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8th 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