RECOMB 2017 Proceedings

Hong Kong, May 3-7, 2017

PC Chair: S. Cenk Sahinalp
Organization Committee: Siu Ming Yiu (chair), Kevin Yip, Alexander Schoenhuth, Paul Medvedev
Keynote Speakers: Colin Collins, Joe Gray, Laxmi Parida, Ben Raphael, Michael Schnall-Levin, Jun Wang

List of Publications

• Boosting Alignment Accuracy by Adaptive Local Realignment. Dan DeBlasio and John Kececioglu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 1-17, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_1
• A Concurrent Subtractive Assembly Approach for Identification of Disease Associated Sub-metagenomes. Wontack Han, Mingjie Wang, Yuzhen Ye.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 18-33, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_2
• A Flow Procedure for the Linearization of Genome Sequence Graphs. David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam M. Novak, Sergei Nikitin, Maria Zueva, Dmitrii Miagkov.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 34-49, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_3
• Dynamic Alignment-Free and Reference-Free Read Compression. Guillaume Holley, Roland Wittler, Jens Stoye, Faraz Hach.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 50-65, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_4
• A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases. Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru, Adam M. Phillippy.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 66-81, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_5
• Determining the Consistency of Resolved Triplets and Fan Triplets. Jesper Jansson, Andrzej Lingas, Ramesh Rajaby, Wing-Kin Sung.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 82-98, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_6
• Progressive Calibration and Averaging for Tandem Mass Spectrometry Statistical Confidence Estimation: Why Settle for a Single Decoy?. Uri Keich and William Stafford Noble.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 99-116, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_7
• Resolving Multicopy Duplications de novo Using Polyploid Phasing. Mark J. Chaisson, Sudipto Mukherjee, Sreeram Kannan, Evan E. Eichler.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 117-133, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_8
• A Bayesian Active Learning Experimental Design for Inferring Signaling Networks. Robert Osazuwa Ness, Karen Sachs, Parag Mallick, Olga Vitek.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 134-156, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_9
• BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces. Adegoke A. Ojewole, Jonathan D. Jou, Vance G. Fowler, Bruce R. Donald.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 157-172, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_10
• Superbubbles, Ultrabubbles and Cacti. Benedict Paten, Adam M. Novak, Erik Garrison, Glenn Hickey.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 173-189, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_11
• EPR-Dictionaries: A Practical and Fast Data Structure for Constant Time Searches in Unidirectional and Bidirectional FM Indices. Christopher Pockrandt, Marcel Ehrhardt, Knut Reinert.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 190-206, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_12
• A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference. Elior Rahmani, Regev Schweiger, Liat Shenhav, Eleazar Eskin, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 207-223, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_13
• Towards Recovering Allele-Specific Cancer Genome Graphs. Ashok Rajaraman and Jian Ma.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 224-240, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_14
• Using Stochastic Approximation Techniques to Efficiently Construct Confidence Intervals for Heritability. Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset, Eran Halperin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 241-256, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_15
• Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees. Brad Solomon and Carl Kingsford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 257-271, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_16
• AllSome Sequence Bloom Trees. Chen Sun, Robert S. Harris, Rayan Chikhi, Paul Medvedev.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 272-286, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_17
• Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-learning Predictive Model. Xiaoqian Wang, Jingwen Yan, Xiaohui Yao, Sungeun Kim, Kwangsik Nho, Shannon L. Risacher, Andrew J. Saykin, Li Shen, Heng Huang, for the ADNI.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 287-302, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_18
• Improving Imputation Accuracy by Inferring Causal Variants in Genetic Studies. Yue Wu, Farhad Hormozdiari, Jong Wha J. Joo, Eleazar Eskin.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 303-317, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_19
• The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-sample Bulk Sequencing Tumor Data. Simone Zaccaria, Mohammed El-Kebir, Gunnar W. Klau, Benjamin J. Raphael.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 318-335, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_20
• Quantifying the Impact of Non-coding Variants on Transcription Factor-DNA Binding. Jingkang Zhao, Dongshunyi Li, Jungkyun Seo, Andrew S. Allen, Raluca Gordân.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 336-352, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_21
• aBayesQR: A Bayesian Method for Reconstruction of Viral Populations Characterized by Low Diversity. Soyeon Ahn and Haris Vikalo.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 353-369, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3_22
• BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions. Phuong Dao, Yoo-Ah Kim, Sanna Madan, Roded Sharan, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 370-371, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• K-mer Set Memory (KSM) Motif Representation Enables Accurate Prediction of the Impact of Regulatory Variants. Yuchun Guo, Kevin Tian, Haoyang Zeng, David K. Gifford.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 372-374, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Network-Based Coverage of Mutational Profiles Reveals Cancer Genes. Borislav H. Hristov and Mona Singh.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 375-376, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Ultra-Accurate Complex Disorder Prediction: Case Study of Neurodevelopmental Disorders. Linh Huynh and Fereydoun Hormozdiari.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 377-378, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Inference of the Human Polyadenylation Code. Michael K.K. Leung, Andrew Delong, Brendan J. Frey.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 379-379, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Folding Membrane Proteins by Deep Transfer learning. Zhen Li, Sheng Wang, Yizhou Yu, Jinbo Xu.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 380-382, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information. Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanging Zhang, Wenhua Kuang, Jian Peng, Ligong Chen, Jianyang Zeng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 383-384, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Epistasis in Genomic and Survival Data of Cancer Patients. Dariusz Matlak and Ewa Szczurek.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 385-386, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Ultra-Fast Identity by Descent Detection in Biobank-Scale Cohorts Using Positional Burrows-Wheeler Transform. Ardalan Naseri, Xiaoming Liu, Shaojie Zhang, Degui Zhi.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 387-388, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Joker de Bruijn: Sequence Libraries to Cover All k-mers Using Joker Characters. Yaron Orenstein, Ryan Kim, Polly Fordyce, Bonnie Berger.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 389-390, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• GATTACA: Lightweight Metagenomic Binning Using Kmer Counting. Victoria Popic, Volodymyr Kuleshov, Michael Snyder, Serafim Batzoglou.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 391-392, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Species Tree Estimation Using ASTRAL: How Many Genes Are Enough?. Shubhanshu Shekhar, Sebastien Roch, Siavash Mirarab.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 393-395, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• Reconstructing Antibody Repertoires from Error-Prone Immunosequencing Datasets. Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Yana Safonova, Pavel A. Pevzner.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 396-397, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• NetREX: Network Rewiring Using EXpression - Towards Context Specific Regulatory Networks. Yijie Wang, Dong-Yeon Cho, Hangnoh Lee, Brian Oliver, Teresa M. Przytycka.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 398-399, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• E Pluribus Unum: United States of Single Cells. Joshua D. Welch, Alexander Hartemink, Jan F. Prins.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 400-401, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3
• ROSE: A Deep Learning Based Framework for Predicting Ribosome Stalling. Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang, Jianyang Zeng.
  • Proceedings: Research in Computational Molecular Biology. RECOMB 2017. Lecture Notes in Computer Science, vol 10229, pp 402-404, Springer, Cham.
    • DOI: 10.1007/978-3-319-56970-3