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BMC Bioinformatics, Volume 12 - Supplements
Volume 12, Number S-1, March 2011
- Yi-Ping Chen, Kwang-Hyun Cho:
The Ninth Asia Pacific Bioinformatics Conference (APBC2011). I1 - Yong Chen, Fenglou Mao, Guojun Li, Ying Xu:
Genome-wide discovery of missing genes in biological pathways of prokaryotes. S1 - Zengyou He
, Hongyu Zhao
, Weichuan Yu
:
Score regularization for peptide identification. S2 - Anita Sarkar
, Sonu Kumar
, Durai Sundar
:
The G protein-coupled receptors in the pufferfish Takifugu rubripes. S3 - Chunfang Zheng, David Sankoff:
On the PATHGROUPS approach to rapid small phylogeny. S4 - Fei Xia, Yong Dou, Guo-Qing Lei, Yusong Tan:
FPGA accelerator for protein secondary structure prediction based on the GOR algorithm. S5 - Laxmi Parida, Pier Francesco Palamara, Asif Javed
:
A minimal descriptor of an ancestral recombinations graph. S6 - Henry Han, Xiaoli Li
:
Multi-resolution independent component analysis for high-performance tumor classification and biomarker discovery. S7 - Euna Jeong, Masao Nagasaki
, Kazuko Ueno, Satoru Miyano
:
Ontology-based instance data validation for high-quality curated biological pathways. S8 - Sung-Chou Li, Wen-Ching Chan, Chun-Hung Lai, Kuo-Wang Tsai
, Chun-Nan Hsu, Yuh-Shan Jou, Hua-Chien Chen, Chun-Hong Chen
, Wen-Chang Lin:
UMARS: Un-MAppable Reads Solution. S9 - Pengyi Yang
, Joshua Wing Kei Ho
, Jean Yee Hwa Yang
, Bing Bing Zhou
:
Gene-gene interaction filtering with ensemble of filters. S10 - Wangshu Zhang, Fengzhu Sun, Rui Jiang
:
Integrating multiple protein-protein interaction networks to prioritize disease genes: a Bayesian regression approach. S11 - William Murad, Rahul Singh, Ten-Yang Yen:
An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis. S12 - Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita, Tatsuya Akutsu
:
A clique-based method for the edit distance between unordered trees and its application to analysis of glycan structures. S13 - Wen-Chieh Chang, J. Gordon Burleigh, David Fernández-Baca, Oliver Eulenstein:
An ILP solution for the gene duplication problem. S14 - Pawel Górecki
, J. Gordon Burleigh, Oliver Eulenstein:
Maximum likelihood models and algorithms for gene tree evolution with duplications and losses. S15 - Nung Kion Lee
, Dianhui Wang:
SOMEA: self-organizing map based extraction algorithm for DNA motif identification with heterogeneous model. S16 - Chu Kang, Yung-Jen Chuang
, Kai Che Tung, Chun Chao, Chuan Yi Tang, Shih Chi Peng, David Shan-Hill Wong:
A genetic algorithm-based boolean delay model of intracellular signal transduction in inflammation. S17 - Byung-Jun Yoon:
Enhanced stochastic optimization algorithm for finding effective multi-target therapeutics. S18 - Xiaoning Qian, Byung-Jun Yoon:
Comparative analysis of protein interaction networks reveals that conserved pathways are susceptible to HIV-1 interception. S19 - Ashish V. Tendulkar, Pramod P. Wangikar:
Characterization and sequence prediction of structural variations in α-helix. S20 - Suparna Mitra
, Paul Rupek, Daniel C. Richter, Tim Urich
, Jack A. Gilbert, Folker Meyer
, Andreas Wilke, Daniel H. Huson:
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. S21 - Zengyou He
, Can Yang
, Guangyu Guo
, Ning Li, Weichuan Yu
:
Motif-All: discovering all phosphorylation motifs. S22 - Keunwan Park, Dongsup Kim:
Modeling allosteric signal propagation using protein structure networks. S23 - Christine Lo, Ali Bashir
, Vikas Bansal, Vineet Bafna
:
Strobe sequence design for haplotype assembly. S24 - Kyoohyoung Rho, Bumjin Kim, Youngjun Jang
, Sanghyun Lee, Taejeong Bae
, Jihae Seo, Chae Hwa Seo, Ji-Hyun Lee, Hyunjung Kang, Ungsik Yu, Sunghoon Kim
, Sanghyuk Lee, Wan Kyu Kim
:
GARNET - gene set analysis with exploration of annotation relations. S25 - Can Yang
, Xiang Wan, Zengyou He
, Qiang Yang, Hong Xue
, Weichuan Yu
:
The choice of null distributions for detecting gene-gene interactions in genome-wide association studies. S26 - Che-Wei Chang
, Ping-Chiang Lyu, Masanori Arita:
Reconstructing phylogeny from metabolic substrate-product relationships. S27 - Shalini John, Sundarapandian Thangapandian, Sugunadevi Sakkiah
, Keun Woo Lee:
Potent bace-1 inhibitor design using pharmacophore modeling, in silico screening and molecular docking studies. S28 - Ivan G. Costa
, Helge G. Roider, Thaís Gaudencio do Rêgo
, Francisco de A. T. de Carvalho
:
Predicting gene expression in T cell differentiation from histone modifications and transcription factor binding affinities by linear mixture models. S29 - Abhinav Grover, Ashutosh Shandilya, Vibhuti Agrawal, Piyush Pratik, Divya Bhasme, Virendra S. Bisaria, Durai Sundar
:
Hsp90/Cdc37 Chaperone/co-chaperone complex, a novel junction anticancer target elucidated by the mode of action of herbal drug Withaferin A. S30 - Jhang-Wei Huang, Jinn-Moon Yang
:
Changed epitopes drive the antigenic drift for influenza A (H3N2) viruses. S31 - Yi-Zhong Weng, Darby Tien-Hao Chang, Yu-Feng Huang
, Chih-Wei Lin:
A study on the flexibility of enzyme active sites. S32 - Kai-Cheng Hsu
, Yen-Fu Chen, Shen-Rong Lin, Jinn-Moon Yang
:
iGEMDOCK: a graphical environment of enhancing GEMDOCK using pharmacological interactions and post-screening analysis. S33 - Igor Chikalov, Peggy Yao, Mikhail Moshkov
, Jean-Claude Latombe:
Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories. S34 - Maxim Totrov
:
Ligand binding site superposition and comparison based on Atomic Property Fields: identification of distant homologues, convergent evolution and PDB-wide clustering of binding sites. S35 - Gang Su, Charles F. Burant
, Christopher W. Beecher, Brian D. Athey
, Fan Meng:
Integrated metabolome and transcriptome analysis of the NCI60 dataset. S36 - Hui Zhao
, Lore Cloots, Tim Van den Bulcke, Yan Wu, Riet De Smet, Valerie Storms, Pieter Meysman
, Kristof Engelen
, Kathleen Marchal
:
Query-based biclustering of gene expression data using Probabilistic Relational Models. S37 - Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon:
PicXAA-R: Efficient structural alignment of multiple RNA sequences using a greedy approach. S38 - Hiroyuki Monji, Satoshi Koizumi, Tomonobu Ozaki, Takenao Ohkawa:
Interaction site prediction by structural similarity to neighboring clusters in protein-protein interaction networks. S39 - Yu Rang Park
, Jihun Kim, Hye Won Lee, Young Jo Yoon, Ju Han Kim:
GOChase-II: correcting semantic inconsistencies from Gene Ontology-based annotations for gene products. S40 - Cho-Yi Chen
, Shui-Tein Chen, Chiou-Shann Fuh
, Hsueh-Fen Juan
, Hsuan-Cheng Huang
:
Coregulation of transcription factors and microRNAs in human transcriptional regulatory network. S41 - Riku Kyogoku, Ryo Fujimoto, Tomonobu Ozaki, Takenao Ohkawa:
A method for supporting retrieval of articles on protein structure analysis considering users' intention. S42 - Sanmin Liu, Lantao Liu, Ugur Uzuner
, Xin Zhou, Manxi Gu, Weibing Shi, Yixiang Zhang, Susie Y. Dai, Joshua S. Yuan:
HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics. S43 - Yongjin Park, Joel S. Bader
:
Resolving the structure of interactomes with hierarchical agglomerative clustering. S44 - Giltae Song
, Chih-Hao Hsu, Cathy Riemer, Webb Miller:
Evaluation of methods for detecting conversion events in gene clusters. S45 - Joo Yoon, Jeonghun Yeom, Heebum Lee, Kyutae Kim, Seungjin Na
, Kunsoo Park, Eunok Paek, Cheolju Lee:
High-throughput peptide quantification using mTRAQ reagent triplex. S46 - Hui-Ling Huang, I-Che Lin, Yi-Fan Liou, Chia-Ta Tsai, Kai-Ti Hsu, Wen-Lin Huang, Shinn-Jang Ho, Shinn-Ying Ho:
Predicting and analyzing DNA-binding domains using a systematic approach to identifying a set of informative physicochemical and biochemical properties. S47 - Yutaka Saito
, Kengo Sato
, Yasubumi Sakakibara:
Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures. S48 - Tsuyoshi Kato, Nozomi Nagano
:
Discriminative structural approaches for enzyme active-site prediction. S49 - Sung-Joon Park
, Kenta Nakai:
A regression analysis of gene expression in ES cells reveals two gene classes that are significantly different in epigenetic patterns. S50 - Young Soo Song, Chan Hee Park, Hee-Joon Chung, Hyunjung Shin, Jihun Kim, Ju Han Kim:
Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases. S51 - Xiao Yang, Srinivas Aluru, Karin S. Dorman
:
Repeat-aware modeling and correction of short read errors. S52 - Jorge Duitama
, Justin Kennedy, Sanjiv Dinakar, Yözen Hernández
, Yufeng Wu, Ion I. Mandoiu
:
Linkage disequilibrium based genotype calling from low-coverage shotgun sequencing reads. S53 - Mingfu Shao, Sheng Wang
, Chao Wang, Xiongying Yuan, Shuai Li, Wei-Mou Zheng, Dongbo Bu:
Incorporating Ab Initio energy into threading approaches for protein structure prediction. S54 - Christina Boucher, Bin Ma:
Closest string with outliers. S55
Volume 12, Number S-2, March 2011
- Isabel Segura-Bedmar
, Paloma Martínez, César de Pablo-Sánchez:
A linguistic rule-based approach to extract drug-drug interactions from pharmacological documents. S1 - Sejoon Lee, Kwang H. Lee, Min Song, Doheon Lee:
Building the process-drug-side effect network to discover the relationship between biological Processes and side effects. S2 - Sara Nasser, Heather E. Cunliffe, Michael A. Black, Seungchan Kim:
Context-specific gene regulatory networks subdivide intrinsic subtypes of breast cancer. S3 - David Martínez, Timothy Baldwin:
Word sense disambiguation for event trigger word detection in biomedicine. S4 - Su Kim, David Martínez
, Lawrence Cavedon
, Lars Yencken:
Automatic classification of sentences to support Evidence Based Medicine. S5 - Jinsoo Lee, Minh-Duc Pham, Jihwan Lee, Wook-Shin Han, Hune Cho, Hwanjo Yu, Jeong-Hoon Lee:
Processing SPARQL queries with regular expressions in RDF databases. S6
Volume 12, Number S-3, May 2011
- Rezarta Islamaj Dogan
, Lana Yeganova
:
Topics in machine learning for biomedical literature analysis and text retrieval. I1 - Neil Barrett, Jens H. Weber-Jahnke:
Building a biomedical tokenizer using the token lattice design pattern and the adapted Viterbi algorithm. S1 - Adrian Benton, Shawndra Hill, Lyle H. Ungar, Annie Chung, Charles E. Leonard, Cristin Freeman, John H. Holmes:
A system for de-identifying medical message board text. S2 - Rezarta Islamaj Dogan
, Aurélie Névéol, Zhiyong Lu:
A context-blocks model for identifying clinical relationships in patient records. S3 - Antonio Jimeno-Yepes
, Bridget T. McInnes, Alan R. Aronson:
Collocation analysis for UMLS knowledge-based word sense disambiguation. S4 - W. John Wilbur, Won Kim:
Improving a gold standard: treating human relevance judgments of MEDLINE document pairs. S5 - Lana Yeganova
, Donald C. Comeau, W. John Wilbur:
Machine learning with naturally labeled data for identifying abbreviation definitions. S6 - Xiaoli Zhang, Jie Zou, Daniel X. Le, George R. Thoma:
A structural SVM approach for reference parsing. S7
Volume 12, Number S-4, July 2011
- José M. G. Izarzugaza, Lisa E. M. Hopcroft
, Anja Baresic, Christine A. Orengo, Andrew C. R. Martin
, Alfonso Valencia:
Characterization of pathogenic germline mutations in human Protein Kinases. S1 - Kirsten Faber, Karl-Heinz Glatting, Phillip J. Mueller, Angela Risch
, Agnes Hotz-Wagenblatt:
Genome-wide prediction of splice-modifying SNPs in human genes using a new analysis pipeline called AASsites. S2 - Emidio Capriotti
, Russ B. Altman:
Improving the prediction of disease-related variants using protein three-dimensional structure. S3 - Philippe E. Thomas, Roman Klinger
, Laura Inés Furlong
, Martin Hofmann-Apitius, Christoph M. Friedrich
:
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. S4 - Jeroen F. J. Laros
, André Blavier
, Johan T. den Dunnen
, Peter E. M. Taschner
:
A formalized description of the standard human variant nomenclature in Extended Backus-Naur Form. S5 - Alexandre Riazanov, Jonas Laurila Bergman, Christopher J. O. Baker
:
Deploying mutation impact text-mining software with the SADI Semantic Web Services framework. S6
Volume 12, Number S-5, July 2011
- Jintao Zhang, Gerald H. Lushington
, Jun Huan:
The BioAssay network and its implications to future therapeutic discovery. S1 - Shao-Ke Lou, Jing-Woei Li
, Hao Qin, Aldrin Kay-Yuen Yim, Leung-Yau Lo, Bing Ni, Kwong-Sak Leung, Stephen Kwok-Wing Tsui
, Ting-Fung Chan
:
Detection of splicing events and multiread locations from RNA-seq data based on a geometric-tail (GT) distribution of intron length. S2 - Sung Yi, Taesung Park:
Integrated analysis of the heterogeneous microarray data. S3 - Yang Liu, Yiu Lee, Michael K. Ng
:
SNP and gene networks construction and analysis from classification of copy number variations data. S4 - Gene P. K. Wu, Keith C. C. Chan
, Andrew K. C. Wong:
Unsupervised fuzzy pattern discovery in gene expression data. S5 - Qinmin Hu, Jimmy X. Huang
, Jun Miao:
A robust approach to optimizing multi-source information for enhancing genomics retrieval performance. S6 - Wei Kong, Xiaoyang Mou, Xiaohua Hu:
Exploring matrix factorization techniques for significant genes identification of Alzheimer's disease microarray gene expression data. S7 - Xiaoshi Yin, Zhoujun Li
, Jimmy X. Huang
, Xiaohua Hu:
Promoting ranking diversity for genomics search with relevance-novelty combined model. S8
Volume 12, Number S-6, July 2011
- Irina Astrovskaya, Bassam Tork, Serghei Mangul, Kelly Westbrooks, Ion I. Mandoiu
, Peter Balfe
, Alex Zelikovsky
:
Inferring viral quasispecies spectra from 454 pyrosequencing reads. S1 - Dan He, Noah Zaitlen, Bogdan Pasaniuc
, Eleazar Eskin, Eran Halperin:
Genotyping common and rare variation using overlapping pool sequencing. S2 - Nathaniel Parrish, Farhad Hormozdiari, Eleazar Eskin:
Assembly of non-unique insertion content using next-generation sequencing. S3 - Yufeng Shen, Yiwei Gu, Itsik Pe'er:
A Hidden Markov Model for Copy Number Variant prediction from whole genome resequencing data. S4
Volume 12, Number S-7, August 2011
- Eric C. Rouchka, Robert M. Flight
, Ramin Homayouni:
Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011. A1 - Lishi Wang, Yan Jiao, Griffin Gibson, Xiaoyun Liu, Yue Huang, Beth Bennett, Kristin Hamre, Robert W. Williams, Weikuan Gu:
Identification of alcohol preference relevant genes in QTL on mouse chromosome 2. A2 - Anindya Bhattacharya, Rajat K. De:
A novel noise handling method to improve clustering of gene expression patterns. A3 - Siyuan Zheng, Zhongming Zhao:
Identifying the key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma using a systems biology approach. A4 - Jason B. Harris, David D. Jenkins, Jonathan Reyles, Stephanie Rickett, Jordan M. Utley, Elizabeth E. Howell
, Jérôme Baudry, Robert J. Hinde:
Determining anion-quadrupole interactions among protein, DNA, and ligand molecules. A5 - Dazhuo Li, Eric C. Rouchka:
Integrative biclustering of heterogeneous datasets using a Bayesian nonparametric model with application to chemogenomics. A6 - Vinhthuy T. Phan, Nam S. Vo, Thomas R. Sutter:
mDAG: a web-based tool for analyzing microarray data with multiple treatments. A7 - Teeradache Viangteeravat, Venkateswara Nagisetty, Matthew N. Anyanwu, Emin Kuscu, Ian M. Brooks, Chanchai McDonald:
Protected Research Information Management Environment (PRIME) provides a secure open source data management option for clinical and scientific research. A8 - Ramy K. Aziz, Bhakti Dwivedi, Mya Breitbart, Robert A. Edwards
:
Phage Eco-Locator: a web tool for visualization and analysis of phage genomes in metagenomic data sets. A9 - Ramy K. Aziz, Rama Saad, Mariam R. Rizkallah:
PharmacoMicrobiomics or how bugs modulate drugs: an educational initiative to explore the effects of human microbiome on drugs. A10 - Laasya Vadlamudi, Lynn A. Jones, Ramin Homayouni:
ColonyTrak: a web tool and database system for managing experimental animal models. A11 - Jonathan Reyles, Charles Phillips:
Comparative studies of high-throughput biological graphs. A12 - Weixi Li, Jerzy W. Jaromczyk:
MSCTrees: a mean-shift based toolkit for cluster analysis of phylogenetic trees. A13 - Leon Dent, Nahed Ismail, Steven Robinson, Gary L. Rogers, Siddharth Pratap
, Dana Marshall:
Next-gen sequencing of multi-drug resistant Acinetobacter baumanii at Nashville General Hospital at Meharry. A14 - Atiq Islam, Khan M. Iftekharuddin, E. Olusegun George:
Gene expression based prototype for automatic tumor prediction. A15 - Robert M. Flight, Jeffrey C. Petruska, Benjamin J. Harrison, Eric C. Rouchka:
categoryCompare: high-throughput data meta-analysis using gene annotations. A16 - David L. Tabb
, Daniel C. Liebler:
Bioinformatic challenges for proteomic biomarkers of cancer. A17 - Vida Abedi, Mohammed Yeasin, Thomas R. Sutter:
Integration of bioinformatics tools in candidate gene prioritization of co-regulated gene sets in Saccharomyces cerevisiae. A18 - Shrikant Pawar
, Cheryl D. Davis, Claire A. Rinehart:
Statistical analysis of microarray gene expression data from a mouse model of toxoplasmosis. A19 - John Kirtley, Eric C. Rouchka, Robert M. Flight, Palaniappan Sethu, John W. Eaton, Robert S. Keynton:
Meta-analysis of gene expression changes in response to radiation exposure. A20
Volume 12, Number S-8, October 2011
- Cecilia N. Arighi
, Zhiyong Lu, Martin Krallinger
, Kevin Bretonnel Cohen, W. John Wilbur, Alfonso Valencia, Lynette Hirschman, Cathy H. Wu
:
Overview of the BioCreative III Workshop. S1 - Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei
, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai
, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illés Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova
, Patrick Ruch
, Martin Romacker, Fabio Rinaldi
, Sanmitra Bhattacharya, Padmini Srinivasan
, Hongfang Liu, Manabu Torii
, Sérgio Matos
, David Campos
, Karin Verspoor
, Kevin M. Livingston, W. John Wilbur:
The gene normalization task in BioCreative III. S2 - Martin Krallinger
, Miguel Vazquez
, Florian Leitner
, David Salgado
, Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto
, Leonardo Briganti, Luana Licata
, Marta Iannuccelli, Luisa Castagnoli
, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi
, Robert Leaman, Graciela Gonzalez
, Sérgio Matos
, Sun Kim, W. John Wilbur, Luis M. Rocha
, Hagit Shatkay, Ashish V. Tendulkar, Shashank Agarwal, Feifan Liu, Xinglong Wang, Rafal Rak, Keith Noto, Charles Elkan, Zhiyong Lu:
The Protein-Protein Interaction tasks of BioCreative III: classification/ranking of articles and linking bio-ontology concepts to full text. S3 - Cecilia N. Arighi
, Phoebe M. Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide
, Pascale Gaudet, Michelle G. Giglio, Ian Harrow
, Eva Huala
, Martin Krallinger
, Ulf Leser, Donghui Li
, Feifan Liu, Zhiyong Lu, Lois J. Maltais, Naoaki Okazaki, Livia Perfetto
, Fabio Rinaldi
, Rune Sætre, David Salgado
, Padmini Srinivasan
, Philippe E. Thomas, Luca Toldo
, Lynette Hirschman, Cathy H. Wu
:
BioCreative III interactive task: an overview. S4 - Chih-Hsuan Wei
, Hung-Yu Kao
:
Cross-species gene normalization by species inference. S5 - Cheng-Ju Kuo, Maurice H. T. Ling
, Chun-Nan Hsu:
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization. S6 - Richard Tzong-Han Tsai
, Po-Ting Lai
:
Multi-stage gene normalization for full-text articles with context-based species filtering for dynamic dictionary entry selection. S7