BMC Bioinformatics, Volume 12 - Supplements

Volume 12, Number S-1, March 2011

Selected articles from the Ninth Asia Pacific Bioinformatics Conference (APBC 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

Fourth International Workshop on Data and Text Mining in Biomedical Informatics (DTMBio) 2010

• 
  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

Machine Learning for Biomedical Literature Analysis and Text Retrieval

• 
  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

Proceedings of the European Conference on Computational Biology (ECCB) 2010 Workshop: Annotation, interpretation and management of mutations (AIMM)

• 
  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

Selected articles from the IEEE International Conference on Bioinformatics and Biomedicine 2010

• 
  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

Proceedings of the First Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (RECOMB-seq)

• 
  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

UT-ORNL-KBRIN Bioinformatics Summit 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

The Third BioCreative - Critical Assessment of Information Extraction in Biology Challenge

• 
  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
• 
  Andrew Chatr-aryamontri, Andrew G. Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers:
  Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases. S8
• 
  Sun Kim, W. John Wilbur:
  Classifying protein-protein interaction articles using word and syntactic features. S9
• 
  Shashank Agarwal, Feifan Liu, Hong Yu:
  Simple and efficient machine learning frameworks for identifying protein-protein interaction relevant articles and experimental methods used to study the interactions. S10
• 
  Xinglong Wang, Rafal Rak, Angelo C. Restificar, Chikashi Nobata, C. J. Rupp, Riza Theresa Batista-Navarro, Raheel Nawaz, Sophia Ananiadou:
  Detecting experimental techniques and selecting relevant documents for protein-protein interactions from biomedical literature. S11
• 
  Anália Lourenço, Michael D. Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay, Luis M. Rocha:
  A linear classifier based on entity recognition tools and a statistical approach to method extraction in the protein-protein interaction literature. S12
• 
  Gerold Schneider, Simon Clematide, Fabio Rinaldi:
  Detection of interaction articles and experimental methods in biomedical literature. S13

Volume 12, Number S-9, October 2011

Proceedings of the Ninth Annual Research in Computational Molecular Biology (RECOMB) Satellite Workshop on Comparative Genomics

• 
  Oliver Attie, Aaron E. Darling, Sophia Yancopoulos:
  The rise and fall of breakpoint reuse depending on genome resolution. S1
• 
  Olivier Tremblay Savard, Denis Bertrand, Nadia El-Mabrouk:
  Evolution of orthologous tandemly arrayed gene clusters. S2
• 
  Chun-Hsi Chen, Hsuan-Yu Lin, Chia-Lin Pan, Feng-Chi Chen:
  The genomic features that affect the lengths of 5' untranslated regions in multicellular eukaryotes. S3
• 
  Jimmy Yang, Tandy J. Warnow:
  Fast and accurate methods for phylogenomic analyses. S4
• 
  Baoyong Wang, Chunfang Zheng, David Sankoff:
  Fractionation statistics. S5
• 
  Matthias Bernt, Martin Middendorf:
  A method for computing an inventory of metazoan mitochondrial gene order rearrangements. S6
• 
  Taoyang Wu, Louxin Zhang:
  Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree. S7
• 
  Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye:
  Genomic distance under gene substitutions. S8
• 
  Dunarel Badescu, Alix Boc, Abdoulaye Baniré Diallo, Vladimir Makarenkov:
  Detecting genomic regions associated with a disease using variability functions and Adjusted Rand Index. S9
• 
  Mahdi Belcaid, Anne Bergeron, Guylaine Poisson:
  The evolution of the tape measure protein: units, duplications and losses. S10
• 
  Jie Lv, Paul Havlak, Nicholas H. Putnam:
  Constraints on genes shape long-term conservation of macro-synteny in metazoan genomes. S11
• 
  Hadas Birin, Tamir Tuller:
  Efficient algorithms for reconstructing gene content by co-evolution. S12
• 
  Marília D. V. Braga, Raphael Machado, Leonardo Costa Ribeiro, Jens Stoye:
  On the weight of indels in genomic distances. S13
• 
  Roy Eric Collins, Hugh Merz, Paul G. Higgs:
  Origin and evolution of gene families in Bacteria and Archaea. S14
• 
  Birte Kehr, David Weese, Knut Reinert:
  STELLAR: fast and exact local alignments. S15
• 
  Cathal Seoighe, Paul K. Korir:
  Evidence for intron length conservation in a set of mammalian genes associated with embryonic development. S16
• 
  Xin Chen, Ruimin Sun, Jiadong Yu:
  Approximating the double-cut-and-join distance between unsigned genomes. S17
• 
  Anasua Sarkar, Hayssam Soueidan, Macha Nikolski:
  Identification of conserved gene clusters in multiple genomes based on synteny and homology. S18
• 
  Chieh Hua Lin, Chun-Yi Lian, Chao A. Hsiung, Feng-Chi Chen:
  Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. S19
• 
  Antoine Thomas, Jean-Stéphane Varré, Aïda Ouangraoua:
  Genome dedoubling by DCJ and reversal. S20
• 
  Roland Wittler, Cédric Chauve:
  Consistency-based detection of potential tumor-specific deletions in matched normal/tumor genomes. S21

Volume 12, Number S-10, October 2011

Proceedings of the Eighth Annual MCBIOS Conference. Computational Biology and Bioinformatics for a New Decade

• 
  Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Stephen Winters-Hilt, Mikhail G. Dozmorov, Ulisses M. Braga-Neto:
  Proceedings of the 2011 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. S1
• 
  Mikhail G. Dozmorov, Jonathan D. Wren:
  High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. S2
• 
  Minjun Chen, Leming M. Shi, Reagan Kelly, Roger Perkins, Hong Fang, Weida Tong:
  Selecting a single model or combining multiple models for microarray-based classifier development? - A comparative analysis based on large and diverse datasets generated from the MAQC-II project. S3
• 
  Fan Zhang, Jake Y. Chen:
  HOMER: a human organ-specific molecular electronic repository. S4
• 
  Ying Wang, Noushin Ghaffari, Charles D. Johnson, Ulisses M. Braga-Neto, Hui Wang, Rui Chen, Huaijun Zhou:
  Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. S5
• 
  Xiaoning Qian, Sayed Mohammad Ebrahim Sahraeian, Byung-Jun Yoon:
  Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. S6
• 
  Venkata Swamy Martha, Zhichao Liu, Li Guo, Zhenqiang Su, Yanbin Ye, Hong Fang, Don Ding, Weida Tong, Xiaowei Xu:
  Constructing a robust protein-protein interaction network by integrating multiple public databases. S7
• 
  Aleksandra Markovets, Damir Herman:
  Analysis of cancer metabolism with high-throughput technologies. S8
• 
  Mohammad Shahrokh Esfahani, Byung-Jun Yoon, Edward R. Dougherty:
  Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. S9
• 
  Noushin Ghaffari, Ivan Ivanov, Xiaoning Qian, Edward R. Dougherty:
  A CoD-based stationary control policy for intervening in large gene regulatory networks. S10
• 
  Halil Bisgin, Zhichao Liu, Hong Fang, Xiaowei Xu, Weida Tong:
  Mining FDA drug labels using an unsupervised learning technique - topic modeling. S11
• 
  Sait Suer, Sinan Kockara, Mutlu Mete:
  An improved border detection in dermoscopy images for density based clustering. S12
• 
  Srisairam Achuthan, Bong Jae Chung, Preetam Ghosh, Vijayaraghavan Rangachari, Ashwin Vaidya:
  A modified Stokes-Einstein equation for Aβ aggregation. S13
• 
  Mikhail G. Dozmorov, Cory B. Giles, Jonathan D. Wren:
  Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. S14
• 
  Karl T. Diedrich, John A. Roberts, Richard H. Schmidt, Chang-Ki Kang, Zang-Hee Cho, Dennis L. Parker:
  Validation of an arterial tortuosity measure with application to hypertension collection of clinical hypertensive patients. S15
• 
  Suzanne J. Matthews, Tiffani L. Williams:
  An efficient and extensible approach for compressing phylogenetic trees. S16
• 
  Shelton D. Griffith, Daniel Quest, Thomas S. Brettin, Robert W. Cottingham:
  Scenario driven data modelling: a method for integrating diverse sources of data and data streams. S17
• 
  Michael L. Mayo, Edward J. Perkins, Preetam Ghosh:
  First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. S18
• 
  Sujoy Roy, Kevin Heinrich, Vinhthuy Phan, Michael W. Berry, Ramin Homayouni:
  Latent Semantic Indexing of PubMed abstracts for identification of transcription factor candidates from microarray derived gene sets. S19
• 
  Ying Li, Ping Gong, Edward J. Perkins, Chaoyang Zhang, Nan Wang:
  RefNetBuilder: a platform for construction of integrated reference gene regulatory networks from expressed sequence tags. S20
• 
  Stephen Winters-Hilt, Evenie Horton-Chao, Eric Morales:
  The NTD Nanoscope: potential applications and implementations. S21
• 
  Xiaofei Nan, Gang Fu, Zhengdong Zhao, Sheng Liu, Ronak Y. Patel, Haining Liu, Pankaj R. Daga, Robert J. Doerksen, Xin Dang, Yixin Chen, Dawn Wilkins:
  Leveraging domain information to restructure biological prediction. S22

Volume 12, Number S-11, November 2011

Highlights from the Seventh International Society for Computational Biology (ISCB) Student Council Symposium 2011

• 
  Priscila Grynberg, Thomas Abeel, Pedro Lopes, Geoff MacIntyre, Lorena Pantano Rubiño:
  Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology. A1
• 
  Kerensa McElroy, Fabio Luciani, Janice Hui, Scott Rice, Torsten Thomas:
  Bacteriophage evolution drives Pseudomonas aeruginosa PAO1 biofilm diversification. A2
• 
  Karin Klotzbücher, Yasushi Kobayashi, Nino Shervashidze, Oliver Stegle, Bertram Müller-Myhsok, Detlef Weigel, Karsten M. Borgwardt:
  Efficient branch-and-bound techniques for two-locus association mapping. A3
• 
  Orion J. Buske, Misko Dzamba, Justin Foong, Lynette Lau, Marc Fiume, Christian Marshall, Susan Walker, Aparna Prasad, Michael Brudno:
  Variant detection and the Autism sequencing project. A4
• 
  Benjamin Goudey, Qiao Wang, Dave Rawlinson, Armita Zarnegar, Eder Kikianty, John Markham, Geoff MacIntyre, Gad Abraham, Linda Stern, Michael Inouye, Izhak Haviv, Adam Kowalczyk:
  Replication of epistatic DNA loci in two case-control GWAS studies using OPE algorithm. A5
• 
  Ben J. Woodcroft, Robert Radloff, Lee M. Yeoh, Kristie-Lee Scanlon, Maria A. Doyle, Giel G. van Dooren, Geoffrey I. McFadden, Christopher J. Tonkin, Terence P. Speed, Stuart A. Ralph:
  An integrative bioinformatic predictor of protein sub-cellular localisation in malaria. A6
• 
  Sebastian J. Schultheiß, Géraldine Jean, Jonas Behr, Regina Bohnert, Philipp Drewe, Nico Görnitz, André Kahles, Pramod Mudrakarta, Vipin T. Sreedharan, Georg Zeller, Gunnar Rätsch:
  Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data. A7
• 
  Margherita Francescatto, Luba Pardo, Patrizia Rizzu, Morana Vitezic, Javier Simón-Sánchez, Hazuki Takahashi, Carsten O. Daub, Piero Carninci, Peter Heutink:
  Profiling transcription initiation in human aged brain using deep-CAGE. A8
• 
  Amit G. Deshwar, Gerald T. Quon, Quaid Morris:
  Computational purification of tumor gene expression data. A9
• 
  Luiz A. Bovolenta, Marcio Luis Acencio, Ney Lemke:
  The development of an open-access database for human transcriptional regulation interactions. A10
• 
  Mrinal Mishra, Ambuj Kumar:
  Computational analysis of genetic network involved in pancreatic cancer in human. A11
• 
  Emre Guney, Baldo Oliva:
  Toward PWAS: discovering pathways associated with human disorders. A12
• 
  Benjamin Y. M. Kwan, Jennifer Y. Y. Kwan, Hon Keung Kwan:
  Spectral classification of short numerical exon and intron sequences. A13

Volume 12, Number S-12, November 2011

Selected articles from the 9th International Workshop on Data Mining in Bioinformatics (BIOKDD)

• 
  Rohit Gupta, Navneet Rao, Vipin Kumar:
  Discovery of error-tolerant biclusters from noisy gene expression data. S1
• 
  Jianhua Ruan, Joseph Perez, Brian Hernandez, Chengwei Lei, Garry Sunter, Valerie M. Sponsel:
  Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. S2
• 
  Bing Han, Xue-wen Chen, Zohreh Talebizadeh:
  FEPI-MB: identifying SNPs-disease association using a Markov Blanket-based approach. S3
• 
  Min Song, Hwanjo Yu, Wook-Shin Han:
  Combining active learning and semi-supervised learning techniques to extract protein interaction sentences. S4
• 
  Fei Xiong, Alan M. Friedman, Chris Bailey-Kellogg:
  Planning combinatorial disulfide cross-links for protein fold determination. S5
• 
  Jorge M. Arevalillo, Hilario Navarro:
  A new method for identifying bivariate differential expression in high dimensional microarray data using quadratic discriminant analysis. S6
• 
  Fengjun Li, Xukai Zou, Peng Liu, Jake Y. Chen:
  New threats to health data privacy. S7

Volume 12, Number S-13, November 2011

Tenth International Conference on Bioinformatics. First ISCB Asia Joint Conference 2011 (InCoB/ISCB-Asia 2011): Bioinformatics

• 
  Shoba Ranganathan, Christian Schönbach, Janet Kelso, Burkhard Rost, Sheila Nathan, Tin Wee Tan:
  Towards big data science in the decade ahead from ten years of InCoB and the 1st ISCB-Asia Joint Conference. S1
• 
  Mohd Firdaus Raih, Anne-Marie Harrison, Peter Willett, Peter J. Artymiuk:
  Novel base triples in RNA structures revealed by graph theoretical searching methods. S2
• 
  Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Hafeezurrehman:
  Building gene expression profile classifiers with a simple and efficient rejection option in R. S3
• 
  Chang Liu, Dong Liang, Ting Gao, Xiaohui Pang, Jingyuan Song, Hui Yao, Jianping Han, Zhihua Liu, Xiaojun Guan, Kun Jiang, Huan Li, Shilin Chen:
  PTIGS-IdIt, a system for species identification by DNA sequences of the psbA-trnH intergenic spacer region. S4
• 
  Michael Fernández, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad:
  Prediction of dinucleotide-specific RNA-binding sites in proteins. S5
• 
  David S. DeLuca, Derin B. Keskin, Guang Zhang, Ellis L. Reinherz, Vladimir Brusic:
  PB1-F2 Finder: scanning influenza sequences for PB1-F2 encoding RNA segments. S6
• 
  Sungwook Choi, Kyungsook Han:
  Prediction of RNA-binding amino acids from protein and RNA sequences. S7
• 
  Mi Kim, Hwa Jeong Seo, Je-Gun Joung, Ju Kim:
  Comprehensive evaluation of matrix factorization methods for the analysis of DNA microarray gene expression data. S8
• 
  Tarini Shankar Ghosh, Monzoorul Haque Mohammed, Hannah Rajasingh, Sudha Chadaram, Sharmila S. Mande:
  HabiSign: a novel approach for comparison of metagenomes and rapid identification of habitat-specific sequences. S9
• 
  Tzong-Yi Lee, Cheng-Tsung Lu, Shu-An Chen, Neil Arvin Bretaña, Tzu-Hsiu Cheng, Min-Gang Su, Kai-Yao Huang:
  Investigation and identification of protein γ-glutamyl carboxylation sites. S10
• 
  Sy Bing Choi, Yahaya M. Normi, Habibah A. Wahab:
  Revealing the functionality of hypothetical protein KPN00728 from Klebsiella pneumoniae MGH78578: molecular dynamics simulation approaches. S11
• 
  Sorayya Malek, Sharifah Syed Ahmad, Sarinder Kaur Singh, Pozi Milow, Aishah Salleh:
  Assessment of predictive models for chlorophyll-a concentration of a tropical lake. S12
• 
  Chengcheng Liu, Mingxi Yao, Christopher W. V. Hogue:
  Near-membrane ensemble elongation in the proline-rich LRP6 intracellular domain may explain the mysterious initiation of the Wnt signaling pathway. S13
• 
  Christopher L. Poirel, Clifford Conley Owens III, T. M. Murali:
  Network-based functional enrichment. S14
• 
  Donny Soh, Difeng Dong, Yike Guo, Limsoon Wong:
  Finding consistent disease subnetworks across microarray datasets. S15
• 
  Chien-Hsiang Hsu, Tse-Yi Wang, Hsueh-Ting Chu, Cheng-Yan Kao, Kuang-Chi Chen:
  A quantitative analysis of monochromaticity in genetic interaction networks. S16
• 
  Jagath C. Rajapakse, Piyushkumar A. Mundra:
  Stability of building gene regulatory networks with sparse autoregressive models. S17
• 
  Tie Du, Wee Puah, Martin Wasser:
  Cell cycle phase classification in 3D in vivo microscopy of Drosophila embryogenesis. S18
• 
  Merlin Veronika, Roy E. Welsch, Alvin Ng, Paul Matsudaira, Jagath C. Rajapakse:
  Correlation of cell membrane dynamics and cell motility. S19
• 
  Sheng-An Lee, Theresa Tsao, Ko-Chun Yang, Han Lin, Yu-Lun Kuo, Chien-Hsiang Hsu, Wen-Kuei Lee, Kuo-Chuan Huang, Cheng-Yan Kao:
  Construction and analysis of the protein-protein interaction networks for schizophrenia, bipolar disorder, and major depression. S20
• 
  Smitha Nair, N. V. Subba Reddy, K. S. Hareesha:
  Exploiting heterogeneous features to improve in silico prediction of peptide status - amyloidogenic or non-amyloidogenic. S21
• 
  Abhinav Grover, Vibhuti Agrawal, Ashutosh Shandilya, Virendra S. Bisaria, Durai Sundar:
  Non-nucleosidic inhibition of Herpes simplex virus DNA polymerase: mechanistic insights into the anti-herpetic mode of action of herbal drug withaferin A. S22
• 
  Usman Sumo Friend Tambunan, N. Bramantya, Arli A. Parikesit:
  In silico modification of suberoylanilide hydroxamic acid (SAHA) as potential inhibitor for class II histone deacetylase (HDAC). S23
• 
  See Ven Lim, Mohd Basyaruddin Abdul Rahman, Bimo Ario Tejo:
  Structure-based and ligand-based virtual screening of novel methyltransferase inhibitors of the dengue virus. S24
• 
  Varun Khanna, Shoba Ranganathan:
  In silico approach to screen compounds active against parasitic nematodes of major socio-economic importance. S25

Volume 12, Number S-14, December 2011

22nd International Conference on Genome Informatics: Bioinformatics

• 
  Masaaki Kotera, Toshiaki Tokimatsu, Minoru Kanehisa, Susumu Goto:
  MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. S1
• 
  Qiong-Yi Zhao, Yi Wang, Yi-Meng Kong, Da Luo, Xuan Li, Pei Hao:
  Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. S2
• 
  Masaaki Shimizu, Hiroshi Nagamochi, Tatsuya Akutsu:
  Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. S3
• 
  Shalini John, Sundarapandian Thangapandian, Mahreen Arooj, Jong Hong, Kwang Kim, Keun Woo Lee:
  Development, evaluation and application of 3D QSAR Pharmacophore model in the discovery of potential human renin inhibitors. S4
• 
  Geoffrey Koh, Ariana Low, Daren Poh, Yujian Yao, Say Ng, Victor Wong, Vincent Vagenende, Kong-Peng Lam, Dong-Yup Lee:
  Integrative analysis workflow for the structural and functional classification of C-type lectins. S5
• 
  Guangyong Zheng, Haibo Wang, Chaochun Wei, Yixue Li:
  iGepros: an integrated gene and protein annotation server for biological nature exploration. S6
• 
  Shin Suzuki, Tomohiro Yasuda, Yuichi Shiraishi, Satoru Miyano, Masao Nagasaki:
  ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information. S7
• 
  Chiyong Kang, Gwan-Su Yi:
  Identification of ubiquitin/ubiquitin-like protein modification from tandem mass spectra with various PTMs. S8
• 
  Tianli Dai, Qi Liu, Jun Gao, Zhiwei Cao, Ruixin Zhu:
  A new protein-ligand binding sites prediction method based on the integration of protein sequence conservation information. S9
• 
  Md Shariful Bhuyan, Xin Gao:
  A protein-dependent side-chain rotamer library. S10

Volume 12, Number S-15, December 2011

Data publishing framework for primary biodiversity data

• 
  Dave Roberts, Tom Moritz:
  A framework for publishing primary biodiversity data. I1
• 
  Tom Moritz, S. Krishnan, Dave Roberts, Peter Ingwersen, Donat Agosti, Lyubomir Penev, Matthew J. Cockerill, Vishwas Chavan:
  Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group. S1
• 
  Vishwas Chavan, Lyubomir Penev:
  The data paper: a mechanism to incentivize data publishing in biodiversity science. S2
• 
  Peter Ingwersen, Vishwas Chavan:
  Indicators for the Data Usage Index (DUI): an incentive for publishing primary biodiversity data through global information infrastructure. S3
• 
  Arturo H. Ariño, Vishwas Chavan, Nick King:
  The Biodiversity Informatics Potential Index. S4
• 
  Anthony Goddard, Nathan Wilson, Phil Cryer, Grant Yamashita:
  Data hosting infrastructure for primary biodiversity data. S5