RECOMB 2017

Registration and Welcome Reception
Regency Ballroom II, Hyatt Regency Hong Kong, Sha Tin
Address: 18 Chak Cheung Street, Sha Tin, N.T.

Registration

Opening Remarks

S01: Precision Health
Session Chair: Eleazar Eskin
[KT] Jun Wang (iCarbonX)

Coffee Break

S02: Sequencing I
Session Chair: Laxmi Parida

1. Sudipto Mukherjee, Mark Chaisson, Sreeram Kannan and Evan Eichler. Resolving multicopy duplications de novo using polyploid phasing
2. Joshua Welch, Alexander Hartemink and Jan Prins. E Pluribus Unum: United States of Single Cells
3. Alexander Shlemov, Sergey Bankevich, Andrey Bzikadze, Yana Safonova and Pavel Pevzner. Reconstructing antibody repertoires from error-prone immunosequencing datasets

Break

S03: Population and Disease Studies I
Session Chair: Fereydoun Hormozdiari

1. Yue Wu, Farhad Hormozdiari, Jong Wha J Joo and Eleazar Eskin. Improving imputation accuracy by inferring causal variants in genetic studies
2. Xiaoqian Wang, Li Shen and Heng Huang. Longitudinal Genotype-Phenotype Association Study via Temporal Structure Auto-Learning Predictive Model

[HT] Elior Rahmani, Noah Zaitlen, Yael Baran, Celeste Eng, Donglei Hu, Joshua Galanter, Sam Oh, Esteban Burchard, Eleazar Eskin, James Zou and Eran Halperin. Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies

Lunch Break (lunch provided)

S04: Translational Science
Session Chair: Siu Ming Yiu
[KT] Colin Collins (Vancouver Prostate Centre)

Coffee Break

S05: Networks and Systems
Session Chair: Kevin Yip

1. Robert Osazuwa Ness, Karen Sachs, Parag Mallick and Olga Vitek. A Bayesian Active Learning Experimental Design for Inferring Signaling Networks
2. Yijie Wang, Dong-Yeon Cho, Hangnoh Lee, Brian Oliver and Teresa Przytycka. NetREX: Network Rewiring using EXpression - Towards Context Specific Regulatory Networks
3. Yunan Luo, Xinbin Zhao, Jingtian Zhou, Jinling Yang, Yanqing Zhang, Wenhua Kuang, Jian Peng, Ligong Chen and Jianyang Zeng. A Network Integration Approach for Drug-Target Interaction Prediction and Computational Drug Repositioning from Heterogeneous Information

Break

S06: Alignment, Search and Compression
Session Chair: Knut Reinert

1. Brad Solomon and Carl Kingsford. Improved Search of Large Transcriptomic Sequencing Databases Using Split Sequence Bloom Trees joint with Chen Sun, Robert Harris, Rayan Chikhi and Paul Medvedev. Allsome Sequence Bloom Trees
2. Guillaume Holley, Roland Wittler, Jens Stoye and Faraz Hach. Dynamic Alignment-free and Reference-free Read Compression
3. Chirag Jain, Alexander Dilthey, Sergey Koren, Srinivas Aluru and Adam Phillippy. A Fast Approximate Algorithm for Mapping Long Reads to Large Reference Databases

Break

Business Meeting
Venue: Room 203, CYT Building

Registration

S07: Network and Pathways
Session Chair: Teresa Przytycka
[KT] Ben Raphael (Princeton)

Coffee Break

S08: Cancer I
Session Chair: Paul Medvedev

1. Phuong Dao, Yoo-Ah Kim, Damian Wojtowicz, Sanna Madan, Roded Sharan and Teresa Przytycka. BeWith: A Between-Within Method for Module Discovery in Cancer using Integrated Analysis of Mutual Exclusivity, Co-occurrence and Functional Interactions
2. Simone Zaccaria, Mohammed El-Kebir, Gunnar Klau and Ben Raphael. The Copy-Number Tree Mixture Deconvolution Problem and Applications to Multi-Sample Bulk Sequencing Tumor Data
3. Ewa Szczurek and Dariusz Matlak. Epistasis in genomic and survival data of cancer patients

Break

S09: Protein-DNA Interactions and Gene Regulation
Session Chair: Mona Singh

1. Jingkang Zhao, Dongshunyi Li, Jungkyun Seo, Andrew Allen and Raluca Gordan. Quantifying the impact of non-coding variants on transcription factor-DNA binding
2. Yuchun Guo, Kevin Tian, Haoyang Zeng and David K. Gifford. K-mer Set Memory (KSM) motif representation enables accurate prediction of the impact of regulatory variants
3. Yaron Orenstein, Ryan Kim, Polly Fordyce and Bonnie Berger. Joker de Bruijn: sequence libraries to cover all k-mers using joker characters

Lunch Break (lunch provided)

S10: Sequencing II
Session Chair: Martin Vingron
[KT] Michael Schnall-Levin (10X Genomics)

Coffee Break

S11: New Directions
Session Chair: Jian Ma

1. Zhen Li, Sheng Wang, Yizhou Yu and Jinbo Xu. Predicting membrane protein contacts from non-membrane proteins by deep transfer learning

[HT] Michael Altenbuchinger, Thorsten Rehberg, Helena Zacharias, Frank Stämmler, Katja Dettmer, Daniela Weber, Andreas Hiergeist, André Gessner, Ernst Holler, Peter Oefner and Rainer Spang. Reference point insensitive molecular data analysis

1. Uri Keich and William Stafford Noble. Progressive calibration and averaging for tandem mass spectrometry statistical confidence estimation: Why settle for a single decoy?
2. Sai Zhang, Hailin Hu, Jingtian Zhou, Xuan He, Tao Jiang and Jianyang Zeng. ROSE: a deep learning based framework for predicting ribosome stalling

Poster Session I [Odd numbered posters]
Venue: The Gastronomy Club, Level 5, CYT Building

Banquet [ticket required]
ClubONE on the Park, Science Park
Address: Shop 061-066, G/F, Building 12W, No. 12 Science Park West Avenue, Hong Kong Science Park, Sha Tin, N.T.

Registration

S12: Early Cancer Detection and Therapy
Session Chair: Cenk Sahinalp
[KT] Joe Gray (OHSU)

Coffee Break

S13: Cancer II
Session Chair: Ben Raphael

1. Ashok Rajaraman and Jian Ma. Towards Recovering Allele-specific Cancer Genome Graphs

[HT] David Amar, Shai Izraeli and Ron Shamir. Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications

1. Borislav Hristov and Mona Singh. Network-based coverage of mutational profiles reveals cancer genes

Break

S14: Epigenomics
Session Chair: Raluca Gordan

[HT] Przemyslaw Szalaj, Zhonghui Tang, Paul Michalski, Michal Pietal, Michal Sadowski, Oskar Luo, Yijun Ruan and Dariusz Plewczynski. 3D-GNOME: high-resolution model of chromatin looping architecture in human genome

1. Elior Rahmani, Regev Schweiger, Liat Shenhav, Eleazar Eskin and Eran Halperin. A Bayesian Framework for Estimating Cell Type Composition from DNA Methylation Without the Need for Methylation Reference
2. Michael Leung, Andrew Delong and Brendan Frey. Inference of the Human Polyadenylation Code

Lunch Break (lunch provided)

S15: Here and Now of Genomic Medicine
Session Chair: Ron Shamir
[KT] Laxmi Parida (IBM Research)

Coffee Break

S16: Population and Disease Studies 2
Session Chair: Jianyang Zeng

1. Linh Huynh and Fereydoun Hormozdiari. Ultra-accurate complex disorder prediction: case study of neurodevelopmental disorders
2. Regev Schweiger, Eyal Fisher, Elior Rahmani, Liat Shenhav, Saharon Rosset and Eran Halperin. Using stochastic approximation techniques to efficiently construct confidence intervals for heritability
3. Ardalan Naseri, Xiaoming Liu, Shaojie Zhang and Degui Zhi. Ultra-fast Identity by Descent Detection in Biobank-Scale Cohorts using Positional Burrows-Wheeler Transform

Break

S17: Genome Data Structures
Session Chair: John Kececioglu

1. Benedict Paten, Adam Novak, Erik Garrison, Eric Dawson and Glenn Hickey. Superbubbles, Ultrabubbles and Cacti
2. David Haussler, Maciej Smuga-Otto, Benedict Paten, Adam Novak, Sergei Nikitin, Maria Zueva and Miagkov Dmitrii. A flow procedure for the linearization of genome variation graphs
3. Christopher Pockrandt, Marcel Ehrhardt and Knut Reinert. EPR-dictionaries: A practical and fast data structure for constant time searches in unidirectional and bidirectional FM-indices

Poster Session II [Even numbered posters]
Venue: The Gastronomy Club, Level 5, CYT Building

Registration

S18: Metagenomics
Session Chair: Wing Kin Sung

1. Victoria Popic, Volodymyr Kuleshov, Michael Snyder and Serafim Batzoglou. GATTACA: Lightweight metagenomic binning using Kmer Counting
2. Soyeon Ahn and Haris Vikalo. aBayesQR: A Bayesian method for reconstruction of viral populations characterized by low diversity
3. Wontack Han, Mingjie Wang and Yuzhen Ye. A concurrent subtractive assembly approach for identification of disease associated sub-metagenomes

Coffee Break

S19: Protein Structure and Proteomics
Session Chair: Serafim Batzoglou

1. Adegoke Ojewole, Jonathan Jou, Vance Fowler and Bruce Donald. BBK* (Branch and Bound over K*): A Provable and Efficient Ensemble-Based Algorithm to Optimize Stability and Binding Affinity over Large Sequence Spaces

[HT1] Sheng Wang, Siqi Sun, Zhen Li, Renyu Zhang and Jinbo Xu. Folding Large Proteins by Ultra-Deep Learning

[HT2]Vikram Alva Kullanja, Johannes Söding and Andrei Lupas. A vocabulary of ancient peptides at the origin of folded proteins

Break

S20: Phylogenetics and Multiple Sequence Alignment
Session Chair: Jinbo Xu

1. Shubhanshu Shekhar, Sebastien Roch and Siavash Mirarab. Species tree estimation using ASTRAL: how many genes are enough?
2. Jesper Jansson, Andrzej Lingas, Ramesh Rajaby and Wing-Kin Sung. Determining the Consistency of Resolved Triplets and Fan Triplets
3. Dan Deblasio and John Kececioglu. Boosting alignment accuracy by adaptive local realignment

Awards Ceremony and Closing Remarks