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ORCID8th BCB 2017: Boston, MA, USA
- Nurit Haspel, Lenore J. Cowen, Amarda Shehu, Tamer Kahveci, Giuseppe Pozzi:
Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2017, Boston, MA, USA, August 20-23, 2017. ACM 2017, ISBN 978-1-4503-4722-8
Session 1: Cancer Genomics and Inferring Phylogenies and Haplotypes
- Paola Bonizzoni
, Simone Ciccolella, Gianluca Della Vedova, Mauricio Soto Gomez:
Beyond Perfect Phylogeny: Multisample Phylogeny Reconstruction via ILP. 1-10 - Yi-Pin Lai, Thomas R. Ioerger:
A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes. 11-20 - Fransiskus Xaverius Ivan, Xinrui Zhou, Akhila Deshpande, Rui Yin, Jie Zheng, Chee Keong Kwoh:
Phylogenetic Tree based Method for Uncovering Co-mutational Site-pairs in Influenza Viruses. 21-26
Session 2: Text Mining and Classification
- Margherita Zorzi, Carlo Combi, Gabriele Pozzani, Ugo Moretti:
Mapping Free Text into MedDRA by Natural Language Processing: A Modular Approach in Designing and Evaluating Software Extensions. 27-35 - Yanshan Wang, Sijia Liu, Majid Rastegar-Mojarad, Liwei Wang, Feichen Shen, Fei Liu, Hongfang Liu:
Dependency and AMR Embeddings for Drug-Drug Interaction Extraction from Biomedical Literature. 36-43 - Adel M. ElMessiry, Zhe Zhang, William O. Cooper, Thomas F. Catron, Jan Karrass, Munindar P. Singh:
Leveraging Sentiment Analysis for Classifying Patient Complaints. 44-51 - Arman Cohan, Allan Fong, Raj M. Ratwani, Nazli Goharian:
Identifying Harm Events in Clinical Care through Medical Narratives. 52-59
Session 3: Proteins and RNA Structure, Dynamics, and Analysis I
- Indika Kahanda, Asa Ben-Hur:
GOstruct 2.0: Automated Protein Function Prediction for Annotated Proteins. 60-66 - Mauricio Oberti, Iosif I. Vaisman:
Identification and Prediction of Intrinsically Disordered Regions in Proteins Using n-grams. 67-72 - Alexander Rosenberg Johansen, Casper Kaae Sønderby, Søren Kaae Sønderby, Ole Winther:
Deep Recurrent Conditional Random Field Network for Protein Secondary Prediction. 73-78
Session 4: Genomic Variation and Disease
- Yao Yao, Zheng Liu, Satpreet Singh, Qi Wei, Stephen A. Ramsey:
CERENKOV: Computational Elucidation of the Regulatory Noncoding Variome. 79-88 - Alan M. Cleary, Indika Kahanda, Brendan Mumey, Joann Mudge, Thiruvarangan Ramaraj:
Exploring Frequented Regions in Pan-Genomic Graphs. 89-97 - Andrew Quitadamo, James Johnson, Xinghua Shi:
Bayesian Hyperparameter Optimization for Machine Learning Based eQTL Analysis. 98-106 - Hussein A. Hejase, Natalie Vande Pol, Gregory M. Bonito, Patrick P. Edger, Kevin J. Liu:
Coal-Miner: A Statistical Method for GWA Studies of Quantitative Traits with Complex Evolutionary Origins. 107-114
Session 5: Clinical Databases and Information Systems
- Chongyu Zhou, Yao Jia, Mehul Motani, Jingwei Chew:
Learning Deep Representations from Heterogeneous Patient Data for Predictive Diagnosis. 115-123 - Hsueh-Chien Cheng, Rainer von Coelln, Ann L. Gruber-Baldini, Lisa M. Shulman, Amitabh Varshney:
Winnow: Interactive Visualization of Temporal Changes in Multidimensional Clinical Data. 124-133 - Francesca Cristiano, Giuseppe Tradigo, Pierangelo Veltri:
Associating Genomics and Clinical Information by Means of Semantic Based Ranking. 134-141 - Fabiana Lorenzi, Rodrigo G. da Rosa, Alessandra Peres, Gilson Pires Dorneles, André Peres, Francesco Ricci:
Tailoring Training for Obese Individuals with Case-Based Reasoning. 142-147
Session 6: Big Data in Bioinformatics I
- Hamid Mushtaq, Frank Liu, Carlos Costa, Gang Liu, H. Peter Hofstee, Zaid Al-Ars:
SparkGA: A Spark Framework for Cost Effective, Fast and Accurate DNA Analysis at Scale. 148-157 - He Zhou, Sunil P. Khatri, Jiang Hu, Frank Liu, Cliff C. N. Sze:
Fast and Highly Scalable Bayesian MDP on a GPU Platform. 158-167 - Chieh Lo, Radu Marculescu:
Inferring Microbial Interactions from Metagenomic Time-series Using Prior Biological Knowledge. 168-177 - Sergio Salinas, Pan Li:
Secure Cloud Computing for Pairwise Sequence Alignment. 178-183
Session 7: Advancing Algorithms and Methods I
- Laraib Malik, Rob Patro:
Rich Chromatin Structure Prediction from Hi-C Data. 184-193 - Alexey Markin, Oliver Eulenstein:
Cophenetic Median Trees Under the Manhattan Distance. 194-202 - Sunyoung Kwon, Sungroh Yoon:
DeepCCI: End-to-end Deep Learning for Chemical-Chemical Interaction Prediction. 203-212
Session 8: Automated Diagnosis and Prediction I
- Ye Yuan, Guangxu Xun, Kebin Jia, Aidong Zhang:
A Multi-view Deep Learning Method for Epileptic Seizure Detection using Short-time Fourier Transform. 213-222 - Alevtina Dubovitskaya, Thierry Buclin, Michael Ignaz Schumacher, Karl Aberer, Yann Thoma:
TUCUXI: An Intelligent System for Personalized Medicine from Individualization of Treatments to Research Databases and Back. 223-232 - Ying Sha, May D. Wang:
Interpretable Predictions of Clinical Outcomes with An Attention-based Recurrent Neural Network. 233-240 - Zhaoheng Ni, Ahmet Cem Yuksel, Xiuyan Ni, Michael I. Mandel, Lei Xie:
Confused or not Confused?: Disentangling Brain Activity from EEG Data Using Bidirectional LSTM Recurrent Neural Networks. 241-246
Session 9: Protein and RNA Structure, Dynamics, and Analysis II
- Roshanak Farhoodi, Max Shelbourne, Rebecca Hsieh, Nurit Haspel, Brian Hutchinson, Filip Jagodzinski:
Predicting the Effect of Point Mutations on Protein Structural Stability. 247-252
Session 10: Advancing Algorithms and Methods II
- Jucheol Moon, Oliver Eulenstein:
Synthesizing Species Trees from Unrooted Gene Trees: A Parameterized Approach. 253-262 - Chelsea J.-T. Ju, Ruirui Li, Zhengliang Wu, Jyun-Yu Jiang, Zhao Yang, Wei Wang:
Fleximer: Accurate Quantification of RNA-Seq via Variable-Length k-mers. 263-272 - Xuefu Wang, Sujun Li, Wenjing Peng, Yehia Mechref, Haixu Tang:
A Sparse Latent Regression Approach for Integrative Analysis of Glycomic and Glycotranscriptomic Data. 273-278 - Pourya Naderi Yeganeh, M. Taghi Mostafavi:
Use of Structural Properties of Underlying Graphs in Pathway Enrichment Analysis of Genomic Data. 279-284
Session 11: Applications to Microbes and Imaging Genetics
- Zheng Xu, Sheng Wang, Feiyun Zhu, Junzhou Huang:
Seq2seq Fingerprint: An Unsupervised Deep Molecular Embedding for Drug Discovery. 285-294 - Ahmed A. Metwally, Patricia W. Finn, Yang Dai, David L. Perkins:
Detection of Differential Abundance Intervals in Longitudinal Metagenomic Data Using Negative Binomial Smoothing Spline ANOVA. 295-304 - Zi Wang, Dali Wang, Husheng Li, Zhirong Bao:
Cell Neighbor Determination in the Metazoan Embryo System. 305-312 - Mostafa M. Abbas, Yasser El-Manzalawy:
Predictive and Comparative Network Analysis of the Gut Microbiota in Type 2 Diabetes. 313-320
Session 12: Systems Biology I
- Lu Zhu, Martin Ester:
Bayesian Collective Markov Random Fields for Subcellular Localization Prediction of Human Proteins. 321-329 - Raghvendra Mall, Ehsan Ullah, Khalid Kunji, Fulvio D'Angelo, Halima Bensmail, Michele Ceccarelli:
Differential Community Detection in Paired Biological Networks. 330-339 - Huey-Eng Chua, Sourav S. Bhowmick, Lisa Tucker-Kellogg:
TINTIN: Exploiting Target Features for Signaling Network Similarity Computation and Ranking. 340-345
Session 13: Knowledge Representation Applications
- Zhila Esna Ashari Esfahani, Kelly A. Brayton, Shira L. Broschat:
Determining Optimal Features for Predicting Type IV Secretion System Effector Proteins for Coxiella burnetii. 346-351 - Hasan M. Jamil:
Knowledge Rich Natural Language Queries over Structured Biological Databases. 352-361 - Nisansa de Silva, Dejing Dou, Jingshan Huang:
Discovering Inconsistencies in PubMed Abstracts through Ontology-Based Information Extraction. 362-371 - Ryan Suderman, William S. Hlavacek:
TRuML: A Translator for Rule-Based Modeling Languages. 372-377
Session 14: Integrative Methods for Genomic Data
- Edward W. Huang, Sheng Wang, Bingxue Li, Ran Zhang, Baoyan Liu, Runshun Zhang, Jie Liu, Xuezhong Zhou, Hongsheng Lin, ChengXiang Zhai:
HEMnet: Integration of Electronic Medical Records with Molecular Interaction Networks and Domain Knowledge for Survival Analysis. 378-387 - Soon Jye Kho, Hima Bindu Yalamanchili, Michael L. Raymer, Amit P. Sheth:
A Novel Approach for Classifying Gene Expression Data using Topic Modeling. 388-393 - Junfeng Liu, Xia Ning:
Differential Compound Prioritization via Bi-Directional Selectivity Push with Power. 394-399
Session 15: Sdequence Analysis and Genome Assembly
- Yi Li, Daniel Quang, Xiaohui Xie:
Understanding Sequence Conservation With Deep Learning. 400-406 - Ilya Y. Zhbannikov, Samuel S. Hunter, James A. Foster, Matthew L. Settles:
SeqyClean: A Pipeline for High-throughput Sequence Data Preprocessing. 407-416 - Nagakishore Jammula, Sriram P. Chockalingam, Srinivas Aluru:
Distributed Memory Partitioning of High-Throughput Sequencing Datasets for Enabling Parallel Genomics Analyses. 417-424 - Kanak Mahadik, Christopher Wright, Milind Kulkarni, Saurabh Bagchi, Somali Chaterji:
Scalable Genomic Assembly through Parallel de Bruijn Graph Construction for Multiple K-mers. 425-431
Session 16: Applications to Healthcare Processes
- Ramyar Saeedi, Keyvan Sasani, Assefaw Hadish Gebremedhin:
Co-MEAL: Cost-Optimal Multi-Expert Active Learning Architecture for Mobile Health Monitoring. 432-441 - Jon B. Long, Yingyuan Zhang, Vladimir Brusic, Lou Chitkushev, Guanglan Zhang:
Antidote Application: An Educational System for Treatment of Common Toxin Overdose. 442-448 - Mengnan Zhao, Christopher C. Yang:
Automated Off-label Drug Use Detection from User Generated Content. 449-454
Session 17: Biological Modeling
- Hannah De Los Santos, Emily J. Collins, Jennifer M. Hurley, Kristin P. Bennett:
Circadian Rhythms in Neurospora Exhibit Biologically Relevant Driven and Damped Harmonic Oscillations. 455-463 - Mansooreh Ahmadian, Shuo Wang, John J. Tyson, Young Cao:
Hybrid ODE/SSA Model of the Budding Yeast Cell Cycle Control Mechanism with Mutant Case Study. 464-473 - Qichun Zhang, Francisco Sepulveda:
RBFNN-based Modelling and Analysis for the Signal Reconstruction of Peripheral Nerve Tissue. 474-479
Session 18: Systems Biology II
- Sriram P. Chockalingam, Maneesha Aluru, Hongqing Guo, Yanhai Yin, Srinivas Aluru:
Reverse Engineering Gene Networks: A Comparative Study at Genome-scale. 480-490 - Sultan Imangaliyev, Evgeni Levin:
Unsupervised Multi-View Feature Selection for Tumor Subtype Identification. 491-499 - Ali Atiia, Corbin Hopper, Jérôme Waldispühl:
Computational Intractability Generates the Topology of Biological Networks. 500-509 - Huiyuan Chen, Jing Li:
A Flexible and Robust Multi-Source Learning Algorithm for Drug Repositioning. 510-515
Session 19: Automated Diagnosys and Prediction II
- Jingyun Choi, Yejin Kim, Hun-Sung Kim, In Young Choi, Hwanjo Yu:
Tensor-Factorization-Based Phenotyping using Group Information: Case Study on the Efficacy of Statins. 516-525 - Hang Wu, May D. Wang:
Infer Cause of Death for Population Health Using Convolutional Neural Network. 526-535 - Richard Platania, Shayan Shams, Seungwon Yang, Jian Zhang, Kisung Lee, Seung-Jong Park:
Automated Breast Cancer Diagnosis Using Deep Learning and Region of Interest Detection (BC-DROID). 536-543 - Viktor Chekh, Peter Soliz, Mark R. Burge, Shuang Luan:
A Physiological Thermal Regulation Model with Application to the Diagnosis of Diabetic Peripheral Neuropathy. 544-549
Session 20: Big Data in Bioinformatics II
- Muaaz Gul Awan, Fahad Saeed:
An Out-of-Core GPU based Dimensionality Reduction Algorithm for Big Mass Spectrometry Data and Its Application in Bottom-up Proteomics. 550-555 - Bjørn Fjukstad, Vanessa Dumeaux, Karina Standahl Olsen, Eiliv Lund, Michael T. Hallett, Lars Ailo Bongo:
Building Applications for Interactive Data Exploration in Systems Biology. 556-561 - Mitchell Dawson, Andrew Zisserman, Christoffer Nellåker:
Mining Faces from Biomedical Literature using Deep Learning. 562-567 - Elham Rastegari, Hesham H. Ali:
A Correlation Network Model Utilizing Gait Parameters for Evaluating Health Levels. 568-574
Poster Session
- Meera Garg:
Study of Antidepressant Molecular Structure Leading to Safer Dosing. 575 - Naveena Yanamala, Marlene S. Orandle, Vamsi K. Kodali, Lindsey M. Bishop, Patti C. Zeidler-Erdely, Jenny R. Roberts, Vincent Castranova, Aaron D. Erdely:
Supervised Machine Learning Approaches Predict and Characterize Nanomaterial Exposures: MWCNT Markers in Lung Lavage Fluid. 576 - Brandon A. Saiz, Padmanabhan Mahadevan:
Prokaryotic Autolysin Database Construction. 578 - Basma Abdelkarim, Vincent Maranda, Guy Drouin:
The Fate of Retrotransposed Processed Genes in Arabidopsis Thaliana. 579 - Basma Abdelkarim, Theodore J. Perkins:
Super-enhancer Dynamics Throughout Myogenesis. 580 - Abdelrahman Hosny, Fatima Zare, Sheida Nabavi:
Varsimlab: A Docker-based Pipeline to Automatically Synthesize Short Reads with Genomic Aberrations. 581 - Neda Hassanpour, Nicholas Alden, Kyongbum Lee, Soha Hassoun:
An Advanced Workflow for Metabolite Annotation. 582 - Salvador Eugenio C. Caoili:
Development of a Polymer-Theoretic Approach to Describing Constraints on Reactions Between Antipeptide Antibodies and Intrinsically Disordered Peptide Antigens: Implications for B-Cell Epitope Prediction. 583 - Huixiao Hong, Carmine Leggett, Suguna Sakkiah:
Development of Nicotinic Acetylcholine Receptor nAChR α7 Binding Activity Prediction Model: Coupling Machine Learning with Competitive Molecular Docking. 584 - Margaret Okomo-Adhiambo, Edward Ramos, Reagan Kelly, Yatish Jain, Roman L. Tatusov, Anna Montmayeur, Gregory Doho, Rachel L. Marine, Terry Fei Fan Ng, Adam Retchless, Steve Oberste, Paul Rota, Xin Wang, Agha N. Khan:
Automated Next Generation Sequencing Bioinformatics Pipelines for Pathogen Discovery and Surveillance. 585 - S. M. Ashiqul Islam, Christopher Michel Kearney, Ankan Choudhury, Erich J. Baker:
Protein Classification using Modified N-Gram and Skip-Gram Models: Extended Abstract. 586 - Xiaoli Jiao, Hiromi Imamichi, Tauseef Rehman, Rishub Nahar, Robin L. Dewar, H. Clifford Lane, Tomozumi Imamichi, Brad T. Sherman:
Self-Tuning Spectral Clustering for Full-length Viral Quasispecies Reconstruction with PacBio Long Reads. 587 - Wen Zou, Weizhong Zhao, James J. Chen, Roger Perkins:
Best Setting of Model Parameters in Applying Topic Modeling on Textual Documents. 588 - Sora Kim, Han Sang Kim, Sangwoo Kim:
Neopepsee: Accurate Genome-level Prediction of Neoantigens by Harnessing Sequence and Amino Acid Immunogenicity Information. 589 - Omid Ghiasvand, Mary Shimoyama:
Novel Unsupervised Named Entity Recognition Used in Text Annotation Tool (OntoMate) At Rat Genome Database. 590 - Fatima Zare, Sardar Ansari, Kayvan Najarian, Sheida Nabavi:
Bias and Noise Cancellation for Robust Copy Number Variation Detection. 591 - Soumi Ray, Adam Wright:
Applying Bayesian Changepoint Model and Hierarchical Divisive Model for Detecting Anomalies in Clinical Decision Support Alert Firing. 592 - Sangkyu Lee, Sarah Kerns, Barry Rosenstein, Harry Ostrer, Joseph O. Deasy, Jung Hun Oh:
Preconditioned Random Forest Regression: Application to Genome-Wide Study for Radiotherapy Toxicity Prediction. 593 - Naveen Mangalakumar, Abed Alkhateeb, Huy Quang Pham, Luis Rueda, Alioune Ngom:
Outlier Genes as Biomarkers of Breast Cancer Survivability in Time-Series Data. 594 - Tamsen Dunn, Gwenn Berry, Dorothea Emig-Agius, Yu Jiang, Anita Iyer, Nitin Udar, Michael Strömberg:
Pisces: An Accurate and Versatile Single Sample Somatic and Germline Variant Caller. 595 - Michael Strömberg, Rajat Roy, Julien Lajugie, Yu Jiang, Haochen Li, Elliott H. Margulies:
Nirvana: Clinical Grade Variant Annotator. 596 - León F. Toro, Laura Pinilla-Mendoza, Rigoberto Ríos-Estepa:
Streptomyces Clavuligerus Constraint-Based Modeling and Gene Expression Analysis for Clavulanic Acid Production. 597 - Dong Liu, Anastasia I. Kousa, Simon R. Tomlinson, C. Clare Blackburn:
Notch Signaling Plays an Important Role in mTEC Specification during Fetal Thymus Development. 598 - Olivia M. Ahern, Rebecca J. Stevick, Li Yuan, Noah M. Daniels:
Analysis of 16S Genomic Data using Graphical Databases. 599 - Varshini Guddanti, Shawn Horvatic, Jie Zhou, Yujia Hu, Bing Ye:
High Dimensional Ensemble Neuronal Activity Pattern Analysis: Visualization and Wave Detection Focused. 600 - Shaojun Tang, Suthee Rapisuwon, Anton Wellstein, Subha Madhavan:
Tumor Neoantigens Derived from RNA Sequencing Analysis. 601 - Sherry Bhalla, Suresh Sharma, Gajendra Pal Singh Raghava:
Challenges in Prediction of different Cancer Stages using Gene Expression Profile of Cancer Patients. 602 - Bruno Dantas, Calmenelias Fleitas, Alexandre Almeida, João Forja, Alexandre P. Francisco, José Simão, Cátia Vaz:
NGSPipes: Fostering Reproducibility and Scalability in Biosciences. 603 - Alexandre P. Francisco, Marta Nascimento, Cátia Vaz:
Dynamic Phylogenetic Inference for Sequence-based Typing Data. 604 - Manal Othman, Sujay Ratna, Anant Tewari, Anthony M. Kang, Katherine Du, Iosif I. Vaisman:
Classification and Prediction of Antimicrobial Peptides Using N-gram Representation and Machine Learning. 605 - Anastasiya Belyaeva, Saradha Venkatachalapathy, Mallika Nagarajan, G. V. Shivashankar, Caroline Uhler:
Network Analysis Identifies Regulatory Hotspots in Regions of Chromosome Interactions. 606 - Ashraf Abou Tabl, Abed Alkhateeb, Waguih H. ElMaraghy, Alioune Ngom:
Machine Learning Model for Identifying Gene Biomarkers for Breast Cancer Treatment Survival. 607 - Zewon Park, Ko-Woon Choi, Doo Won Seo, Sunae Ryu, Jong Gu Lee, Woo Yong Oh:
Genome-Wide Association Study (GWAS) for the Infliximab Responsiveness in Korean Inflammatory Bowel Disease Patients. 608-609 - Ali Foroughi Pour, Lori A. Dalton:
Integrating Prior Information with Bayesian Feature Selection. 610 - Lei Li, Mukul S. Bansal:
An Integrated Reconciliation Framework for Domain, Gene, and Species Level Evolution. 611 - Soumya Kundu, Mukul S. Bansal:
Assessing the Impact of Uncertain Gene Tree Rooting on Phylogenetic Reconciliation Using a Simulation Framework. 612 - Alexander J. Paul, Dylan Lawrence, Tae-Hyuk Ahn:
Overlap Graph Reduction for Genome Assembly using Apache Spark. 613 - Blake Camp, Jaya Mandivarapu, Jay Mehta, Nagashayana Ramamurthy, James Wingo, Anu G. Bourgeois, Xiaojun Cao, Rajshekhar Sunderraman:
A Cross-Platform System Architecture for Form Design and Data Analytics for Public Health. 614 - Aly Valliani, Ameet Soni:
Deep Residual Nets for Improved Alzheimer's Diagnosis. 615 - Yashita Jain, Shanshan Ding:
Integrative Sufficient Dimension Reduction Methods for Multi-Omics Data Analysis. 616 - Huy Quang Pham, Luis Rueda, Alioune Ngom:
Predicting Breast Cancer Outcome under Different Treatments by Feature Selection Approaches. 617 - Ibrahim Youssef, Anna M. Ritz:
Breaking Ties in Weighted Interactomes. 618 - Ahmed Metwally, Christian Ascoli, Kalista Andropolis, Ravi Ranjan, Yang Dai, Thomas Ferkol, Patricia W. Finn, David L. Perkins:
Microbiome Dynamics as Predictors of Lung Transplant Rejection. 619 - Aseel Awdeh, Theodore J. Perkins:
Analysis of Controls in ChIP-seq. 620 - Alex V. Kotlar, Cristina E. Trevino, Michael E. Zwick, David J. Cutler, Thomas S. Wingo:
SeqAnt: Cloud-Based Whole-Genome Annotation and Search. 621 - Linfeng Liu, Soha Hassoun:
A Tool for Predicting the Dark Side of Enzymes. 622