Volume 11, Number S-1, 2010

Selected articles from the Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)

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  Laxmi Parida, Gene Myers: APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010. 0
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  Henry Han: Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery. 1
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  Vinod Chandra, Reshmi Girijadevi, Achuthsankar S. Nair, Sreenadhan S. Pillai, Radhakrishna M. Pillai: MTar: a computational microRNA target prediction architecture for human transcriptome. 2
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  Darby Tien-Hao Chang, Yu-Tang Syu, Po-Chang Lin: Predicting the protein-protein interactions using primary structures with predicted protein surface. 3
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  Xiaowen Liu, Baozhen Shan, Lei Xin, Bin Ma: Better score function for peptide identification with ETD MS/MS spectra. 4
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  Pengyi Yang, Bing Bing Zhou, Zili Zhang, Albert Y. Zomaya: A multi-filter enhanced genetic ensemble system for gene selection and sample classification of microarray data. 5
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  Nitin Bhardwaj, Mark Gerstein, Hui Lu: Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. 6
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  Soja Saghar Soman, Krishnankutty Chandrika Sivakumar, Easwaran Sreekumar: Molecular dynamics simulation studies and in vitro site directed mutagenesis of avian beta-defensin Apl_AvBD2. 7
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  Junhee Seok, Amit Kaushal, Ronald W. Davis, Wenzhong Xiao: Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships. 8
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  Jian-Yi Yang, Zhen-Ling Peng, Xin Chen: Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. 9
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  Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida, Dongsup Kim: PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. 10
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  Christina Boucher, James King: Fast motif recognition via application of statistical thresholds. 11
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  Suparna Mitra, Max Schubach, Daniel H. Huson: Short clones or long clones? A simulation study on the use of paired reads in metagenomics. 12
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  Sayak Ganguli, Manjita Mazumder, Protip Basu, Paushali Roy, Sayani Mitra, Abhijit Datta: In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. 13
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  Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong, Sunhee Park, Pamela J. Green, D. Janine Sherrier, Andrew Farmer, Greg May, Blake C. Meyers, Dong Xu, Gary Stacey: Prediction of novel miRNAs and associated target genes in Glycine max. 14
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  Suzanne Matthews, Tiffani L. Williams: MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees. 15
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  Matteo Comin, Davide Verzotto: Classification of protein sequences by means of irredundant patterns. 16
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  Suyu Mei, Wang Fei: Amino acid classification based spectrum kernel fusion for protein subnuclear localization. 17
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  Can Yang, Xiang Wan, Qiang Yang, Hong Xue, Weichuan Yu: Identifying main effects and epistatic interactions from large-scale SNP data via adaptive group Lasso. 18
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  Sneh Lata, Nitish K. Mishra, Gajendra P. S. Raghava: AntiBP2: improved version of antibacterial peptide prediction. 19
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  Yongjin Li, Jagdish Chandra Patra: Integration of multiple data sources to prioritize candidate genes using discounted rating system. 20
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  Wen-Ching Chan, Po-Huang Liang, Yan-Ping Shih, Ueng-Cheng Yang, Wen-chang Lin, Chun-Nan Hsu: Learning to predict expression efficacy of vectors in recombinant protein production. 21
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  Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q. Zhang: SFSSClass: an integrated approach for miRNA based tumor classification. 22
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  Byungkyu Park, Kyungsook Han: An ontology-based search engine for protein-protein interactions. 23
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  Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, Ramanathan Sowdhamini: HORI: a web server to compute Higher Order Residue Interactions in protein structures. 24
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  Chia-Hao Chin, Shu-Hwa Chen, Chin-Wen Ho, Ming-Tat Ko, Chung-Yen Lin: A hub-attachment based method to detect functional modules from confidence-scored protein interactions and expression profiles. 25
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  Aridaman Pandit, Somdatta Sinha: Using genomic signatures for HIV-1 sub-typing. 26
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  Martin Bader: Genome rearrangements with duplications. 27
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  Daniel G. Brown, Daniil Golod: Decoding HMMs using the k best paths: algorithms and applications. 28
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  Sumeet Agarwal, Candida Vaz, Alok Bhattacharya, Ashwin Srinivasan: Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM). 29
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  Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret: Heuristics for the inversion median problem. 30
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  Hiroto Saigo, Masahiro Hattori, Hisashi Kashima, Koji Tsuda: Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. 31
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  Yezhou Huang, Shao Li: Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network. 32
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  Limin Li, Wai-Ki Ching, Takako Yamaguchi, Kiyoko F. Aoki-Kinoshita: A weighted q-gram method for glycan structure classification. 33
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  Zaixin Lu, Zhiyu Zhao, Bin Fu: Efficient protein alignment algorithm for protein search. 34
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  Jayesh Pandey, Mehmet Koyutürk, Ananth Grama: Functional characterization and topological modularity of molecular interaction networks. 35
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  S. P. T. Krishnan, Sim Sze Liang, Bharadwaj Veeravalli: Towards high performance computing for molecular structure prediction using IBM Cell Broadband Engine - an implementation perspective. 36
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  Won-Hyoung Chung, Seong-Bae Park: Hit integration for identifying optimal spaced seeds. 37
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  Adi Mano, Tamir Tuller, Oded Béjà, Ron Y. Pinter: Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways. 38
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  Abu Zafer M. Dayem Ullah, Kathleen Steinhöfel: A hybrid approach to protein folding problem integrating constraint programming with local search. 39
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  Daniel G. Brown, Jakub Truszkowski: New decoding algorithms for Hidden Markov Models using distance measures on labellings. 40
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  Giovanni Ciriello, Claudio Gallina, Concettina Guerra: Analysis of interactions between ribosomal proteins and RNA structural motifs. 41
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  Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein: Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. 42
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  Vishwesh V. Kulkarni, Venkatesh Kareenhalli, Pushkar Malakar, Lucy Y. Pao, Michael G. Safonov, Ganesh A. Viswanathan: Stability analysis of the GAL regulatory network in Saccharomyces cerevisiae and Kluyveromyces lactis. 43
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  Kamal Al-Nasr, Weitao Sun, Jing He: Structure prediction for the helical skeletons detected from the low resolution protein density map. 44
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  Yixuan Chen, Xin Li, Jing Li: A novel approach for haplotype-based association analysis using family data. 45
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  Lei Zhang, James Bailey, Arun Siddharth Konagurthu, Kotagiri Ramamohanarao: A fast indexing approach for protein structure comparison. 46
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  Yang Yang, Jiayuan Zhao, Robyn L. Morgan, Wenbo Ma, Tao Jiang: Computational prediction of type III secreted proteins from gram-negative bacteria. 47
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  Nitish K. Mishra, Gajendra P. S. Raghava: Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information. 48
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  M. S. Vijayabaskar, Saraswathi Vishveshwara: Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks. 49
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  Tina P. George, Tessamma Thomas: Discrete wavelet transform de-noising in eukaryotic gene splicing. 50
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  Padmapriya Paragi-Vedanthi, Mukesh Doble: Comparison of PGH₂ binding site in prostaglandin synthases. 51
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  Chih-Hung Hsieh, Darby Tien-Hao Chang, Cheng-Hao Hsueh, Chi-Yeh Wu, Yen-Jen Oyang: Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm. 52
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  Aarti Garg, Rupinder Tewari, Gajendra P. S. Raghava: Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis. 53
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  Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret: Estimating true evolutionary distances under rearrangements, duplications, and losses. 54
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  Kalidas Yeturu, Tapani Utriainen, Graham J. L. Kemp, Nagasuma Chandra: An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. 55
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  Mitra Kabir, Nasimul Noman, Hitoshi Iba: Reverse engineering gene regulatory network from microarray data using linear time-variant model. 56
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  Thahir P. Mohamed, Jaime G. Carbonell, Madhavi Ganapathiraju: Active learning for human protein-protein interaction prediction. 57
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  Hatice U. Osmanbeyoglu, Jessica A. Wehner, Jaime G. Carbonell, Madhavi Ganapathiraju: Active machine learning for transmembrane helix prediction. 58
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  Xianjun Dong, Altuna Akalin, Yogita Sharma, Boris Lenhard: Translog, a web browser for studying the expression divergence of homologous genes. 59
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  Daniel Merkle, Martin Middendorf, Nicolas Wieseke: A parameter-adaptive dynamic programming approach for inferring cophylogenies. 60
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  Corban G. Rivera, Rachit Vakil, Joel S. Bader: NeMo: Network Module identification in Cytoscape. 61
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  Michael R. Mehan, Juan Nunez-Iglesias, Chao Dai, Michael S. Waterman, Xianghong Jasmine Zhou: An integrative modular approach to systematically predict gene-phenotype associations. 62
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  Melvin Zhang, Hon Wai Leong: Bidirectional best hit r-window gene clusters. 63
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  Pingzhao Hu, Hui Jiang, Andrew Emili: Predicting protein functions by relaxation labelling protein interaction network. 64
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  Ravi Gupta, Priyankara Wikramasinghe, Anirban Bhattacharyya, Francisco A. Perez, Sharmistha Pal, Ramana V. Davuluri: Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. 65
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  Jianjun Hu, Fan Zhang: BayesMotif: de novo protein sorting motif discovery from impure datasets. 66
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  Anil Sorathiya, Andrea Bracciali, Pietro Liò: Formal reasoning on qualitative models of coinfection of HIV and Tuberculosis and HAART therapy. 67

Volume 11, Number S-2, 2010

Third International Workshop on Data and Text Mining in Bioinformatics (DTMBio) 2009

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  Isabel Segura-Bedmar, Mario Crespo, César de Pablo-Sánchez, Paloma Martínez: Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents. 1
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  Chan-seok Jeong, Dongsup Kim: Linear predictive coding representation of correlated mutation for protein sequence alignment. 2
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  Ali Zeeshan Ijaz, Min Song, Doheon Lee: MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge. 3
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  Younghoon Kim, Imhoi Koo, Byung Hwa Jung, Bong Chul Chung, Doheon Lee: Multivariate classification of urine metabolome profiles for breast cancer diagnosis. 4
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  Bin Yang, Yu Peng, Henry Chi-Ming Leung, Siu-Ming Yiu, Jing-Chi Chen, Francis Yuk-Lun Chin: Unsupervised binning of environmental genomic fragments based on an error robust selection of l-mers. 5
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  Hwanjo Yu, Taehoon Kim, Jinoh Oh, Ilhwan Ko, Sungchul Kim, Wook-Shin Han: Enabling multi-level relevance feedback on PubMed by integrating rank learning into DBMS. 6
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  Yanpeng Li, Xiaohua Hu, Hongfei Lin, Zhihao Yang: Learning an enriched representation from unlabeled data for protein-protein interaction extraction. 7

Volume 11, Number S-3, 2010

Selected articles from the 2009 IEEE International Conference on Bioinformatics and Biomedicine

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  Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng: SeqRate: sequence-based protein folding type classification and rates prediction. 1
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  Daniel Duanqing Wu, Xiaohua Hu, E. K. Park, Xiaofeng Wang, Jiali Feng, Xindong Wu: Exploratory analysis of protein translation regulatory networks using hierarchical random graphs. 2
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  Young-Rae Cho, Aidong Zhang: Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. 3
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  Minoo Aminian, Amina Shabbeer, Kristin P. Bennett: A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages. 4
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  Bing Han, Meeyoung Park, Xue-wen Chen: A Markov blanket-based method for detecting causal SNPs in GWAS. 5
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  Brian E. Howard, Steffen Heber: Towards reliable isoform quantification using RNA-SEQ data. 6
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  Fadi Towfic, Susan VanderPlas, Casey A. Oliver, Oliver Couture, Christopher K. Tuggle, M. Heather West Greenlee, Vasant Honavar: Detection of gene orthology from gene co-expression and protein interaction networks. 7
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  Xiaohong Wang, Jun Huan, Aaron M. Smalter, Gerald H. Lushington: Application of kernel functions for accurate similarity search in large chemical databases. 8
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  Dong-Chul Kim, Xiaoyu Wang, Chin-Rang Yang, Jean Gao: Learning biological network using mutual information and conditional independence. 9
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  Jeffrey Martin, Wenhan Zhu, Karla D. Passalacqua, Nicholas H. Bergman, Mark Borodovsky: Bacillus anthracis genome organization in light of whole transcriptome sequencing. 10

Volume 11, Number S-4, 2010

UT-ORNL-KBRIN Bioinformatics Summit 2010

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  Eric C. Rouchka, Robert M. Flight, Claire Rinehart: Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010. I1
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  Peilin Jia, Zhongming Zhao: Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia. O1
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  Ramy K. Aziz: Subsystems-based servers for rapid annotation of genomes and metagenomes. O2
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  Steven J. M. Jones, Janessa Laskin, Yvonne Y. Li, Obi L. Griffith, Jianghong An, Mikhail Bilenky, Yaron S. N. Butterfield, Timothee Cezard, Eric Chuah, Richard Corbett, Anthony P. Fejes, Malachi Griffith, John Yee, Montgomery Martin, Michael Mayo, Nataliya Melnyk, Ryan D. Morin, Trevor J. Pugh, Tesa Severson, Sohrab P. Shah, Margaret Sutcliffe, Angela Tam, Jefferson Terry, Nina Thiessen, Thomas Thomson, Richard Varhol, Thomas Zeng, Yongjun Zhao, Richard A. Moore, David G. Huntsman, Inanç Birol, Martin Hirst, Robert A. Holt, Marco A. Marra: Genomic analysis of a rare human tumor. O3
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  Ronald M. Adkins, Julia Krushkal, Steven Zeisel, Chandrika Piyathilake, Fran Tylavsky, Grant Somes: Association of genomewide newborn DNA methylation patterns with maternal and newborn characteristics. O4
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  Sudhir Naswa, Gary L. Rogers Jr., Rachel M. Lynch, Stephen A. Kania, Suchita Das, Elissa J. Chesler, Arnold M. Saxton, Brynn H. Voy, Michael A. Langston: Inferring gene coexpression networks for low dose ionizing radiation using graph theoretical algorithms and systems genetics. O5
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  Robert L. Hettich, Alison L. Russell, Nathan Verberkmoes, Manesh Shah, Claire Fraser-Liggett, Janet K. Jansson: Integrating experimental and computational approaches for the proteogenomic characterizations of microbial communities. O6
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  Xusheng Wang, Richa Agarwala, John A. Capra, Zugen Chen, Deanna M. Church, Daniel C. Ciobanu, Zhengsheng Li, Lu Lu, Khyobeni Mozhui, Megan K. Mulligan, Stanley F. Nelson, Katherine S. Pollard, William Taylor, Donald B. Thomason, Robert W. Williams: High-throughput sequencing of the DBA/2J mouse genome. O7
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  Stephen J. Coleman, Zheng Zeng, Jinze Liu, James N. MacLeod: Analysis of equine protein-coding gene structure and expression by RNA-sequencing. O8
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  Gipsy Majumdar, Rajendra Raghow: Epigenetic control of signaling networks involved in interleukin-18-induced cardiac hypertrophy and its attenuation by pan-histone deacetylase inhibitors. P1
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  Mei Liu, Joshua C. Denny, Subramani Mani, Yukun Chen, Yong Hu, Hua Xu: Identifying potential drugs that induce QT prolongation using electronic medical records. P2
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  LiPeng Bi, Chad Groce, Cheryl Davis: Molecular analysis of Trypanosoma cruzi isolates obtained from raccoons in Warren and Barren counties of Kentucky. P3
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  Zhi-Liang Hu, Rex Fernando, Dorian Garrick, James M. Reecy: SNPlotz: a generic genome plot tool to aid the SNP association studies. P4
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  Teeradache Viangteeravat, Ian M. Brooks, Somchan Vuthipadadon, Emin Kuscu, Naga Nagisetty, Ebony Smith, Ramin Homayouni, Chanchai McDonald: Slim-Prim: an integrated data system for clinical and translational research. P5
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  Elissaveta G. Arnaoudova, Jerzy W. Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida: Phylotree - a toolkit for computing experiments with distance-based methods for genome coevolution. P6
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  Nan Zhao, Jean-Luc Ferrer, Xiaofeng Zhuang, Feng Chen: Comparative functional genomic study of substrate specificity evolution of the SABATH family of methyltransferases in plants. P7
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  Ramy Karam Aziz: In silico analysis of a family of extracellular polysaccharide deacetylases involved in virulence of pathogenic gram-positive cocci. P8
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  Daniel Harris, Jerzy W. Jaromczyk, Christopher L. Schardl: Experimenting with database segmentation size vs time performance for mpiBLAST on an IBM HS21 blade cluster. P9
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  Dexter T. Duncan, Naresh Prodduturi, Bing Zhang: WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. P10
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  Julia Krushkal, Ronald M. Adkins, Yanhua Qu, Jeanette Peeples, Sreedhar Sontineni, Ching Leang, Peter Brown, Nelson D. Young, Toshiyuki Ueki, Katy Juarez, Derek R. Lovley: Bioinformatic analysis of gene regulation in the metal-reducing bacterial family Geobacteraceae. P11
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  Ramy K. Aziz, Bruce J. Aronow, William L. Taylor, Sarah Rowe, Rita Kansal, Mark J. Walker, Malak Kotb: Integrating neighbor clustering, coexpression clustering and subsystems analysis to define dynamic changes in regulatory networks associated with group A streptococcal sociomicrobiology and niche adaptation. P12
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  Shephali Bhatnagar, Siva K. Panguluri, Robert F. Lundy, Ashok Kumar: Pleiotropy of tumor necrosis factor-alpha in C2C12 myotubes: in vitro studies on genes, networks and pathways involved in TNF-alpha induced skeletal muscle atrophy. P13
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  Rachel M. Adams, Jason B. Harris, Jeremy J. Jay, Beth G. Johnson, Miriam L. Land, Loren J. Hauser: Developing measures for microbial genome assembly quality control. P14
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  Ejike Anyanwu, Kaitlyn Cole, Karlee Driver, Anthony Falcone, Elizabeth Farnsworth, Benjamin Howard, Brittney Howard, Courtney Howard, Rodney A. King, Jordan Olberding, Mackenzie Perkins, Claire Rinehart, Heidi Sayre, Tyler Scaff, Sarah Schrader, Prasanna Tamarapu Parthasarathy, Cynthia Tope: Sequence and annotation of the Wizard007 mycobacterium phage genome. P15
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  Leon Dent, Dana Marshall, Robert Hulette, Siddharth Pratap: Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes. P16
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  Fridtjof Thomas, Stanley Pounds: A Bayesian change-point algorithm for detecting copy number alteration. P17
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  Huazhang Guo, Larry Tague, Ramesh Ray, Gabor Tigyi: A two-step approach to qPCR experimental design and software for data analysis. P18
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  Jesse D. Ziebarth, Bao Li, Isao Miyairi, Yan Cui: Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection. P19
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  Rodney A. King, Claire Rinehart, Prasanna Tamarapu Parthasarathy: The HHMI National Genomics Research Initiative at Western Kentucky University. P20
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  Gary L. Rogers, Pablo Moscato, Michael A. Langston: Graph algorithms for machine learning: a case-control study based on prostate cancer populations and high throughput transcriptomic data. P21
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  Indranil Mitra, Yan Cui: Understanding molecular recognition and epitope prediction from Information Theoretic approach. P22
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  Hung-Chung Huang, Siyuan Zheng, Zhongming Zhao: Application of Pearson correlation coefficient (PCC) and Kolmogorov-Smirnov distance (KSD) metrics to identify disease-specific biomarker genes. P23
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  Sally R. Ellingson, Charles A. Phillips, Randy Glenn, Douglas Swanson, Thomas Ha, Daniel Goldowitz, Michael A. Langston: Serendipitous discoveries in microarray analysis. P24
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  S. Waigel, Xiaohong Li, Yinlu Chen, Vennila Arumugam, Nigel G. F. Cooper, Wolfgang Zacharias: The UofL Microarray Facility: merger and new location. P25
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  Michael E. Smith, Huifang Sun, Julie B. Schuck, Shunsuke Moriyama: Growth hormone induces proliferation in the zebrafish inner ear. P26
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  Sally Ellingson, Joe Hughes, Dylan Storey, Rick Weber, Nathan Verberkmoes: Development of tools for the automated analysis of spectra generated by tandem mass spectrometry. P27
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  Ahmed Abo-Bakr Mahmoud, Ramy K. Aziz: Do pathogenic bacteria encode more secreted proteins than their non-pathogenic relatives? P28
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  Jing Li, Zeqiang Ma, Robbert J. C. Slebos, David L. Tabb, Daniel C. Liebler, Bing Zhang: Enabling proteomics-based identification of human cancer variations. P29
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  Bing Wang, Fahim Mohammad, Jun Zhang, Xinmin Yin, Eric C. Rouchka, Xiang Zhang: Statistical analysis of multiple significance test methods for differential proteomics. P30
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  Christy M. Gearheart, Eric C. Rouchka, Benjamin Arazi: Design of a DNA-based shift register. P31

Volume 11, Number S-5, October 2010

Workshop on Advances in Bio Text Mining

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  Thomas Abeel, Sofie Van Landeghem, Roser Morante, Vincent Van Asch, Yves Van de Peer, Walter Daelemans, Yvan Saeys: Highlights of the BioTM 2010 workshop on advances in bio text mining. I1
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  Martin Krallinger, Ashish V. Tendulkar, Florian Leitner, Andrew Chatr-aryamontri, Alfonso Valencia: The PPI affix dictionary (PPIAD) and BioMethod Lexicon: importance of affixes and tags for recognition of entity mentions and experimental protein interactions. O1
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  Senay Kafkas, Ekrem Varoglu, Dietrich Rebholz-Schuhmann, Bahar Taneri: Functional variation of alternative splice forms in their protein interaction networks: a literature mining approach. P1
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  Filip Ginter, Jari Björne, Sampo Pyysalo: Event extraction on PubMed scale. O2
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  Borut Sluban, Nada Lavrac: Supporting the search for cross-context links by outlier detection methods. P2
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  K. Cohen: Integrating text mining into high-throughput assay analysis. O3
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  Bert Verslyppe, Wim De Smet, Paul De Vos, Bernard De Baets, Peter Dawyndt: Semantic integration of isolation habitat and location in StrainInfo. P3
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  Jean-Marc Neefs: Pitfalls in applying text mining to scientific literature. O4
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  Matjaz Jursic, Igor Mozetic, Miha Grcar, Bojan Cestnik, Nada Lavrac: Identification of concepts bridging diverse biomedical domains. P4
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  Maté Ongenaert, Luc Dehaspe: Integrating automated literature searches and text mining in biomarker discovery. O5
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  Illés Solt, Domonkos Tikk, Ulf Leser: Species identification for gene name normalization. P5
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  Sampo Pyysalo: Entities, relations, events: representing biomolecular semantics. O6
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  Yifei Chen, Feng Liu, Bernard Manderick: BioLMiner and the BioCreative II.5 challenge. P6
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  Tomoko Ohta, Takuya Matsuzaki, Naoaki Okazaki, Makoto Miwa, Rune Sætre, Sampo Pyysalo, Jun'ichi Tsujii: Medie and Info-pubmed: 2010 update. P7
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  Domonkos Tikk, Peter Palaga, Ulf Leser: A fast and effective dependency graph kernel for PPI relation extraction. P8
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  Isabel Segura-Bedmar, Paloma Martínez, César de Pablo-Sánchez: Extracting drug-drug interactions from biomedical texts. P9

Volume 11, Number S-6, October 2010

Proceedings of the Seventh Annual MCBIOS Conference. Bioinformatics: Systems, Biology, Informatics and Computation

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  Jonathan D. Wren, Doris M. Kupfer, Edward J. Perkins, Susan Bridges, Daniel Berleant: Proceedings of the 2010 MidSouth Computational Biology and Bioinformatics Society (MCBIOS) Conference. S1
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  Shuju Bai, Tianchuan Du, Ebrahim Khosravi: Applying internal coordinate mechanics to model the interactions between 8R-lipoxygenase and its substrate. S2
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  Ulrich Melcher: Assessing constancy of substitution rates in viruses over evolutionary time. S3
• 
  Hong Fang, Joshua Xu, Don Ding, Scott A. Jackson, Isha R. Patel, Jonathan G. Frye, Wen Zou, Rajesh Nayak, Steven Foley, James J. Chen, Zhenqiang Su, Yanbin Ye, Steve Turner, Steve Harris, Guangxu Zhou, Carl Cerniglia, Weida Tong: An FDA bioinformatics tool for microbial genomics research on molecular characterization of bacterial foodborne pathogens using microarrays. S4
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  Don Ding, Lei Xu, Hong Fang, Huixiao Hong, Roger Perkins, Steve Harris, Edward D. Bearden, Leming Shi, Weida Tong: The EDKB: an established knowledge base for endocrine disrupting chemicals. S5
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  Joshua Xu, Carolyn Wise, Vijayalakshmi Varma, Hong Fang, Baitang Ning, Huixiao Hong, Weida Tong, Jim Kaput: Two new ArrayTrack libraries for personalized biomedical research. S6
• 
  Ao Zhou, Fan Zhang, Jake Y. Chen: PEPPI: a peptidomic database of human protein isoforms for proteomics experiments. S7
• 
  Junjie Su, Byung-Jun Yoon, Edward R. Dougherty: Identification of diagnostic subnetwork markers for cancer in human protein-protein interaction network. S8
• 
  Mais Ammari, Fiona M. McCarthy, Bindu Nanduri, Lesya M. Pinchuk: Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences. S9
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  Zhining Wen, Charles Wang, Quan Shi, Ying Huang, Zhenqiang Su, Huixiao Hong, Weida Tong, Leming Shi: Evaluation of gene expression data generated from expired Affymetrix GeneChip^® microarrays using MAQC reference RNA samples. S10
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  Tansel Halic, Sinan Kockara, Coskun Bayrak, Richard Rowe: Mixed reality simulation of rasping procedure in artificial cervical disc replacement (ACDR) surgery. S11
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  Ugur Uzuner, Weibing Shi, Lantao Liu, Sanmin Liu, Susie Y. Dai, Joshua S. Yuan: Enzyme structure dynamics of xylanase I from Trichoderma longibrachiatum. S12
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  Arun Rawat, Kurt A. Gust, Mohamed O. Elasri, Edward J. Perkins: Quail Genomics: a knowledgebase for Northern bobwhite. S13
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  Elina Tjioe, Michael W. Berry, Ramin Homayouni: Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization). S14
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  Daniel Quest, Miriam L. Land, Thomas S. Brettin, Robert W. Cottingham: Next generation models for storage and representation of microbial biological annotation. S15
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  Ranjit Kumar, Bindu Nanduri: HPIDB - a unified resource for host-pathogen interactions. S16
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  Charles Bland, Abigail Newsome, Aleksandra Markovets: Promoter prediction in E. coli based on SIDD profiles and Artificial Neural Networks. S17
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  Samuel A. Smits, Cleber C. Ouverney: Phylometrics: a pipeline for inferring phylogenetic trees from a sequence relationship network perspective. S18
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  Vijender Chaitankar, Preetam Ghosh, Edward J. Perkins, Ping Gong, Chaoyang Zhang: Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. S19
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  Cyriac Kandoth, Fikret Erçal, Ronald L. Frank: A framework for automated enrichment of functionally significant inverted repeats in whole genomes. S20
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  Denise R. Koessler, Debra J. Knisley, Jeff Knisley, Teresa W. Haynes: A predictive model for secondary RNA structure using graph theory and a neural network. S21
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  Chao Di, Wenying Xu, Zhen Su, Joshua S. Yuan: Comparative genome analysis of PHB gene family reveals deep evolutionary origins and diverse gene function. S22
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  Mutlu Mete, Nikolay Metodiev Sirakov: Lesion detection in demoscopy images with novel density-based and active contour approaches. S23
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  Preetam Ghosh, Amit Kumar, Bhaswati Datta, Vijayaraghavan Rangachari: Dynamics of protofibril elongation and association involved in Aβ. S24
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  Rowena Y. Kelley, Cathy R. Gresham, Jonathan Harper, Susan M. Bridges, Marilyn Warburton, Leigh K. Hawkins, Olga Pechanova, Bela Peethambaran, Tibor Pechan, Dawn S. Luthe, J. E. Mylroie, Arunkanth Ankala, Seval Ozkan, W. B. Henry, W. Paul Williams: Integrated database for identifying candidate genes for Aspergillus flavus resistance in maize. S25
• 
  Sinan Kockara, Mutlu Mete, Bernard Chen, Kemal Aydin: Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images. S26
• 
  Yi Jia, Jun Huan: Constructing non-stationary Dynamic Bayesian Networks with a flexible lag choosing mechanism. S27
• 
  Christopher A. Bottoms, Sherry Flint-Garcia, Michael D. McMullen: IView: introgression library visualization and query tool. S28
• 
  Prashanti Manda, McKinley G. Freeman, Susan M. Bridges, T. J. Jankun-Kelly, Bindu Nanduri, Fiona M. McCarthy, Shane C. Burgess: GOModeler- A tool for hypothesis-testing of functional genomics datasets. S29

Volume 11, Number S-7, October 2010

Ninth International Conference on Bioinformatics (InCoB2010): Bioinformatics

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  Christian Schönbach, Kenta Nakai, Tin Wee Tan, Shoba Ranganathan: InCoB2010 - 9^th International Conference on Bioinformatics at Tokyo, Japan, September 26-28, 2010. S1
• 
  Kohji Okamura, Kazuaki A. Matsumoto, Kenta Nakai: Gradual transition from mosaic to global DNA methylation patterns during deuterostome evolution. S2
• 
  Yutaka Saito, Kengo Sato, Yasubumi Sakakibara: Robust and accurate prediction of noncoding RNAs from aligned sequences. S3
• 
  Daniel Tay, Kunde Ramamoorthy Govindarajan, Asif M. Khan, Terenze Ong, Hanif M. Samad, Wei Soh, Minyan Tong, Fan Zhang, Tin Wee Tan: T3SEdb: data warehousing of virulence effectors secreted by the bacterial Type III Secretion System. S4
• 
  Huqun, Shun-ichiro Fukuyama, Hiroyuki Morino, Hiroshi Miyazawa, Tomoaki Tanaka, Tomoko Suzuki, Masakazu Kohda, Hideshi Kawakami, Yasushi Okazaki, Kuniaki Seyama, Koichi Hagiwara: A quantitatively-modeled homozygosity mapping algorithm, qHomozygosityMapping, utilizing whole genome single nucleotide polymorphism genotyping data. S5
• 
  Ting-wen Chen, Timothy H. Wu, Wailap V. Ng, Wen-chang Lin: DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection. S6
• 
  Shunsuke Teraguchi, Ashwini Patil, Daron M. Standley: Intrinsically disordered domains deviate significantly from random sequences in mammalian proteins. S7
• 
  Min Wu, Xiaoli Li, Hon Nian Chua, Chee-Keong Kwoh, See-Kiong Ng: Integrating diverse biological and computational sources for reliable protein-protein interactions. S8
• 
  Gaurav Kumar, Shoba Ranganathan: Network analysis of human protein location. S9
• 
  Haijun Gong, Paolo Zuliani, Anvesh Komuravelli, James R. Faeder, Edmund M. Clarke: Analysis and verification of the HMGB1 signaling pathway. S10
• 
  Timothy H. Wu, Ian Chang, Li-chieh Chu, Hsuan-Cheng Huang, Wailap V. Ng: Modularity of Escherichia coli sRNA regulation revealed by sRNA-target and protein network analysis. S11
• 
  Wu Wu, Feng Wang, Maw Chang: Sensitivity analysis of dynamic biological systems with time-delays. S12
• 
  Marzio Pennisi, Francesco Pappalardo, Arianna Palladini, Giordano Nicoletti, Patrizia Nanni, Pierluigi Lollini, Santo Motta: Modeling the competition between lung metastases and the immune system using agents. S13
• 
  Tarini Shankar Ghosh, Monzoorul Haque Mohammed, Sharmila S. Mande: DiScRIBinATE: a rapid method for accurate taxonomic classification of metagenomic sequences. S14
• 
  Shanthi Nagarajan, Hyunah Choo, Yong Cho, Kye Jung Shin, Kwang-Seok Oh, Byung Lee, Ae Pae: IKKβ. S15
• 
  Usman Tambunan, Evi Wulandari: Identification of a better Homo sapiens Class II HDAC inhibitor through binding energy calculations and descriptor analysis. S16

Volume 11, Number S-8, October 2010

Proceedings of the Neural Information Processing Systems (NIPS) Workshop on Machine Learning in Computational Biology (MLCB)

• 
  Pavel P. Kuksa, Vladimir Pavlovic: Efficient motif finding algorithms for large-alphabet inputs. S1
• 
  Jonathan E. Bronson, Jake M. Hofman, Jingyi Fei, Ruben L. Gonzalez, Chris H. Wiggins: Graphical models for inferring single molecule dynamics. S2
• 
  Giorgio Guzzetta, Giuseppe Jurman, Cesare Furlanello: A machine learning pipeline for quantitative phenotype prediction from genotype data. S3
• 
  Eddie Y. T. Ma, Christopher J. F. Cameron, Stefan C. Kremer: Classifying and scoring of molecules with the NGN: new datasets, significance tests, and generalization. S4
• 
  Christian Widmer, Nora C. Toussaint, Yasemin Altun, Gunnar Rätsch: Inferring latent task structure for Multitask Learning by Multiple Kernel Learning. S5
• 
  Cornelia Caragea, Doina Caragea, Adrian Silvescu, Vasant Honavar: Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models. S6
• 
  Nora C. Toussaint, Christian Widmer, Oliver Kohlbacher, Gunnar Rätsch: Exploiting physico-chemical properties in string kernels. S7
• 
  Sudhir Raman, Thomas J. Fuchs, Peter J. Wild, Edgar Dahl, Joachim M. Buhmann, Volker Roth: Infinite mixture-of-experts model for sparse survival regression with application to breast cancer. S8

Volume 11, Number S-9, October 2010

Selected Proceedings of the 2010 AMIA Summit on Translational Bioinformatics

• 
  Eneida A. Mendonça, Peter Tarczy-Hornoch: Selected proceedings of the 2010 Summit on Translational Bioinformatics. S1
• 
  Hsun-Hsien Chang, Michael McGeachie, Gil Alterovitz, Marco Ramoni: Mapping transcription mechanisms from multimodal genomic data. S2
• 
  Philip R. O. Payne, Kun Huang, Kristin Keen-Circle, Abhisek Kundu, Jie Zhang, Tara Borlawsky: Multi-dimensional discovery of biomarker and phenotype complexes. S3
• 
  David P. Chen, Joel Dudley, Atul J. Butte: Latent physiological factors of complex human diseases revealed by independent component analysis of clinarrays. S4
• 
  Jie Zhang, Yang Xiang, Liya Ding, Kristin Keen-Circle, Tara Borlawsky, Hatice Gulcin Ozer, Ruoming Jin, Philip R. O. Payne, Kun Huang: Using gene co-expression network analysis to predict biomarkers for chronic lymphocytic leukemia. S5
• 
  Alexander A. Morgan, Purvesh Khatri, Richard Jones, Minnie M. Sarwal, Atul J. Butte: Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. S6
• 
  Rave Harpaz, Herbert S. Chase, Carol Friedman: Mining multi-item drug adverse effect associations in spontaneous reporting systems. S7
• 
  Ronilda Lacson, Michael Mbagwu, Hisham Yousif, Lucila Ohno-Machado: Assessing the quality of annotations in asthma gene expression experiments. S8
• 
  Nicholas P. Tatonetti, Joel Dudley, Hersh Sagreiya, Atul J. Butte, Russ B. Altman: An integrative method for scoring candidate genes from association studies: application to warfarin dosing. S9
• 
  Casey Lynnette Overby, Peter Tarczy-Hornoch, Jim Hoath, Ira J. Kalet, David L. Veenstra: Feasibility of incorporating genomic knowledge into electronic medical records for pharmacogenomic clinical decision support. S10
• 
  Xinan Yang, Younghee Lee, Yong Huang, James L. Chen, H. Rosie Xing, Yves A. Lussier: Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. S11
• 
  Eric C. Rouchka, Diego E. Montoya-Durango, Vilius Stribinskis, Kenneth S. Ramos, Ted Kalbfleisch: Assessment of genetic variation for the LINE-1 retrotransposon from next generation sequence data. S12

Volume 11, Number S-10, December 2010

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

• 
  Christiaan Klijn, Magali Michaut, Thomas Abeel: Highlights from the 6th International Society for Computational Biology Student Council Symposium at the 18th Annual International Conference on Intelligent Systems for Molecular Biology. I1
• 
  Peter Vanhee, Francois Stricher, Lies Baeten, Erik Verschueren, Luis Serrano, Frederic Rousseau, Joost Schymkowitz: Modeling protein-peptide interactions using protein fragments: fitting the pieces? O1
• 
  Mark D. McDowall, Michelle S. Scott, Geoffrey J. Barton: Human protein-protein interaction prediction. P1
• 
  Xiaofan F. Li, Iain H. Moal, Paul A. Bates: Bridging the gaps: atomic simulation of macromolecular environment brings together protein docking, interaction kinetics and the crowding effects. O2
• 
  Shweta Shah, Nick Sahinidis: Exploiting physical properties in protein structure alignment. O3
• 
  Fuxiao Xin, Steven Myers, Yong Fuga Li, David N. Cooper, Sean D. Mooney, Predrag Radivojac: Structure-based kernels for the prediction of catalytic residues and their involvement in human inherited disease. O4
• 
  Jessica L. Larson, Guo-Cheng Yuan: A hidden Markov model for detecting multi-gene chromatin domains. O5
• 
  Praveen Surendran, Alice V. Stanton, Denis C. Shields: Genome wide association study of nonsynonymous Single Nucleotide Polymorphisms for seven common diseases. O6
• 
  Geoff MacIntyre, James Bailey, Izhak Haviv, Adam Kowalczyk: is-rSNP: a novel technique for in silico regulatory SNP detection. O7
• 
  Jonas Behr, Regina Bohnert, Georg Zeller, Gabriele Schweikert, Lisa Hartmann, Gunnar Rätsch: Next generation genome annotation with mGene.ngs. O8
• 
  Hannes Hettling, Jaap Heringa, Johannes H. G. M. van Beek: Analysis of the functional properties of the creatine kinase system using a multiscale 'sloppy' modeling approach. O9
• 
  María P. Magariños, John P. Overington, Santiago J. Carmona, Dhanasekaran Shanmugam, Maria A. Doyle, Stuart A. Ralph, Gregory J. Crowther, Christiane Hertz-Fowler, Solomon Nwaka, Matthew Berriman, David S. Roos, Wesley C. Van Voorhis, Fernán Agüero: Designing and implementing chemoinformatic approaches in TDR Targets Database: linking genes to chemical compounds in tropical disease causing pathogens. O10
• 
  Santiago J. Carmona, Paula Sartor, Maria Leguizamón, Oscar Campetella, Fernán Agüero: A computational pipeline for diagnostic biomarker discovery in the human pathogen Trypanosoma cruzi. O11
• 
  Sophia Banton, Zvi Roth, Mirjana Pavlovic: A bioengineering approach for rational vaccine design towards the Ebola Virus. O12

Volume 11, Number S-11, December 2010

Proceedings of the 21st International Conference on Genome Informatics (GIW2010)

• 
  Yao Yu, Tao Xu, Yongtao Yu, Pei Hao, Xuan Li: Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. S1
• 
  Lee Sael, Daisuke Kihara: Improved protein surface comparison and application to low-resolution protein structure data. S2
• 
  Liping Jing, Michael K. Ng: Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology. S3
• 
  Yang Zhao, Morihiro Hayashida, Tatsuya Akutsu: Integer programming-based method for grammar-based tree compression and its application to pattern extraction of glycan tree structures. S4
• 
  Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie: TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interactions and protein post-translational modifications information. S5
• 
  Shao Li, Bo Zhang, Duo Jiang, Yingying Wei, Ningbo Zhang: Herb network construction and co-module analysis for uncovering the combination rule of traditional Chinese herbal formulae. S6
• 
  Hao Zheng, Hongwei Wu: Gene-centric association analysis for the correlation between the guanine-cytosine content levels and temperature range conditions of prokaryotic species. S7
• 
  He Quan Sun, Malcolm Yoke-Hean Low, Wen-Jing Hsu, Jagath C. Rajapakse: RecMotif: a novel fast algorithm for weak motif discovery. S8
• 
  Yixiang Shi, Yi-Xue Li, Yuan-Yuan Li: Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution. S9
• 
  Minzhu Xie, Jing Li, Tao Jiang: Accurate HLA type inference using a weighted similarity graph. S10
• 
  Jiandong Ding, Shuigeng Zhou, Jihong Guan: MiRenSVM: towards better prediction of microRNA precursors using an ensemble SVM classifier with multi-loop features. S11
• 
  Dan He, Nicholas A. Furlotte, Eleazar Eskin: Detection and reconstruction of tandemly organized de novo copy number variations. S12
• 
  Tao Xu, Jie Ping, Yao Yu, Fudong Yu, Yongtao Yu, Pei Hao, Xuan Li: Revealing parasite influence in metabolic pathways in Apicomplexa infected patients. S13
• 
  Kang Ning, Alexey I. Nesvizhskii: The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. S14
• 
  Wanlin Liu, Dong Li, Qijun Liu, Yunping Zhu, Fuchu He: A novel parametric approach to mine gene regulatory relationship from microarray datasets. S15
• 
  Yun-Qin Chen, Hui Yu, Yi-Xue Li, Yuan-Yuan Li: Sorting out inherent features of head-to-head gene pairs by evolutionary conservation. S16

Volume 11, Number S-12, December 2010

Proceedings of the 11th Annual Bioinformatics Open Source Conference (BOSC) 2010

• 
  Ronald C. Taylor: An overview of the Hadoop/MapReduce/HBase framework and its current applications in bioinformatics. S1
• 
  Brian D. O'Connor, Barry Merriman, Stanley F. Nelson: SeqWare Query Engine: storing and searching sequence data in the cloud. S2
• 
  Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Hui Li, Bingjing Zhang, Tak-Lon Wu, Yang Ruan, Saliya Ekanayake, Adam Hughes, Geoffrey Fox: Hybrid cloud and cluster computing paradigms for life science applications. S3
• 
  Enis Afgan, Dannon Baker, Nathan Coraor, Brad Chapman, Anton Nekrutenko, James Taylor: Galaxy CloudMan: delivering cloud compute clusters. S4
• 
  Steffen Möller, Hajo N. Krabbenhöft, Andreas Tille, David Paleino, Alan Williams, Katy Wolstencroft, Carole A. Goble, Richard Holland, Dominique Belhachemi, Charles Plessy: Community-driven computational biology with Debian Linux. S5
• 
  Jens Lichtenberg, Kyle Kurz, Xiaoyu Liang, Rami Al-ouran, Lev Neiman, Lee J. Nau, Joshua D. Welch, Edwin Jacox, Thomas Bitterman, Klaus Ecker, Laura Elnitski, Frank Drews, Stephen Lee, Lonnie R. Welch: WordSeeker: concurrent bioinformatics software for discovering genome-wide patterns and word-based genomic signatures. S6
• 
  Mark D. Wilkinson, E. Luke McCarthy, Benjamin P. Vandervalk, David Withers, Edward A. Kawas, Soroush Samadian: SADI, SHARE, and the in silico scientific method. S7
• 
  Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov, Martin Kuiper: ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. S8
• 
  Jianjiong Gao, Dong Xu: The Musite open-source framework for phosphorylation-site prediction. S9
• 
  Tiago Antao: interPopula: a Python API to access the HapMap Project dataset. S10
• 
  Laurent Gautier: An intuitive Python interface for Bioconductor libraries demonstrates the utility of language translators. S11
• 
  Morris A. Swertz, Martijn Dijkstra, Tomasz Adamusiak, K. Joeri van der Velde, Alexandros Kanterakis, Erik T. Roos, Joris Lops, Gudmundur A. Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J. Brookes, Engbert O. de Brock, Ritsert C. Jansen, Helen E. Parkinson: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button. S12
• 
  Ryan J. Kelly, David E. Vincent, Iddo Friedberg: IPRStats: visualization of the functional potential of an InterProScan run. S13