default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBMC Bioinformatics, Volume 13 - Supplements
Volume 13, Number S-1, January 2012
- Albert Burger, Adrian Paschke, Paolo Romano
, M. Scott Marshall, Andrea Splendiani:
Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010. S1 - E. Luke McCarthy, Benjamin P. Vandervalk, Mark D. Wilkinson:
SPARQL Assist language-neutral query composer. S2 - Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper:
Gauging triple stores with actual biological data. S3 - Mohameth-François Sy, Sylvie Ranwez, Jacky Montmain, Armelle Regnault, Michel Crampes, Vincent Ranwez:
User centered and ontology based information retrieval system for life sciences. S4 - Simon Jupp, Matthew Horridge, Luigi Iannone, Julie Klein, Stuart Owen, Joost Schanstra, Katy Wolstencroft, Robert Stevens:
Populous: a tool for building OWL ontologies from templates. S5 - Rafael Berlanga Llavori, Ernesto Jiménez-Ruiz, Victoria Nebot:
Exploring and linking biomedical resources through multidimensional semantic spaces. S6 - Abdelaali 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. S7 - Kenneth McLeod, Gus Ferguson, Albert Burger:
Argudas: lessons for argumentation in biology based on a gene expression use case. S8 - Alejandra N. González-Beltrán, Ben Tagger, Anthony Finkelstein:
Federated ontology-based queries over cancer data. S9 - Matthew Holford, Jamie P. McCusker, Kei-Hoi Cheung, Michael Krauthammer:
A semantic web framework to integrate cancer omics data with biological knowledge. S10
Volume 13, Number S-2, March 2012
- Robert A. Colvin, Jundong Liu:
Preface. I1 - Xiaogang Wu, Hui Huang, Madhankumar Sonachalam, Sina Reinhard, Jeffrey Shen, Ragini Pandey, Jake Y. Chen:
Reordering based integrative expression profiling for microarray classification. S1 - Zhi 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. S2 - Jeremy 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. S3 - Fernando Farfán, Jun Ma, Maureen A. Sartor, George Michailidis, H. V. Jagadish:
THINK Back: KNowledge-based Interpretation of High Throughput data. S4 - Franziska Jentzsch, Jennifer V. Hines:
Interfacing medicinal chemistry with structural bioinformatics: implications for T box riboswitch RNA drug discovery. S5 - Juan Esquivel-Rodríguez, Daisuke Kihara:
Evaluation of multiple protein docking structures using correctly predicted pairwise subunits. S6 - Lee Sael, Daisuke Kihara:
Constructing patch-based ligand-binding pocket database for predicting function of proteins. S7 - Richard C. McEachin, Keerthi S. Sannareddy, James D. Cavalcoli, Alla Karnovsky, Jacqueline M. Vink, Maureen A. Sartor:
Convergence of genetic influences in comorbidity. S8 - Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, Geoffrey C. Fox:
Interpolative multidimensional scaling techniques for the identification of clusters in very large sequence sets. S9 - Ariful Azad, Saumyadipta Pyne, Alex Pothen:
Matching phosphorylation response patterns of antigen-receptor-stimulated T cells via flow cytometry. S10 - Mark R. Dalman, Anthony Deeter, Gayathri Nimishakavi, Zhong-Hui Duan:
Fold change and p-value cutoffs significantly alter microarray interpretations. S11 - Yang Xiang, Cun-Quan Zhang, Kun Huang:
Predicting glioblastoma prognosis networks using weighted gene co-expression network analysis on TCGA data. S12 - Lauren S. Mogil, Kamil Slowikowski, Howard M. Laten:
Computational and experimental analyses of retrotransposon-associated minisatellite DNAs in the soybean genome. S13
Volume 13, Number S-3, March 2012
- Li An, Haibin Ling, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou:
Learning pair-wise gene functional similarity by multiplex gene expression maps. S1 - Ferhat Ay, Michael Dang, Tamer Kahveci:
Metabolic network alignment in large scale by network compression. S2 - Lu He, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for optimizing cross-overs in DNA shuffling. S3 - Richard Jang, Xin Gao, Ming Li:
Combining automated peak tracking in SAR by NMR with structure-based backbone assignment from 15N-NOESY. S4 - Yuan Li, Shaojie Zhang:
Predicting folding pathways between RNA conformational structures guided by RNA stacks. S5 - Adriana Muñoz, David Sankoff:
Detection of gene expression changes at chromosomal rearrangement breakpoints in evolution. S6 - R. Mitchell Parry, John H. Phan, May D. Wang:
Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems. S7 - Marco Pellegrini, Maria Elena Renda, Alessio Vecchio:
Ab initio detection of fuzzy amino acid tandem repeats in protein sequences. S8 - Corban G. Rivera, Brett M. Tyler, T. M. Murali:
Sensitive detection of pathway perturbations in cancers. S9 - Boon-Siew Seah, Sourav S. Bhowmick, C. Forbes Dewey Jr., Hanry Yu:
FUSE: a profit maximization approach for functional summarization of biological networks. S10 - Yu-Keng Shih, Srinivasan Parthasarathy:
Scalable global alignment for multiple biological networks. S11 - Yanni Sun, Osama Aljawad, Jikai Lei, Alex Liu:
Genome-scale NCRNA homology search using a Hamming distance-based filtration strategy. S12 - Jeremy R. Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan:
Comparative analysis and visualization of multiple collinear genomes. S13 - Lei Yang, En Cheng, Z. Meral Özsoyoglu:
Efficient path-based computations on pedigree graphs with compact encodings. S14 - Youngik Yang, Kenneth P. Nephew, Sun Kim:
A novel k-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. S15
Volume 13, Number S-4, March 2012
- Paolo Romano, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics. I1 - Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame:
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. S1 - Emanuele Bramucci, Alessandro Paiardini, Francesco Bossa, Stefano Pascarella:
PyMod: sequence similarity searches, multiple sequence-structure alignments, and homology modeling within PyMOL. S2 - Marco Pellegrini, Maria Elena Renda, Alessio Vecchio:
Tandem repeats discovery service (TReaDS) applied to finding novel cis-acting factors in repeat expansion diseases. S3 - Paolo 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. S4 - Daniele Segagni, Valentina Tibollo, Arianna Dagliati, Alberto Zambelli, Silvia G. Priori, Riccardo Bellazzi:
An ICT infrastructure to integrate clinical and molecular data in oncology research. S5 - Renato Umeton, Giuseppe Nicosia, C. Forbes Dewey Jr.:
OREMPdb: a semantic dictionary of computational pathway models. S6 - Achille Zappa, Andrea Splendiani, Paolo Romano:
Towards linked open gene mutations data. S7 - Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio:
Fine-tuning anti-tumor immunotherapies via stochastic simulations. S8 - Lorenzo Lazzerini-Ospri, Pasquale Stano, Pier Luigi Luisi, Roberto Marangoni:
Characterization of the emergent properties of a synthetic quasi-cellular system. S9 - Fabio Mavelli:
Stochastic simulations of minimal cells: the Ribocell model. S10 - Susanna Zucca, Lorenzo Pasotti, Giuliano Mazzini, Maria Gabriella Cusella De Angelis, Paolo Magni:
Characterization of an inducible promoter in different DNA copy number conditions. S11 - Domenico 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. S12 - Andrea 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. S13 - Marco 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. S14 - Francesco Maria Calabrese, Domenico Simone, Marcella Attimonelli:
Primates and mouse NumtS in the UCSC Genome Browser. S15 - Raluca 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. S16 - Valerio 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. S17 - Federico 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. S18 - Anna Vangone, Romina Oliva, Luigi Cavallo:
CONS-COCOMAPS: a novel tool to measure and visualize the conservation of inter-residue contacts in multiple docking solutions. S19 - Fabio Fioravanti, Manuela Helmer-Citterich, Enrico Nardelli:
Modeling gene regulatory network motifs using statecharts. S20 - Arianna 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. S21 - Tiziana 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. S22
Volume 13, Number S-5, April 2012
- Yingfeng 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. S1 - Yuri 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. S2 - Yuhong 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. S3 - Mayank Daga, Wu-chun Feng:
Multi-dimensional characterization of electrostatic surface potential computation on graphics processors. S4 - Hsiu 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. S5 - Peter Clote, Feng Lou, William Andrew Lorenz:
Maximum expected accuracy structural neighbors of an RNA secondary structure. S6 - Piotr Dittwald, Jerzy Ostrowski, Jakub Karczmarski, Anna Gambin:
Inferring serum proteolytic activity from LC-MS/MS data. S7 - Sumit Kumar Jha, Christopher James Langmead:
Exploring behaviors of stochastic differential equation models of biological systems using change of measures. S8
Volume 13, Number S-6, April 2012
- Chengxi Ye, Zhanshan (Sam) Ma, Charles H. Cannon, Mihai Pop, Douglas W. Yu:
Exploiting sparseness in de novo genome assembly. S1 - Roye Rozov, Eran Halperin, Ron Shamir:
MGMR: leveraging RNA-Seq population data to optimize expression estimation. S2 - Anatoly Efros, Eran Halperin:
Haplotype reconstruction using perfect phylogeny and sequence data. S3 - Ekaterina Khrameeva, Mikhail S. Gelfand:
Biases in read coverage demonstrated by interlaboratory and interplatform comparison of 117 mRNA and genome sequencing experiments. S4 - Gustavo 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. S5 - Jin Zhang, Jiayin Wang, Yufeng Wu:
An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data. S6 - Jón Sveinbjörnsson, Bjarni V. Halldórsson:
PAIR: polymorphic Alu insertion recognition. S7 - Matthew D. Edwards, David K. Gifford:
High-resolution genetic mapping with pooled sequencing. S8 - Thomas Bonfert, Gergely Csaba, Ralf Zimmer, Caroline C. Friedel:
A context-based approach to identify the most likely mapping for RNA-seq experiments. S9 - Layla Oesper, Anna M. Ritz, Sarah J. Aerni, Ryan Drebin, Benjamin J. Raphael:
Reconstructing cancer genomes from paired-end sequencing data. S10 - Boyko 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. S11
Volume 13, Number S-7, May 2012
- M. Michael Gromiha, De-Shuang Huang:
Introduction: advanced intelligent computing theories and their applications in bioinformatics. I1 - M. 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. S1 - Jingyan 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. S2 - Ying-Ke Lei, Zhuhong You, Zhen Ji, Lin Zhu, De-Shuang Huang:
Assessing and predicting protein interactions by combining manifold embedding with multiple information integration. S3 - Xuesong Wang, Lijing Li, Yuhu Cheng:
An overlapping module identification method in protein-protein interaction networks. S4 - Guangyu Cui, Chao Fang, Kyungsook Han:
Prediction of protein-protein interactions between viruses and human by an SVM model. S5 - Zhi-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. S6 - Yin-Ying Wang, Ke-Jia Xu, Jiangning Song, Xing-Ming Zhao:
Exploring drug combinations in genetic interaction network. S7 - Yu-Ting Hsiao, Wei-Po Lee:
Inferring robust gene networks from expression data by a sensitivity-based incremental evolution method. S8 - Vitoantonio 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. S9 - Byungkyu 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. S10 - Wassim Ayadi, Mourad Elloumi, Jin-Kao Hao:
Pattern-driven neighborhood search for biclustering of microarray data. S11 - Kwang Su Jung, Sanghoon Moon, Young Kim, Bong-Jo Kim, Kiejung Park:
Genovar: a detection and visualization tool for genomic variants. S12
Volume 13, Number S-8, May 2012
- Jessie Kennedy, Jos B. T. M. Roerdink:
Highlights of the 1st IEEE Symposium on Biological Data Visualization. S1 - Julian Heinrich, Corinna Vehlow, Florian Battke, Günter Jäger, Daniel Weiskopf, Kay Nieselt:
iHAT: interactive Hierarchical Aggregation Table for Genetic Association Data. S2 - Adam M. Smith, Wen Xu, Yao Sun, James R. Faeder, G. Elisabeta Marai:
RuleBender: integrated modeling, simulation and visualization for rule-based intracellular biochemistry. S3 - Hendrik 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. S4 - Trevor Paterson, Martin Graham, Jessie B. Kennedy, Andy Law:
VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees. S5 - Philip Livengood, Ross Maciejewski, Wei Chen, David S. Ebert:
OmicsVis: an interactive tool for visually analyzing metabolomics data. S6 - David Mayerich, Christopher Björnsson, Jonothan Taylor, Badrinath Roysam:
NetMets: software for quantifying and visualizing errors in biological network segmentation. S7 - Christopher 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. S8
Volume 13, Number S-9, June 2012
- Yann Christinat, Bernard M. E. Moret:
Inferring transcript phylogenies. S1 - Qinmin Hu, Jimmy X. Huang, Xiaohua Hu:
Modeling and mining term association for improving biomedical information retrieval performance. S2 - Xijun Liang, Zhonghang Xia, Li-Wei Zhang, Fang-Xiang Wu:
Inference of gene regulatory subnetworks from time course gene expression data. S3 - Weimin Luo, Keith C. C. Chan:
Discovering patterns in drug-protein interactions based on their fingerprints. S4 - Sohee 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. S5 - Kristopher L. Patton, David J. John, James L. Norris:
Bayesian probabilistic network modeling from multiple independent replicates. S6 - Jingchun Sun, Yonghui Wu, Hua Xu, Zhongming Zhao:
DTome: a web-based tool for drug-target interactome construction. S7 - Zhenyu Yang, David Sankoff:
Generalized adjacency and the conservation of gene clusters in genetic networks defined by synthetic lethals. S8
Volume 13, Number S-10, June 2012
- Jianer Chen, Ion I. Mandoiu, Raj Sunderraman, Jianxin Wang, Alexander Zelikovsky:
Guest Editors' Introduction. S1 - Fei Guo, Lusheng Wang:
Computing the protein binding sites. S2 - Andrea Szabóová, Ondrej Kuzelka, Filip Zelezný, Jakub Tolar:
Prediction of DNA-binding propensity of proteins by the ball-histogram method using automatic template search. S3 - X