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ORCIDBMC Bioinformatics, Volume 11 - Supplements
Volume 11, Number S-1, 2010
- Laxmi Parida, Gene Myers:
APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010. 0 - Henry Han:
Nonnegative principal component analysis for mass spectral serum profiles and biomarker discovery. 1 - Vinod S. S. Chandra
, Reshmi Girijadevi, Achuthsankar S. Nair, Sreenadhan S. Pillai, Radhakrishna M. Pillai:
MTar: a computational microRNA target prediction architecture for human transcriptome. 2 - Darby Tien-Hao Chang, Yu-Tang Syu, Po-Chang Lin:
Predicting the protein-protein interactions using primary structures with predicted protein surface. 3 - Xiaowen Liu, Baozhen Shan, Lei Xin, Bin Ma:
Better score function for peptide identification with ETD MS/MS spectra. 4 - 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 - Nitin Bhardwaj, Mark Gerstein, Hui Lu:
Genome-wide sequence-based prediction of peripheral proteins using a novel semi-supervised learning technique. 6 - 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 - Junhee Seok, Amit Kaushal, Ronald W. Davis, Wenzhong Xiao:
Knowledge-based analysis of microarrays for the discovery of transcriptional regulation relationships. 8 - Jianyi Yang, Zhen-Ling Peng, Xin Chen:
Prediction of protein structural classes for low-homology sequences based on predicted secondary structure. 9 - Inkyung Jung, Akihisa Matsuyama, Minoru Yoshida, Dongsup Kim:
PostMod: sequence based prediction of kinase-specific phosphorylation sites with indirect relationship. 10 - Christina Boucher, James King:
Fast motif recognition via application of statistical thresholds. 11 - Suparna Mitra, Max Schubach, Daniel H. Huson:
Short clones or long clones? A simulation study on the use of paired reads in metagenomics. 12 - (Withdrawn) In silico screening of herbal and nanoparticle lead compounds for effectivity against H5N1, H1N1 neuraminidase and telomerase. 13
- 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 - Suzanne J. Matthews, Tiffani L. Williams:
MrsRF: an efficient MapReduce algorithm for analyzing large collections of evolutionary trees. 15 - Matteo Comin, Davide Verzotto:
Classification of protein sequences by means of irredundant patterns. 16 - Suyu Mei, Wang Fei:
Amino acid classification based spectrum kernel fusion for protein subnuclear localization. 17 - 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 - Sneh Lata, Nitish K. Mishra, Gajendra P. S. Raghava:
AntiBP2: improved version of antibacterial peptide prediction. 19 - Yongjin Li, Jagdish Chandra Patra:
Integration of multiple data sources to prioritize candidate genes using discounted rating system. 20 - 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 - Ramkrishna Mitra, Sanghamitra Bandyopadhyay, Ujjwal Maulik, Michael Q. Zhang:
SFSSClass: an integrated approach for miRNA based tumor classification. 22 - Byungkyu Park, Kyungsook Han:
An ontology-based search engine for protein-protein interactions. 23 - Pandurangan Sundaramurthy, Khader Shameer, Raashi Sreenivasan, Sunita Gakkhar, Ramanathan Sowdhamini:
HORI: a web server to compute Higher Order Residue Interactions in protein structures. 24 - 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 - Aridaman Pandit, Somdatta Sinha:
Using genomic signatures for HIV-1 sub-typing. 26 - Martin Bader:
Genome rearrangements with duplications. 27 - Daniel G. Brown, Daniil Golod:
Decoding HMMs using the k best paths: algorithms and applications. 28 - Sumeet Agarwal, Candida Vaz, Alok Bhattacharya, Ashwin Srinivasan:
Prediction of novel precursor miRNAs using a context-sensitive hidden Markov model (CSHMM). 29 - Vaibhav Rajan, Andrew Wei Xu, Yu Lin, Krister M. Swenson, Bernard M. E. Moret:
Heuristics for the inversion median problem. 30 - Hiroto Saigo, Masahiro Hattori, Hisashi Kashima, Koji Tsuda:
Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. 31 - Yezhou Huang, Shao Li:
Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network. 32 - Limin Li, Wai-Ki Ching, Takako Yamaguchi, Kiyoko F. Aoki-Kinoshita:
A weighted q-gram method for glycan structure classification. 33 - Zaixin Lu, Zhiyu Zhao, Bin Fu:
Efficient protein alignment algorithm for protein search. 34 - Jayesh Pandey, Mehmet Koyutürk, Ananth Grama:
Functional characterization and topological modularity of molecular interaction networks. 35 - 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 - Won-Hyoung Chung, Seong-Bae Park:
Hit integration for identifying optimal spaced seeds. 37 - 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 - Abu Zafer M. Dayem Ullah, Kathleen Steinhöfel:
A hybrid approach to protein folding problem integrating constraint programming with local search. 39 - Daniel G. Brown, Jakub Truszkowski:
New decoding algorithms for Hidden Markov Models using distance measures on labellings. 40 - Giovanni Ciriello, Claudio Gallina, Concettina Guerra:
Analysis of interactions between ribosomal proteins and RNA structural motifs. 41 - Mukul S. Bansal, J. Gordon Burleigh, Oliver Eulenstein:
Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models. 42 - 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 - Kamal Al-Nasr, Weitao Sun, Jing He:
Structure prediction for the helical skeletons detected from the low resolution protein density map. 44 - Yixuan Chen, Xin Li, Jing Li:
A novel approach for haplotype-based association analysis using family data. 45 - Lei Zhang, James Bailey, Arun Siddharth Konagurthu, Kotagiri Ramamohanarao:
A fast indexing approach for protein structure comparison. 46 - Yang Yang, Jiayuan Zhao, Robyn L. Morgan, Wenbo Ma, Tao Jiang:
Computational prediction of type III secreted proteins from gram-negative bacteria. 47 - Nitish K. Mishra, Gajendra P. S. Raghava:
Prediction of FAD interacting residues in a protein from its primary sequence using evolutionary information. 48 - M. S. Vijayabaskar, Saraswathi Vishveshwara:
Comparative analysis of thermophilic and mesophilic proteins using Protein Energy Networks. 49 - Tina P. George, Tessamma Thomas:
Discrete wavelet transform de-noising in eukaryotic gene splicing. 50 - Padmapriya Paragi-Vedanthi, Mukesh Doble:
Comparison of PGH2 binding site in prostaglandin synthases. 51 - 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 - Aarti Garg, Rupinder Tewari, Gajendra P. S. Raghava:
Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis. 53 - Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard M. E. Moret:
Estimating true evolutionary distances under rearrangements, duplications, and losses. 54 - Kalidas Yeturu, Tapani Utriainen, Graham J. L. Kemp, Nagasuma R. Chandra:
An automated framework for understanding structural variations in the binding grooves of MHC class II molecules. 55 - Mitra Kabir, Nasimul Noman, Hitoshi Iba:
Reverse engineering gene regulatory network from microarray data using linear time-variant model. 56 - Thahir P. Mohamed, Jaime G. Carbonell, Madhavi Ganapathiraju:
Active learning for human protein-protein interaction prediction. 57 - Hatice U. Osmanbeyoglu, Jessica A. Wehner, Jaime G. Carbonell, Madhavi Ganapathiraju:
Active machine learning for transmembrane helix prediction. 58 - Xianjun Dong, Altuna Akalin, Yogita Sharma, Boris Lenhard:
Translog, a web browser for studying the expression divergence of homologous genes. 59 - Daniel Merkle, Martin Middendorf, Nicolas Wieseke:
A parameter-adaptive dynamic programming approach for inferring cophylogenies. 60 - Corban G. Rivera, Rachit Vakil, Joel S. Bader:
NeMo: Network Module identification in Cytoscape. 61 - 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 - Melvin Zhang, Hon Wai Leong:
Bidirectional best hit r-window gene clusters. 63 - Pingzhao Hu, Hui Jiang, Andrew Emili:
Predicting protein functions by relaxation labelling protein interaction network. 64 - 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 - Jianjun Hu, Fan Zhang:
BayesMotif: de novo protein sorting motif discovery from impure datasets. 66 - 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
- Isabel Segura-Bedmar, Mario Crespo, César de Pablo-Sánchez, Paloma Martínez:
Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents. 1 - Chan-seok Jeong, Dongsup Kim:
Linear predictive coding representation of correlated mutation for protein sequence alignment. 2 - Ali Zeeshan Ijaz, Min Song, Doheon Lee:
MKEM: a Multi-level Knowledge Emergence Model for mining undiscovered public knowledge. 3 - Younghoon Kim, Imhoi Koo, Byung Hwa Jung, Bong Chul Chung, Doheon Lee:
Multivariate classification of urine metabolome profiles for breast cancer diagnosis. 4 - 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 - 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 - 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
- Guan Ning Lin, Zheng Wang, Dong Xu, Jianlin Cheng:
SeqRate: sequence-based protein folding type classification and rates prediction. 1 - 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 - Young-Rae Cho, Aidong Zhang:
Identification of functional hubs and modules by converting interactome networks into hierarchical ordering of proteins. 3 - Minoo Aminian, Amina Shabbeer, Kristin P. Bennett:
A conformal Bayesian network for classification of Mycobacterium tuberculosis complex lineages. 4 - Bing Han, Meeyoung Park, Xue-wen Chen:
A Markov blanket-based method for detecting causal SNPs in GWAS. 5 - Brian E. Howard, Steffen Heber:
Towards reliable isoform quantification using RNA-SEQ data. 6 - Fadi Towfic, Susan VanderPlas, Casey A. Oliver, Oliver Couture, Christopher K. Tuggle, M. Heather West Greenlee, Vasant G. Honavar:
Detection of gene orthology from gene co-expression and protein interaction networks. 7 - Xiaohong Wang, Jun Huan, Aaron M. Smalter, Gerald H. Lushington:
Application of kernel functions for accurate similarity search in large chemical databases. 8 - Dong-Chul Kim, Xiaoyu Wang, Chin-Rang Yang, Jean Gao:
Learning biological network using mutual information and conditional independence. 9 - 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
- Eric C. Rouchka, Robert M. Flight, Claire Rinehart:
Proceedings of the ninth annual UT-ORNL-KBRIN Bioinformatics Summit 2010. I1 - Peilin Jia, Zhongming Zhao:
Pathway- and network-based analysis of GWAS data revealed susceptibility gene sets to schizophrenia. O1 - Ramy K. Aziz:
Subsystems-based servers for rapid annotation of genomes and metagenomes. O2 - 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 - 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 - 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 - 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 - 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 - Stephen J. Coleman, Zheng Zeng, Jinze Liu, James N. MacLeod:
Analysis of equine protein-coding gene structure and expression by RNA-sequencing. O8 - 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 - 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 - LiPeng Bi, Chad Groce, Cheryl Davis:
Molecular analysis of Trypanosoma cruzi isolates obtained from raccoons in Warren and Barren counties of Kentucky. P3 - Zhi-Liang Hu, Rex Fernando, Dorian Garrick, James M. Reecy:
SNPlotz: a generic genome plot tool to aid the SNP association studies. P4 - 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 - 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 - 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 - Ramy Karam Aziz:
In silico analysis of a family of extracellular polysaccharide deacetylases involved in virulence of pathogenic gram-positive cocci. P8 - Daniel R. Harris, Jerzy W. Jaromczyk, Christopher L. Schardl:
Experimenting with database segmentation size vs time performance for mpiBLAST on an IBM HS21 blade cluster. P9 - Dexter T. Duncan, Naresh Prodduturi, Bing Zhang:
WebGestalt2: an updated and expanded version of the Web-based Gene Set Analysis Toolkit. P10 - 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 - 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 - 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 - 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 - 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 - Leon Dent, Dana Marshall, Robert Hulette, Siddharth Pratap:
Next-gen sequencing of multi-drug resistant Acinetobacter baumannii to determine antibiotic resistance genotypes. P16 - Fridtjof Thomas, Stanley Pounds:
A Bayesian change-point algorithm for detecting copy number alteration. P17 - Huazhang Guo, Larry Tague, Ramesh Ray, Gabor Tigyi:
A two-step approach to qPCR experimental design and software for data analysis. P18 - Jesse D. Ziebarth, Bao Li, Isao Miyairi, Yan Cui:
Linking genotype to phenotype with Bayesian network modeling of Chlamydia infection. P19