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6. BCB 2015: Atlanta, GA, USA
- Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2015, Atlanta, GA, USA, September 9-12, 2015. ACM 2015, ISBN 978-1-4503-3853-0
Regular papers
- Xun Lu, Aston Zhang, Carl A. Gunter, Daniel Fabbri, David M. Liebovitz
, Bradley A. Malin:
Discovering de facto diagnosis specialties. 7-16 - Aika Terada, Hanyoung Kim, Jun Sese:
High-speed westfall-young permutation procedure for genome-wide association studies. 17-26 - Cen Wan
Two methods for constructing a gene ontology-based feature network for a Bayesian network classifier and applications to datasets of aging-related genes. 27-36 - Minghan Chen, Fei Li, Kartik Subramanian, John J. Tyson, Yang Cao:
Two-dimensional model of bipolar PopZ polymerization in caulobacter crescentus. 37-46 - Zihe Chen, Hu Ding, Danyang Chen, Xiangyu Wang, Andrew J. Fritz, Nitasha Sehgal, Ronald Berezney, Jinhui Xu:
Mining k-median chromosome association graphs from a population of heterogeneous cells. 47-56 - Subrata Saha, Sanguthevar Rajasekaran:
HECTOR: a novel paradigm for correcting short reads. 57-66 - Sanghoon Lee, Yanjun Zhao, Mohamed Eid Mahmoud Masoud, Maria Valero, Semra Kul, Saeid Belkasim:
Domain specific information retrieval and text mining in medical document. 67-76 - Nikhil Yadav, Christian Poellabauer
Portable neurological disease assessment using temporal analysis of speech. 77-85 - Haitham Gabr, Alin Dobra
Estimating reachability in dense biological networks. 86-95 - Michael Uelschen, Heinz-Josef Eikerling:
A mobile sensor system for gait analysis supporting the assessment of rehabilitation measures. 96-105 - Aseel Awdeh, Hilary Phenix, Mads Kærn, Theodore J. Perkins:
The potential power of dynamics in epistasis analysis. 106-115 - Andrei Todor, Alin Dobra
Counting motifs in probabilistic biological networks. 116-125 - Veronika Strnadová-Neeley, Aydin Buluç
Efficient data reduction for large-scale genetic mapping. 126-135 - Ayat Hatem, Kamer Kaya, Jeffrey D. Parvin, Kun Huang, Ümit V. Çatalyürek:
MICA: MicroRNA integration for active module discovery. 136-145 - Shi Qiao, Mehmet Koyutürk
Integrated querying of disparate association and interaction data in biomedical applications. 146-155 - Suruchi Deodhar, Jiangzhuo Chen, Mandy L. Wilson, Keith R. Bisset, Christopher L. Barrett, Madhav V. Marathe:
EpiCaster: an integrated web application for situation assessment and forecasting of global epidemics. 156-165 - Qingming Tang, Sheng Wang
Bermuda: de novo assembly of transcripts with new insights for handling uneven coverage. 166-175 - Md Abdul Alim, Ahmet Ay, Md Mahmudul Hasan, My T. Thai, Tamer Kahveci:
Multiple reference networks improve accuracy of signaling network construction. 176-185 - Peihua Chen, Weiheng Huang, Wei Shao, Hongmin Cai
Discrimination of recurrent CNVs from individual ones from multisample aCGH by jointly constrained minimization. 186-193 - Darya Filippova, Carl Kingsford:
Rapid, separable compression enables fast analyses of sequence alignments. 194-201 - Feng Chen, Noman Mohammed, Shuang Wang, Wenbo He, Samuel Cheng, Xiaoqian Jiang:
Cloud-assisted distributed private data sharing. 202-211 - Hui Li, Xiaoyi Li, Xiaowei Jia, Murali Ramanathan, Aidong Zhang:
Bone disease prediction and phenotype discovery using feature representation over electronic health records. 212-221 - Deukhyun Cha, Qin Zhang, Jesmin Jahan Tithi, Alexander Rand, Rezaul Alam Chowdhury, Chandrajit L. Bajaj:
Accelerated molecular mechanical and solvation energetics on multicore CPUs and manycore GPUs. 222-231 - Alexej Gossmann
Identification of significant genetic variants via SLOPE, and its extension to group SLOPE. 232-240 - Shaolong Cao, Huaizhen Qin, Alexej Gossmann
Unified tests for fine scale mapping and identifying sparse high-dimensional sequence associations. 241-249 - Daniel Riofrío
Particle swarm optimization for radiation therapy planning. 250-257 - Anthony Rios
Convolutional neural networks for biomedical text classification: application in indexing biomedical articles. 258-267 - Shufan Ji, Xing Tian, Jin Chen:
Improving biological significance of gene expression biclusters with key missing genes. 268-277 - Segun Jung, Hongjian Jin, Ramana V. Davuluri:
Identification of candidate regulatory SNPs by integrative analysis for prostate cancer genome data. 278-285 - Dan He, Laxmi Parida:
SAME: a sampling-based multi-locus epistasis algorithm for quantitative genetic trait prediction. 286-295 - Chao Ji, Yong Fuga Li, Earl P. Bellinger
A maximum-likelihood approach to absolute protein quantification in mass spectrometry. 296-305 - Dong Nie, Elizabeth A. Shank, Vladimir Jojic:
A deep framework for bacterial image segmentation and classification. 306-314 - Dingcheng Li, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Yanshan Wang
A frequency-filtering strategy of obtaining PHI-free sentences from clinical data repository. 315-324 - Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi
Fast and efficient compression of high-throughput sequencing reads. 325-334 - Elisabetta Bergamini, Romina D'Aurizio
CNVScan: detecting borderline copy number variations in NGS data via scan statistics. 335-344 - Kun Wang, Kan Cao, Sridhar Hannenhalli:
Chromatin and genomic determinants of alternative splicing. 345-354 - Xuefeng Cui, Hiroyuki Kuwahara, Shuai Cheng Li
Compare local pocket and global protein structure models by small structure patterns. 355-365 - Guopeng Wei, Connor Walsh, Irina Cazan, Radu Marculescu
Molecular tweeting: unveiling the social network behind heterogeneous bacteria populations. 366-375 - Marzieh Ayati
Assessing the collective disease association of multiple genomic loci. 376-385 - Chihwen Cheng, May D. Wang
Improving personalized clinical risk prediction based on causality-based association rules. 386-392 - Chanchala D. Kaddi, May D. Wang
Developing robust predictive models for head and neck cancer across microarray and RNA-seq data. 393-402 - Asish Ghoshal, Ananth Grama, Saurabh Bagchi, Somali Chaterji:
An ensemble SVM model for the accurate prediction of non-canonical MicroRNA targets. 403-412 - Sherif Elmeligy Abdelhamid, Chris J. Kuhlman, Gizem Korkmaz, Madhav V. Marathe, S. S. Ravi:
EDISON: a web application for computational health informatics at scale. 413-422 - Adib Shafi, Michele Donato, Sorin Draghici
A systems biology approach for the identification of significantly perturbed genes. 423-432 - NhatHai Phan, Dejing Dou, Hao Wang, David Kil, Brigitte Piniewski:
Ontology-based deep learning for human behavior prediction in health social networks. 433-442 - Dan Gusfield:
Persistent phylogeny: a galled-tree and integer linear programming approach. 443-451 - Dan F. DeBlasio
Ensemble multiple sequence alignment via advising. 452-461 - Cheng Yang, Po-Yen Wu, Li Tong, John H. Phan, May D. Wang
The impact of RNA-seq aligners on gene expression estimation. 462-471
Posters
- U. Deok Seo, Yoo-Joo Choi, Ku-Jin Kim:
Updating channel adjacent amino acids for a flexible protein molecule. 472-473 - Pugalendhi GaneshKumar
Intelligent F-information for genetic swarm algorithm based fuzzy expert system. 474-475 - Yue Hou, Lee Cooper, Scott Wilkinson, Adam I. Marcus, Daniel J. Brat:
Spatiotemporal visualization of cell membrane dynamics and protein colocalization reveals correlation between membrane dynamics and metastatic invasion. 476-477 - K. Jason Crandall, Matthew Shake
Bingocize® 3.0: a game based platform for promoting wellness in older adults. 478-479 - Bin Xue:
Improving MiRNA prediction accuracy by deep learning strategies. 480-481 - Juan Antonio García-Martín, Peter Clote:
Poster abstract: RNA thermodynamic conformational entropy. 482-483 - Erin C. Macaulay
Methylome meets maternity ward: predicting pre-eclampsia in early pregnancy. 484-485 - Namjin Gu, Yongmin Kim, Ryan W. Kim:
Detection of a fusion gene using soft-clipping reads in exome-sequencing data. 486 - Nikolai V. Ivanov, Carine Poussin, Stéphanie Boué, Florian Martin, Alain Sewer, Bjoern Titz
The systems toxicology challenge: how to leverage omics data to predict mechanisms of toxicity? 487 - Pugalendhi GaneshKumar, Ku-Jin Kim:
Computational support system for personalized medicine. 488-489 - Joseph Crawford, Yihan Sun, Tijana Milenkovic:
Fair evaluation of global network aligners. 490 - Kristen R. Petersen, David A. Streett, Alida T. Gerritsen, Samuel S. Hunter, Matthew L. Settles:
Super deduper, fast PCR duplicate detection in fastq files. 491-492 - Sen Yao, Robert M. Flight, Eric C. Rouchka, Hunter N. B. Moseley
A less biased analysis of metalloproteins' coordination geometries. 493-494 - Salvador Eugenio C. Caoili:
Analogy-based entropic similarity between observations and/or predictions (AESOP): an entropically weighted information-theoretic measure for benchmarking computational accuracy. 495-496 - Megan Druce, Paula Sommer, Philippe Le Mercier, Chantal Hulo, Patrick Masson, Tulio de Oliveira:
Human immunodeficiency virus (HIV) proteomics resource at BioAfrica. 497-498 - Shivani Goel, Sara Kalvala:
PlasMatch: a tool for choosing usable restriction enzymes and plasmid backbones. 499-500 - Amir H. Bayegan, Peter Clote:
Structural diversity measures for RNA. 501-502 - Yarong Gu, Xianying Liu, Qiang Zhu, Youchao Dong, C. Titus Brown, Sakti Pramanik:
A new method for DNA sequencing error verification and correction via an on-disk index tree. 503-504 - Ahmet Süreyya Rifaioglu, Tunca Dogan
Unsupervised identification of redundant domain entries in InterPro database using clustering techniques. 505-506 - Xuefeng Cui, Hammad Naveed, Xin Gao
Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces. 507-508 - Rangjiao Roger Liu, Anuradha Lakshminarayana, Daniel Durkin, Sara Patterson, Craig Hanna, Grace A. Stafford, Guruprasad Ananda, Krishna M. Karuturi, Susan M. Mockus:
Clinical knowledgebase to interprete genomic variations from targeted exome sequencing of patient tumor samples. 509 - Robert W. Cottingham
The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological function. 510 - Dustin Atchley, Juan Gutierrez:
A robotics approach to analysis of non-isotropic random walks. 511 - Shane E. Sawyer, Bhanu Rekepalli, Mitchel D. Horton, R. Glenn Brook:
HPC-BLAST: distributed BLAST for xeon phi clusters. 512-513 - Pranav Srinivas:
Boolean network modeling for systematic identification of anticancer drug resistance in colorectal cancer. 514 - Jesmin Jahan Tithi, Rezaul Alam Chowdhury:
Efficient computation of distance incorporated codon autocorrelation (DICA) score using fast Fourier transform. 515-516 - Wen-Ran Zhang, Francesco Marchetti:
A logical exposition of dirac 3-polarizer experiment and its potential impact on computational biology. 517-518 - Joseph Nalluri, Pratip Rana
Determining influential miRNA targets in diseases using influence diffusion model. 519-520 - Gideon Nimako
A data assurance model for syndromic monitoring infectious diseases in developing countries. 521-522 - David A. Streett, Kristen R. Petersen, Alida T. Gerritsen, Samuel S. Hunter, Matthew L. Settles:
expHTS: analysis of high throughput sequence data in an experimental framework. 523-524 - Raehoon Jeong, Ameet Soni:
A comprehensive analysis of classification algorithms for cancer prediction from gene expression. 525-526 - Cheng Yang, Shi Qiao, Z. Meral Özsoyoglu:
An exploratory graph query interface for biomedical data. 527-528 - Hsin-Yi Cindy Yeh, Shawna L. Thomas, Nancy M. Amato:
Using motion planning to rank ligand binding affinity. 529-530 - Sungchul Bae, Il Kon Kim, Dong Geun Suh:
eClaim System based on IHE XDR. 531-532 - Anhong He, Benika Hall, Jia Wen, Yingbin Liang, Xinghua Shi:
Sequential parallel LASSO models for eQTL analysis. 533-534 - Jilong Li, Jie Hou, Lin Sun, Jordan Maximillian Wilkins, Yuan Lu, Chad E. Niederhuth, Benjamin Ryan Merideth, Thomas P. Mawhinney, Valeri V. Mossine, Michael Greenlief, John C. Walker, William R. Folk, Mark Hannink, Dennis B. Lubahn, James A. Birchler, Jianlin Cheng:
From gigabyte to kilobyte: a bioinformatics protocol for mining large RNA-Seq transcriptomics data. 535-536 - Jilong Li, Renzhi Cao, Jianlin Cheng:
MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction. 537 - Kanak Mahadik, Wei Tang, Saurabh Bagchi, Folker Meyer:
Do specialized distributed frameworks for bioinformatics applications obtain better performance over generic ones? 538 - Valerie Diane V. Valeriano
Application of a systematic exoproteogenomic profiling workflow on lactobacillus mucosae LM1. 539-540 - Do-Youn Lee, Il Kon Kim, Dong Geun Suh:
Consolidated CDA-based care record summary definition and HIE system tools. 541-542 - Jonathan Rice, Kortni Dees, Adam Thrash
Investigating genome similarity through cross mapping percentage. 543-544 - Cody L. Arbuckle, Milton L. Greenberg, Erik Linstead:
Detection and tracking of T cells in time-lapse imaging. 545-546 - Saima Sultana Tithi, Mohammad Shabbir Hasan:
Modeling ebola outbreak: a case study on 2014 outbreak in sierra leone. 547-548 - Guangming Xing, Qinglong Sun:
Greedy topological sorting on questionnaire directed acyclic graph and its application in patient surveys. 549-550 - Tumaini Kilimba, Gideon Nimako
Data everywhere: an integrated longitudinal data visualization platform for health and demographic surveillance sites. 551-552 - Xiaolong Sun, Juyoung Park, Kyungtae Kang:
Arrhythmia classification using nearest neighbor search with principal component analysis. 553-555 - Henry Dewhurst, Matthew Torres:
Structural analysis of PTM hotspots (SAPH-ire): a tool for the prediction of regulatory post-translational modification elements in protein families. 556 - Elizabeth Brooks, Alison Scoville
An extensible software infrastructure for testing the evolutionary consequences of developmental interactions. 557-558 - Junqi Yin, R. Glenn Brook, Lonnie D. Crosby
fMRI image registration with AFNI's 3dQwarp. 559-560
Workshop ParBio
- Pietro Hiram Guzzi, Marianna Milano, Swarup Roy
Towards the assessment of GRN algorithms based on (disease) ontology. 561-567 - Giuseppe Agapito
Efficient learning of association rules from human phenotype ontology. 568-573 - Wilfredo Lugo, Jaime Seguel:
A fast and accurate parallel algorithm for genome mapping assembly aimed at massively parallel sequencers. 574-581 - Urmi Bhayani, John A. Springer:
Toward an analytical framework for proteomics software. 582-588 - Giuseppe Tradigo, Barbara Calabrese
Voice signal features analysis and classification: looking for new diseases related parameters. 589-596 - Armen Abnousi, Shira L. Broschat, Ananth Kalyanaraman:
An alignment-free approach to cluster proteins using frequency of conserved k-mers. 597-606
Workshop CHS
- Sherry Emery, Christophe G. Giraud-Carrier:
Introduction to the workshop on computational health science. 607-609 - Nikhil Devraj, Michael Chary:
How do Twitter, Wikipedia, and Harrison's principles of medicine describe heart attacks? 610-614 - Rose Yesha, Aryya Gangopadhyay:
A method for analyzing health behavior in online forums. 615-621 - Qianyi Zhan, Sherry Emery, Philip S. Yu:
How TV advertising and social network help tobacco control campaigns influence more. 622-625
Workshop BigLS
- Charles A. Phillips, Kai Wang, Jason A. Bubier
Scalable multipartite subgraph enumeration for integrative analysis of heterogeneous experimental functional genomics data. 626-633 - Michael Camara, Oliver Bonham-Carter, Janyl Jumadinova
A multi-agent system with reinforcement learning agents for biomedical text mining. 634-643
Workshop CNB-MAC
- Daniel N. Mohsenizadeh, Roozbeh Dehghannasiri
An experimental design to reduce dynamics uncertainty in genomic networks. 644-645 - Haitham Gabr, Juan Carlos Rivera-Mulia
Computing interaction probabilities in signaling networks. 646 - Hyundoo Jeong, Byung-Jun Yoon:
Identifying molecular complexes in biological networks through context sensitive network querying. 647 - Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon:
Computational identification of key functional genes associated with fusarium verticillioides pathogenicity. 648 - Yijie Wang, Xiaoning Qian:
A computational framework for finding functional modules across multiple biological networks. 649-650 - Ali Foroughi Pour, Lori A. Dalton:
Optimal bayesian feature filtering. 651-652 - Meltem Apaydin, Bo Zeng, Shaogang Ren, Xiaoning Qian:
A computationally efficient solution strategy for optimal gene knockouts for targeted overproduction. 653-654 - Lei Huang, Li Liao, Cathy H. Wu:
Inference of protein-protein interaction networks from multiple heterogeneous data. 655
Workshop GMDM
- Mike Wallinga:
Multi-core dynamic parallelism for multiple sequence alignment and counting metrics. 656-657 - Quoc-Nam Tran:
Selection of genes using long-term influence and sensitivity analysis. 658-664 - Manjari Mukhopadhyay, Raunaq Malhotra, Raj Acharya:
A generalized lattice model for clustering metagenomic sequences. 665-672
Workshop industrial track - KDDBHI
- Vincent A. Emanuele II, David Lloyd:
Building and implementing data science products to change healthcare IT. 673 - Xin Deng, Donghui Wu:
Senior health management through internet of things and real-time big data analytics. 674 - Nong Shang:
A bayesian nonparametric approach for latent class regression analysis. 675 - Yiheng Liang, Armin R. Mikler:
Learning causal structures with background knowledge in health data. 676 - Xin Deng, Donghui Wu:
Big data and predictive modeling topics in healthcare. 677
Demos
- Jiajie Peng, Hongxiang Li, Yadong Wang, Jin Chen:
A web tool for measuring gene semantic similarities by combining gene ontology and gene co-function networks. 678-679
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