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4. BCB 2013: Washington, DC, USA
- Jing Gao:
ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics. ACM-BCB 2013, Washington, DC, USA, September 22-25, 2013. ACM 2013, ISBN 978-1-4503-2434-2
Regular Papers
- Haitham Gabr, Andrei Todor, Helia Zandi
, Alin Dobra
PReach: Reachability in Probabilistic Signaling Networks. 3 - Solon P. Pissis
MoTeX: A word-based HPC tool for MoTif eXtraction. 13 - Tijana Milenkovic, Han Zhao, Fazle Elahi Faisal:
Global Network Alignment In The Context Of Aging. 23 - Yuri Pirola
Haplotype-based prediction of gene alleles using pedigrees and SNP genotypes. 33 - Hui Li, Xiaoyi Li, Murali Ramanathan, Aidong Zhang:
A Semi-Supervised Learning Approach to Integrated Salient Risk Features for Bone Diseases. 42 - Md Mahmudul Hasan, Tamer Kahveci:
Color distribution can accelerate network alignment. 52 - David E. Robbins, Alexander Grüneberg, Helena F. Deus
TCGA Toolbox: an Open Web App Framework for Distributing Big Data Analysis Pipelines for Cancer Genomics. 62 - Raul I. Ramos-Garcia, Adam W. Hoover:
A Study of Temporal Action Sequencing During Consumption of a Meal. 68 - Elena G. Randou, Daniel Veltri
Binary Response Models for Recognition of Antimicrobial Peptides. 76 - Viktor Chekh, Shuang (Sean) Luan, Mark R. Burge, Cesar Carranza
Quantitative Early Detection of Diabetic Foot. 86 - Jinghua Gu, Jianhua Xuan, Xiao Wang, Ayesha N. Shajahan, Leena Hilakivi-Clarke, Robert Clarke
Reconstructing transcriptional regulatory networks by probabilistic network component analysis. 96 - Debswapna Bhattacharya, Jianlin Cheng
Protein Structure Refinement by Iterative Fragment Exchange. 106 - Tin Chi Nguyen
MarkovBin: An Algorithm to Cluster Metagenomic Reads Using a Mixture Modeling of Hierarchical Distributions. 115 - Nan Deng, Dongxiao Zhu:
Detecting various types of differential splicing events using RNA-Seq data. 124 - Noah M. Daniels, Andrew Gallant, Norman Ramsey, Lenore J. Cowen:
MRFy: Remote Homology Detection for Beta-Structural Proteins Using Markov Random Fields and Stochastic Search. 133 - Michael A. DeJesus
Improving discrimination of essential genes by modeling local insertion frequencies in transposon mutagenesis data. 144 - Yongtao Ye
GLProbs: Aligning multiple sequences adaptively. 152 - Xiao Zhu, Henry C. M. Leung, Francis Y. L. Chin, Siu-Ming Yiu, Guangri Quan, Bo Liu, Yadong Wang:
PERGA: A Paired-End Read Guided De Novo Assembler for Extending Contigs Using SVM Approach. 161 - Himanshu Chandola, Bruce Randall Donald, Chris Bailey-Kellogg:
Simultaneous determination of subunit and complex structures of symmetric homo-oligomers from ambiguous NMR data. 171 - Ulisses Dias
Greedy Randomized Search Procedure to Sort Genomes using Symmetric, Almost-Symmetric and Unitary Inversions. 181 - Shaolong Cao, Huaizhen Qin, Hong-Wen Deng, Yu-Ping Wang:
A generalized sparse regression model with adjustment of pedigree structure for variant detection from next generation sequencing data. 191 - Manabu Torii
Text Mining of Protein Phosphorylation Information Using a Generalizable Rule-Based Approach. 201 - Ehsan Ullah, Calvin Hopkins, Shuchin Aeron, Soha Hassoun:
Decomposing Biochemical Networks Into Elementary Flux Modes Using Graph Traversal. 211 - A. Ercüment Çiçek, Xinjian Qi, Ali Cakmak
PathCase-MAW: An Online Metabolic Network Analysis Workbench. 219 - Yu Zhou, Yann Ponty
Flexible RNA design under structure and sequence constraints using formal languages. 229 - Ellen M. Voorhees
The TREC Medical Records Track. 239 - Mark F. Rogers, Christina Boucher, Asa Ben-Hur
SpliceGrapherXT: From Splice Graphs to Transcripts Using RNA-Seq. 247 - Ariful Azad, Arif M. Khan, Bartek Rajwa, Saumyadipta Pyne, Alex Pothen
Classifying Immunophenotypes With Templates From Flow Cytometry. 256 - Kang Li, Suxin Guo, Jing Gao, Aidong Zhang:
An Ensemble Model for Mobile Device based Arrhythmia Detection. 266 - En-Shiun Annie Lee, Andrew K. C. Wong:
Classifying Proteins by Amino Acid Variations of Sequential Patterns. 276 - Ayat Hatem, Kamer Kaya, Ümit V. Çatalyürek
PRASE: PageRank-based Active Subnetwork Extraction. 286 - Vanja Paunic, Michael S. Steinbach
Evaluation of Label Dependency for the Prediction of HLA Genes. 296 - Hao Wang, Geet Duggal, Rob Patro, Michelle Girvan, Sridhar Hannenhalli, Carl Kingsford:
Topological properties of chromosome conformation graphs reflect spatial proximities within chromatin. 306 - Sujun Li, Randy J. Arnold, Haixu Tang, Predrag Radivojac:
Improving phosphopeptide identification in shotgun proteomics by supervised filtering of peptide-spectrum matches. 316 - Jie Zhou, Anthony Brunson, John Winans, Kirk L. Duffin, Nicholas T. Karonis:
Performance Model Selection for Learning-based Biological Image Analysis on a Cluster. 324 - Andrew K. Rider, Nitesh V. Chawla
An Ensemble Topic Model for Sharing Healthcare Data and Predicting Disease Risk. 333 - Anas Abu-Doleh, Erik Saule, Kamer Kaya, Ümit V. Çatalyürek
Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs. 341 - Daniel M. Savel, Thomas LaFramboise, Ananth Grama, Mehmet Koyutürk
Suffix-Tree Based Error Correction of NGS Reads Using Multiple Manifestations of an Error. 351 - Anurag Nagar, Michael Hahsler
Genomic Sequence Fragment Identification using Quasi-Alignment. 359 - Guillermo Palma, Maria-Esther Vidal
Measuring Relatedness Between Scientific Entities in Annotation Datasets. 367 - Kun Wang, Avinash Das Sahu, Zheng-Mei Xiong, Kan Cao, Sridhar Hannenhalli:
Identification of gene clusters with phenotype-dependent expression with application to normal and premature ageing. 377 - Min Wu
Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer. 384 - Jennifer D'Souza, Vincent Ng:
Temporal Relation Identification and Classification in Clinical Notes. 392
Short Papers
- Carl Barton, Tomás Flouri
GapsMis: flexible sequence alignment with a bounded number of gaps. 402 - Luis D. Lopez, Jingyi Yu, Cecilia N. Arighi, Manabu Torii
An Image-Text Approach for Extracting Experimental Evidence of Protein-Protein Interactions in the Biomedical Literature. 412 - Abdallah Eteleeb, Robert M. Flight
An Island-Based Approach for Differential Expression Analysis. 419 - Brian S. Olson, Amarda Shehu
Multi-Objective Stochastic Search for Sampling Local Minima in the Protein Energy Surface. 430 - Yu-Keng Shih, Srinivasan Parthasarathy
Identifying protein complexes in AP-MS data with negative evidence via soft Markov clustering. 440 - Le Shu, Tianyang Ma, Longin Jan Latecki
Stable Feature Selection with Minimal Independent Dominating Sets. 450 - Rukhsana Yeasmin, Jesmin Jahan Tithi, Jeffrey Chen, Steven Skiena
Designing Autocorrelated Genes. 458 - Giuseppe Agapito
Cloud4SNP: Distributed Analysis of SNP Microarray Data on the Cloud. 468 - Paul M. Bodily, Mark J. Clement, Quinn Snell, Jared C. Price, Stanley Fujimoto, Nozomu Okuda:
Application of a MAX-CUT Heuristic to the Contig Orientation Problem in Genome Assembly. 476 - Ketan K. Mane, Phillips Owen, Charles Schmitt
Visual Analytics to Optimize Patient-Population Evidence Delivery for Personalized Care. 484 - Yang Lei, Ramgopal R. Mettu
A Confidence Measure for Model Fitting with X-Ray Crystallography Data. 489 - Thiago da Silva Arruda, Ulisses Dias
Heuristics for the Sorting by Length-Weighted Inversion Problem. 498 - Prapaporn Techa-angkoon, Yanni Sun
glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity. 508 - Igor Akushevich, Julia Kravchenko, Kenneth Gersing, Ketan K. Mane:
Predictive model of the treatment effect for patients with major depressive disorder. 518 - W. Lewis Collier, Jean-Yves Hervé, Lenore Martin
Towards Independent Particle Reconstruction from Cryogenic Transmission Electron Microscopy. 525 - Jikai Lei
ChainKnot: a comparative H-type pseudoknot prediction tool using multiple ab initio folding tools. 535 - Nan Du, Marc R. Knecht, Paras N. Prasad
A Framework for Identifying Affinity Classes of Inorganic Materials Binding Peptide Sequences. 545 - Suzanne Renick Gallagher, Debra S. Goldberg:
Clustering Coefficients in Protein Interaction Hypernetworks. 552 - Suxin Guo, Sheng Zhong, Aidong Zhang:
A Privacy Preserving Markov Model for Sequence Classification. 561 - Jue Mo, Sana Siddiqui, Stuart Maudsley
Classification of Alzheimer Diagnosis from ADNI Plasma Biomarker Data. 569 - Richard Beal, Donald A. Adjeroh, Ahmed Abbasi
The Forward Stem Matrix: An Efficient Data Structure for Finding Hairpins in RNA Secondary Structures. 575 - Catherine E. Welsh, Chen-Ping Fu, Fernando Pardo-Manuel de Villena, Leonard McMillan
Fine-Scale Recombination Mapping of High-Throughput Sequence Data. 585 - Shunping Huang, Chia-Yu Kao, Leonard McMillan
Transforming Genomes Using MOD Files with Applications. 595 - James Holt, Shunping Huang, Leonard McMillan
Read Annotation Pipeline for High-Throughput Sequencing Data. 605 - Vishakha Sharma, Adriana B. Compagnoni, Matthew Libera, Agnieszka K. Muszanska, Henk J. Busscher, Henny C. van der Mei:
Simulating Anti-adhesive and Antibacterial Bifunctional Polymers for Surface Coating using BioScape. 613 - Raghu Chandramohan, Po-Yen Wu, John H. Phan, May D. Wang
Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence Data. 623 - Andrew J. Proctor, Cody A. Stevens, Samuel S. Cho:
GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly. 633 - Thair Judeh, Thaer Jayyousi, Lipi R. Acharya, Robert G. Reynolds, Dongxiao Zhu:
Gene Set Cultural Algorithm: A Cultural Algorithm Approach to Reconstruct Networks from Gene Sets. 641
Posters
- F. O. Atanu, E. Oveido-Orta, K. A. Watson:
Predicting protein transport mechanism and immune response using spatial protein motifs and epitopes: a case study of Chlamydophila MOMP. 649 - Peter B. McGarvey, Baris E. Suzek
In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases. 650 - Pietro Hiram Guzzi, Simone Truglia, Marianna Milano, Pierangelo Veltri
Modularity and community detection in Semantic Similarity Networks trough Spectral Based Transformation and Markov Clustering. 652 - Serdar Bozdag, Aiguo Li, Gregory Riddick, Yuri Kotliarov
Age-Specific Signatures of Glioblastoma at the Genomic, Genetic, and Epigenetic levels. 654 - Difei Wang, Kevin Rosso, Shruti Rao, Lei Song, Varun Singh, Shailendra Singh, Michael Harris, Subha Madhavan:
SNP2Structure: A public database for mapping and modeling nsSNPs on human protein structures. 655 - Krithika Bhuvaneshwar
An integrated pharmacogenomic analysis of doxorubicin response using genotype information on DMET genes. 657 - En-Shiun Annie Lee:
Classifying Proteins by Amino Acid Variations of Sequence Patterns. 659 - Tijana Milenkovic, Han Zhao, Fazle Elahi Faisal:
Using Global Network Alignment In The Context Of Aging. 661 - Fazle Elahi Faisal, Tijana Milenkovic:
Dynamic networks reveal key players in aging. 662 - Ruolin Liu, Julie A. Dickerson:
Computational methods for alternative splicing detection using RNA-seq. 663 - Xi Wen, Hong Wang, Weiming Zhai:
Computer Assisted Surgery-Planning for Microwave Ablation. 664 - Masahito Ohue, Yuri Matsuzaki, Takehiro Shimoda, Takashi Ishida, Yutaka Akiyama
Improvement of Protein-Protein Interaction Prediction by Integrating Template-Based and Template-Free Protein Docking. 666 - Takehiro Shimoda, Masahito Ohue, Yuri Matsuzaki, Takayuki Fujiwara, Nobuyuki Uchikoga, Takashi Ishida, Yutaka Akiyama
The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments. 667 - Jesse R. Walsh
Semi-automated Constraint-based Metabolic Model Generation. 668 - Divya Mistry, Julie A. Dickerson:
Incorporating Gene Annotations as Node Metadata to Improve Network Centrality Measures for Better Node Ranking. 669 - Irina Hashmi, Amarda Shehu
Protein-protein Docking Using Information from Native Interaction Interfaces. 670 - Joseph Nalluri, Bhanu K. Kamapantula, Preetam Ghosh
Determining miRNA-disease associations using bipartite graph modelling. 672 - Tamer Aldwairi
Statistical Methods for Ambiguous Sequence Mappings. 674 - Brigitte Hofmeister, Brian R. King:
ngPhylo: N-Gram Modeled Proteins with Substitution Matrices for Phylogenetic Analysis. 676 - Debswapna Bhattacharya, Jianlin Cheng
Automated protein structure refinement using i3Drefine software and its assessment in CASP10. 678 - Rudy Clausen, Amarda Shehu
A PCA-guided Search Algorithm to Probe the Conformational Space of the Ras Protein. 679 - Haris Godil, Sonya Davey, Raj Shekhar:
A Novel Algorithm for Feature Detection and Hiding from Ultrasound Images. 681 - Leonid Zaslavsky, Boris Fedorov, Tatiana A. Tatusova:
Bacterial pan-genomes: data representation and analysis. 683 - Charles L. Cole, Brian R. King:
Using Machine Learning to Predict the Health of HIV-Infected Patients. 684 - Nan Deng, Dongxiao Zhu:
RNA-Seq analyses to reveal the human transcriptome landscape. 686 - Jeffrey A. Thompson, Clare Bates Congdon:
Initial Results In Using de Novo Motif Inference to Detect Cis-Regulatory Modules. 687 - Daifeng Wang, Eric Pan, Gang Fang, Sunita Kumari, Fei He, Doreen Ware, Sergei Maslov
Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar. 689 - Andrei Todor, Haitham Gabr, Alin Dobra
Reachability analysis in large probabilistic biological networks. 691 - Bui The Quang, Nguyen Hong Quang, Emmanuel Medernach, Vincent Breton
Scheduling of virtual screening application on multi-user pilot-agent platform on grid/cloud to optimize the stretch. 692 - Afzal Godil, Zhouhui Lian, Asim Wagan
Exploring Local Features and the Bag-of-Visual-Words Approach for Bioimage Classification. 694 - Arshia A. Khan, John Grillo:
Quality of Care and Electronic Health Record Systems. 696 - Manish Pandit, Luis Rueda, Alioune Ngom:
Prediction of Biological Protein-protein Interaction Types Using Short-Linear Motifs. 698 - Bingqing Xie, Gady Agam, Natalia Maltsev, T. Conrad Gilliam:
Conditional Random Field for Candidate Gene Prioritization. 700 - Mosaab Daoud
Quantum Sequence Analysis: A New Alignment-free Technique For Analyzing Sequences in Feature Space. 702 - David Solti, Haijun Zhai:
Predicting Breast Cancer Patient Survival Using Machine Learning. 704 - Chuming Chen
ngsShoRT: A Software for Pre-processing Illumina Short Read Sequences for De Novo Genome Assembly. 706 - Arshia A. Khan, John Grillo:
Role of Quality in Electronic Health Record Systems. 708 - Roozbeh Manshaei
Sparse and Stable Reconstruction of Genetic Regulatory Networks Using Time Series Gene Expression Data. 710 - Amritanjali, Gadadhar Sahoo
Listing Sorting Sequences of Reversals and Translocations. 712 - Pietro Hiram Guzzi, Marco Mina, Concettina Guerra, Mario Cannataro
Modularity and community detection in Semantic Similarity Networks trough Spectral Based Transformation and Markov Clustering. 714 - Ilya Y. Zhbannikov, Joseph W. Brown, James A. Foster
decisivatoR: an R infrastructure package that addresses the problem of phylogenetic decisiveness. 716 - Adele P. Peskin, Joe Chalfoun, Karen Kafadar, John T. Elliott:
Estimating the Number of Manually Segmented Cellular Objects Required to Evaluate the Performance of a Segmentation Algorithm. 718 - Calvin Hopkins, Soha Hassoun:
Abstraction of Kinetic Models For Biochemical Networks. 720 - Sanderz Fung:
Co-occurrence Clusters of Aligned Pattern Clusters. 721 - William W. Lau, Calvin A. Johnson, Sara Lioi, Joseph A. Mindell
Three-Dimensional Spot Detection in Ratiometric Fluorescence Imaging For Measurement of Subcellular Organelles. 722 - Todd A. Gibson, Debra S. Goldberg:
Evaluating theoretical models of protein interaction network evolution without seed graphs. 724 - José Juan Tapia, James R. Faeder
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models. 726 - Natasa Miskov-Zivanov, Paolo Zuliani, Edmund M. Clarke, James R. Faeder
Studies of biological networks with statistical model checking: application to immune system cells. 728 - Peter Z. Revesz
An Algorithm for Constructing Hypothetical Evolutionary Trees Using Common Mutation Similarity Matrices. 730 - Jun Tan, Donald A. Adjeroh:
Predicting Protein Families using Protein Shape Context. 733
Workshop CSBW
- Majid Masso
Fast and Accurate Structure-Based Prediction of Resistance to the HIV-1 Integrase Inhibitor Raltegravir. 735 - Jeffrey Chyan, Mark Moll
Improving the Prediction of Kinase Binding Affinity Using Homology Models. 741 - Kamal Al-Nasr, Lin Chen, Desh Ranjan, Mohammad Zubair, Dong Si, Jing He
A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps. 749 - Rudy Clausen, Amarda Shehu
Exploring the Structure Space of Wildtype Ras Guided by Experimental Data. 756 - Dong Si, Jing He
Beta-sheet Detection and Representation from Medium Resolution Cryo-EM Density Maps. 764 - Irina Hashmi, Amarda Shehu
Informatics-driven Protein-protein Docking. 771 - Filip Jagodzinski, Bahar Akbal-Delibas, Nurit Haspel:
An Evolutionary Conservation & Rigidity Analysis Machine Learning Approach for Detecting Critical Protein Residues. 779 - Dong Luo, Nurit Haspel:
Multi-Resolution Rigidity-Based Sampling of Protein Conformational Paths. 786 - Brian Orndorff, Filip Jagodzinski:
A Combined Molecular Dynamics, Rigidity Analysis Approach for Studying Protein Complexes. 793
Workshop ECF
- Benjamin Audit, Antoine Baker, Rasha E. Boulos
Relating mammalian replication program to large-scale chromatin folding. 799 - Sven Bilke, Yevgeniy Gindin, Paul S. Meltzer:
Chromatin structure fully determines replication timing program in human cells. 811 - Michael M. Hoffman, Orion J. Buske, Jie Wang, Zhiping Weng, Jeff A. Bilmes, William Stafford Noble:
Unsupervised pattern discovery in human chromatin structure through genomic segmentation. 813
Workshop ICIW
- Francesco Pappalardo
iAtheroSim: atherosclerosis process simulator on smart devices. 815 - En-Shiun Annie Lee, Fiona J. Whelan
Characterizing Amino Acid Variations of Scavenger Receptors by Class Information Gain. 818 - Ping Zhang
Biomarkers in Immunology: from Concepts to Applications. 826 - Jing Sun, Guanglan Zhang, Lars Rønn Olsen, Ellis L. Reinherz, Vladimir Brusic
Landscape of neutralizing assessment of monoclonal antibodies against dengue virus. 836 - Guanglan Zhang, Angelika Riemer, Derin B. Keskin, Lou Chitkushev, Ellis L. Reinherz, Vladimir Brusic
HPVdb: a Data Mining System for Knowledge Discovery in Human Papillomavirus with Applications in T cell Immunology and Vaccinology. 843 - Parvez Singh Slathia
DNA Vaccine Design for Chikungunya Virus Based On the Conserved Epitopes Derived from Structural Protein. 849 - Salvador Eugenio C. Caoili:
Defining Functional Redundancy of Epitope Data as Potential Antigenic Cross-Reactivity. 851
Workshop IWBNA
- Kathryn Dempsey, Hesham H. Ali:
Identifying Pathway Proteins in Networks using Convergence. 853 - Kun Zhao, Abdoul Sylla:
A Neural-network Algorithm for All k Shortest Paths Problem. 861 - Sanderz Fung, En-Shiun Annie Lee, Andrew K. C. Wong:
Revealing Protein Structures by Co-Occurrence Clustering of Aligned Pattern Clusters. 869 - Suhaib Mohammed:
Comparative analysis of network algorithms to address modularity with gene expression temporal data. 876
Workshop ParBio
- Takehiro Shimoda, Takashi Ishida, Shuji Suzuki, Masahito Ohue
MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs. 883 - Aditi A. Magikar, John A. Springer:
pXAlign: A parallel implementation of XAlign. 890
Health Informatics Symposium
- Qian Cheng, Joshua Juen, Yanen Li, Valentin Prieto-Centurion, Jerry A. Krishnan, Bruce R. Schatz:
GaitTrack: Health Monitoring of Body Motion from Spatio-Temporal Parameters of Simple Smart Phones. 897 - Jason H. D. Cho, Q. Vera Liao, Yunliang Jiang, Bruce R. Schatz:
Aggregating Personal Health Messages for Scalable Comparative Effectiveness Research. 907 - Simon Diemert, Morgan Price, Jens H. Weber:
Locating Discharge Medications in Natural Language Summaries. 917 - Oliver Bonham-Carter, Lotfollah Najjar, Dhundy Bastola:
Evidence of a Pathway of Reduction in Bacteria: Reduced Quantities of Restriction Sites Impact tRNA Activity in a Trial Set. 926 - Allen C. Lin, Meng-Hsiu Chang, Mike Y. Chen, Travis Yu, Lih-ching Chou, Dian-Je Tsai, Jackey Wang:
Mobility Patterns of Doctors Using Electronic Health Records on iPads. 933 - Eamon Johnson, W. Christopher Baughman, Gultekin Özsoyoglu:
Modeling Incidental Findings in Radiology Records. 940 - Paul D. Martin, Aviel D. Rubin, Rafae Bhatti:
Enforcing Minimum Necessary Access in Healthcare Through Integrated Audit and Access Control. 946
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