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2. BCB 2011: Chicago, IL, USA
- Robert Grossman, Andrey Rzhetsky, Sun Kim, Wei Wang:
ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 11, Chicago, IL, USA - July 31 - August 03, 2011. ACM 2011, ISBN 978-1-4503-0796-3 - Boon-Siew Seah, Sourav S. Bhowmick
, C. Forbes Dewey Jr., Hanry Yu
Fuse: towards multi-level functional summarization of protein interaction networks. 2-11 - Iman Rezaeian, Luis Rueda:
Biological assessment of grid and spot detection in cDNA microarray images. 12-19 - Changjiang Zhang, Kimberly Forsten-Williams, Michael Fannon, Wensheng Shen, Jun Zhang:
Parallel simulation of multiple proteins through a bioreactor coupled with biochemical reactions. 20-28 - R. Mitchell Parry, John H. Phan, May D. Wang
Win percentage: a novel measure for assessing the suitability of machine classifiers for biological problems. 29-38 - Zanoni Dias, Ulisses Dias
Using inversion signatures to generate draft genome sequence scaffolds. 39-48 - Yin Tang, Fei Wang:
Neural system modeling and simulation using hybrid functional Petri net. 49-58 - Corban G. Rivera, Brett M. Tyler, T. M. Murali:
Sensitive detection of pathway perturbations in cancers: extended abstract. 59-68 - Taehyong Kim, Murali Ramanathan, Lawrence Bone, Aidong Zhang:
Mathematical network model for bone mineral density (BMD) and bone quality assessment. 69-75 - Richard Jang, Xin Gao
Combining ambiguous chemical shift mapping with structure-based backbone and NOE assignment from 15N-NOESY. 76-86 - Marco Pellegrini
Detecting fuzzy amino acid tandem repeats in protein sequences. 87-95 - Yu-Keng Shih, Srinivasan Parthasarathy
Scalable multiple global network alignment for biological data. 96-105 - Xia Ning, Michael A. Walters, George Karypis
Improved machine learning models for predicting selective compounds. 106-115 - Toshiaki Namiki, Tsuyoshi Hachiya, Hideaki Tanaka, Yasubumi Sakakibara:
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads. 116-124 - Andrey N. Chernikov, Nikos Chrisochoides:
Tetrahedral image-to-mesh conversion for biomedical applications. 125-134 - Artem Sokolov, Asa Ben-Hur
Multi-view prediction of protein function. 135-142 - Lu He, Alan M. Friedman, Chris Bailey-Kellogg:
Algorithms for optimizing cross-overs in DNA shuffling. 143-152 - Basak Oztan, Lindsey M. Polizzotti, Cemal Çagatay Bilgin, Kira M. Henderson, George E. Plopper, Bülent Yener:
Classification of breast cancer grades through quantitative characterization of ductal structure morphology in three-dimensional cultures. 153-161 - Maryam Haghighi, Sylvia C. Boyd:
A fast method for large-scale multichromosomal breakpoint median problems. 162-171 - Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
Inference of tumor phylogenies from genomic assays on heterogeneous samples. 172-181 - Li An, Haibin Ling, Zoran Obradovic, Desmond J. Smith, Vasileios Megalooikonomou:
Identifying pair-wise gene functional similarity by multiplex gene expression maps and supervised learning. 182-190 - Shruthi Prabhakara, Raj Acharya:
A two-way multi-dimensional mixture model for clustering metagenomic sequences. 191-200 - Minoo Aminian, Amina Shabbeer, Kane Hadley, Cagri Ozcaglar, Scott L. Vandenberg, Kristin P. Bennett:
Knowledge-based Bayesian network for the classification of Mycobacterium tuberculosis complex sublineages. 201-208 - Osama Aljawad, Yanni Sun
NcRNA homology search using Hamming distance seeds. 209-217 - Jianlong Qi, Tom Michoel
An integrative approach to infer regulation programs in a transcription regulatory module network. 218-225 - Aaron Smalter Hall, Jun Huan, Gerald H. Lushington
Similarity boosting for label noise tolerance in protein-chemical interaction prediction. 226-234 - Lei Yang, En Cheng, Z. Meral Özsoyoglu:
Using compact encodings for path-based computations on pedigree graphs. 235-244 - Yuan Li, Shaojie Zhang
Predicting folding pathways between RNA conformational structures guided by RNA stacks. 245-253 - Ye Tian, Bai Zhang, Ie-Ming Shih, Yue Joseph Wang:
Knowledge-guided differential dependency network learning for detecting structural changes in biological networks. 254-263 - Ameet Soni, Jude W. Shavlik:
Probabilistic ensembles for improved inference in protein-structure determination. 264-273 - Michael Dang, Ferhat Ay
A novel framework for large scale metabolic network alignments by compression. 274-283 - Huey-Eng Chua, Qing Zhao, Sourav S. Bhowmick
Pani: a novel algorithm for fast discovery of putative target nodes in signaling networks. 284-288 - Leif Ellingson
An efficient algorithm for matching protein binding sites for protein function prediction. 289-293 - Luis C. González, Dennis R. Livesay, Donald J. Jacobs:
Improving protein flexibility predictions by combining statistical sampling with a mean-field virtual Pebble Game. 294-298 - Chengcheng Shen, Ying Liu:
A tripartite clustering analysis on microRNA, gene and disease model. 299-303 - Woo-Hyuk Jang, Suk Hoon Jung, Bo-ra Hyun, Dong-Soo Han:
Modeling of multi domain contribution to protein interaction. 304-308 - Majid Masso
Sequence-based prediction of HIV-1 coreceptor usage: utility of n-grams for representing gp120 V3 loops. 309-314 - Shilpa Nadimpalli
Formatt: correcting protein multiple structural alignments by sequence peeking. 315-319 - Anupam Ghosh
A fuzzy entropy based approach for development of gene prediction networks (GPNs): detecting altered dependency in carcinogenic state. 320-324 - Yixuan Chen, Jing Li
Generation of synthetic data in evaluating interactions for association studies. 325-329 - Tomás Flouri
DynMap: mapping short reads to multiple related genomes. 330-334 - Jeremy W. Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan
Dynamic visualization and comparative analysis of multiple collinear genomic data. 335-339 - Shulin Yang, Linda G. Shapiro, Michael L. Cunningham, Matthew L. Speltz, Su-In Lee:
Classification and feature selection for craniosynostosis. 340-344 - Akther Shermin, Hasan Jamil
A scalable approach for inferring transcriptional regulation in the yeast cell cycle. 345-349 - Omar Odibat, Chandan K. Reddy
Ranking differential genes in co-expression networks. 350-354 - Songjian Lu, Xinghua Lu:
A graph model and an exact algorithm for finding transcription factor modules. 355-359 - Lei Shi, Aidong Zhang:
An ACO based functional module detection algorithm for protein interaction networks. 360-365 - Youngik Yang:
A novel K-mer mixture logistic regression for methylation susceptibility modeling of CpG dinucleotides in human gene promoters. 366-370 - Lindsey Bell, Jinfeng Zhang, Xufeng Niu:
Mixture of logistic models and an ensemble approach for protein-protein interaction extraction. 371-375 - Noor Alaydie, Chandan K. Reddy
A Bayesian integration model for improved gene functional inference from heterogeneous data sources. 376-380 - Michael Hamilton, A. S. N. Reddy, Asa Ben-Hur
Kernel methods for Calmodulin binding and binding site prediction. 381-386 - Ali Cakmak
Computational interpretation of metabolomics measurements: steady-state metabolic network dynamics analysis. 387-392 - Adriana Muñoz, David Sankoff:
Changes in gene expression near evolutionary breakpoints. 393-398 - Jie Zhou, Hanchuan Peng:
Counting cells in 3D confocal images based on discriminative models. 399-403 - M. Leigh Fanning, Joanne Macdonald
ISO: numeric representation of nucleic acid form. 404-408 - A. Ercüment Çiçek, Gultekin Özsoyoglu:
Resolving observation conflicts in steady state metabolic network dynamics analysis. 409-414 - Xuan Liu, Shing-Wan Choi
Detection of novel tandem duplication with next-generation sequencing. 415-419 - Vinicio Reynoso, Catherine Putonti:
Mapping short sequencing reads to distant relatives. 420-424 - Hiroyuki Kuwahara, Chris J. Myers
Erlang-delayed stochastic chemical kinetic formalism for efficient analysis of biological systems with non-elementary reaction effects. 425-429 - Qiong Cheng, Mitsunori Ogihara
Inferring conflict-sensitive phosphorylation dynamics. 430-434 - Günhan Gülsoy, Bhavik Gandhi, Tamer Kahveci:
Topology aware coloring of gene regulatory networks. 435-440 - Li C. Xue, Rafael A. Jordan, Yasser El-Manzalawy, Drena Dobbs
Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study. 441-445 - Emmett Sprecher, Sudipa Sarkar, Steven H. Kleinstein, Murli Narayan, Eric P. Winer, David Tuck, Kimberly Lezon-Geyda, Ian Krop, Lyndsay Harris:
Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors. 446-450 - Yuan Li, Aaron L. Halpern, Shaojie Zhang:
TreeLign: simultaneous stepwise alignment and phylogenetic positioning, with its application to automatic phylogenetic assignment of 16S rRNAs. 451-456 - Chih Lee, Chun-Hsi Huang:
Geometric visualization of TF binding sites in context. 457-461 - Kavishwar B. Wagholikar
Human gene/protein synonym dictionary from WikiLinks. 462-464 - Paolo Atzeni
Experimentation of an automatic resolution method for protein abbreviations in full-text papers. 465-467 - Chee Keong Kwoh, Lakshmi Chandrasekaran:
Phylogenetic and mutational analysis of 2008, 2009 & 2010 neuraminidase of H1N1 influenza A. 468-470 - Jia Wu, Raymond Tse, Carrie Heike
Learning to compute the plane of symmetry for human faces. 471-474 - Zhi-Liang Hu, Xiaolin Wu, James M. Reecy:
Extension of Animal QTLdb: QTL meta-analysis on the fly. 475-477 - Sabareesh Subramaniam, Sriraam Natarajan, Alessandro Senes:
A machine learning based approach to improve sidechain optimization. 478-480 - Ling Chen, Wei Liu:
An effective approach for mining frequent patterns in multiple biological sequences. 481-483 - Thomas K. F. Wong, Hui-Ting Yu, Bay-Yuan Hsu, Tak Wah Lam
Algorithms for pseudoknot classification. 484-486 - Yam Ki Cheung, Ovidiu Daescu, Lech Papiez:
Volume matching with application in medical treatment planning. 487-489 - Tomás Flouri
Approximate string-matching with a single gap for sequence alignment. 490-492 - Yifeng Liu, Zhaochen Guo, Xiaodi Ke, Osmar R. Zaïane:
Protein subcellular localization prediction with associative classification and multi-class SVM. 493-495 - Ondrej Kuzelka
Gaussian logic and its applications in bioinformatics. 496-498 - Osamu Maruyama:
Heterodimeric protein complex identification. 499-501 - George Mathew, Zoran Obradovic:
Constraint graphs as security filters for privacy assurance in medical transactions. 502-504 - Christian Baudet, Zanoni Dias:
Partial enumeration of solutions traces for the problem of sorting by signed reversals. 505-507 - Kuan Yang, João Carlos Setubal
A whole genome simulator of prokaryote genome evolution. 508-510 - Daniel Johnson, Kun Wang, Carole L. Cramer, Xiuzhen Huang:
Graph-based approach for gene markers and applications in next-generation sequencing data analysis. 511-513 - Tu-Liang Lin
Evaluating the quality of conformation sampling methods using experimental residual dipolar coupling data. 514-518 - Alpna Agarwal, Eron Oronsaye, Arthur Nadas, Susan Zolla-Pazner
CCR5/CXCR4 discriminating sites in the HIV-1 gp120 core. 519-521 - Ho-Sun Shon, Kyung-Sook Yang, Che Woo Yoo, Keun Ho Ryu:
Feature selection method using WF-LASSO for gene expression data analysis. 522-524 - Maragaille R. Capiroso, Marla A. Endriga, Valerie Diane V. Valeriano
A molecular systems analysis of HOX PPI networks in hematopoiesis and leukemogenesis. 525-527 - Angel Bravo-Salgado, Jessica Beckham, Armin R. Mikler:
Modeling malaria: stretch-delay effect of temperature in the sporogonic cycle and disease dynamics. 528-530 - Nan Du, Kang Li, Supriya D. Mahajan, Stanley A. Schwartz, Bindukumar B. Nair, Chiu Bin Hsiao, Aidong Zhang:
Gene Co-Adaboost: a semi-supervised approach for classifying gene expression data. 531-535 - Natasa Miskov-Zivanov, Andrew Bresticker, Deepa Krishnaswamy
Emulation of biological networks in reconfigurable hardware. 536-540 - Todd H. Stokes, Richard A. Moffitt, May D. Wang
SecureMed-ID: memorable and private identifiers for off-site access to medical records. 541-543 - Fethullah Karabiber, Kevin Weeks, Oleg V. Favorov
Automated peak alignment for nucleic acid capillary electrophoresis data by dynamic programming. 544-546 - Zhonghua Jiang, George Karypis
Automatic detection of vaccine adverse reactions by incorporating historical medical conditions. 547-549 - Heung-Seon Oh
Extracting targets and attributes of medical findings from radiology reports in a mixture of languages. 550-552 - Vishal Bahirwani, Doina Caragea
Study on regulatory motifs in Arabidopsis thaliana. 553-555 - Li C. Xue, Rasna R. Walia
Improving protein-RNA interface prediction by combining sequence homology based method with a naive Bayes classifier: preliminary results. 556-558 - Suely Oliveira
Clustering for bioinformatics via matrix optimization. 559-563
Immunoinformatics and Computational Immunology Workshop
- Francesca Cordero
Cancer stem cell based adjuvant for oncoantingen-driven vaccination. 564-568 - Salvador Eugenio C. Caoili:
Affinity limits in B-cell epitope prediction for immunity mediated by antipeptide antibodies. 569-578 - Christopher S. Eickhoff, Matthew Ardito, Eric Gustafson, William D. Martin, Daniel F. Hoft:
Generation of novel Chagas vaccines: evolving studies/work in progress. 579-583 - Nora C. Toussaint
T-cell epitope prediction based on self-tolerance. 584-588 - Leonard Moise, Matthew Ardito, William D. Martin, Eric Gustafson, Alan Rothman, Anne S. De Groot
Immunoinformatic discovery of potential cross-reactive T cell epitopes in the measles genome. 589-593 - Dan He, Pratima Kunwar, Eleazar Eskin, Helen Horton, Peter B. Gilbert, Tomer Hertz
Using HLA binding prediction algorithms for epitope mapping in HIV vaccine clinical trials. 594-601 - Guanglan Zhang, Melisa L. Budde, Jennifer J. Lhost, David H. O'Connor
PREDmafa: a system for prediction of peptide binding to several MHC class I molecules in cynomolgus macaques. 602-606 - Yohan Kim, Jonathan W. Yewdell, Bjoern Peters:
Determining positional bias of MHC class I restricted T-cell epitopes in viral antigens. 607-611
Workshop on Semantic Applied Technologies on Biomedical Informatics
- Alejandro Rodríguez González
Designing an ontology to support the creation of diagnostic decision support system. 612-616 - María Del Carmen Legaz-García, José Antonio Miñarro-Giménez
Using ontologies for supporting genomic sequence annotation projects. 617-625 - José María Álvarez Rodríguez
Application of the spreading activation technique for recommending concepts of well-known ontologies in medical systems. 626-635 - Nate Blaylock, William de Beaumont, James F. Allen, Hyuckchul Jung:
Towards an OWL-based framework for extracting information from clinical texts. 636-640
Workshop on Biomolecular Network Analysis
- Edward Casey Kenley, Lyles Kirk, Young-Rae Cho:
Differentiating party and date hubs in protein interaction networks using semantic similarity measures. 641-645 - Saeed Salem, Loqmane Seridi
CLARM: an integrative approach for functional modules discovery. 646-650 - Kim Jong Kwang:
Brain tumor pathway identification by integrating transcriptome and interactome data. 651-655 - Pietro Hiram Guzzi, Pierangelo Veltri
Experimental evaluation of OntoPIN: an ontology-annotated PPI database. 656-660
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