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ORCID5. 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, Nathan Edwards, Mark Danielsen, Peter Uetz, Cathy H. Wu:
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, Vijay Huddar:
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, Chee-Keong Kwoh:
Fast dendrogram-based OTU clustering using sequence embedding. 63-72 - Mahdieh Khanmohammadi, Rasmus Waagepetersen, Nicoletta Nava, Jens Rondel Nyengaard, Jon Sporring:
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, Joël Kuiper, Byron C. Wallace:
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, Abeer Madbouly, Vipin Kumar:
Amb-EM: a SNP-based prediction of HLA alleles using ambiguous HLA data. 104-113 - Pawel Górecki, Jaroslaw Paszek, Oliver Eulenstein:
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, Robert Leaman, Zhiyong Lu:
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, Gulcin Irim, Berrin Aktekin, Canan Aykut-Bingöl:
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, Manuel E. Lladser, Robin D. Dowell:
FStitch: a fast and simple algorithm for detecting nascent RNA transcripts. 174-183 - Luca Pireddu, Simone Leo, Nicola Soranzo, Gianluigi Zanetti:
A Hadoop-Galaxy adapter for user-friendly and scalable data-intensive bioinformatics in Galaxy. 184-191 - Prateek Jindal, Dan Roth, Carl A. Gunter:
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, John D. Kececioglu:
Learning parameter sets for alignment advising. 230-239 - Marzieh Ayati, Mehmet Koyutürk:
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, Jayanta Mukhopadhyay:
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, Nadine Kabbani, Amarda Shehu:
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, Joseph Helsing, Armin R. Mikler:
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, Zanoni Dias:
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, Andre Rodrigues Oliveira, Zanoni 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, Eric C. Rouchka:
A comparison of combined p-value methods for gene differential expression using RNA-seq data. 417-425 - Huey-Eng Chua, Sourav S. Bhowmick, Lisa Tucker-Kellogg:
One feature doesn't fit all: characterizing topological features of targets in signaling networks. 426-435 - Fan Zhang, Chee Keong Kwoh, Min Wu, Jie Zheng:
Data-driven prediction of cancer cell fates with a nonlinear model of signaling pathways. 436-444 - Ziyi Guo, Trevor Kuhlengel, Steven R. Stinson, Seth Blumenthal, Brian Yuan Chen, Soutir Bandyopadhyay:
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, Karen Hovsepian, Syed Monowar Hossain, Emre Ertin, Ashley Kennedy, David H. Epstein, Kenzie Preston, Michelle Jobes, J. Gayle Beck, Satish Kedia, Kenneth D. Ward, Mustafa al'Absi, Santosh Kumar:
Are we there yet?: feasibility of continuous stress assessment via wireless physiological sensors. 479-488 - Julia Warnke, Hesham H. Ali:
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, Peter J. Sadowski, Pierre Baldi:
Deep autoencoder neural networks for gene ontology annotation predictions. 533-540 - Raed I. Seetan, Anne M. Denton, Omar Al Azzam, Ajay Kumar, Muhammad Javed Iqbal, Shahryar F. Kianian:
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, Dhundy Kiran Bastola:
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, Rasna R. Walia, Carla M. Mann, Robert L. Jernigan, Vasant G. Honavar, Drena Dobbs:
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, Guanglan Zhang:
Antidote application: an educational system for treatment of common toxin overdose. 598-599 - Jesmin Jahan Tithi, Pramod Ganapathi, Aakrati Talati, Rezaul Alam Chowdhury:
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, Sairam Behera, Malachy Campbell, Harkamal Walia, Jitender S. Deogun:
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, Hongfang Liu, Scott Leischow:
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, Carl A. Gunter, Dan Roth:
Detecting privacy-sensitive events in medical text. 617-620 - Md. Aashikur Rahman Azim, Costas S. Iliopoulos, Mohammad Sohel Rahman, M. Samiruzzaman:
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, William Crosby:
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, Wooyoung Kim:
Genome dynamics in coevolved genomes: database management system for tracing mutations. 633-634 - Ahmed Abdelzaher, Preetam Ghosh, Ahmad F. Al Musawi, David S. Jackson, John A. Palesis, Jonathan P. DeShazo:
Care coordination metrics of patients sharing among physicians: a social network analytic approach. 635-636 - Daniel Malmer, Phillip Andrew Richmond, Aaron Odell, Richard Radcliffe, Robin D. Dowell:
Inferring ancestry in mouse genomes using a hidden Markov model. 637-638 - Xiang Ji, Soon Ae Chun, James Geller:
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, Luca Soldaini, Andrew Yates, Nazli Goharian, Ophir Frieder:
On clinical decision support. 651-652
Workshop BigLS
- Abhishek Biswas, David Gauthier, Desh Ranjan, Mohammad Zubair:
Big data challenges for estimating genome assembler quality. 653-660 - Etienne Z. Gnimpieba, Abalo Chango, Carol M. Lushbough:
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, Bjoern Peters:
The interplay of sequence conservation and T cell immune recognition. 739-743 - Francesco Pappalardo, Marzio Pennisi, Abdul Mateen Rajput, Ferdinando Chiacchio, Santo Motta:
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, Hesham H. Ali:
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, Etienne Z. Gnimpieba, Carol Lushbough:
Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison. 797-804 - Mario Cannataro, Pietro Hiram Guzzi:
A taxonomy for bioinformatics tools: exploiting semantics, parallelism, and services for analyzing omics data. 805-812 - Pietro Cinaglia, Manuela Macrí, Barbara Calabrese, Patrizia Vizza, Giuseppe Tradigo, Pierangelo Veltri:
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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