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ORCIDBMC 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