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5. BCB 2014: Newport Beach, California, USA
- Pierre Baldi, Wei Wang:
Proceedings of the 5th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB '14, Newport Beach, California, USA, September 20-23, 2014. ACM 2014, ISBN 978-1-4503-2894-4
Regular papers
- Ryan Cobb, Rasha Elhesha, J. Gordon Burleigh, Tamer Kahveci:
Extracting phylogenetic signals from multi-labeled gene trees and its significance for species tree construction. 3-12 - Adele P. Peskin, Steven P. Lund
, Ya-Shian Li-Baboud, Michael Halter, Anne L. Plant, Peter Bajcsy:
Automated ranking of stem cell colonies by translating biological rules to computational models. 13-22 - Norman Goodacre
Docking features for predicting binding loss due to protein mutation. 23-32 - Jason H. D. Cho, Parikshit Sondhi, Chengxiang Zhai, Bruce R. Schatz:
Resolving healthcare forum posts via similar thread retrieval. 33-42 - Sakyajit Bhattacharya, Vaibhav Rajan
A novel classification method for predicting acute hypotensive episodes in critical care. 43-52 - Joshua Juen, Qian Cheng, Bruce R. Schatz:
Towards a natural walking monitor for pulmonary patients using simple smart phones. 53-62 - Thuy-Diem Nguyen, Bertil Schmidt
Fast dendrogram-based OTU clustering using sequence embedding. 63-72 - Mahdieh Khanmohammadi, Rasmus Waagepetersen
Analysing the distribution of synaptic vesicles using a spatial point process model. 73-78 - Shaolong Cao, Huaizhen Qin, Jian Li, Hong-Wen Deng, Yu-Ping Wang:
Scaled sparse high-dimensional tests for localizing sequence variants. 79-87 - Iain James Marshall
Automating risk of bias assessment for clinical trials. 88-95 - Anima Singh, Girish N. Nadkarni, John V. Guttag, Erwin P. Bottinger:
Leveraging hierarchy in medical codes for predictive modeling. 96-103 - Vanja Paunic, Michael S. Steinbach
Amb-EM: a SNP-based prediction of HLA alleles using ambiguous HLA data. 104-113 - Pawel Górecki
Unconstrained gene tree diameters for deep coalescence. 114-121 - Julian Dymacek, Nancy Lan Guo:
Integrated miRNA and mRNA analysis of time series microarray data. 122-127 - Zhiyong Wang, Jinbo Xu, Xinghua Shi:
CNVnet: combining sparse learning and biological networks to capture joint effect of copy number variants. 128-137 - Chih-Hsuan Wei
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine. 138-146 - Chia-Yu Kao, Chen-Ping Fu, Leonard McMillan
InstantGenotype: a non-parametric model for genotype inference using microarray probe intensities. 147-154 - Nimit Dhulekar, Basak Oztan, Bülent Yener, Haluk O. Bingol
Graph-theoretic analysis of epileptic seizures on scalp EEG recordings. 155-163 - Boyoung Yoo, Huili Chen, Fazle Elahi Faisal, Tijana Milenkovic:
Improving identification of key players in aging via network de-noising. 164-173 - Joseph Azofeifa, Mary A. Allen
FStitch: a fast and simple algorithm for detecting nascent RNA transcripts. 174-183 - Luca Pireddu
A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy. 184-191 - Prateek Jindal
Joint inference for end-to-end coreference resolution for clinical notes. 192-201 - Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin:
IPED2: inheritance path based pedigree reconstruction algorithm for complicated pedigrees. 202-210 - Chihwen Cheng, Nikhil Chanani, Kevin O. Maher, May D. Wang
icuARM-II: improving the reliability of personalized risk prediction in pediatric intensive care units. 211-219 - Thomas Zhang, Jason H. D. Cho, Chengxiang Zhai:
Understanding user intents in online health forums. 220-229 - Dan F. DeBlasio
Learning parameter sets for alignment advising. 230-239 - Marzieh Ayati
Prioritization of genomic locus pairs for testing epistasis. 240-248 - Anna M. Ritz, T. M. Murali:
Pathway analysis with signaling hypergraphs. 249-258
Short papers
- Sourya Bhattacharyya
Couplet supertree by equivalence partitioning of taxa set and DAG formation. 259-268 - Rudy Clausen, Amarda Shehu:
A multiscale hybrid evolutionary algorithm to obtain sample-based representations of multi-basin protein energy landscapes. 269-278 - Irina Hashmi, Daniel Veltri
Knowledge-based search and multi-objective filters: proposed structural models of GPCR dimerization. 279-288 - Bahar Akbal-Delibas, Marc Pomplun, Nurit Haspel:
AccuRMSD: a machine learning approach to predicting structure similarity of docked protein complexes. 289-296 - Aleksandar Poleksic, Paul Gray:
Utilizing twilight zone sequence similarities to increase the accuracy of protein 3D structure comparison. 297-303 - Amy Webb, Aaron Albin, Zhan Ye, Majid Rastegar-Mojarad, Kun Huang, Jeffrey D. Parvin, Wolfgang Sadee, Lang Li, Simon M. Lin, Yang Xiang:
Mining massive SNP data for identifying associated SNPs and uncovering gene relationships. 304-313 - Zixing Wang, Peng Qiu, Wenlong Xu, Yin Liu:
Spectral feature selection and its application in high dimensional gene expression studies. 314-320 - Sheng Wang, Yanen Li, Duncan C. Ferguson, Chengxiang Zhai:
SideEffectPTM: an unsupervised topic model to mine adverse drug reactions from health forums. 321-330 - Qian Cheng, Joshua Juen, Bruce R. Schatz:
Using mobile phones to simulate pulse oximeters: gait analysis predicts oxygen saturation. 331-340 - Krzysztof Drewniak
A method for reducing the severity of epidemics by allocating vaccines according to centrality. 341-350 - Stuart Price, Bruce L. Golden, Edward A. Wasil, Hao Howard Zhang:
Data mining to aid beam angle selection for intensity-modulated radiation therapy. 351-359 - Gustavo Rodrigues Galvão
Approximation algorithms for sorting by signed short reversals. 360-369 - Annamalai Natarajan, Edward Gaiser, Gustavo Angarita, Robert Malison, Deepak Ganesan, Benjamin M. Marlin
Conditional random fields for morphological analysis of wireless ECG signals. 370-379 - Aditya Vaidya, Angel Bravo-Salgado, Armin R. Mikler:
Modeling climate-dependent population dynamics of mosquitoes to guide public health policies. 380-389 - Suzanne Renick Gallagher, Debra S. Goldberg:
Large highly connected clusters in protein-protein interaction networks. 390-399 - Ulisses Dias
An improved algorithm for the sorting by reversals and transpositions problem. 400-409 - Xi Wen, Hong Wang, Weiming Zhai:
Dynamic coordinate registration method for image-guided surgery. 410-415 - Abdallah M. Eteleeb, Hunter N. B. Moseley
A comparison of combined p-value methods for gene differential expression using RNA-seq data. 417-425 - Huey-Eng Chua, Sourav S. Bhowmick
One feature doesn't fit all: characterizing topological features of targets in signaling networks. 426-435 - Fan Zhang
Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways. 436-444 - Ziyi Guo, Trevor Kuhlengel
A flexible volumetric comparison of protein cavities can reveal patterns in ligand binding specificity. 445-454 - Janani Venugopalan, Chihwen Cheng, May D. Wang
MotionTalk: personalized home rehabilitation system for assisting patients with impaired mobility. 455-463 - James Holt, Leonard McMillan
Constructing burrows-wheeler transforms of large string collections via merging. 464-471 - Chen-Ping Fu, Fernando Pardo-Manuel de Villena, Leonard McMillan
Quantitative trait loci mapping with microarray marker intensities. 472-478 - Md. Mahbubur Rahman, Rummana Bari, Amin Ahsan Ali, Moushumi Sharmin, Andrew Raij
Are we there yet?: feasibility of continuous stress assessment via wireless physiological sensors. 479-488 - Julia Warnke
Focus: a new multilayer graph model for short read analysis and extraction of biologically relevant features. 489-498 - Paul M. Bodily, Mark J. Clement, Quinn Snell, M. Stanley Fujimoto, Perry G. Ridge:
Haplotype-centered mapping for improved alignments and genetic association studies. 499-505 - Jake Drew, Michael Hahsler
Strand: fast sequence comparison using mapreduce and locality sensitive hashing. 506-513 - John H. Phan, Sonal Kothari, May D. Wang
omniClassifier: a desktop grid computing system for big data prediction modeling. 514-523 - Rami Alroobi, Saeed Salem:
Discovering dysregulated phenotype-related gene patterns. 524-532 - Davide Chicco
Deep autoencoder neural networks for gene ontology annotation predictions. 533-540 - Raed I. Seetan, Anne M. Denton, Omar Al Azzam
A noise-aware method for building radiation hybrid maps. 541-550 - K. E. Ravikumar, Kavishwar B. Wagholikar, Hongfang Liu:
Challenges in adapting text mining for full text articles to assist pathway curation. 551-558 - Karthik Tangirala, Doina Caragea
Community detection-based features for sequence classification. 559-568 - Chelsea J.-T. Ju, Zhuangtian Zhao, Wei Wang
PseudoLasso: leveraging read alignment in homologous regions to correct pseudogene expression estimates via RNASeq. 569-578
Posters
- Fazle Elahi Faisal, Tijana Milenkovic:
Dynamic networks reveal key players in aging. 579 - Fazle Elahi Faisal, Han Zhao, Tijana Milenkovic:
Global network alignment in the context of aging. 580 - Juli Petereit, Karen Schlauch:
A powerful and robust co-expression network analysis algorithm. 581 - Scott McGrath
DTC genetic testing and consumer comprehension. 582-583 - Zeynep Kosaloglu-Yalçin, Inka Zoernig, Niels Halama, Eliana Ruggiero, Benedikt Brors, Dirk Jäger:
The epitope landscape of CRC liver metastases analyzed by whole-exome sequencing and in silico epitope prediction. 584 - Rahul Shubhra Mandal, Atri Ta, Santasabuj Das:
In silico designing and experimental validation of a potential small molecule inhibitor against vibrio cholerae AphB: a LysR-type transcriptional regulator. 585 - Pranav Srinivas:
Apoptosis centric Bayesian network perturbation analysis of signaling pathways in colorectal cancer for synergistic drug targets discovery. 586 - Robert Leaman, Zhiyong Lu:
Disease named entity recognition and normalization with DNorm. 587 - Shiyuyun Tang, Alexandre Lomsadze, Mark Borodovsky:
Identification of protein coding regions in RNA transcripts. 588 - Jeffrey R. Long, Qingxiang Yan, Brett Trost, Anthony J. Kusalik:
The UniFrac significance test generates different outputs given semantically equivalent inputs. 589 - Chih-Hsuan Wei, Hung-Yu Kao, Zhiyong Lu:
Text mining tools for assisting literature curation. 590-591 - Kannan Sankar
An analysis of conformational changes upon RNA-protein binding. 592-593 - Roberto A. Cárdenas-Ovando, Héctor A. Rueda-Zárate, Julieta Noguez-Monroy, Claudia Rangel-Escareño:
Dose and time relationship through probabilistic graphical models of gene expression time course toxicogenomics data. 594-595 - Rimma Shakhbatyan, Himanshu Sharma, Ellen Tsai, Mark J. Bowser, Birgit Funke, Matthew S. Lebo:
Validation and implementation of whole-exome sequencing bioinformatics processes for clinical applications. 596-597 - Jon Long, Yingyuan Zhang, Lubomir T. Chitkushev, Vladimir Brusic
Antidote application: an educational system for treatment of common toxin overdose. 598-599 - Jesmin Jahan Tithi, Pramod Ganapathi
High-performance recursive dynamic programming for bioinformatics using MM-like flexible kernels. 600-601 - Rachid Ounit, Timothy J. Close, Steve Wanamaker, Stefano Lonardi
CLARK, accurate and efficient classification of DNA sequences. 602 - Natasha Pavlovikj, Kevin Begcy
Comparing and optimizing transcriptome assembly pipeline for diploid wheat. 603-604 - Matthew Seeley, Mark J. Clement, Christophe G. Giraud-Carrier, Quinn Snell, Paul M. Bodily, Stanley Fujimoto:
A structured approach to ensemble learning for Alzheimer's disease prediction. 605-606 - Dingcheng Li, Janet Okamoto
An author topic analysis on NCI DCP/DCCPS PIs. 607-608 - Seyed Hamid Mirebrahim, Timothy J. Close, Stefano Lonardi:
De novo assembly of ultra-deep sequencing data. 609 - Farhad Hormozdiari, Emrah Kostem, Eun Yong Kang, Bogdan Pasaniuc, Eleazar Eskin:
Identifying causal variants at loci with multiple signals of association. 610-611 - Marianna Milano, Pietro Hiram Guzzi, Pierangelo Veltri, Mario Cannataro:
A web-based tool to analyze semantic similarity networks. 612-613 - Changhui Yan, Wen Cheng:
Graph methods for protein-nucleotide interactions. 614 - Sepideh Mazrouee, Wei Wang
Individual haplotyping prediction agreements. 615-616 - Prateek Jindal
Detecting privacy-sensitive events in medical text. 617-620 - Md. Aashikur Rahman Azim
A fast and lightweight filter-based algorithm for circular pattern matching. 621-622 - Aadithya V. Karthik, David Soloveichik, Sayak Ray, Baruch Sterin, Alan Mishchenko, Robert K. Brayton, Jaijeet Roychowdhury:
NINJA: boolean modelling and formal verification of tiered-rate chemical reaction networks (extended abstract). 623-624 - Mina Maleki, Luis Rueda, Mohammad Haj Dezfulian
Computational analysis of the stability of SCF ligases employing domain information. 625-626 - Jeffrey A. Thompson, Christine Duarte, Peter Marks, Clare Bates Congdon:
An automated pipeline for discovering gene expression patterns associated with increased cancer survival time. 627-628 - Yuliang Geng, Xue-wen Chen, Dongxiao Zhu:
A novel semi-supervised learning approach to analyzing metagenomic reads. 629-630 - Craig Estep, Jaeil Yi, Anna M. Ritz, T. M. Murali:
GraphSpace: sharing and collaborating through networks on the web. 631-632 - Sahith Sai Nareddy, Erik Westover, Kristina Hillesland
Genome dynamics in coevolved genomes: database management system for tracing mutations. 633-634 - Ahmed Abdelzaher, Preetam Ghosh
Care coordination metrics of patients sharing among physicians: a social network analytic approach. 635-636 - Daniel Malmer, Phillip Andrew Richmond
Inferring ancestry in mouse genomes using a hidden Markov model. 637-638 - Xiang Ji, Soon Ae Chun
A collaborative filtering approach to assess individual condition risk based on patients' social network data. 639-640 - Tianchuan Du, Alvaro J. González, Qinghua Wang, Hongzhan Huang, Li Liao, Cathy H. Wu
DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions. 641-642 - Jeffrey A. Thompson, Craig R. Lessard, Samuel McFarland, Robert L. Morris, Clare Bates Congdon:
A workflow for the computational identification of candidate regulatory elements in noncoding DNA. 643-644 - Venkata Pasupuleti, Jie Zhou:
Multi-channel synapse validation on confocal images of mammalian neurons. 645-646 - Suzanne Renick Gallagher, Micah Dombrower, Debra S. Goldberg:
Using 2-node hypergraph clustering coefficients to analyze disease-gene networks. 647-648 - Chuqiao Ren, Brian R. King:
Predicting protein contact maps by bagging decision trees. 649-650 - Arman Cohan
On clinical decision support. 651-652
Workshop BigLS
- Abhishek Biswas
Big data challenges for estimating genome assembler quality. 653-660 - Etienne Z. Gnimpieba
RNA-seq gene and transcript expression analysis using the BioExtract server and iPlant collaborative. 661-669 - Urmi Bhayani, John A. Springer:
AlignMR: mass spectrometry peak alignment using Hadoop MapReduce. 670-672 - Gregory Ditzler, Gail L. Rosen
Feature subset selection for inferring relative importance of taxonomy. 673-679 - Jason E. McDermott
Promises and challenges in analysis of biological big data. 680
Workshop CNB-MAC
- Navadon Khunlertgit, Byung-Jun Yoon:
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. 681 - Mohammadmahdi R. Yousefi, Lori A. Dalton:
Optimal cancer prognosis under network uncertainty. 682-683 - Hyundoo Jeong, Byung-Jun Yoon:
A novel context-sensitive random walk model for estimating node correspondence between two biological networks. 684 - Mansuck Kim, Huan Zhang, Charles Woloshuk, Won-Bo Shim, Byung-Jun Yoon:
Computational identification of functional network modules associated with the pathogenicity of Fusarium verticillioides. 685 - Amin Ahmadi Adl, Xiaoning Qian:
Network-regularized bi-clique finding for tumor stratification. 686-687 - Yijie Wang, Xiaoning Qian:
Biological network clustering by robust NMF. 688-689
Workshop CSBW
- Dong Si, Jing He
Orientations of beta-strand traces and near maximum twist. 690-694 - Hui Dong, Gregory S. Chirikjian:
A computational model for data acquisition in SAXS. 695-702 - Ziyi Guo, Brian Yuan Chen:
Variational Bayesian clustering on protein cavity conformations for detecting influential amino acids. 703-710 - Kamal Al-Nasr, Jing He
Construction of protein backbone pieces using segment-based FBCCD and Cryo-EM skeleton. 711-716 - Aaron Lindsey, Hsin-Yi Cindy Yeh, Chih-Peng Wu, Shawna L. Thomas, Nancy M. Amato:
Improving decoy databases for protein folding algorithms. 717-724
Workshop ICIW
- Salvador Eugenio C. Caoili:
An integrative framework for structure-based prediction of biological effects mediated by antipeptide antibodies. 725-732 - Sinu Paul, John Sidney, Bjoern Peters, Alessandro Sette:
Development and validation of a broad scheme for prediction of HLA class II restricted T cell epitopes. 733-738 - Anne Bresciani, Jason Greenbaum, Cecilia S. Lindestam Arlehamn, Alessandro Sette, Morten Nielsen
The interplay of sequence conservation and T cell immune recognition. 739-743 - Francesco Pappalardo
Relapsing-remitting multiple scleroris and the role of vitamin D: an agent based model. 744-748 - Sandra Andorf, Jennifer B. Bollyky, Patrick J. Dunn, Jeffrey A. Wiser, Sanchita Bhattacharya, Atul J. Butte:
Towards the characterization of normal peripheral immune cells with data from ImmPort. 749-750 - Ravi D. Shankar, Sandra Andorf, Sanchita Bhattacharya, Jeffrey A. Wiser, Atul J. Butte:
RImmPort: enabling ready-for-analysis immunology research data. 751
Workshop IWBNA
- Md Mahmudul Hasan, Tamer Kahveci:
Incremental network querying in biological networks. 752-759 - Sean West
On the impact of data integration and edge enrichment in mining significant signals from biological networks. 760-767 - Francesca Cristiano, Pierangelo Veltri
An R-based tool for miRNA data analysis and correlation with clinical ontologies. 768-773 - Oliver Bonham-Carter, Ishwor Thapa, Dhundy Bastola:
Evidence of post translational modification bias extracted from the tRNA and corresponding amino acid interplay across a set of diverse organisms. 774-781 - Mathialakan Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba
Heuristic parallelizable algorithm for similarity based biosystems comparison. 782-789
Workshop ParBio
- Mathialakan Thavappiragasam, Carol M. Lushbough, Etienne Z. Gnimpieba
Automatic biosystems comparison using semantic and name similarity. 790-796 - Nick Weinandt, Laura M. Jackson
Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison. 797-804 - Mario Cannataro
A taxonomy for bioinformatics tools: exploiting semantics, parallelism, and services for analyzing omics data. 805-812 - Pietro Cinaglia
A system for ubiquitous distributed acquisition of voice alteration samples through a mobile application. 813-818
Demo
- Peehoo Dewan, Naveen Ashish, Arthur W. Toga:
A schema-matching tool for Alzheimer's disease data integration. 819-820 - Robert W. Cottingham:
The DOE systems biology knowledgebase (KBase): progress towards a system for collaborative and reproducible inference and modeling of biological function. 821
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