Journal: BMC Bioinformatics

Volume 13, Issue S-9

0 -- 0Weimin Luo, Keith C. C. Chan. Discovering patterns in drug-protein interactions based on their fingerprints
0 -- 0Qinmin Hu, Jimmy Huang, Xiaohua Hu. Modeling and mining term association for improving biomedical information retrieval performance
0 -- 0Kristopher L. Patton, David J. John, James L. Norris. Bayesian probabilistic network modeling from multiple independent replicates
0 -- 0Yann Christinat, Bernard M. E. Moret. Inferring transcript phylogenies
0 -- 0Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao. DTome: a web-based tool for drug-target interactome construction
0 -- 0Sohee Oh, Jaehoon Lee, Min-Seok Kwon, Bruce Weir, Kyooseob Ha, Taesung Park. A novel method to identify high order gene-gene interactions in genome-wide association studies: Gene-based MDR
0 -- 0Zhenyu Yang, David Sankoff. Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals
0 -- 0Xijun Liang, Zhonghang Xia, Li-Wei Zhang, Fang-Xiang Wu. Inference of gene regulatory subnetworks from time course gene expression data

Volume 13, Issue S-8

0 -- 0Jessie Kennedy, Jos B. T. M. Roerdink. Highlights of the 1st IEEE Symposium on Biological Data Visualization
0 -- 0David Mayerich, Christopher Björnsson, Jonothan Taylor, Badrinath Roysam. NetMets: software for quantifying and visualizing errors in biological network segmentation
0 -- 0Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai. RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry
0 -- 0Hendrik Strobelt, Enrico Bertini, Joachim Braun, Oliver Deussen, Ulrich Groth, Thomas U. Mayer, Dorit Merhof. HiTSEE KNIME: a visualization tool for hit selection and analysis in high-throughput screening experiments for the KNIME platform
0 -- 0Julian Heinrich, Corinna Vehlow, Florian Battke, Günter Jäger, Daniel Weiskopf, Kay Nieselt. iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data
0 -- 0Philip Livengood, Ross Maciejewski, Wei Chen 0001, David S. Ebert. OmicsVis: an interactive tool for visually analyzing metabolomics data
0 -- 0Trevor Paterson, Martin Graham, Jessie B. Kennedy, Andy Law. VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees
0 -- 0Christopher W. Bartlett, Soo Yeon Cheong, Liping Hou, Jesse Paquette, Pek Yee Lum, Günter Jäger, Florian Battke, Corinna Vehlow, Julian Heinrich, Kay Nieselt, Ryo Sakai, Jan Aerts, William C. Ray. An eQTL biological data visualization challenge and approaches from the visualization community

Volume 13, Issue S-7

0 -- 0M. Michael Gromiha, De-Shuang Huang. Introduction: advanced intelligent computing theories and their applications in bioinformatics
0 -- 0Yu-Ting Hsiao, Wei-Po Lee. Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method
0 -- 0Guangyu Cui, Chao Fang, Kyungsook Han. Prediction of protein-protein interactions between viruses and human by an SVM model
0 -- 0Ying-Ke Lei, Zhuhong You, Zhen Ji, Lin Zhu, De-Shuang Huang. Assessing and predicting protein interactions by combining manifold embedding with multiple information integration
0 -- 0Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao. Exploring drug combinations in genetic interaction network
0 -- 0M. Michael Gromiha, K. Harini, R. Sowdhamini, Kazuhiko Fukui. Relationship between amino acid properties and functional parameters in olfactory receptors and discrimination of mutants with enhanced specificity
0 -- 0Xuesong Wang, Lijing Li, Yuhu Cheng. An overlapping module identification method in protein-protein interaction networks
0 -- 0Zhi-Ping Liu, Jiguang Wang, Yu-Qing Qiu, Ross K. K. Leung, Xiang-Sun Zhang, Stephen Kwok-Wing Tsui, Luonan Chen. Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs
0 -- 0Byungkyu Park, Wook Lee, Kyungsook Han. Modeling the interactions of Alzheimer-related genes from the whole brain microarray data and diffusion tensor images of human brain
0 -- 0Wassim Ayadi, Mourad Elloumi, Jin-Kao Hao. Pattern-driven neighborhood search for biclustering of microarray data
0 -- 0Vitoantonio Bevilacqua, Paolo Pannarale, Mirko Abbrescia, Claudia Cava, Angelo Paradiso, Stefania Tommasi. Comparison of data-merging methods with SVM attribute selection and classification in breast cancer gene expression
0 -- 0Jingyan Wang, Xin Gao, Quanquan Wang, Yongping Li. ProDis-ContSHC: learning protein dissimilarity measures and hierarchical context coherently for protein-protein comparison in protein database retrieval
0 -- 0Kwang Su Jung, Sanghoon Moon, Young Kim, Bong-Jo Kim, Kiejung Park. Genovar: a detection and visualization tool for genomic variants

Volume 13, Issue S-6

0 -- 0Chengxi Ye, Zhanshan (Sam) Ma, Charles H. Cannon, Mihai Pop, Douglas W. Yu. Exploiting sparseness in de novo genome assembly
0 -- 0Jón Sveinbjörnsson, Bjarni V. Halldórsson. PAIR: polymorphic Alu insertion recognition
0 -- 0Anatoly Efros, Eran Halperin. Haplotype reconstruction using perfect phylogeny and sequence data
0 -- 0Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel. A context-based approach to identify the most likely mapping for RNA-seq experiments
0 -- 0Layla Oesper, Anna M. Ritz, Sarah J. Aerni, Ryan Drebin, Benjamin J. Raphael. Reconstructing cancer genomes from paired-end sequencing data
0 -- 0Boyko Kakaradov, Hui Yuan Xiong, Leo J. Lee, Nebojsa Jojic, Brendan J. Frey. Challenges in estimating percent inclusion of alternatively spliced junctions from RNA-seq data
0 -- 0Roye Rozov, Eran Halperin, Ron Shamir. MGMR: leveraging RNA-Seq population data to optimize expression estimation
0 -- 0Ekaterina Khrameeva, Mikhail S. Gelfand. Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments
0 -- 0Matthew D. Edwards, David K. Gifford. High-resolution genetic mapping with pooled sequencing
0 -- 0Gustavo Akio Tominaga Sacomoto, Janice Kielbassa, Rayan Chikhi, Raluca Uricaru, Pavlos Antoniou, Marie-France Sagot, Pierre Peterlongo, Vincent Lacroix. KISSPLICE: de-novo calling alternative splicing events from RNA-seq data
0 -- 0Jin Zhang, Jiayin Wang, Yufeng Wu. An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data

Volume 13, Issue S-5

0 -- 0Mayank Daga, Wu-chun Feng. Multi-dimensional characterization of electrostatic surface potential computation on graphics processors
0 -- 0Peter Clote, Feng Lou, William Andrew Lorenz. Maximum expected accuracy structural neighbors of an RNA secondary structure
0 -- 0Yingfeng Wang, Amir Manzour, Pooya Shareghi, Timothy I. Shaw, Ying Wai Li, Russell L. Malmberg, Liming Cai. Stable stem enabled Shannon entropies distinguish non-coding RNAs from random backgrounds
0 -- 0Yuri Pirola, Raffaella Rizzi, Ernesto Picardi, Graziano Pesole, Gianluca Della Vedova, Paola Bonizzoni. PIntron: a fast method for detecting the gene structure due to alternative splicing via maximal pairings of a pattern and a text
0 -- 0Yuhong Zhang, Sanchit Misra, Ankit Agrawal, Md. Mostofa Ali Patwary, Wei-keng Liao, Zhiguang Qin, Alok N. Choudhary. Accelerating pairwise statistical significance estimation for local alignment by harvesting GPU's power
0 -- 0Piotr Dittwald, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin. Inferring serum proteolytic activity from LC-MS/MS data
0 -- 0Hsiu J. Ho, Tsung I. Lin, Hannah H. Chang, Steven B. Haase, Sui Huang, Saumyadipta Pyne. Parametric modeling of cellular state transitions as measured with flow cytometry
0 -- 0Sumit Kumar Jha, Christopher James Langmead. Exploring behaviors of stochastic differential equation models of biological systems using change of measures

Volume 13, Issue S-4

0 -- 0Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio. Fine-tuning anti-tumor immunotherapies via stochastic simulations
0 -- 0Marco Falda, Stefano Toppo, Alessandro Pescarolo, Enrico Lavezzo, Barbara Di Camillo, Andrea Facchinetti, Elisa Cilia, Riccardo Velasco, Paolo Fontana. Argot2: a large scale function prediction tool relying on semantic similarity of weighted Gene Ontology terms
0 -- 0Marco Pellegrini, Maria Elena Renda, Alessio Vecchio. Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases
0 -- 0Lorenzo Lazzerini-Ospri, Pasquale Stano, Pier Luigi Luisi, Roberto Marangoni. Characterization of the emergent properties of a synthetic quasi-cellular system
0 -- 0Paolo Romano, Manuela Helmer-Citterich. Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics
0 -- 0Francesco Maria Calabrese, Domenico Simone, Marcella Attimonelli. Primates and mouse NumtS in the UCSC Genome Browser
0 -- 0Arianna Consiglio, Massimo Carella, Giorgio De Caro, Gianfranco Delle Foglie, Candida Giovannelli, Giorgio Grillo, Massimo Ianigro, Flavio Licciulli, Orazio Palumbo, Ada Piepoli, Elena Ranieri, Sabino Liuni. BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments
0 -- 0Fabio Mavelli. Stochastic simulations of minimal cells: the Ribocell model
0 -- 0Anna Vangone, Romina Oliva, Luigi Cavallo. CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions
0 -- 0Fabio Fioravanti, Manuela Helmer-Citterich, Enrico Nardelli. Modeling gene regulatory network motifs using statecharts
0 -- 0Paolo Pannarale, Domenico Catalano, Giorgio De Caro, Giorgio Grillo, Pietro Leo, Graziano Pappadà, Francesco Rubino, Gaetano Scioscia, Flavio Licciulli. GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity database
0 -- 0Federico Fogolari, Alessandra Corazza, Vijaylakshmi Yarra, Anusha Jalaru, Paolo Viglino, Gennaro Esposito. Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii
0 -- 0Susanna Zucca, Lorenzo Pasotti, Giuliano Mazzini, Maria Gabriella Cusella De Angelis, Paolo Magni. Characterization of an inducible promoter in different DNA copy number conditions
0 -- 0Achille Zappa, Andrea Splendiani, Paolo Romano 0001. Towards linked open gene mutations data
0 -- 0Andrea Cornero, Massimo Acquaviva, Paolo Fardin, Rogier Versteeg, Alexander Schramm, Alessandra Eva, Maria Bosco, Fabiola Blengio, Sara Barzaghi, Luigi Varesio. Design of a multi-signature ensemble classifier predicting neuroblastoma patients' outcome
0 -- 0Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame. Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
0 -- 0Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa, Stefano Pascarella. PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL
0 -- 0Valerio Bianchi, Pier Federico Gherardini, Manuela Helmer-Citterich, Gabriele Ausiello. Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities
0 -- 0Raluca Mihaela Andrei, Marco Callieri, Maria Francesca Zini, Tiziana Loni, Giuseppe Maraziti, Mike Chen Pan, Monica Zoppè. Intuitive representation of surface properties of biomolecules using BioBlender
0 -- 0Tiziana Sanavia, Fabio Aiolli, Giovanni Da San Martino, Andrea Bisognin, Barbara Di Camillo. Improving biomarker list stability by integration of biological knowledge in the learning process
0 -- 0Domenico Catalano, Domenico Pignone, Gabriella Sonnante, Mariella M. Finetti-Sialer. In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus
0 -- 0Renato Umeton, Giuseppe Nicosia, Charles Forbes Dewey Jr.. OREMPdb: a semantic dictionary of computational pathway models
0 -- 0Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Silvia G. Priori, Riccardo Bellazzi. An ICT infrastructure to integrate clinical and molecular data in oncology research

Volume 13, Issue S-3

0 -- 0Yu-Keng Shih, Srinivasan Parthasarathy. Scalable global alignment for multiple biological networks
0 -- 0Lei Yang, En Cheng, Z. Meral Özsoyoglu. Efficient path-based computations on pedigree graphs with compact encodings
0 -- 0Jeremy R. Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan. Comparative analysis and visualization of multiple collinear genomes
0 -- 0Ferhat Ay, Michael Dang, Tamer Kahveci. Metabolic network alignment in large scale by network compression
0 -- 0Boon-Siew Seah, Sourav S. Bhowmick, Charles Forbes Dewey Jr., Hanry Yu. FUSE: a profit maximization approach for functional summarization of biological networks
0 -- 0Corban G. Rivera, Brett M. Tyler, T. M. Murali. Sensitive detection of pathway perturbations in cancers
0 -- 0Li An, Haibin Ling, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou. Learning pair-wise gene functional similarity by multiplex gene expression maps
0 -- 0Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu. Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy
0 -- 0Lu He, Alan M. Friedman, Chris Bailey-Kellogg. Algorithms for optimizing cross-overs in DNA shuffling
0 -- 0Youngik Yang, Kenneth P. Nephew, Sun Kim. A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters
0 -- 0Marco Pellegrini, Maria Elena Renda, Alessio Vecchio. Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
0 -- 0Adriana Muñoz, David Sankoff. Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution
0 -- 0R. Mitchell Parry, John H. Phan, May D. Wang. Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems
0 -- 0Richard Jang, Xin Gao, Ming Li. 15N-NOESY
0 -- 0Yuan Li, Shaojie Zhang. Predicting folding pathways between RNA conformational structures guided by RNA stacks

Volume 13, Issue S-2

0 -- 0Juan Esquivel-Rodríguez, Daisuke Kihara. Evaluation of multiple protein docking structures using correctly predicted pairwise subunits
0 -- 0Richard C. McEachin, Keerthi S. Sannareddy, James D. Cavalcoli, Alla Karnovsky, Jacqueline M. Vink, Maureen A. Sartor. Convergence of genetic influences in comorbidity
0 -- 0Jeremy W. Prokop, Thomas C. Leeper, Zhong-Hui Duan, Amy Milsted. Amino acid function and docking site prediction through combining disease variants, structure alignments, sequence alignments, and molecular dynamics: a study of the HMG domain
0 -- 0Robert A. Colvin, Jundong Liu. Preface
0 -- 0Yang Xiang, Cun-Quan Zhang, Kun Huang. Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data
0 -- 0Xiaogang Wu, Hui Huang 0007, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen. Reordering based integrative expression profiling for microarray classification
0 -- 0Mark R. Dalman, Anthony Deeter, Gayathri Nimishakavi, Zhong-Hui Duan. Fold change and p-value cutoffs significantly alter microarray interpretations
0 -- 0Fernando Farfán, Jun Ma, Maureen A. Sartor, George Michailidis, H. V. Jagadish. THINK Back: KNowledge-based Interpretation of High Throughput data
0 -- 0Zhi Han, Lu Tian, Thierry Pécot, Tim Hui-Ming Huang, Raghu Machiraju, Kun Huang. A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
0 -- 0Lauren S. Mogil, Kamil Slowikowski, Howard M. Laten. Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome
0 -- 0Franziska Jentzsch, Jennifer V. Hines. Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery
0 -- 0Lee Sael, Daisuke Kihara. Constructing patch-based ligand-binding pocket database for predicting function of proteins
0 -- 0Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, Geoffrey Fox. Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets
0 -- 0Ariful Azad, Saumyadipta Pyne, Alex Pothen. Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry

Volume 13, Issue S-19

0 -- 0Xiaolong Wu, Yun Heo, Izzat El Hajj, Wen-mei W. Hwu, Deming Chen, Jian Ma. TIGER: tiled iterative genome assembler
0 -- 0Yves Gagnon, Mathieu Blanchette, Nadia El-Mabrouk. A flexible ancestral genome reconstruction method based on gapped adjacencies
0 -- 0Mingfu Shao, Yu Lin. Approximating the edit distance for genomes with duplicate genes under DCJ, insertion and deletion
0 -- 0Katharina Jahn, Henner Sudek, Jens Stoye. Multiple genome comparison based on overlap regions of pairwise local alignments
0 -- 0Maribel Hernandez-Rosales, Marc Hellmuth, Nicolas Wieseke, Katharina T. Huber, Vincent Moulton, Peter F. Stadler. From event-labeled gene trees to species trees
0 -- 0Maryam Haghighi, David Sankoff. Medians seek the corners, and other conjectures
0 -- 0Hyun Jung Park, Luay Nakhleh. Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria
0 -- 0Daniel Doerr, Annelyse Thévenin, Jens Stoye. Gene family assignment-free comparative genomics
0 -- 0Poly H. da Silva, Raphael Machado, Simone Dantas, Marília D. V. Braga. Restricted DCJ-indel model: sorting linear genomes with DCJ and indels
0 -- 0Krister M. Swenson, Nadia El-Mabrouk. Gene trees and species trees: irreconcilable differences
0 -- 0Filippo Utro, Omar Cornejo, Donald Livingstone, Juan Motamayor, Laxmi Parida. ARG-based genome-wide analysis of cacao cultivars
0 -- 0Mathieu Blanchette. Exploiting ancestral mammalian genomes for the prediction of human transcription factor binding sites
0 -- 0Sergey Aganezov Jr., Max A. Alekseyev. On pairwise distances and median score of three genomes under DCJ
0 -- 0Olivier Tremblay Savard, Krister M. Swenson. A graph-theoretic approach for inparalog detection
0 -- 0Ahmad Mahmoody, Crystal L. Kahn, Benjamin J. Raphael. Reconstructing genome mixtures from partial adjacencies
0 -- 0Nicolas Maillet, Claire Lemaitre, Rayan Chikhi, Dominique Lavenier, Pierre Peterlongo. Compareads: comparing huge metagenomic experiments
0 -- 0Katharina Jahn, Chunfang Zheng, Jakub Kovác, David Sankoff. A consolidation algorithm for genomes fractionated after higher order polyploidization
0 -- 0Ján Manuch, Murray Patterson, Roland Wittler, Cedric Chauve, Eric Tannier. Linearization of ancestral multichromosomal genomes

Volume 13, Issue S-18

0 -- 0Heewook Lee, Ellen Popodi, Patricia L. Foster, Haixu Tang. Detecting structural variants involving repetitive elements: capturing transposition events of IS elements in the genome of Escherichia coli
0 -- 0Kyle D. Bemis, Livia Eberlin, Christina Ferreira, R. Cooks, Olga Vitek. Spatial segmentation and feature selection for desi imaging mass spectrometry data with spatially-aware sparse clustering
0 -- 0Jing Gong, Yin Tong, Hong-mei Zhang, An-Yuan Guo. miRNASNP: a database of miRNA related SNPs and their effects on miRNA function
0 -- 0Kyungtaek Lim, Yoshikazu Furuta, Ichizo Kobayashi. Unexpected variations in translation initiation machinery
0 -- 0Alexander Goncearenco, Priscila Grynberg, Olga B. Botvinnik, Geoff Macintyre, Thomas Abeel. Highlights from the Eighth International Society for Computational Biology (ISCB) Student Council Symposium 2012
0 -- 0Ignacio S. Caballero, Gracia Bonilla, Judy Y. Yen, John H. Connor. Diagnosing Lassa virus infection by tracking the antiviral response
0 -- 0Oliver Voggenreiter, Stefan Bleuler, Wilhelm Gruissem. Exact biclustering algorithm for the analysis of large gene expression data sets
0 -- 0Ernesto Iacucci, Léon-Charles Tranchevent, Dusan Popovic, Georgios A. Pavlopoulos, Bart De Moor, Reinhard Schneider 0002, Yves Moreau. A bioinformatics e-dating story: computational prediction and prioritization of receptor-ligand pairs
0 -- 0Shruthi Viswanath, Chengyong Yang. Color call improvement in next generation sequencing using multi-class support vector machines
0 -- 0Yingying Wei, Xia Li, Qianfei Wang, Hongkai Ji. iASeq: integrating multiple chip-seq datasets for detecting allele-specific binding
0 -- 0Tulip Nandu, Meeta Pradhan, Mathew J. Palakal. Elucidating gene signatures that control the circadian rhythm in cyanobacteria using bioinformatics methods
0 -- 0Serghei Mangul, Adrian Caciula, Dumitru Brinza, Ion I. Mandoiu, Alex Zelikovsky. TRIP: a method for novel transcript reconstruction from paired-end RNA-seq reads
0 -- 0Huy Q. Dinh. Epi-letters - how to describe epigenetic signatures

Volume 13, Issue S-17

0 -- 0Felix A. Kruger, Raghd Rostom, John P. Overington. Mapping small molecule binding data to structural domains
0 -- 0Mahmoud ElHefnawi, Mohammad ElGamacy, Mohamed Fares. Multiple virtual screening approaches for finding new Hepatitis c virus RNA-dependent RNA polymerase inhibitors: Structure-based screens and molecular dynamics for the pursue of new poly pharmacological inhibitors
0 -- 0Kevin Lim, Limsoon Wong. CMPF: Class-switching minimized pathfinding in metabolic networks
0 -- 0Mohamed El-Kalioby, Mohamed Abouelhoda, Jan Krüger, Robert Giegerich, Alexander Sczyrba, Dennis P. Wall, Peter J. Tonellato. Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package
0 -- 0Liang Zhao, Limsoon Wong, Lanyuan Lu, Steven C. H. Hoi, Jinyan Li. B-cell epitope prediction through a graph model
0 -- 0Chuan Hock Koh, Sucheendra K. Palaniappan, P. S. Thiagarajan, Limsoon Wong. Improved statistical model checking methods for pathway analysis
0 -- 0Mostafa M. Abbas, Mohamed Abouelhoda, Hazem M. Bahig. A hybrid method for the exact planted (l, d) motif finding problem and its parallelization
0 -- 0Masaomi Nakamura, Tsuyoshi Hachiya, Yutaka Saito, Kengo Sato, Yasubumi Sakakibara. An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds
0 -- 0Emily Chia-Yu Su, Jia-Ming Chang, Cheng-Wei Cheng, Ting-Yi Sung, Wen-Lian Hsu. Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing
0 -- 0Mogeeb A. A. Mosleh, Hayat Manssor, Sorayya Malek, Pozi Milow, Aishah Salleh. A preliminary study on automated freshwater algae recognition and classification system
0 -- 0Je-Gun Joung, Soo-Jin Kim, Soo-Yong Shin, Byoung-Tak Zhang. A probabilistic coevolutionary biclustering algorithm for discovering coherent patterns in gene expression dataset
0 -- 0Bhyravabhotla Jayaram, Tanya Singh, Goutam Mukherjee, Abhinav Mathur, Shashank Shekhar, Vandana Shekhar. Sanjeevini: a freely accessible web-server for target directed lead molecule discovery
0 -- 0Minho Lee, Dongsup Kim. Large-scale reverse docking profiles and their applications
0 -- 0Rithvik Vinekar, Chandra Verma, Indira Ghosh. Functional relevance of dynamic properties of Dimeric NADP-dependent Isocitrate Dehydrogenases
0 -- 0Christian Schönbach, Sissades Tongsima, Jonathan Chan, Vladimir Brusic, Tin Wee Tan, Shoba Ranganathan. InCoB2012 Conference: from biological data to knowledge to technological breakthroughs
0 -- 0Carlo Bianca, Ferdinando Chiacchio, Francesco Pappalardo, Marzio Pennisi. Mathematical modeling of the immune system recognition to mammary carcinoma antigen
0 -- 0Saowaluck Kaewkamnerd, Chairat Uthaipibull, Apichart Intarapanich, Montri Pannarut, Sastra Chaotheing, Sissades Tongsima. An automatic device for detection and classification of malaria parasite species in thick blood film
0 -- 0Ranjeeta Menon, Gagan Garg, Robin B. Gasser, Shoba Ranganathan. TranSeqAnnotator: large-scale analysis of transcriptomic data
0 -- 0Devendra Kumar Biswal, Manish Debnath, Shakti Kumar, Pramod Tandon. Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding
0 -- 0Sungin Park, Soo-Yong Shin, Kyu Baek Hwang. CFMDS: CUDA-based fast multidimensional scaling for genome-scale data
0 -- 0Rambabu Chinta, Joo Huang Tan, Martin Wasser. The study of muscle remodeling in Drosophila metamorphosis using in vivo microscopy and bioimage informatics
0 -- 0Atima Tharatipyakul, Somrak Numnark, Duangdao Wichadakul, Supawadee Ingsriswang. ChemEx: information extraction system for chemical data curation
0 -- 0En-Yu Lai, Wei-Bung Wang, Tao Jiang, Kun-Pin Wu. A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree
0 -- 0Sriganesh Srihari, Hon Wai Leong. Temporal dynamics of protein complexes in PPI Networks: a case study using yeast cell cycle dynamics
0 -- 0Hui-Ling Huang, Phasit Charoenkwan, Te-Fen Kao, Hua-Chin Lee, Fang-Lin Chang, Wen-Lin Huang, Shinn-Jang Ho, Li-Sun Shu, Wen-Liang Chen, Shinn-Ying Ho. Prediction and analysis of protein solubility using a novel scoring card method with dipeptide composition
0 -- 0Chian Teo, Steven R. Shave, Adam Thean Chor, Abu Salleh, Mohd Basyaruddin Abdul Rahman, Malcolm D. Walkinshaw, Bimo A. Tejo. Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening

Volume 13, Issue S-16

0 -- 0D. R. Mani, Susan E. Abbatiello, Steven A. Carr. Statistical characterization of multiple-reaction monitoring mass spectrometry (MRM-MS) assays for quantitative proteomics
0 -- 0Marina Bessarabova, Alexander Ishkin, Lellean JeBailey, Tatiana Nikolskaya, Yuri Nikolsky. Knowledge-based analysis of proteomics data
0 -- 0Ann L. Oberg, Douglas W. Mahoney. Statistical methods for quantitative mass spectrometry proteomic experiments with labeling
0 -- 0Kyowon Jeong, Sangtae Kim, Nuno Bandeira. False discovery rates in spectral identification
0 -- 0Melissa Key. A tutorial in displaying mass spectrometry-based proteomic data using heat maps
0 -- 0Yuliya V. Karpievitch, Alan R. Dabney, Richard D. Smith. Normalization and missing value imputation for label-free LC-MS analysis
0 -- 0Juergen Cox, Matthias Mann. 1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data
0 -- 0Yong Fuga Li, Predrag Radivojac. Computational approaches to protein inference in shotgun proteomics
0 -- 0Timothy Clough, Safia Thaminy, Susanne Ragg, Ruedi Aebersold, Olga Vitek. Statistical protein quantification and significance analysis in label-free LC-MS experiments with complex designs
0 -- 0Theodore Alexandrov. MALDI imaging mass spectrometry: statistical data analysis and current computational challenges
0 -- 0Sven Nahnsen, Oliver Kohlbacher. In silico design of targeted SRM-based experiments
0 -- 0Viktor Granholm, William Stafford Noble, Lukas Käll. A cross-validation scheme for machine learning algorithms in shotgun proteomics
0 -- 0Kelvin Ma, Olga Vitek, Alexey I. Nesvizhskii. A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet

Volume 13, Issue S-15

0 -- 0Fan Zhang, Renee Drabier. IPAD: the Integrated Pathway Analysis Database for Systematic Enrichment Analysis
0 -- 0Andrey Ptitsyn, Leonid L. Moroz. Computational workflow for analysis of gain and loss of genes in distantly related genomes
0 -- 0Halil Bisgin, Zhichao Liu, Reagan Kelly, Hong Fang, Xiaowei Xu, Weida Tong. Investigating drug repositioning opportunities in FDA drug labels through topic modeling
0 -- 0Jonathan D. Wren, Mikhail G. Dozmorov, Dennis Burian, Rakesh Kaundal, Susan Bridges, Doris M. Kupfer. Proceedings of the 2012 MidSouth computational biology and bioinformatics society (MCBIOS) conference
0 -- 0Zhifa Liu, Brandon M. Malone, Changhe Yuan. Empirical evaluation of scoring functions for Bayesian network model selection
0 -- 0Dongxia Yao, Qiang Wei, Wenying Xu, Ryan D. Syrenne, Joshua S. Yuan, Zhen Su. Comparative genomic analysis of NAC transcriptional factors to dissect the regulatory mechanisms for cell wall biosynthesis
0 -- 0Ruchi Verma, Ulrich Melcher. A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins
0 -- 0Hui Huang 0007, Xiaogang Wu, Madhankumar Sonachalam, Sammed N. Mandape, Ragini Pandey, Karl F. MacDorman, Ping Wan, Jake Y. Chen. PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries
0 -- 0Gang Fu, Xiaofei Nan, Haining Liu, Ronak Y. Patel, Pankaj R. Daga, Yixin Chen, Dawn Wilkins, Robert J. Doerksen. Implementation of multiple-instance learning in drug activity prediction
0 -- 0Tibor Pechan, Steven R. Gwaltney. Calculations of relative intensities of fragment ions in the MSMS spectra of a doubly charged penta-peptide
0 -- 0Gaihua Zhang, Zhen Su. Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization
0 -- 0Lifeng Zhang, Daniel Berleant, Yi Wang, Ling Li, Diane J. Cook, Eve Syrkin Wurtele. BirdsEyeView (BEV): graphical overviews of experimental data
0 -- 0Joseph S. Reddy, Ranjit Kumar, James M. Watt, Mark L. Lawrence, Shane C. Burgess, Bindu Nanduri. Transcriptome profile of a bovine respiratory disease pathogen: Mannheimia haemolytica PHL213
0 -- 0Yixiang Zhang, Sanmin Liu, Susie Y. Dai, Joshua S. Yuan. Integration of shot-gun proteomics and bioinformatics analysis to explore plant hormone responses

Volume 13, Issue S-14

0 -- 0Irene Sánchez-Linares, Horacio Emilio Pérez Sánchez, José M. Cecilia, José M. García. High-Throughput parallel blind Virtual Screening using BINDSURF
0 -- 0Pietro Liò, Nicola Paoletti, Mohammad Ali Moni, Kathryn Atwell, Emanuela Merelli, Marco Viceconti. Modelling osteomyelitis
0 -- 0Damiano Piovesan, Giuseppe Profiti, Pier Luigi Martelli, Rita Casadio. The human "magnesome": detecting magnesium binding sites on human proteins
0 -- 0Francesco Sambo, Emanuele Trifoglio, Barbara Di Camillo, Gianna Maria Toffolo, Claudio Cobelli. Bag of Naïve Bayes: biomarker selection and classification from genome-wide SNP data
0 -- 0Paola Lecca, Daniele Morpurgo. Modelling non-homogeneous stochastic reaction-diffusion systems: the case study of gemcitabine-treated non-small cell lung cancer growth
0 -- 0Ivan Merelli, Federica Viti, Luciano Milanesi. IBDsite: a Galaxy-interacting, integrative database for supporting inflammatory bowel disease high throughput data analysis
0 -- 0Sophie Coutant, Chloé Cabot, Arnaud Lefebvre, Martine Léonard, Élise Prieur-Gaston, Dominique Campion, Thierry Lecroq, Hélène Dauchel. EVA: Exome Variation Analyzer, an efficient and versatile tool for filtering strategies in medical genomics
0 -- 0Lina Fatima Soualmia, Élise Prieur-Gaston, Zied Moalla, Thierry Lecroq, Stéfan Jacques Darmoni. Matching health information seekers' queries to medical terms
0 -- 0Vladan Mijatovic, Ilaria Iacobucci, Marco Sazzini, Luciano Xumerle, Antonio Mori, Pier Franco Pignatti, Giovanni Martinelli, Giovanni Malerba. Imputation reliability on DNA biallelic markers for drug metabolism studies
0 -- 0Alberto Malovini, Nicola Barbarini, Riccardo Bellazzi, Francesca De Michelis. Hierarchical Naive Bayes for genetic association studies
0 -- 0Matteo Re, Giorgio Valentini. Cancer module genes ranking using kernelized score functions
0 -- 0Francesca Nadalin, Francesco Vezzi, Alberto Policriti. GapFiller: a de novo assembly approach to fill the gap within paired reads
0 -- 0Riccardo Bellazzi, Marco Masseroli, Shawn Murphy, Amnon Shabo, Paolo Romano. Clinical Bioinformatics: challenges and opportunities
0 -- 0Xian Yang, Rui Han, Yike Guo, Jeremy T. Bradley, Benita Cox, Robert Dickinson, Richard Kitney. Modelling and performance analysis of clinical pathways using the stochastic process algebra PEPA

Volume 13, Issue S-13

0 -- 0Jiexin Zhang, Kevin R. Coombes. Sources of variation in false discovery rate estimation include sample size, correlation, and inherent differences between groups
0 -- 0Guoshuai Cai, Hua Li, Yue Lu, Xuelin Huang, Juhee Lee, Peter Müller, Yuan Ji, Shoudan Liang. Accuracy of RNA-Seq and its dependence on sequencing depth
0 -- 0Kevin Riehle, Cristian Coarfa, Andrew R. Jackson, Jun Ma, Arpit Tandon, Sameer Paithankar, Sriram Raghuraman, Toni-Ann Mistretta, Delphine Saulnier, Sabeen Raza, Maria Diaz, Robert Shulman, Kjersti Aagaard, James Versalovic, Aleksandar Milosavljevic. The Genboree Microbiome Toolset and the analysis of 16S rRNA microbial sequences
0 -- 0Catherine H. Schein, David M. Bowen, Jessica A. Lewis, Kyung Choi, Aniko Paul, Gerbrand J. van der Heden van Noort, Wenzhe Lu, Dmitri V. Filippov. Physicochemical property consensus sequences for functional analysis, design of multivalent antigens and targeted antivirals
0 -- 0Peng Qiu, Li Zhang. Identification of markers associated with global changes in DNA methylation regulation in cancers
0 -- 0Kenneth Sundberg, Mark J. Clement, Quinn Snell, Dan Ventura, Michael Whiting, Keith A. Crandall. Phylogenetic search through partial tree mixing
0 -- 0Jorge R. Herskovic, Devika Subramanian, Trevor Cohen, Pamela A. Bozzo-Silva, Charles F. Bearden, Elmer V. Bernstam. Graph-based signal integration for high-throughput phenotyping
0 -- 0Priyakshi Mahanta, Hasin Afzal Ahmed, Dhruba K. Bhattacharyya, Jugal K. Kalita. An effective method for network module extraction from microarray data
0 -- 0Yuan Ji, Riten Mitra, Fernando Quintana, Alejandro Jara, Peter Müller, Ping Liu, Yue Lu, Shoudan Liang. BM-BC: a Bayesian method of base calling for Solexa sequence data
0 -- 0Bong-Hyun Kim, Bhadrachalam Chitturi, Nick V. Grishin. Self consistency grouping: a stringent clustering method
0 -- 0Bradley M. Broom, Kim-Anh Do, Devika Subramanian. Model averaging strategies for structure learning in Bayesian networks with limited data

Volume 13, Issue S-12

0 -- 0Yan Jiao, Yonghui Ma, Xiaoyun Liu, Weikuan Gu. Evaluation of potential role of vitamin C in differential skeletal development between female and male mice using a mouse model
0 -- 0Dana Marshall, Jianan Dong, Leon Dent, Siddharth Pratap. The antibiotic resistance proteome of Acinetobacter baumanii MDR isolate MMC#4
0 -- 0Uta Ziegler, Yuanan Diao, Claus Ernst, Anthony Montemayor. Computational investigation of DNA packing in confinement
0 -- 0Marc Beck, Roman V. Yampolskiy. DNA as a medium for hiding data
0 -- 0Jonathan Babbage, Naga Nagisetty, Steven P. Larmore, Jacqueline Fiore. Delivering informatics for clinical research in developing countries
0 -- 0Chandrajit Lahiri, Pawar Shrikant, Radhakrishnan Sabarinathan, M. Ashraf, Dipshikha Chakravortty. Identifying indispensable proteins of the type III secretion systems of Salmonella enterica serovar Typhimurium strain LT2
0 -- 0Matt Gannon, Rachel Stevens, Molly Griffith, Mark Bardgett. The effects of early-life risperidone administration on forebrain neurotrophin expression during adulthood
0 -- 0Fusheng Zhao, Yonghui Ma, Yan Jiao, Lishi Wang, Yue Huang, Wei Wei, Weikuan Gu. Identification of hearing loss relevant genes in QTL on mouse chromosome 16
0 -- 0Farid Yaghouby, Ting Zhang, Martin Striz, James Crawford, Kevin Donohue, Bruce O'Hara, Sridhar Sunderam. Experimental and computational analysis of mouse sleep-wake dynamics
0 -- 0Neil Moore, Jerzy W. Jaromczyk, Christopher L. Schardl. Finding long protein products of alternatively spliced genes
0 -- 0Christopher Burton, Sujin Kim. The development of a three-frame timeline for clinical concepts extracted from discharge summaries
0 -- 0Benjamin J. Harrison, Robert M. Flight, Abdallah Eteleeb, Eric C. Rouchka, Jeffrey C. Petruska. RNASeq profiling of UTR expression during neuronal plasticity
0 -- 0Paul A. Harris. Research Electronic Data Capture (REDCap) - planning, collecting and managing data for clinical and translational research
0 -- 0Eric C. Rouchka, Robert M. Flight, Hunter N. B. Moseley. Proceedings of the Eleventh Annual UT-ORNL-KBRIN Bioinformatics Summit 2012
0 -- 0Caroline Rempe, Charles R. Budinoff, T. Effler, Alison Buchan. The influence of sample biases on estimations of marine microbial diversity
0 -- 0Lishi Wang, Wenli Lu, Rachel Scheib, Yue Huang, Xiaoyun Liu, Linda Myers, Lu Lu, Robert W. Williams, Yan Jiao, Weikuan Gu. QTLs for bone mineral density of femurs and tibias in recombinant inbred strains derived from C57BL/6J and DBA/2J inbred strains
0 -- 0Nourtan Abdeltawab, Lu Lu, Robert W. Williams, Malak Kotb. Meta-analysis of genes within QTLs of group A streptococcal sepsis and their expression QTLs reveal pathways modulating host differential response to streptococcal sepsis
0 -- 0Denise R. Koessler, Elizabeth G. Johnson, Jordan M. Utley, Harry A. Richards, Cynthia B. Peterson. Building better interdisciplinary scientists: creating graduate level courses to address the communication gap in interdisciplinary research
0 -- 0Gopinath Rajadinakaran, Huifang Sun, Claire Rinehart, Eric C. Rouchka, Michael E. Smith. Regulation of cell proliferation and apoptosis by growth hormone during zebrafish auditory hair cell regeneration
0 -- 0Behrouz Madahian, Robert C. Klesges, Lisa Klesges, Ramin Homayouni. System dynamics modeling of childhood obesity
0 -- 0Wenyuan Zhao, Tieqian Zhao, Yuanjian Chen, Yao Sun. Temporal and spatial relationship of gene expression in the infarcted rat heart
0 -- 0Yue Huang, Lishi Wang, Robert W. Williams, Weikuan Gu, Yan Jiao. Evaluation of potential role of Atp5g3 in modulating alcohol preference and obesity
0 -- 0Yonghui Ma, Yan Jiao, Fusheng Zhao, Weikuan Gu. Evaluation of gene expression in muscle in mouse model lacking of vitamin C synthesis
0 -- 0Alexander Kemper, Musa Hindi, Kenneth S. Ramos, Theodore S. Kalbfleisch. Comprehensive characterization of an individual's LINE-1 insertion profile using next generation sequencing data

Volume 13, Issue S-11

0 -- 0Robert Bossy, Julien Jourde, Alain-Pierre Manine, Philippe Veber, Érick Alphonse, Maarten van de Guchte, Philippe Bessières, Claire Nedellec. BioNLP Shared Task - The Bacteria Track
0 -- 0Halil Kilicoglu, Sabine Bergler. Biological event composition
0 -- 0Andreas Vlachos, Mark Craven. Biomedical event extraction from abstracts and full papers using search-based structured prediction
0 -- 0David McClosky, Sebastian Riedel, Mihai Surdeanu, Andrew McCallum, Christopher D. Manning. Combining joint models for biomedical event extraction
0 -- 0Sampo Pyysalo, Tomoko Ohta, Rafal Rak, Dan Sullivan, Chunhong Mao, Chunxia Wang, Bruno W. S. Sobral, Jun'ichi Tsujii, Sophia Ananiadou. Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011
0 -- 0Zorana Ratkovic, Wiktoria Golik, Pierre Warnier. Event extraction of bacteria biotopes: a knowledge-intensive NLP-based approach
0 -- 0Jin-Dong Kim, Ngan Nguyen, Yue Wang, Jun'ichi Tsujii, Toshihisa Takagi, Akinori Yonezawa. The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011
0 -- 0Jari Björne, Filip Ginter, Tapio Salakoski. University of Turku in the BioNLP'11 Shared Task
0 -- 0Sofie Van Landeghem, Jari Björne, Thomas Abeel, Bernard De Baets, Tapio Salakoski, Yves Van de Peer. Semantically linking molecular entities in literature through entity relationships

Volume 13, Issue S-10

0 -- 0Pavol Jancura, Eleftheria Mavridou, Enrique Carrillo-de Santa Pau, Elena Marchiori. A methodology for detecting the orthology signal in a PPI network at a functional complex level
0 -- 0John D. Eblen, Charles A. Phillips, Gary L. Rogers, Michael A. Langston. The maximum clique enumeration problem: algorithms, applications, and implementations
0 -- 0Pavel Skums, Zoya Dimitrova, David S. Campo, Gilberto Vaughan, Livia Rossi, Joseph C. Forbi, Jonny Yokosawa, Alex Zelikovsky, Yuri Khudyakov. Efficient error correction for next-generation sequencing of viral amplicons
0 -- 0Ruchi Chaudhary, J. Gordon Burleigh, Oliver Eulenstein. Efficient error correction algorithms for gene tree reconciliation based on duplication, duplication and loss, and deep coalescence
0 -- 0Andrea Szabóová, Ondrej Kuzelka, Filip Zelezný, Jakub Tolar. Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search
0 -- 0Fei Guo, Lusheng Wang. Computing the protein binding sites
0 -- 0Jianer Chen, Ion I. Mandoiu, Raj Sunderraman, Jianxin Wang, Alexander Zelikovsky. Guest Editors' Introduction
0 -- 0Harris T. Lin, J. Gordon Burleigh, Oliver Eulenstein. Consensus properties for the deep coalescence problem and their application for scalable tree search
0 -- 0Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu. High-performance blob-based iterative three-dimensional reconstruction in electron tomography using multi-GPUs
0 -- 0Matej Holec, Jirí Kléma, Filip Zelezný, Jakub Tolar. Comparative evaluation of set-level techniques in predictive classification of gene expression samples
0 -- 0Jonathan Q. Jiang, Maoying Wu. Predicting multiplex subcellular localization of proteins using protein-protein interaction network: a comparative study
0 -- 0Pingzhao Hu, Shelley B. Bull, Hui Jiang 0001. Gene network modular-based classification of microarray samples
0 -- 0Chunfang Zheng, David Sankoff. Gene order in rosid phylogeny, inferred from pairwise syntenies among extant genomes
0 -- 0Vadim Mozhayskiy, Ilias Tagkopoulos. Guided evolution of in silico microbial populations in complex environments accelerates evolutionary rates through a step-wise adaptation
0 -- 0Wen-Chieh Chang 0002, Sudheer Vakati, Roland Krause, Oliver Eulenstein. Exploring biological interaction networks with tailored weighted quasi-bicliques
0 -- 0Jieyue He, Chaojun Li, Baoliu Ye, Wei Zhong. Efficient and accurate greedy search methods for mining functional modules in protein interaction networks
0 -- 0Pawel Górecki, Oliver Eulenstein. Algorithms: simultaneous error-correction and rooting for gene tree reconciliation and the gene duplication problem
0 -- 0Vadim Mozhayskiy, Ilias Tagkopoulos. Horizontal gene transfer dynamics and distribution of fitness effects during microbial in silico evolution
0 -- 0Jeremy J. Jay, John D. Eblen, Yun Zhang, Mikael Benson, Andy D. Perkins, Arnold M. Saxton, Brynn H. Voy, Elissa J. Chesler, Michael A. Langston. A systematic comparison of genome-scale clustering algorithms
0 -- 0Zhan Zhou, Jianying Gu, Yong-Quan Li, Yufeng Wang. Genome plasticity and systems evolution in Streptomyces

Volume 13, Issue S-1

0 -- 0Kenneth McLeod, Gus Ferguson, Albert Burger. Argudas: lessons for argumentation in biology based on a gene expression use case
0 -- 0Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens. Populous: a tool for building OWL ontologies from templates
0 -- 0Albert Burger, Adrian Paschke, Paolo Romano 0001, M. Scott Marshall, Andrea Splendiani. Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010
0 -- 0Mohameth-François Sy, Sylvie Ranwez, Jacky Montmain, Armelle Regnault, Michel Crampes, Vincent Ranwez. User centered and ontology based information retrieval system for life sciences
0 -- 0Matthew Holford, James P. McCusker, Kei-Hoi Cheung, Michael Krauthammer. A semantic web framework to integrate cancer omics data with biological knowledge
0 -- 0Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper. Gauging triple stores with actual biological data
0 -- 0Alejandra González Beltrán, Ben Tagger, Anthony Finkelstein. Federated ontology-based queries over cancer data
0 -- 0E. Luke McCarthy, Benjamin P. Vandervalk, Mark Wilkinson. SPARQL Assist language-neutral query composer
0 -- 0Abdelaali Briache, Kamar Marrakchi, Amine Kerzazi, Ismael Navas Delgado, Badr Din Rossi Hassani, Khalid Lairini, José Francisco Aldana Montes. Transparent mediation-based access to multiple yeast data sources using an ontology driven interface
0 -- 0Rafael Berlanga Llavori, Ernesto Jiménez-Ruiz, Victoria Nebot. Exploring and linking biomedical resources through multidimensional semantic spaces