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ORCID1. BCB 2010: Niagara Falls, NY, USA
- Aidong Zhang, Mark Borodovsky, Gultekin Özsoyoglu, Armin R. Mikler:
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, BCB 2010, Niagara Falls, NY, USA, August 2-4, 2010. ACM 2010, ISBN 978-1-4503-0438-2
Keynote speeches, panel and tutorials
- Mark Gerstein:
Analysis of molecular networks. 1 - Bob Cottingham:
Bioinformatics - transition from algorithmic to data intensive science. 2 - Vipin Kumar:
Personalized medicine - challenges and opportunities for informatics research. 3-4 - Jing Li, Kun Huang:
Next generation sequencing data analysis. 5 - Patrick Wang:
Intelligent pattern recognition and applications. 6
Regular papers
- Fatih Altiparmak, Michael Gibas, Hakan Ferhatosmanoglu:
Relationship preserving feature selection for unlabelled clinical trials time-series. 7-16 - Irtisha Singh
, Öznur Tastan, Judith Klein-Seetharaman:
Comparison of virus interactions with human signal transduction pathways. 17-24 - Getiria Onsongo, Hongwei Xie, Timothy J. Griffin, John V. Carlis:
Relational operators for prioritizing candidate biomarkers in high-throughput differential expression data. 25-34 - Yue Li, Gary S. Tyson, Jinfeng Zhang:
Effect of sequences on the shape of protein energy landscapes. 35-42 - Jeremy W. Wang, Kyle J. Moore, Qi Zhang, Fernando Pardo-Manuel de Villena, Wei Wang, Leonard McMillan:
Genome-wide compatible SNP intervals and their properties. 43-52 - Yifeng Li, Numanul Subhani, Alioune Ngom, Luis Rueda:
Alignment-based versus variation-based transformation methods for clustering microarray time-series data. 53-61 - Wei Liu, Anuj Srivastava, Jinfeng Zhang:
Protein structure alignment using elastic shape analysis. 62-70 - Pamela F. Marcott, Jacquelyn S. Fetrow, Richard F. Loeser, Edward E. Allen:
Computational modeling of the effects of oxidative stress on the IGF-1 signaling pathway in human articular chondrocytes. 71-78 - Adrienne Breland, Karen Schlauch, Monica N. Nicolescu, Frederick C. Harris Jr.:
An annotated k-deep prefix tree for (1-k)-mer based sequence comparisons. 79-85 - Choujun Zhan, Lam Fat Yeung:
A parameter estimation approach for non-linear systems biology models using spline approximation. 86-91 - Nirmalya Bandyopadhyay, A. Mark Settles, Tamer Kahveci:
RepFrag: a graph based method for finding repeats and transposons from fragmented genomes. 92-101 - Ferhat Ay, Tamer Kahveci:
Functional similarities of reaction sets in metabolic pathways. 102-111 - Vamsi Kundeti, Sanguthevar Rajasekaran, Hieu Dinh:
On the border length minimization problem (BLMP) on a square array. 112-119 - Shaolei Teng, Hong Luo, Liangjiang Wang:
Random forest-based prediction of protein sumoylation sites from sequence features. 120-126 - Sharlee Climer, Alan R. Templeton, Weixiong Zhang:
SplittingHeirs: inferring haplotypes by optimizing resultant dense graphs. 127-136 - Ali Cakmak, Arun Dsouza, Richard W. Hanson, Z. Meral Özsoyoglu:
Analyzing metabolite measurements for automated prediction of underlying biological mechanisms. 137-146 - Markus Chimani, Sven Rahmann, Sebastian Böcker:
Exact ILP solutions for phylogenetic minimum flip problems. 147-153 - Kimon Frousios, Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis, German Tischler:
REAL: an efficient REad ALigner for next generation sequencing reads. 154-159 - Jorge Duitama, Thomas Huebsch, Gayle McEwen, Eun-Kyung Suk, Margret R. Hoehe:
ReFHap: a reliable and fast algorithm for single individual haplotyping. 160-169 - Bin Yang, Yu Peng, Henry C. M. Leung, Siu-Ming Yiu, Junjie Qin, Ruiqiang Li, Francis Y. L. Chin:
MetaCluster: unsupervised binning of environmental genomic fragments and taxonomic annotation. 170-179 - Bin Song, Sanjay Ranka, Tamer Kahveci:
Enzymatic target identification with dynamic states. 180-187 - Li An, Desmond J. Smith, Hongbo M. Xie, Vasileios Megalooikonomou, Zoran Obradovic:
Identifying gene functions using functional expression profiles obtained by voxelation. 188-197 - J. Gordon Burleigh, Mukul S. Bansal, Oliver Eulenstein, Todd J. Vision:
Inferring species trees from gene duplication episodes. 198-203 - Trilce Estrada, Roger S. Armen, Michela Taufer:
Automatic selection of near-native protein-ligand conformations using a hierarchical clustering and volunteer computing. 204-213 - Dong Yue, Hui Liu, Mingzhu Lu, Philip Chen, Yidong Chen, Yufei Huang:
A Bayesian decision fusion approach for microRNA target prediction. 214-221 - Daniel A. Ashlock, Sheridan K. Houghten:
Ring optimization of edit metric codes in DNA. 222-229 - Kuan Yang, João C. Setubal:
Homology prediction refinement and reconstruction of gene content and order of ancestral bacterial genomes. 230-236 - Tae-Hyuk Ahn, Adrian Sandu:
Parallel stochastic simulations of budding yeast cell cycle: load balancing strategies and theoretical analysis. 237-246 - Venu Satuluri, Srinivasan Parthasarathy, Duygu Ucar:
Markov clustering of protein interaction networks with improved balance and scalability. 247-256 - Cornelia Caragea, Adrian Silvescu, Doina Caragea, Vasant G. Honavar:
Semi-supervised sequence classification using abstraction augmented Markov models. 257-264 - Doruk Bozdag, Ashwin S. Kumar, Ümit V. Çatalyürek:
Comparative analysis of biclustering algorithms. 265-274 - Omar Odibat, Chandan K. Reddy, Craig N. Giroux:
Differential biclustering for gene expression analysis. 275-284 - Ameet Soni, Craig A. Bingman, Jude W. Shavlik:
Guiding belief propagation using domain knowledge for protein-structure determination. 285-294 - Xuefeng Zhou, Jianhua Ruan, Weixiong Zhang:
Promoter prediction based on a multiple instance learning scheme. 295-301 - Fangrui Ma, Jitender S. Deogun:
The solution space of genome sequence alignment and LIS graph decomposition. 302-311 - Ankit Agrawal, Alok N. Choudhary, Xiaoqiu Huang:
Derived distribution points heuristic for fast pairwise statistical significance estimation. 312-321 - Mi-Young Kim, Qing Dou, Osmar R. Zaïane, Randy Goebel:
Unsupervised mapping of sentences to biomedical concepts based on integrated information retrieval model and clustering. 322-329
Short papers
- Isa Kemal Pakatci, Wei Wang, Leonard McMillan:
Gene set analysis using principal components. 330-333 - Ulisses Dias, Zanoni Dias:
An improved 1.375-approximation algorithm for the transposition distance problem. 334-337 - Jinchao Feng, Kebin Jia:
Spectrally resolved bioluminescence tomography with Huber-Markov random-field regularization. 338-341 - Ying-Wooi Wan, Swetha Bose, James Denvir, Nancy Lan Guo:
A novel network model for molecular prognosis. 342-345 - Jun Wang, Maozu Guo:
A graph and hierarchical clustering based approach for population structure inference. 346-349 - Qian Xiang, Xianhua Dai:
Modeling the competitive effects of nucleosomes on transcription factors binding. 350-353 - Guo-Zheng Li, Mingyu You, Lei Ge, Jack Y. Yang, Mary Qu Yang:
Feature selection for semi-supervised multi-label learning with application to gene function analysis. 354-357 - Nishanth Ulhas Nair, Navin Goyal, Nagasuma R. Chandra:
Enhanced flux balance analysis to model metabolic networks. 358-361 - Jinane Mounsef, Lina J. Karam, Patricia Estes, Daniela Zamescu:
Shape analysis and classification of lgl-type and wild-type neurons. 362-365 - Emad Y. Ramadan, Christopher Osgood, Alex Pothen:
Discovering overlapping modules and bridge proteins in proteomic networks. 366-369 - Syed Toufeeq Ahmed, Radhika Nair, Chintan Patel, Sheela P. Kanwar, Jörg Hakenberg, Hasan Davulcu:
Semantic classification and dependency parsing enabled automated bio-molecular event extraction from text. 370-373 - Rachel A. Black, David J. John, Jacquelyn S. Fetrow, James L. Norris:
Examining effects of variability on systems biology modeling algorithms. 374-377 - Yang Liu, Michael K. Ng, Jin Zhou:
SNP specific extraction and analysis using shrunken dissimilarity measure. 378-381 - Zejin Jason Ding, Yan-Qing Zhang:
An effective filtering gene selection method for microarray data via shuffling and statistical analysis. 382-385 - Yu Zhang, Xiuwen Liu, Justin A. Fincher, Jonathan H. Dennis:
DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoost. 386-389 - Jason E. McDermott, Bob Baddeley, Susan L. Stevens, Antonio Sanfilippo, Rick Riensche, Mary P. Stenzel-Poore, Ronald C. Taylor, Russ Jensen:
An integrated approach to predictive genomic analytics. 390-393 - Tiina Manninen, Daniel X. Keller:
Comparison of discrete- and continuous-state stochastic methods to model neuronal signal transduction. 394-397 - Kathryn Dempsey, Benjamin Currall, Richard Hallworth, Hesham H. Ali:
An intelligent data-centric approach toward identification of conserved motifs in protein sequences. 398-401 - Michael Krone, Carsten Dachsbacher, Thomas Ertl:
Parallel computation and interactive visualization of time-varying solvent excluded surfaces. 402-405 - Wendy Ashlock, Suprakash Datta:
Using Fourier phase analysis on genomic sequences to identify retroviruses. 406-409 - Vijender Chaitankar, Preetam Ghosh, Chaoyang Zhang, Ping Gong, Edward J. Perkins:
Effects of cDNA microarray time-series data size on gene regulatory network inference accuracy. 410-413 - Davide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi:
Compositional modelling of signalling pathways in timed concurrent constraint programming. 414-417 - Narayan Ganesan, Roger D. Chamberlain, Jeremy Buhler, Michela Taufer:
Accelerating HMMER on GPUs by implementing hybrid data and task parallelism. 418-421 - Mehdi Kargar, Aijun An:
Evaluation of different complexity measures for signal detection in genome sequences. 422-425 - Qinmin Vivian Hu, Jimmy Xiangji Huang:
Genomics information retrieval using a Bayesian model for learning and re-ranking. 426-429 - Ping Gong, Fuliang Xie, Baohong Zhang, Edward J. Perkins:
In silico identification of microRNAs from expressed sequence tags of three earthworm species. 430-434 - Mahesh Visvanathan, Sasidhar R. Siddam, In-Hee Lee, Gerald H. Lushington, George R. Bousfield:
Systematic data integration platform for functional glycomics. 435-438
Posters
- Changjiang Zhang, Kimberly Forsten-Williams, Bing Zhao, Michael Fannon, Jun Zhang:
Coupling between heparan sulfate proteoglycans and FGF-2 receptors is key to FGF-2 capture under flow: a computational study. 439-441 - Alex Rudniy, Min Song, James Geller:
Shortest path edit distance for detecting duplicate biological entities. 442-444 - Tianchuan Du, Shuju Bai, Ebrahim Khosravi:
Docking arachidonic acid to 8R-lipoxygenase using internal coordinate mechanics. 445-447 - Heejoon Chae, Kwangmin Choi, Sun Kim, Haleh Ashki:
EGGSlicer: predicting biologically meaningful gene sets from gene clusters using gene ontology information. 448-450 - Preetam Ghosh, Amit Kumar, Bhaswati Datta, Vijayaraghavan Rangachari:
Estimating the dynamics of protofibril elongation involved in Aβ42 peptide aggregation in Alzheimer's disease. 451-453 - En Cheng, Ali Cakmak, Z. Meral Özsoyoglu:
Efficient query evaluation for DAG-shaped hierarchies. 454-456 - Guillaume Santini, Henry Soldano, Joël Pothier:
Use of ternary similarities in graph based clustering for protein structural family classification. 457-459 - Mei Xiao, Jung Soh, Morgan L. Taschuk, Andrei L. Turinsky, Trish E. Parsons, Benedikt Hallgrímsson, Christoph W. Sensen:
Visualization of biological shape transformation by 3D model morphing. 460-462 - Fan Zhang, Mu Wang, Jake Y. Chen:
Breast cancer plasma protein biomarker discovery by coupling LC-MS/MS proteomics and systems biology. 463-465 - Haoni Li, Peng Li, Chaoyang Zhang, Nan Wang, Ping Gong, Edward J. Perkins:
Performance evaluation of the time-delayed dynamic Bayesian network approach to inferring gene regulatory networks from time series microarray data. 466-468 - Justin A. Fincher, Gary Tyson, Jonathan H. Dennis:
A computational exploration of gene regulation by nucleosome position. 469-471 - Jingshan Huang, Ming Tan, Dejing Dou, Lei He, Christopher Townsend, Patrick J. Hayes:
Ontology for MicroRNA Target prediction in human cancer. 472-474 - Marko Gosak, Marko Marhl, Christelle Guibert, Marie Billaud, Etienne Roux:
Pulmonary artery smooth muscle responses to KCl under normoxic and hypoxic conditions studied by means of a spatial network model. 475-477 - Wolfgang Hankeln, Pier Luigi Buttigieg, Ivaylo Kostadinov, Renzo Kottmann, Pelin Yilmaz, Melissa Beth Duhaime, Frank Oliver Glöckner:
Applying graph theoretic approaches to microbial metagenomes: ecological perspectives on function. 478-480 - Cen Li, Suk Jai Seo, Ralph Butler:
Hunting for truly relevant articles in bioinformatics literature: a preliminary study. 481-483 - Alex Rodionov, Alexandr Bezginov, Jonathan Rose, Elisabeth R. M. Tillier:
Faster coevolution detection of proteins using maximum similar cliques. 484-486 - David Hala, Duane B. Huggett, Dalma Martinovic:
In silico predicted essential genes required for zebrafish (Danio rerio) steroid hormone production. 487-489 - Mohamad Qayoom, Qi Zhang, Christopher Taylor:
F-statistics algorithm for gene clustering evaluation. 490-492 - Jaegyoon Ahn, Youngmi Yoon, Sanghyun Park:
A novel cancer classifier based on differentially expressed gene network. 493-495 - Caroline Baroukh, Anthony Rowe, Yike Guo:
Process calculi for systems biology. 496-497 - Bradley W. Poland, Panayiotis Zagouras, Snehal Naik, Eric Fauman, Karl Richter, Robert M. Peitzsch:
Alzheimer's disease target selection: a data integration approach. 498 - Hyunsoo Kim, Ramana V. Davuluri:
Data mining of mRNA-Seq and small RNA-Seq data to find microRNA targets. 499-501
Workshop on Gene Network and Pathway Generation and Analysis
- Tao Huang, Guohui Ding, Yixue Li, Lei Liu, Eugene Tan, Hongyue Dai, Qi Liu, Zhidong Tu, Lu Xie:
Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma. 502-507 - Mahesh Visvanathan, Shanker Rao, Vijay Anand, Gerald H. Lushington, Michael Netzer, Christian Baumgartner, George R. Bousfield:
A multi-tier data mining workflow to analyze the age related shift from diglycosylated- to tetra-glycosylated-FSH secretion by the anterior pituitary. 508-514 - Ronald C. Taylor, Bob Baddeley, Antonio Sanfilippo, Rick Riensche, Marc Verhagen, Jason E. McDermott, Russ Jensen:
Learning biological networks via bootstrapping with optimized go-based gene similarity. 515-519 - Chifeng Ma, Hung-I Harry Chen, Yufei Huang, Yidong Chen:
Constructing a compound mode-of-action network for personalized drug effectiveness prediction. 520-528 - Laura Elnitski, Jens Lichtenberg, Lonnie R. Welch:
Regulatory network nodes of check point factors in DNA repair pathways. 529-536 - Mudita Singhal, Anuj R. Shah, Joshua N. Adkins, Roslyn Brown:
Using support vector machine for improving protein-protein interaction prediction utilizing domain interactions. 537-545 - Praneeth Uppalapati, Yang Xiang, Kun Huang:
Predicting prognostic markers for glioma using gene co-expression network analysis. 546-551 - An Zhou, Larry David, Roger Simon:
De novo proteomics of neuronal ischemic tolerance. 552-555
Workshop on Graph Theoretic Approaches for Biological Network Analysis
- Emad Y. Ramadan, Sudhir Perincheri, David Tuck:
A hyper-graph approach for analyzing transcriptional networks in breast cancer. 556-562 - Taehyong Kim, Murali Ramanathan, Aidong Zhang:
A graph-based approach for computational model of bone microstructure. 563-568 - José P. Pinto, Isabel Rocha, Miguel Rocha:
A software tool for network topology analysis under a metabolic engineering perspective. 569-578 - Emad Y. Ramadan, Sudhir Perincheri, David Tuck:
Crosstalk measures for analyzing biological networks in breast cancer. 579-586 - Young-Rae Cho:
Topological analysis of structural roles of proteins in interactome networks. 587-593 - Adrienne Breland, Karen Schlauch, Mehmet Hadi Gunes, Frederick C. Harris Jr.:
Fast graph approaches to measure influenza transmission across geographically distributed host types. 594-601
Immunoinformatics and Computational Immunology Workshop
- Salvador Eugenio C. Caoili:
B-cell epitope prediction for peptide-based vaccine design: towards a paradigm of biological outcomes. 602-610 - Matthew Ardito, Songhua Zhang, William D. Martin, Steven F. Moss, Anne S. De Groot, Leonard Moise:
Immunoinformatic-driven H. pylori vaccine design. 611-615 - Matthew Ardito, Leonard Moise, William D. Martin, Anne S. De Groot:
Immunoinformatic approach to a multi-pathogen genome-derived epitope-driven vaccine. 616-620 - Michael T. Zimmermann, Aris Skliros, Saras Saraswathi, Andrzej Kloczkowski, Robert L. Jernigan:
Immunoglobulin functional motions and their effects on the complementarity determining regions. 621-626 - Chen Yanover, Mari Malkki, Ted Gooley, Effie W. Petersdorf, Philip Bradley:
How do amino acid mismatches affect the outcome of hematopoietic cell transplants?: a structural perspective. 627-633 - Peng Wang, Björn Peters, John Sidney, Alessandro Sette:
An automatic computational pipeline to display MHC binding motifs. 634-641 - David K. Crockett, Perry G. Ridge:
A novel representation of HLA allele specificity and prediction algorithm for HLA class I binding. 642-643 - Perry G. Ridge, David K. Crockett:
Feature selection for characterizing HLA class I peptide motif anchors. 644-645 - Anat Zvi, David Lewinsohn, Deborah Lewinsohn, Avigdor Shafferman:
Whole-genome immunoinformatic analysis of Mycobacterium tuberculosis towards large scale identification of immunodominant CD8 epitopes. 646 - Andreas Heinzel, Johannes Söllner, Suszan Szathmary:
Application of systems biology for understanding of disease and selection of molecular targets for therapy. 647 - Sinu Paul, Helen Piontkivska:
Highly conserved and associated HIV-1 CTL and T-Helper epitopes in global HIV-1 population: potential candidates for multi-epitope HIV-1 vaccine. 648 - Francesco Pappalardo, Marzio Pennisi, Santo Motta:
Universal immune system simulator framework (UISS). 649-650 - Anna Chailyan, Davide Cirillo, Paolo Marcatili, Anna Tramontano:
Structural landscape of immunoglobulin lambda light chains. 651-652 - Ataur R. Katebi, Pawel Gniewek, Michael T. Zimmermann, Saras Saraswathi, Zhenming Gong, Christopher K. Tuggle, Andrzej Kloczkowski, Robert L. Jernigan:
Immunological implications of a structural analysis of two different porcine IL1β proteins expressed in macrophages and embryos. 653-655 - Alpna Agarwal, Susan Zolla-Pazner, James Swetnam, Timothy Cardozo:
Effective neutralization and neutralization epitope masking signatures for four anti-V3 mAbs. 656 - Sanchita Bhattacharya, Shai Shen-Orr, Holden T. Maecker, Laura Lazzeroni, Gary E. Swan, J. David Clark, Martin S. Angst, Atul J. Butte, Mark M. Davis:
Immunological response in normal healthy twins across age. 657 - Claus Lundegaard, M. Buggert, A. C. Karlsson, Ole Lund, Carina Perez, Morten Nielsen:
PopCover: a method for selecting of peptides with optimal population and pathogen coverage. 658-659 - Yasser El-Manzalawy, Vasant G. Honavar:
A framework for developing epitope prediction tools. 660-662 - Sarah K. Kummerfeld, Jason A. Hackney, Michael J. Townsend, Hilary F. Clark:
Rheumatoid Arthritis molecular heterogeneity. 663
Workshop on Protein-Protein Interaction Data: Management, Querying and Analysis
- Mario Cannataro, Pietro Hiram Guzzi, Pierangelo Veltri:
Using RDF for managing protein-protein interaction data. 664-670 - Vera Tomaino, Pietro Hiram Guzzi, Mario Cannataro, Pierangelo Veltri:
Experimental comparison of biclustering algorithms for PPI networks. 671-676 - Maria Persico:
A combinatorics based solution for input generation in the context of classification frameworks aimed to learning interacting protein class. 684-689
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