoyan A. Qu, Ranga Chandra Gudivada, Anil G. Jegga, Eric K. Neumann, Bruce J. Aronow. Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships
0 -- 0Cecilia N. Arighi, Hongfang Liu, Darren A. Natale, Winona C. Barker, Harold J. Drabkin, Judith A. Blake, Barry Smith, Cathy H. Wu. TGF-beta signaling proteins and the Protein Ontology
0 -- 0Tim Beck, Hugh Morgan, Andrew Blake, Sara Wells, John M. Hancock, Ann-Marie Mallon. Practical application of ontologies to annotate and analyse large scale raw mouse phenotype data
0 -- 0Christopher Brewster, Simon Jupp, Joanne S. Luciano, David Shotton, Robert D. Stevens, Ziqi Zhang. Issues in learning an ontology from text
0 -- 0Robert Hoehndorf, Joshua Bacher, Michael Backhaus, Sergio E. Gregorio Jr., Frank Loebe, Kay Prüfer, Alexandr Uciteli, Johann Visagie, Heinrich Herre, Janet Kelso. BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology
0 -- 0Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian D. Athey, Stanley J. Watson, Fan Meng. Open Biomedical Ontology-based Medline exploration

Volume 10, Issue S-4

0 -- 0Seung-Jin Sul, Suzanne Matthews, Tiffani L. Williams. Using tree diversity to compare phylogenetic heuristics
0 -- 0Jung Hun Oh, Jean Gao. A kernel-based approach for detecting outliers of high-dimensional biological data
0 -- 0Pavel P. Kuksa, Pai-Hsi Huang, Vladimir Pavlovic. Efficient use of unlabeled data for protein sequence classification: a comparative study
0 -- 0Oscar Harari, Coral del Val, Rocío Romero-Záliz, Dongwoo Shin, Henry Huang, Eduardo A. Groisman, Igor Zwir. Identifying promoter features of co-regulated genes with similar network motifs
0 -- 0Junwan Liu, Zhoujun Li, Xiaohua Hu, Yiming Chen. Biclustering of microarray data with MOSPO based on crowding distance
0 -- 0Xiaotong Lin, Mei Liu, Xue-wen Chen. Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms
0 -- 0Li An, Hongbo Xie, Mark H. Chin, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou. Analysis of multiplex gene expression maps obtained by voxelation
0 -- 0Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang, Luonan Chen. Modeling post-transcriptional regulation activity of small non-coding RNAs in ::::Escherichia coli::::
0 -- 0Feng Luo, Bo Li, Xiu-Feng Wan, Richard H. Scheuermann. Core and periphery structures in protein interaction networks
0 -- 0Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant Honavar. Mixture of experts models to exploit global sequence similarity on biomolecular sequence labeling

Volume 10, Issue S-3

0 -- 0Ankit Agrawal, Xiaoqiu Huang. Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty
0 -- 0Jay Urbain, Ophir Frieder, Nazli Goharian. Passage relevance models for genomics search
0 -- 0Weisi Duan, Min Song, Alexander Yates. Fast max-margin clustering for unsupervised word sense disambiguation in biomedical texts
0 -- 0Jorge Amigo, Christopher Phillips, Antonio Salas, Ángel Carracedo. Viability of in-house datamarting approaches for population genetics analysis of SNP genotypes
0 -- 0Hojung Nam, Ki-Young Lee, Doheon Lee. Identification of temporal association rules from time-series microarray data sets
0 -- 0Sangwoo Kim, Doheon Lee. Mining metastasis related genes by primary-secondary tumor comparisons from large-scale databases

Volume 10, Issue S-2

0 -- 0Benjamin J. Keller, Richard C. McEachin. Identifying hypothetical genetic influences on complex disease phenotypes
0 -- 0Nigam H. Shah, Clement Jonquet, Annie P. Chiang, Atul J. Butte, Rong Chen, Mark A. Musen. Ontology-driven indexing of public datasets for translational bioinformatics
0 -- 0Yael Garten, Russ B. Altman. Pharmspresso: a text mining tool for extraction of pharmacogenomic concepts and relationships from full text
0 -- 0Peter L. Elkin, Mark S. Tuttle, Brett E. Trusko, Steven H. Brown. BioProspecting: novel marker discovery obtained by mining the bibleome
0 -- 0Alberto Malovini, Angelo Nuzzo, Fulvia Ferrazzi, Annibale A. Puca, Riccardo Bellazzi. Phenotype forecasting with SNPs data through gene-based Bayesian networks
0 -- 0Daniel L. Rubin, Ion-Florin Talos, Michael Halle, Mark A. Musen, Ron Kikinis. Computational neuroanatomy: ontology-based representation of neural components and connectivity
0 -- 0Isaac Kunz, Ming-Chin Lin, Lewis Frey. Metadata mapping and reuse in caBIG:::TM:::
0 -- 0Jianji Yang, Aaron M. Cohen, William R. Hersh. Evaluation of a gene information summarization system by users during the analysis process of microarray datasets
0 -- 0Vitali Sintchenko, Blanca Gallego, Grace Chung, Enrico W. Coiera. Towards bioinformatics assisted infectious disease control
0 -- 0Yueyi I. Liu, Paul H. Wise, Atul J. Butte. The "etiome": identification and clustering of human disease etiological factors
0 -- 0Atul J. Butte, Indra Neil Sarkar, Marco Ramoni, Yves A. Lussier, Olga G. Troyanskaya. Selected proceedings of the First Summit on Translational Bioinformatics 2008
0 -- 0Parsa Mirhaji, Min Zhu, Mattew Vagnoni, Elmer V. Bernstam, Jiajie Zhang, Jack W. Smith. Ontology driven integration platform for clinical and translational research
0 -- 0Hannah J. Tipney, Sonia M. Leach, Weiguo Feng, Richard Spritz, Trevor Williams, Lawrence Hunter. Leveraging existing biological knowledge in the identification of candidate genes for facial dysmorphology
0 -- 0Lee T. Sam, Eneida A. Mendonça, Jianrong Li, Judith A. Blake, Carol Friedman, Yves A. Lussier. PhenoGO: an integrated resource for the multiscale mining of clinical and biological data
0 -- 0Yang Liu, Lee T. Sam, Jianrong Li, Yves A. Lussier. Robust methods for accurate diagnosis using pan-microbiological oligonucleotide microarrays

Volume 10, Issue S-15

1 -- 0Shoba Ranganathan. Towards a career in bioinformatics
2 -- 0Khar Heng Choo, Tin Wee Tan, Shoba Ranganathan. A comprehensive assessment of N-terminal signal peptides prediction methods
3 -- 0Woo-Yeon Kim, Sang-Yoon Kim, Tae Hyung Kim, Sung-Min Ahn, Ha Na Byun, Deokhoon Kim, Dae-Soo Kim, Yong Seok Lee, Ho Ghang, Daeui Park, Byoung-Chul Kim, Chulhong Kim, Sunghoon Lee, Seong-Jin Kim, Jong Bhak. Gevab: a prototype genome variation analysis browsing server
4 -- 0Merlin Veronika, James Evans, Paul Matsudaira, Roy Welsch, Jagath C. Rajapakse. Sub-population analysis based on temporal features of high content images
5 -- 0Byungwook Lee, Doheon Lee. Protein comparison at the domain architecture level
6 -- 0Shubhra Ghosh Dastidar, David P. Lane, Chandra S. Verma. Modulation of p53 binding to MDM2: computational studies reveal important roles of Tyr100
7 -- 0Cheng-Ju Kuo, Maurice H. T. Ling, Kuan-Ting Lin, Chun-Nan Hsu. BIOADI: a machine learning approach to identifying abbreviations and definitions in biological literature
8 -- 0Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho, Wen-Lian Hsu. Protein subcellular localization prediction of eukaryotes using a knowledge-based approach
9 -- 0Richard Tzong-Han Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan, Wen-Lian Hsu. HypertenGene: extracting key hypertension genes from biomedical literature with position and automatically-generated template features
10 -- 0Varun Khanna, Shoba Ranganathan. Physicochemical property space distribution among human metabolites, drugs and toxins
11 -- 0In-Hwan Paik, Jeongheui Lim, Byung-Sun Chun, Seon-Duck Jin, Jae-Pyoung Yu, Joon-Woo Lee, Jong Bhak, Woon Kee Paek. The Korean Bird Information System (KBIS) through open and public participation
12 -- 0Shen Jean Lim, Asif Mohammad Khan, Mark De Silva, Kuan Siong Lim, Yongli Hu, Chay Hoon Tan, Tin Wee Tan. The implementation of e-learning tools to enhance undergraduate bioinformatics teaching and learning: a case study in the National University of Singapore

Volume 10, Issue S-14

1 -- 0Indra Neil Sarkar. Biodiversity Informatics: the emergence of a field
2 -- 0Vishwas Chavan, Peter Ingwersen. Towards a data publishing framework for primary biodiversity data: challenges and potentials for the biodiversity informatics community
3 -- 0Andrew W. Hill, Robert P. Guralnick, Paul Flemons, Reed Beaman, John Wieczorek, Ajay Ranipeta, Vishwas Chavan, David Remsen. Location, location, location: utilizing pipelines and services to more effectively georeference the world s biodiversity data
4 -- 0Mehrdad Hajibabaei, Gregory A. C. Singer. Googling DNA sequences on the World Wide Web
5 -- 0Roderic D. M. Page. bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
6 -- 0Vincent S. Smith, Simon D. Rycroft, Kehan T. Harman, Ben Scott, David Roberts. Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life
7 -- 0Paola Bertolazzi, Giovanni Felici, Emanuel Weitschek. Learning to classify species with barcodes
8 -- 0Ka Hou Chu, Minli Xu, Chi Pang Li. Rapid DNA barcoding analysis of large datasets using the composition vector method
9 -- 0Pavel P. Kuksa, Vladimir Pavlovic. Efficient alignment-free DNA barcode analytics
10 -- 0Frederic Austerlitz, Olivier David, Brigitte Schaeffer, Kevin Bleakley, Madalina Olteanu, Raphael Leblois, Michel Veuille, Catherine Laredo. DNA barcode analysis: a comparison of phylogenetic and statistical classification methods

Volume 10, Issue S-13

0 -- 0Nils Gehlenborg, Alvis Brazma. Visualization of large microarray experiments with space maps
0 -- 0Sebastian J. Schultheiß, Wolfgang Busch, Jan Lohmann, Oliver Kohlbacher, Gunnar Rätsch. KIRMES: kernel-based identification of regulatory modules in euchromatic sequences
0 -- 0Rayan Chikhi, Dominique Lavenier. Paired-end read length lower bounds for genome re-sequencing
0 -- 0Walter Pirovano, Anneke van der Reijden, K. Anton Feenstra, Jaap Heringa. Structure and function analysis of flexible alignment regions in proteins
0 -- 0Inken Wohlers, Lars Petzold, Francisco S. Domingues, Gunnar W. Klau. PAUL: protein structural alignment using integer linear programming and Lagrangian relaxation
0 -- 0Van Du Tran, Philippe Chassignet, Jean-Marc Steyaert. Prediction of super-secondary structure in alpha-helical and beta-barrel transmembrane proteins
0 -- 0Teresa Szczepinska, Krzysztof Pawlowski. Looking for chromosome spatial organization rules in microarray gene expression data
0 -- 0José Caldas, Nils Gehlenborg, Ali Faisal, Alvis Brazma, Samuel Kaski. Probabilistic retrieval and visualization of biologically relevant microarray experiments
0 -- 0Regina Bohnert, Jonas Behr, Gunnar Rätsch. Transcript quantification with RNA-Seq data
0 -- 0Thomas Abeel, Jeroen de Ridder, Lucia Peixoto. Highlights from the 5:::th :::International Society for Computational Biology Student Council Symposium at the 17:::th :::Annual International Conference on Intelligent Systems for Molecular Biology and the 8:::th :::European Conference on Computational B
0 -- 0Tom A. Williams, Brian E. Caffrey, Xiaowei Jiang, Christina Toft, Mario A. Fares. Phylogenomic inference of functional divergence
0 -- 0Nikolay Samusik, Yannis Kalaidzidis, Marino Zerial. A method for validation for clustering of phenotypic gene knockdown profiles using protein-protein interactions information
0 -- 0Martina Koeva, E. Camilla Forsberg, Joshua M. Stuart. Core stemness mechanisms revealed through homology
0 -- 0Phil Hyoun Lee, Jae-Yoon Jung, Hagit Shatkay. Functionally informative tag SNP selection using a pareto-optimal approach: playing the game of life

Volume 10, Issue S-12

0 -- 0Luciano Milanesi, Paolo Romano 0001, Gastone C. Castellani, Daniel Remondini, Pietro Liò. Trends in modeling Biomedical Complex Systems
1 -- 0Chiara Balestrieri, Lilia Alberghina, Marco Vanoni, Ferdinando Chiaradonna. Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes
2 -- 0Ivan Merelli, Andrea Caprera, Alessandra Stella, Marcello Del Corvo, Luciano Milanesi, Barbara Lazzari. The Human EST Ontology Explorer: a tissue-oriented visualization system for ontologies distribution in human EST collections
3 -- 0Federica Chiappori, Pasqualina D Ursi, Ivan Merelli, Luciano Milanesi, Ermanna Rovida. In silico saturation mutagenesis and docking screening for the analysis of protein-ligand interaction: the Endothelial Protein C Receptor case study
4 -- 0Filippo Menolascina, Domenico Bellomo, Thomas Maiwald, Vitoantonio Bevilacqua, Caterina Ciminelli, Angelo Paradiso, Stefania Tommasi. Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering
5 -- 0Angelo Nuzzo, Alberto Riva, Riccardo Bellazzi. Phenotypic and genotypic data integration and exploration through a web-service architecture
6 -- 0Emanuel Schwarz, F. Markus Leweke, Sabine Bahn, Pietro Liò. Clinical bioinformatics for complex disorders: a schizophrenia case study
7 -- 0Marco Mesiti, Ernesto Jiménez-Ruiz, Ismael Sanz, Rafael Berlanga Llavori, Paolo Perlasca, Giorgio Valentini, David Manset. XML-based approaches for the integration of heterogeneous bio-molecular data
8 -- 0Ettore Mosca, Gloria Bertoli, Eleonora Piscitelli, Laura Vilardo, Rolland A. Reinbold, Ileana Zucchi, Luciano Milanesi. Identification of functionally related genes using data mining and data integration: a breast cancer case study
9 -- 0Michele Ceccarelli, Antonio d Acierno, Angelo Facchiano. A scale space approach for unsupervised feature selection in mass spectra classification for ovarian cancer detection
10 -- 0Luca Corradi, Valentina Mirisola, Ivan Porro, Livia Torterolo, Marco Fato, Paolo Romano 0001, Ulrich Pfeffer. Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data
11 -- 0Alessandra Tiengo, Nicola Barbarini, Sonia Troiani, Luisa Rusconi, Paolo Magni. A Perl procedure for protein identification by Peptide Mass Fingerprinting
12 -- 0Concita Cantarella, Leandra Sepe, Francesca Fioretti, Maria Carla Ferrari, Giovanni Paolella. Analysis and modelling of motility of cell populations with MotoCell
13 -- 0Federico M. Stefanini, Danila Coradini, Elia Biganzoli. Conditional independence relations among biological markers may improve clinical decision as in the case of triple negative breast cancers
14 -- 0Liliana Ironi, Luigi Panzeri. A computational framework for qualitative simulation of nonlinear dynamical models of gene-regulatory networks
15 -- 0Matteo D Antonio, Marco Masseroli. Extraction, integration and analysis of alternative splicing and protein structure distributed information
16 -- 0Roberta Alfieri, Matteo Barberis, Ferdinando Chiaradonna, Daniela Gaglio, Luciano Milanesi, Marco Vanoni, Edda Klipp, Lilia Alberghina. Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation
17 -- 0Alejandro Real-Chicharro, Iván Ruiz Mostazo, Ismael Navas Delgado, Amine Kerzazi, Othmane Chniber, Francisca Sánchez-Jiménez, Miguel Angel Medina, José Francisco Aldana Montes. Protopia: a protein-protein interaction tool

Volume 10, Issue S-11

1 -- 0Jonathan D. Wren, Yuriy Gusev, Raphael D. Isokpehi, Daniel Berleant, Ulisses Braga-Neto, Dawn Wilkins, Susan Bridges. Proceedings of the 2009 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference
2 -- 0Teresia J. Buza, Ranjit Kumar, Cathy R. Gresham, Shane C. Burgess, Fiona M. McCarthy. Facilitating functional annotation of chicken microarray data
3 -- 0Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L. Reichel, Nathan R. Stewart, Ryan D. Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W. Sykes, Jason N. Burris, Joseph J. Bozell, (Max) Zong-Ming Cheng, Douglas G. Hayes, Nicole Labbe, Mark Davis, C. Neal Stewart Jr., Joshua S. Yuan. Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom
4 -- 0Andy D. Perkins, Michael A. Langston. Threshold selection in gene co-expression networks using spectral graph theory techniques
5 -- 0Sudhir R. Chowbina, Xiaogang Wu, Fan Zhang, Peter M. Li, Ragini Pandey, Harini N. Kasamsetty, Jake Y. Chen. HPD: an online integrated human pathway database enabling systems biology studies
6 -- 0Andrey A. Ptitsyn. Computational analysis of gene expression space associated with metastatic cancer
7 -- 0T. J. Jankun-Kelly, Andrew D. Lindeman, Susan M. Bridges. Exploratory visual analysis of conserved domains on multiple sequence alignments
8 -- 0Lauren A. Bright, Shane C. Burgess, Bhanu Chowdhary, Cyprianna E. Swiderski, Fiona M. McCarthy. Structural and functional-annotation of an equine whole genome oligoarray
9 -- 0Bart H. J. van den Berg, Chamali Thanthiriwatte, Prashanti Manda, Susan M. Bridges. Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data
10 -- 0Amin Zollanvari, Mary Jane Cunningham, Ulisses Braga-Neto, Edward R. Dougherty. Analysis and modeling of time-course gene-expression profiles from nanomaterial-exposed primary human epidermal keratinocytes
11 -- 0Natàlia Garcia-Reyero, Ira R. Adelman, Dalma Martinovic, Li Liu, Nancy D. Denslow. Site-specific impacts on gene expression and behavior in fathead minnows (::::Pimephales promelas::::) exposed ::::in situ ::::to streams adjacent to sewage treatment plants
12 -- 0Zhiguang Li, Zhenqiang Su, Zhining Wen, Leming M. Shi, Tao Chen. Microarray platform consistency is revealed by biologically functional analysis of gene expression profiles
13 -- 0Mutlu Mete, Leah Hennings, Horace J. Spencer, Umit Topaloglu. Automatic identification of angiogenesis in double stained images of liver tissue
14 -- 0Shweta S. Chavan, Michael A. Bauer, Marco Scutari, Radhakrishnan Nagarajan. NATbox: a network analysis toolbox in R
15 -- 0Bernard Chen, Matthew Johnson. Protein local 3D structure prediction by Super Granule Support Vector Machines (Super GSVM)
16 -- 0Xin Zhou, Zhen Su, R. Douglas Sammons, Yanhui Peng, Patrick J. Tranel, C. Neal Stewart Jr., Joshua S. Yuan. Novel software package for cross-platform transcriptome analysis (CPTRA)
17 -- 0Ken Pendarvis, Ranjit Kumar, Shane C. Burgess, Bindu Nanduri. An automated proteomic data analysis workflow for mass spectrometry
18 -- 0Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao, Eve Syrkin Wurtele. PathBinder - text empirics and automatic extraction of biomolecular interactions
19 -- 0Cuilan Gao, Xin Dang, Yixin Chen, Dawn Wilkins. Graph ranking for exploratory gene data analysis
20 -- 0Brandon M. Malone, Andy D. Perkins, Susan M. Bridges. Integrating phenotype and gene expression data for predicting gene function

Volume 10, Issue S-10

1 -- 0Albert Burger, Paolo Romano, Adrian Paschke, Andrea Splendiani. Semantic Web Applications and Tools for Life Sciences, 2008 - Introduction
2 -- 0James P. McCusker, Joshua A. Phillips, Alejandra González Beltrán, Anthony Finkelstein, Michael Krauthammer. Semantic web data warehousing for caGrid
3 -- 0Nadia Anwar, Ela Hunt. ::::Francisella tularensis novicida ::::proteomic and transcriptomic data integration and annotation based on semantic web technologies
4 -- 0Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga Llavori, Dietrich Rebholz-Schuhmann. Reuse of terminological resources for efficient ontological engineering in Life Sciences
5 -- 0María del Mar Roldán García, Ismael Navas Delgado, Amine Kerzazi, Othmane Chniber, Joaquin J. Molina-Castro, José Francisco Aldana Montes. KA-SB: from data integration to large scale reasoning
6 -- 0George Zheng, Athman Bouguettaya. Service-based analysis of biological pathways
7 -- 0Heiko Dietze, Michael Schroeder. GoWeb: a semantic search engine for the life science web
8 -- 0Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen. Bio-jETI: a framework for semantics-based service composition
9 -- 0Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn J. Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans. Structuring and extracting knowledge for the support of hypothesis generation in molecular biology
10 -- 0Kei-Hoi Cheung, H. Robert Frost, M. Scott Marshall, Eric Prud hommeaux, Matthias Samwald, Jun Zhao, Adrian Paschke. A journey to Semantic Web query federation in the life sciences
11 -- 0Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper. BioGateway: a semantic systems biology tool for the life sciences
12 -- 0Karen Sutherland, Kenneth McLeod, Gus Ferguson, Albert Burger. Knowledge-driven enhancements for task composition in bioinformatics
13 -- 0José Antonio Miñarro-Giménez, Marisa Madrid, Jesualdo Tomás Fernández-Breis. OGO: an ontological approach for integrating knowledge about orthology
14 -- 0Helen Oliver, Gayo Diallo, Ed de Quincey, Dimitra Alexopoulou, Bianca Habermann, Patty Kostkova, Michael Schroeder, Simon Jupp, Khaled Khelif, Robert Stevens, Gawesh Jawaheer, Gemma Madle. A user-centred evaluation framework for the Sealife semantic web browsers

Volume 10, Issue S-1

0 -- 0Smitha Dharan, Achuthsankar S. Nair. Biclustering of gene expression data using reactive greedy randomized adaptive search procedure
0 -- 0Corinna Kolárik, Roman Klinger, Martin Hofmann-Apitius. Identification of histone modifications in biomedical text for supporting epigenomic research
0 -- 0Krister M. Swenson, Yokuki To, Jijun Tang, Bernard M. E. Moret. Maximum independent sets of commuting and noninterfering inversions
0 -- 0Chengpeng Bi. DNA motif alignment by evolving a population of Markov chains
0 -- 0Wentian Li, Annette Lee, Peter K. Gregersen. Copy-number-variation and copy-number-alteration region detection by cumulative plots
0 -- 0Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein. Triplet supertree heuristics for the tree of life
0 -- 0Wenhui Huang, Pengyuan Wang, Zhen Liu, Liqing Zhang. Identifying disease associations via genome-wide association studies
0 -- 0Krister M. Swenson, Bernard M. E. Moret. Inversion-based genomic signatures
0 -- 0Daniel H. Huson, Daniel C. Richter, Suparna Mitra, Alexander F. Auch, Stephan C. Schuster. Methods for comparative metagenomics
0 -- 0Fenix W. D. Huang, Linda Y. M. Li, Christian M. Reidys. Sequence-structure relations of pseudoknot RNA
0 -- 0Rui Jiang, Wanwan Tang, Xuebing Wu, Wenhui Fu. A random forest approach to the detection of epistatic interactions in case-control studies
0 -- 0Michael Q. Zhang, Michael S. Waterman, Xuegong Zhang. The Seventh Asia Pacific Bioinformatics Conference (APBC2009)
0 -- 0Benjamin G. Jackson, Patrick S. Schnable, Srinivas Aluru. Parallel short sequence assembly of transcriptomes
0 -- 0Dongxiao Zhu. Semi-supervised gene shaving method for predicting low variation biological pathways from genome-wide data
0 -- 0Pengfei Han, Xiuzhen Zhang, Zhi-Ping Feng. Predicting disordered regions in proteins using the profiles of amino acid indices
0 -- 0An-Min Zou, Fang-Xiang Wu, Jiarui Ding, Guy G. Poirier. Quality assessment of tandem mass spectra using support vector machine (SVM)
0 -- 0Unyanee Poolsap, Yuki Kato, Tatsuya Akutsu. Prediction of RNA secondary structure with pseudoknots using integer programming
0 -- 0Chin-Hsien Tai, James J. Vincent, Changhoon Kim, Byungkook Lee. SE: an algorithm for deriving sequence alignment from a pair of superimposed structures
0 -- 0Reija Autio, Matti Saarela, Anna-Kaarina Järvinen, Sampsa Hautaniemi, Jaakko Astola. Advanced analysis and visualization of gene copy number and expression data
0 -- 0Sabah Kadri, Veronica Hinman, Panayiotis V. Benos. HHMMiR: efficient ::::de novo ::::prediction of microRNAs using hierarchical hidden Markov models
0 -- 0Md. Rafiul Hassan, M. Maruf Hossain, James Bailey, Geoff Macintyre, Joshua Wing Kei Ho, Kotagiri Ramamohanarao. A voting approach to identify a small number of highly predictive genes using multiple classifiers
0 -- 0Taiji Suzuki, Masashi Sugiyama, Takafumi Kanamori, Jun Sese. Mutual information estimation reveals global associations between stimuli and biological processes
0 -- 0Sebastian Böcker, Sebastian Briesemeister, Gunnar W. Klau. On optimal comparability editing with applications to molecular diagnostics
0 -- 0Jan Freudenberg, Mingyi Wang, Yaning Yang, Wentian Li. Partial correlation analysis indicates causal relationships between GC-content, exon density and recombination rate in the human genome
0 -- 0Hong-Hee Won, Inho Park, Eunjung Lee, Jong Won Kim, Doheon Lee. Comparative analysis of the JAK/STAT signaling through erythropoietin receptor and thrombopoietin receptor using a systems approach
0 -- 0Yanni Zhu, Xiaotong Shen, Wei Pan. Network-based support vector machine for classification of microarray samples
0 -- 0Chun-Chi Liu, Jianjun Hu, Mrinal Kalakrishnan, Haiyan Huang, Xianghong Jasmine Zhou. Integrative disease classification based on cross-platform microarray data
0 -- 0Yan Fu, Wei Jia, Zhuang Lu, Haipeng Wang, Zuofei Yuan, Hao Chi, You Li, Liyun Xiu, Wenping Wang, Chao Liu, Leheng Wang, Ruixiang Sun, Wen Gao, Xiaohong Qian, Simin He. Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
0 -- 0Liling Zhao, Jihua Wang, Xianghua Dou, Zanxia Cao. Studying the unfolding process of protein G and protein L under physical property space
0 -- 0Feng Yue, Jian Shi, Jijun Tang. Simultaneous phylogeny reconstruction and multiple sequence alignment
0 -- 0Fei Xia, Yong Dou, Xingming Zhou, Xuejun Yang, Jiaqing Xu, Yang Zhang. Fine-grained parallel RNAalifold algorithm for RNA secondary structure prediction on FPGA
0 -- 0Chih Lee, Ali Abdool, Chun-Hsi Huang. PCA-based population structure inference with generic clustering algorithms
0 -- 0Wouter Meuleman, Judith Y. M. N. Engwegen, Marie-Christine W. Gast, Lodewyk F. A. Wessels, Marcel J. T. Reinders. Analysis of mass spectrometry data using sub-spectra
0 -- 0Zixiang Xu, Xiao Sun, Shihai Yu. Genome-scale analysis to the impact of gene deletion on the metabolism of ::::E. coli::::: constraint-based simulation approach
0 -- 0Hong Sun, Tijl De Bie, Valerie Storms, Qiang Fu, Thomas Dhollander, Karen Lemmens, Annemieke Verstuyf, Bart De Moor, Kathleen Marchal. ModuleDigger: an itemset mining framework for the detection of ::::cis::::-regulatory modules
0 -- 0Wendi Wang, Peiheng Zhang, Xinchun Liu. Short read DNA fragment anchoring algorithm
0 -- 0Guan Ning Lin, Zhipeng Cai, Guohui Lin, Sounak Chakraborty, Dong Xu. ComPhy: prokaryotic composite distance phylogenies inferred from whole-genome gene sets
0 -- 0Martin Bader. Sorting by reversals, block interchanges, tandem duplications, and deletions
0 -- 0Yinglei Lai, Sarah E. Eckenrode, Jin-Xiong She. A statistical framework for integrating two microarray data sets in differential expression analysis
0 -- 0Martin H. van Vliet, Lodewyk F. A. Wessels, Marcel J. T. Reinders. Knowledge driven decomposition of tumor expression profiles
0 -- 0Robert Warren, David Sankoff. Genome aliquoting with double cut and join
0 -- 0Yi Jia, Jun Huan, Vincent Buhr, Jintao Zhang, Leonidas N. Carayannopoulos. Towards comprehensive structural motif mining for better fold annotation in the "twilight zone" of sequence dissimilarity
0 -- 0Søren Besenbacher, Christian N. S. Pedersen, Thomas Mailund. A fast algorithm for genome-wide haplotype pattern mining
0 -- 0Pei Hao, SiYuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li. Human gene expression sensitivity according to large scale meta-analysis
0 -- 0Jhang-Wei Huang, Chwan-Chuen King, Jinn-Moon Yang. Co-evolution positions and rules for antigenic variants of human influenza A/H3N2 viruses
0 -- 0Gunnar W. Klau. A new graph-based method for pairwise global network alignment
0 -- 0Zhiming Dai, Xianhua Dai, Qian Xiang, Jihua Feng, Yangyang Deng, Jiang Wang, Caisheng He. Transcriptional interaction-assisted identification of dynamic nucleosome positioning
0 -- 0Kelvin Xi Zhang, B. F. Francis Ouellette. GAIA: a gram-based interaction analysis tool - an approach for identifying interacting domains in yeast
0 -- 0Erdahl T. Teber, Jason Y. Liu, Sara Ballouz, Diane Fatkin, Merridee A. Wouters. Comparison of automated candidate gene prediction systems using genes implicated in type 2 diabetes by genome-wide association studies
0 -- 0Jian Tian, Ningfeng Wu, Jun Guo, Yunliu Fan. Prediction of amyloid fibril-forming segments based on a support vector machine
0 -- 0Dimitrios P. Papamichail, Georgios P. Papamichail. Improved algorithms for approximate string matching (extended abstract)
0 -- 0Quan Long, Qingrun Zhang, Jurg Ott. Detecting disease-associated genotype patterns
0 -- 0Jing Chen, Guangcheng Xi. An unsupervised partition method based on association delineated revised mutual information
0 -- 0Brian J. Parker, Jiayu Wen. Predicting microRNA targets in time-series microarray experiments via functional data analysis
0 -- 0Francis Y. L. Chin, Henry C. M. Leung, Wei-Lin Li, Siu-Ming Yiu. Finding optimal threshold for correction error reads in DNA assembling
0 -- 0Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang, Minghua Deng. REMAS: a new regression model to identify alternative splicing events from exon array data
0 -- 0Chi Yu Chan, C. Steven Carmack, Dang D. Long, Anil Maliyekkel, Yu Shao, Igor B. Roninson, Ye Ding. A structural interpretation of the effect of GC-content on efficiency of RNA interference
0 -- 0Weitao Sun, Jing He. Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures
0 -- 0G. X. Yu. Pathogenic ::::Bacillus anthracis ::::in the progressive gene losses and gains in adaptive evolution
0 -- 0Quan Wang, Lin Wan, Dayong Li, Lihuang Zhu, Minping Qian, Minghua Deng. Searching for bidirectional promoters in ::::Arabidopsis thaliana::::
0 -- 0Tomasz Gambin, Krzysztof Walczak 0002. A new classification method using array Comparative Genome Hybridization data, based on the concept of Limited Jumping Emerging Patterns
0 -- 0Yanping Xi, Yi-Ping Phoebe Chen, Ming Cao, Weirong Wang, Fei Wang. Analysis on relationship between extreme pathways and correlated reaction sets
0 -- 0Reija Autio, Sami Kilpinen, Matti Saarela, Olli-P. Kallioniemi, Sampsa Hautaniemi, Jaakko Astola. Comparison of Affymetrix data normalization methods using 6, 926 experiments across five array generations
0 -- 0Jun Wang, Maozu Guo, Chun-yu Wang. CGTS: a site-clustering graph based tagSNP selection algorithm in genotype data
0 -- 0Fan Yang, Hua-zhen Wang, Hong Mi, Cheng-de Lin, Wei-Wen Cai. Using random forest for reliable classification and cost-sensitive learning for medical diagnosis
0 -- 0Hongning Wang, Minlie Huang, Xiaoyan Zhu. Extract interaction detection methods from the biological literature
0 -- 0Jisu Kim, De-Shuang Huang, Kyungsook Han. Finding motif pairs in the interactions between heterogeneous proteins via bootstrapping and boosting
0 -- 0Thai Quang Tung, Doheon Lee. A method to improve protein subcellular localization prediction by integrating various biological data sources
0 -- 0Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit, Genographic Consortium. Minimizing recombinations in consensus networks for phylogeographic studies
0 -- 0Wensheng Zhang, Hong-Bin Fang, Jiuzhou Song. Principal component tests: applied to temporal gene expression data
0 -- 0Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen, Tao Jiang. Computational prediction of novel non-coding RNAs in ::::Arabidopsis thaliana::::
0 -- 0Je-Gun Joung, Zhangjun Fei. Computational identification of condition-specific miRNA targets based on gene expression profiles and sequence information
0 -- 0Qian Xu, Derek Hao Hu, Hong Xue, Weichuan Yu, Qiang Yang. Semi-supervised protein subcellular localization
0 -- 0Mohammad Sajjad Hossain, Navid Azimi, Steven Skiena. Crystallizing short-read assemblies around seeds
0 -- 0Krongsakda Phakthanakanok, Khanok Ratanakhanokchai, Khin Lay Kyu, Pornthep Sompornpisut, Aaron Watts, Surapong Pinitglang. A computational analysis of SARS cysteine proteinase-octapeptide substrate interaction: implication for structure and active site binding mechanism