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10th BCB 2019: Niagara Falls, NY, USA
- Xinghua Mindy Shi, Michael Buck, Jian Ma, Pierangelo Veltri:
Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, BCB 2019, Niagara Falls, NY, USA, September 7-10, 2019. ACM 2019, ISBN 978-1-4503-6666-3
Keynote&Invited Talks
- Mark Borodovsky:
New Machine Learning Algorithms for Genome Annotation. 1 - Christina S. Leslie:
Decoding Epigenomic Programs in Immunity and Cancer. 2-3 - Heng Huang:
Large-Scale Machine Learning Algorithms for Biomedical Data Science. 4
Session 1: Translational Bioinformatics I
- Hannah De Los Santos, Kristin P. Bennett, Jennifer M. Hurley:
ENCORE: A Visualization Tool for Insight into Circadian Omics. 5-14 - Kaniz Fatema Madhobi, Methun Kamruzzaman
, Ananth Kalyanaraman, Eric Lofgren, Rebekah Moehring
A Visual Analytics Framework for Analysis of Patient Trajectories. 15-24 - Gaëtan Dissez
Drug Repositioning Predictions by Non-Negative Matrix Tri-Factorization of Integrated Association Data. 25-33 - Olatunji Oni, Sanzheng Qiao:
Model-Agnostic Interpretation of Cancer Classification with Multi-Platform Genomic Data. 34-41
Session 2: Structural Bioinformatics I
- Fei Wang
Human Protein Complex Signatures for Drug Repositioning. 42-50 - John Lazarsfeld, Jonathan Rodríguez, Mert Erden, Yuelin Liu, Lenore J. Cowen:
Majority Vote Cascading: A Semi-Supervised Framework for Improving Protein Function Prediction. 51-60 - Allison M. Rossetto, Wenjin Zhou:
GANDALF: A Prototype of a GAN-based Peptide Design Method. 61-66
Session 3: Biological Networks
- Huiyuan Chen, Sudha K. Iyengar, Jing Li:
Large-scale Analysis of Drug Combinations by Integrating Multiple Heterogeneous Information Networks. 67-76 - Alexey Markin, Tavis K. Anderson, Venkata Sai Krishna Teja Vadali, Oliver Eulenstein:
Robinson-Foulds Reticulation Networks. 77-86 - Ali Jazayeri, Muge Capan
Network-Based Modeling of Sepsis: Quantification and Evaluation of Simultaneity of Organ Dysfunctions. 87-96 - Yuanfang Ren, Aisharjya Sarkar, Ahmet Ay, Alin Dobra
Finding Conserved Patterns in Multilayer Networks. 97-102
Session 4: Translational Bioinformatics II
- Hao-Ren Yao, Der-Chen Chang, Ophir Frieder, Wendy Huang, Tian-Shyug Lee:
Multiple Graph Kernel Fusion Prediction of Drug Prescription. 103-112 - Md. Rezaul Karim, Michael Cochez
Drug-Drug Interaction Prediction Based on Knowledge Graph Embeddings and Convolutional-LSTM Network. 113-123 - Cole A. Lyman
Feedback Regulation of Immune Response to Maximum Exercise in Gulf War Illness. 124-129 - Lena Ara, Xiao Luo, Alan Sawchuk, Dave Rollins:
Automate the Peripheral Arterial Disease Prediction in Lower Extremity Arterial Doppler Study using Machine Learning and Neural Networks. 130-135
Session 5: Structural Bioinformatics II
- Zhen Li, Chongming Ni, Jinbo Xu, Xin Gao
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. 136-143 - Jose Lugo-Martinez
Integration of Heterogeneous Experimental Data Improves Global Map of Human Protein Complexes. 144-153 - Ahmed Bin Zaman, Prasanna Venkatesh Parthasarathy, Amarda Shehu:
Using Sequence-Predicted Contacts to Guide Template-free Protein Structure Prediction. 154-160 - Jonas Pfab, Dong Si:
Automated Threshold Selection for Cryo-EM Density Maps. 161-166
Session 6: High-throughput Sequencing Data
- Dan F. DeBlasio
Practical Universal k-mer Sets for Minimizer Schemes. 167-176 - C. Shane Elder, Catherine E. Welsh:
MitoMut: An Efficient Approach to Detecting Mitochondrial DNA Deletions from Paired-end Next-generation Sequencing Data. 177-182 - Anwica Kashfeen, Harper B. Fauni, Timothy A. Bell, Fernando Pardo-Manuel de Villena, Leonard McMillan
ELITE: Efficiently Locating Insertions of Transposable Elements. 183-189
Session 7: Deep Learning I
- Patrick Luckett, Thomas Watts, Jeffrey Todd McDonald, Lee M. Hively, Ryan Benton
A Deep Learning Approach to Phase-Space Analysis for Seizure Detection. 190-196 - Bo Peng, Xia Ning:
Deep Learning for High-Order Drug-Drug Interaction Prediction. 197-206 - Fariba Khoshghalbvash, Jean X. Gao:
Integrative Feature Ranking by Applying Deep Learning on Multi Source Genomic Data. 207-216 - Junjie Chen
A Sparse Convolutional Predictor with Denoising Autoencoders for Phenotype Prediction. 217-222
Session 8: Medical Informatics I
- Tianfan Fu, Tian Gao, Cao Xiao, Tengfei Ma, Jimeng Sun:
PEARL: Prototype Learning via Rule Learning. 223-232 - Fenglong Ma, Shiran Zhong, Jing Gao, Ling Bian:
Influenza-Like Symptom Prediction by Analyzing Self-Reported Health Status and Human Mobility Behaviors. 233-242 - Saket Gurukar, Srikanta Bedathur:
Time-series as Background Data for Relating Medical Diagnoses Terms. 243-252 - Ramin Ramazi, Christine Perndorfer, Emily Soriano, Jean-Philippe Laurenceau, Rahmatollah Beheshti
Multi-modal Predictive Models of Diabetes Progression. 253-258
Session 9: Regulatory Genomics I
- Mattia Prosperi, Taj Azarian, Judith A. Johnson, Marco Salemi, Franco Milicchio, Marco Oliva:
Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus. 259-268 - Farhad Maleki
Gene Set Databases: A Fountain of Knowledge or a Siren Call? 269-278 - Cagatay Dursun
PhenoGeneRanker: A Tool for Gene Prioritization Using Complete Multiplex Heterogeneous Networks. 279-288 - Hua-Ting Yao
Exponentially Few RNA Structures are Designable. 289-298
Session 10: Deep Learning II
- Yue Guo, Jason L. Stein, Guorong Wu, Ashok K. Krishnamurthy:
SAU-Net: A Universal Deep Network for Cell Counting. 299-306 - Chih-Hsuan Wei, Kyubum Lee
Biomedical Mention Disambiguation using a Deep Learning Approach. 307-313 - Seyedroohollah Hosseini, Xuan Guo:
Deep Convolutional Neural Network for Automated Detection of Mind Wandering using EEG Signals. 314-319 - Abhishek Kumar Dubey, Jacob D. Hinkle
Extraction of Tumor Site from Cancer Pathology Reports using Deep Filters. 320-327
Session 11: Medical Informatics II
- Zelalem Gero, Joyce C. Ho:
NamedKeys: Unsupervised Keyphrase Extraction for Biomedical Documents. 328-337 - Qiuhao Lu, Nisansa de Silva, Sabin Kafle, Jiazhen Cao, Dejing Dou, Thien Huu Nguyen, Prithviraj Sen, Brent Hailpern, Berthold Reinwald, Yunyao Li:
Learning Electronic Health Records through Hyperbolic Embedding of Medical Ontologies. 338-346 - Magdalyn E. Elkin, Whitney Angelica Andrews, Xingquan Zhu
Network Analysis and Recommendation for Infectious Disease Clinical Trial Research. 347-356
Session 12: Regulatory Genomics II
- Mira Barshai, Yaron Orenstein:
Predicting G-Quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks. 357-365 - Banabithi Bose, Serdar Bozdag:
miRDriver: A Tool to Infer Copy Number Derived miRNA-Gene Networks in Cancer. 366-375 - Alisa Yurovsky, Bruce Futcher, Steven Skiena
Pre-Phaser: Precise Cell-Cycle Phase Detector for scRNA-seq. 376-382
Session 13: Deep Learning III
- Nur Hafieza Ismail, Mengnan Du, Diego Martinez, Zhe He
Multivariate Multi-step Deep Learning Time Series Approach in Forecasting Parkinson's Disease Future Severity Progression. 383-389 - Michael Segundo Ortiz
Dynamic Cluster-based Retrieval and Discovery for Biomedical Literature. 390-396 - Fei He, Duolin Wang, Yulia Innokenteva, Olha Kholod
Extracting Molecular Entities and Their Interactions from Pathway Figures Based on Deep Learning. 397-404
Session 14: Medical Informatics III
- Priyanka Gandhi, Xiao Luo, Susan Storey, Zuoyi Zhang, Zhi Han, Kun Huang:
Identifying Symptom Clusters in Breast Cancer and Colorectal Cancer Patients using EHR Data. 405-413 - Morteza Pourreza Shahri, Gillian Reynolds
PPPred: Classifying Protein-phenotype Co-mentions Extracted from Biomedical Literature. 414-422 - Fatima Zare, Sheida Nabavi:
Copy Number Variation Detection Using Total Variation. 423-428 - Sheng Wang, Yuzhi Guo
SMILES-BERT: Large Scale Unsupervised Pre-Training for Molecular Property Prediction. 429-436
Session 15: High-throughput Sequencing Data II
- Simone Ciccolella
Effective Clustering for Single Cell Sequencing Cancer Data. 437-446 - Nagakishore Jammula, Srinivas Aluru:
ParRefCom: Parallel Reference-based Compression of Paired-end Genomics Read Datasets. 447-456 - Patrick Perkins, Steffen Heber:
Using a Novel Negative Selection Inspired Anomaly Detection Algorithm to Identify Corrupted Ribo-seq and RNA-seq Samples. 457-465
Session 16: Bioimages&Functional Annotation
- Anirudh Choudhary, Hang Wu, Li Tong, May D. Wang
Learning to Evaluate Color Similarity for Histopathology Images using Triplet Networks. 466-474 - Dina Abdelhafiz
Residual Deep Learning System for Mass Segmentation and Classification in Mammography. 475-484 - Juan Carlos Vizcarra, Ryan Place, Li Tong, David A. Gutman, May Dongmei Wang
Fusion In Breast Cancer Histology Classification. 485-493
Session 17: Comparative Genomics&Cancer Phylogenetics
- Rasha Elhesha, Aisharjya Sarkar, Pietro Cinaglia, Christina Boucher, Tamer Kahveci:
Co-evolving Patterns in Temporal Networks of Varying Evolution. 494-503 - Qiqige Wuyun, Nicholas W. VanKuren, Marcus Kronforst, Sean P. Mullen, Kevin J. Liu
Scalable Statistical Introgression Mapping Using Approximate Coalescent-Based Inference. 504-513 - Misagh Kordi, Soumya Kundu, Mukul S. Bansal
On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic Reconciliation. 514-523 - Shorya Consul, Haris Vikalo
Reconstructing Intra-Tumor Heterogeneity via Convex Optimization and Branch-and-Bound Search. 524-529
Poster Session
- Amy R. Lazarte, Samuel B. Fey, Anna M. Ritz:
Modeling Phytoplankton Movement and Fitness in Lakes. 530 - Guinevere Sieradzki, Sabrina Mierswa, Jung Lee:
Application of Comparative Biosequence Analysis to Understand Antibiotic Resistance in Superbug. 531 - Abhinav Kaushik, Diane Dunham, Monali Manohar, Kari C. Nadeau, Sandra Andorf:
A Novel Workflow for Semi-supervised Annotation of Cell-type Clusters in Mass Cytometry Data. 532 - Qingyu Chen, Jingcheng Du, Sun Kim, W. John Wilbur, Zhiyong Lu:
Evaluation of Five Sentence Similarity Models on Electronic Medical Records. 533 - Salvador Eugenio C. Caoili:
Toward a Sequence-Based Physicochemical Approach to Variable-Length B-Cell Epitope Prediction for Antipeptide Paratopes Recognizing Flexibly Disordered Targets: Insights Drawn from Protein Folding Modeled as Polymer Collapse. 534 - Qiqige Wuyun, Nicholas W. VanKuren, Marcus Kronforst, Sean P. Mullen, Kevin J. Liu:
Scalable Statistical Introgression Mapping Using Approximate Coalescent-Based Inference. 535 - Sutanu Bhattacharya
Contact-assisted Protein Threading: An Evolving New Direction. 536 - Buwani Manuweera, Joann Mudge, Indika Kahanda
Poster: Pangenome-Wide Association Studies with Frequented Regions. 537 - Moran Xu, Dianlin Hu, Weiwen Wu:
ℓ0DL: Joint Image Gradient ℓ0-norm With Dictionary Learning for Limited-angle CT. 538 - Mira Barshai, Yaron Orenstein:
Predicting G-quadruplexes from DNA Sequences Using Multi-Kernel Convolutional Neural Networks. 539 - Chih-Hsuan Wei, Alexis Allot, Robert Leaman, Zhiyong Lu:
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles. 540 - Abdullah Al Mamun, Ananda Mohan Mondal:
Long Non-coding RNA Based Cancer Classification using Deep Neural Networks. 541 - Tianfan Fu, Tian Gao, Cao Xiao, Tengfei Ma
PEARL: Prototype Learning via Rule Learning. 542 - Ali Jazayeri, Muge Capan
Simulating Uncertainty of Early Warning Scores in Sepsis Detection. 543 - Tasmia Aqila, Ananda Mohan Mondal:
Pseudotime Based Analysis of Cancer Dynamics. 544 - Raihanul Bari Tanvir, Mona Maharjan, Ananda Mohan Mondal:
Community Based Cancer Biomarker Identification from Gene Co-expression Network. 545 - Yasunobu Nohara, Koutarou Matsumoto, Hidehisa Soejima, Naoki Nakashima:
Explanation of Machine Learning Models Using Improved Shapley Additive Explanation. 546 - Zhen Li, Chongming Ni, Jinbo Xu, Xin Gao, Shuguang Cui, Sheng Wang:
Transmembrane Topology Identification by Fusing Evolutionary and Co-evolutionary Information with Cascaded Bidirectional Transformers. 547
Highlights
- Jianlin Cheng:
Introduction to 2019 ACM-BCB Highlights Session. 548 - Richard C. Tillquist, Manuel E. Lladser:
Low-Dimensional Representation of Genomic Sequences. 549 - Marzieh Ayati, Danica Wiredja, Daniela Schlatzer, Sean Maxwell, Ming Li, Mehmet Koyutürk, Mark R. Chance:
CoPhosK: A Method for Comprehensive Kinase Substrate Annotation using Co-phosphorylation Analysis. 550 - Jianlin Cheng:
Protein Tertiary Structure Modeling Driven by Deep Learning and Contact Distance Prediction in CASP13. 551 - Hyun-Hwan Jeong, Seon Young Kim, Maxime W. C. Rousseaux, Huda Y. Zoghbi, Zhandong Liu:
Beta-Binomial Modeling of CRISPR Pooled Screen Data Identifies Target Genes with Greater Sensitivity and fewer False Negatives. 552 - Sutanu Bhattacharya
How Effective is Contact-assisted Protein Threading? 553
Tutorials
- Daniel Veltri, Kevin Molloy:
Employing Deep Learning to Study Biomolecules. 554 - Richard C. Tillquist:
Low-Dimensional Representation of Biological Sequence Data. 555 - Antony Pearson:
Extracting Structure from Contaminated Symbolic Data. 556 - Arvind Singh Mer
Machine Learning for Biomarker Discovery in Cancer Pharmacogenomics Data. 557 - May D. Wang
Tutorial: Causal Inference in Biomedical Data Analytics - Basics and Recent Advances. 558 - Daniel J. Blankenberg
You Wrote It, Now Get It Used: Publishing Your Software with Galaxy and Bioconda. 559 - Dan Gusfield:
Integer Linear Programming in Computational and Systems Biology: Tutorial. 560
8th Workshop on Computational Advances in Molecular Epidemiology
- Yury Khudyakov, Ion I. Mandoiu, Pavel Skums, Alexander Zelikovsky
Workshop on Computational Advances in Molecular Epidemiology. 561
Computational Structural Bioinformatics Workshop 2019
- Ahmed Bin Zaman, Parastoo Kamranfar, Carlotta Domeniconi, Amarda Shehu:
Decoy Ensemble Reduction in Template-free Protein Structure Prediction. 562-567 - Hunter Read, Dylan Carpenter, Sam Herr, Filip Jagodzinski:
PETRA: Protein-ligand Complex Engineering Through Rigidity Analysis. 568-573 - Elizabeth West, Kyle Daling, Courtney Miller, Wes Rosales, Sasa Vukovic, Filip Jagodzinski:
CONSEQUENCES: CONstrained SEQUENCE alignmentS With Multiple User Weights. 574-579 - Zhenni Zhao, Xinqi Gong:
Trimer Protein-Protein Complex Interface Interacting Residue Pairs Prediction Using Deep Learning Approach. 580-585 - Lin Chen, Jing He:
A Histogram-based Outlier Profile for Atomic Structures Derived from Cryo-Electron Microscopy. 586-591 - Fardina Fathmiul Alam, Taseef Rahman, Amarda Shehu:
Learning Reduced Latent Representations of Protein Structure Data. 592-597 - Amir Vajdi, Arpita Joshi, Nurit Haspel:
Integrating Co-Evolutionary Information in Monte Carlo Based Method for Proteins Trajectory Simulation. 598-603 - Jinbu Wang, Brian Y. Chen:
On Conformations of Peptides Bound to Class I Major Histocompatibility Complexes. 604-610 - Devan Bicher, Brian Y. Chen:
A Volumetric Survey of Cavities and Electrostatic Patterns in Protein-RNA Binding Sites. 611-617
2019 Workshop on Microbiomics, Metagenomics, and Metabolomics
- Soha Hassoun, Yasser El-Manzalawy, Georg Gerber, David Koslicki, Gail Rosen:
Workshop on Microbiomics, Metagenomics, and Metabolomics. 618
MODI - Machine Learning Models for Multi-omics Data Integration
- Massimiliano S. Tagliamonte, Sheldon G. Waugh, Mattia Prosperi, Volker Mai
An Integrated Approach for Efficient Multi-Omics Joint Analysis. 619-625 - Tarik Elamsy:
Machine Learning Approach for Predicting Metastatic Sites of Prostate Cancer. 626 - Buwani Manuweera, Joann Mudge, Indika Kahanda
Pangenome-Wide Association Studies with Frequented Regions. 627-632 - Osama Hamzeh, Luis Rueda:
A Gene-disease-based Machine Learning Approach to Identify Prostate Cancer Biomarkers. 633-638 - Huy Quang Pham, Jurko Guba, Mousa Gawanmeh, Lisa A. Porter
A Network-based Machine Learning Approach for Identifying Biomarkers of Breast Cancer Survivability. 639-644 - Abed Alkhateeb, Nazia Fatima, Govindaraja Atikukke, Sabeena Misra, Luis Rueda:
A Deep Learning Model to Identify a Genomic Signature Driving Sporadic Colorectal Cancer in Young Adults. 645 - Taban Eslami, Fahad Saeed:
Auto-ASD-Network: A Technique Based on Deep Learning and Support Vector Machines for Diagnosing Autism Spectrum Disorder using fMRI Data. 646-651
8th International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio)
- Giuseppe Agapito
ParBio'19 - 8th Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine. 652 - Zheming Jin, Hal Finkel:
Simulation of Random Network of Hodgkin and Huxley Neurons with Exponential Synaptic Conductances on an FPGA Platform. 653-657 - Marianna Milano, Pietro Hiram Guzzi, Mario Cannataro:
Towards Local Alignment of Multiple Networks: Multi-GLAlign. 658-662 - Rodrigo Crespo-Cepeda, Giuseppe Agapito
Challenges and Opportunities of Amazon Serverless Lambda Services in Bioinformatics. 663-668 - Chao-Jung Wu, Amine M. Remita, Abdoulaye Baniré Diallo:
MirLibSpark: A Scalable NGS Plant MicroRNA Prediction Pipeline for Multi-Library Functional Annotation. 669-674 - Marty Humphrey, Vincent Lin, Shweta Notani, Jose Mattos:
Leveraging the Cloud for Intelligent Clinical Data Registries. 675-682 - Xingzhi Niu, Dimitar Kumanov, Ling-Hong Hung, Wes Lloyd, Ka Yee Yeung:
Leveraging Serverless Computing to Improve Performance for Sequence Comparison. 683-687 - Marzia Settino
Using GMQL-Web for Querying, Downloading and Integrating Public with Private Genomic Datasets. 688-693
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