Top Banner  

















The conference proceedings (Lecture Notes in Computer Science, Volume 7821, 2013) is now online. You can find information about it at or access the online version at A subscription to Springer products is required in order for you to download full text.

Pdf version of the RECOMB 2013 book of abstracts is available here.

RECOMB 2013 Program

RECOMB-Seq 2013 Program

April 6 (Saturday)
  18:00-20:00 Reception (all registered participants), Wenjin Hotel
April 7 (Sunday)
  9:00-18:00 On-site registration
  10:00-10:10 Opening Remarks
Xuegong Zhang (Tsinghua University, China)
  10:10-11:10 Keynote Talk. Chair: Sorin Istrail (Brown University, USA)
Deborah A. Nickerson
University of Washington, USA
Next-Generation Human Genetics
  11:10-12:10 Session 1: Population Genomics
Chair: Francis Chin (University of Hongkong, China)
  11:10-11:30 Emrah Kostem and Eleazar Eskin
Efficiently Identifying Significant Associations in Genome-wide Association Studies
  11:30-11:50 Jesse Rodriguez, Serafim Batzoglou and Sivan Bercovici
An Accurate Method for Inferring Relatedness in Large Datasets of Unphased Genotypes via an Embedded Likelihood-Ratio Test
  11:50-12:10 Itamar Eskin, Farhad Hormozdiari, Lucia Conde, Chris Skibola, Jacques Riby, Eleazar Eskin and Eran Halperin
eALPS: Estimating Abundance Levels in Pooled Sequencing Using Available Genotyping Data
  12:10-14:30 Lunch Break and Poster Session
  12:10-13:30 Poster Setup (Guidelines)
  13:30-14:30 Poster Session 1
  14:30-15:30 Keynote Talk. Chair: Xuegong Zhang (Tsinghua University, China)<
Chung-I Wu
Chinese Academy of Sciences, China
University of Chicago, USA
Active migration driving evolution --- Adaptive invasion and diversification of multifocal tumors
  15:30-16:10 Session 2: Evolutionary Genomics
Chair: Louxin Zhang (National University of Singapore)
  15:30-15:50 Yufeng Wu
An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees
  15:50-16:10 Jesper Jansson, Chuanqi Shen and Wing-Kin Sung
An Optimal Algorithm for Building the Majority Rule Consensus Tree
  16:10-16:30 Tea Break
  16:30-17:50 Session 3: Computational Methods for Genomics
Co-Chairs: Roded Sharan (Tel Aviv University, Israel) and Lei Li (Chinese Academy of Sciences, China)
  16:30-16:50 Dan He, Zhanyong Wang, Laxmi Parida and Eleazar Eskin
IPED: Inheritance Path based Pedigree Reconstruction Algorithm using Genotype Data
  16:50-17:10 Shijian Chen, Anqi Wang and Lei Li
SEME: A Fast Mapper of Illumina Sequencing Reads with Statistical Evaluation
  17:10-17:30 Alina Munteanu and Raluca Gordan
Distinguishing between Genomic Regions Bound by Paralogous Transcription Factors
  17:30-17:50 Po-Ru Loh, Michael Baym and Bonnie Berger (highlight talk)
Compressive Genomics
  17:50 Removal of Poster Session 1
April 8 (Monday)
  8:30-18:00 On-site registration
  9:00-10:00 Keynote Talk. Chair: Martin Vingron (Max-Planck-Institute for Molecular Genetics, Germany)
Takashi Gojobori
National Institute of Genetics, Japan
Time-Course Big Data in Environmental Metagenomics for Monitoring Dynamic Changes of Marine Microorganism Diversity
  10:00-10:40 Session 4: Comparative Genomics
Chair: Xiujie Wang (Institute of Genetics and Developmental Biology, China)
  10:00-10:20 Mukul S. Bansal, Eric J Alm and Manolis Kellis
Reconciliation Revisited: Handling Multiple Optima when Reconciling with Duplication, Transfer, and Loss
  10:20-10:40 Roy Ronen, Nitin Udpa, Eran Halperin and Vineet Bafna
Learning Natural Selection from the Site Frequency Spectrum
  10:40-11:00 Tea Break
  11:00-12:20 Session 5: Cancer Genomics
Co-Chairs: Ben Raphael (Brown University, USA) and Jingdong Han (Chinese Academy of Sciences, China
  11:00-11:20 Dong-Yeon Cho and Teresa Przytycka
Dissecting Cancer Heterogeneity with a Probabilistic Genotype-Phenotype Model
  11:20-11:40 Fabio Vandin, Alexandra Papoutsaki, Ben Raphael and Eli Upfal
Genome-Wide Survival Analysis of Somatic Mutations in Cancer
  11:40-12:00 Raheleh Salari, Syed Shayon Saleh, Dorna Kashef-Haghighi, David Khavari, Daniel E Newburger, Robert E West, Arend Sidow and Serafim Batzoglou
Inference of Tumor Phylogenies with Improved Somatic Mutation Discovery
  12:00-12:20 Layla Oesper, Ahmad Mahmoody and Ben Raphael
Estimating Tumor Purity and Cancer Subpopulations from High-Throughput DNA Sequencing Data
  12:20-14:30 Lunch Break and Poster Session
  12:20-13:30 Poster Setup (Guidelines)
  13:30-14:30 Poster Session 2
  14:30-16:10 Session 6: RNA and Chromosome Structure I
Co-Chairs: Michal Linial (Hebrew University of Jerusalem, Israel) and Xiaowo Wang (Tsinghua University, China)
  14:30-14:50 Raheleh Salari, Damian Wojtowicz, Jie Zheng, David Levens, Yitzhak Pilpel and Teresa Przytycka (highlight talk)
Teasing Apart Translational and Transcriptional Components of Stochastic Variations in Eukaryotic Gene Expression
  14:50-15:10 Sebastian Will, Christina Schmiedl, Milad Miladi, Mathias Mohl and Rolf Backofen
SPARSE: Quadratic Time Simultaneous Alignment and Folding of RNAs Without Sequence-Based Heuristics
  15:10-15:30 Evan Senter, Saad Sheikh, Ivan Dotu, Yann Ponty and Peter Clote
Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches
  15:30-15:50 Vladimir Reinharz, Yann Ponty and Jerume Waldispuhl
A Linear Inside-Outside Algorithm for Correcting Sequencing Errors in Structured RNA Sequences
  15:50-16:10 Yitzhak Freindman, Ohad Balaga and Michal Linial (highlight talk)
Cellular Regulation by Teamwork of microRNAs
  16:10-16:30 Tea Break
  16:30-17:10 Session 7: RNA and Chromosome Structure II
Chair: Xie Zhen (Tsinghua University, China)
  16:30-16:50 Audrey M. Michel, Kingshuk Roy Choudhury, Andrew E. Firth, Nicholas T. Ingolia, John F. Atkins and Pavel V. Baranov (highlight talk)
Observation of Dually Decoded Regions of the Human Genome Using Ribosome Profiling Data
  16:50-17:10 Zhizhuo Zhang, Guoliang Li, Kim-Chuan Toh and Wing-Kin Sung
Inference of Spatial Organizations of Chromosomes Using Semi-definite Embedding Approach and Hi-C Data
  17:10-18:00 Business meeting (all participants)
  18:00 Removal of Poster Session 2
April 9 (Tuesday)
  8:30-13:30 On-site registration
  9:00-10:00 Keynote Talk 4. Chair: Michael Waterman (University of Southern California, USA)
Scott Fraser
University of Southern California, USA
Pushing the Limits of Biological Imaging, Sensing and Manipulation
  10:00-10:40 Session 8: Molecular Networks I
Chair: Minghua Deng (Peking University, China)
  10:00-10:20 Mohammad Javad Sadeh, Giusi Moffa and Rainer Spang
Considering Unknown Unknowns - Reconstruction of Non-confoundable Causal Relations in Biological Networks
  10:20-10:40 Ngoc Hieu Tran, Kwok Pui Choi and Louxin Zhang
Counting Motifs in the Entire Biological Network from Noisy and Incomplete Data
  10:40-11:00 Tea Break
  11:00-12:40 Session 9: Molecular Networks II
Chairs: Hyunju Lee (Gwangju Institute of Science and Technology, Korea) and Rui Jiang (Tsinghua University, China)
  11:00-11:20 DKriti Puniyani and Eric Xing
NP-MuScL: Unsupervised Global Prediction of Interaction Networks From Multiple Data Sources
  11:20-11:40 Ali A Faruqi, William A Bryant and John W Pinney
Analysis of Metabolic Evolution in Bacteria Using Whole-Genome Metabolic Models
  11:40-12:00 Qiangfeng Cliff Zhang, Donald Petrey, Lei Deng, Andrea Califano and Barry Honig (highlight talk)
On the Integration of Structural and Systems Biology: Structure-Based Prediction of Protein–Protein Interactions on a Genome-Wide Scale
  12:00-12:20 Shihua Zhang, Chun-Chi Liu, Wenyuan Li, Hui Shen, Peter W. Laird and Xianghong Jasmine Zhou (highlight talk)
Discovery of Multi-Dimensional Modules by Integrative Analysis of Cancer Genomic Data
  12:20-12:40 Bartek Wilczynski, Ya-Hsin Liu, Zhen Xuan Yeo and Eileen E. M. Furlong (highlight talk)
Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State
  12:40-13:30 Lunch Break
  13:30-17:30 Great Wall Tour (all registered participants, reservation required)
  18:30-20:30 Banquet (full registration only)
April 10 (Wednesday)
  8:30-18:00 On-site registration
  9:00-10:00 Keynote Talk 5
Chair: Fengzhu Sun (University of Southern California, USA)
Nadia Rosenthal
Monash University in Melbourne, Australia
Enhancing Mammalian Regeneration
  10:00-10:40 Session 10: Epigenomics
Chair: Teresa Przytycka (NIH, USA)
  10:00-10:20 Christopher Reeder and David Gifford
High Resolution Modeling of Chromatin Interactions
  10:20-10:40 Michael Stevens, Jeffrey Cheng, Mingchao Xie, Joseph Costello and Ting Wang
MethylCRF: an Algorithm for Estimating Absolute Methylation Levels at Single CpG Resolution from Methylation Enrichment and Restriction Enzyme Sequencing Methods
  10:40-11:00 Tea Break
  11:00-12:20 Session 11: Protein Structure
Co-Chairs: Knut Reinert (Freie Universität Berlin, Germany) and Lusheng Wang (City University of Hongkong, China)
  11:00-11:20 Chittaranjan Tripathy, Anthony Yan, Pei Zhou and Bruce Donald
Extracting Structural Information from Residual Chemical Shift Anisotropy: Analytic Solutions for Peptide Plane Orientations and Applications to Determine Protein Structure
  11:20-11:40 Fei Guo, Shuai Cheng Li, Wenji Ma and Lusheng Wang
Detecting Protein Conformational Changes in Interactions via Scaling Known Structures
  11:40-12:00 Dong Xu, Hua Li and Yang Zhang
Fast and Accurate Calculation of Protein Depth by Euclidean Distance Transform
  12:00-12:20 Shuigeng Zhou
Boosting Prediction Performance of Protein-Protein Interaction Hot Spots by Using Structural Neighborhood Properties
  12:20-13:15 Lunch Break
  13:15-13:35 Industry talk. Chair: Jin Gu (Tsinghua University, China)
Hubert Ding
Healthcare Leading Architect, Healthcare Strategy and Solution, Intel Corporation
Compute for Personalized Medicine
  13:40-14:40 Keynote Talk. Chair: Ron Shamir (Tel Aviv University, Israel)
Xiaoliang Sunney Xie
Harvard University, USA
Life at the Single Molecule Level
  14:40-15:40 Session 12: Image Analysis and Comparative Epigenomics
Chair: Russell Schwartz (Carnegie Mellon U, USA)
  14:40-15:00 Yinyin Yuan, Henrik Failmezger, Oscar M. Rueda, H. Raza Ali, Stefan Gräf, Suet-Feung Chin, Roland F. Schwarz, Christina Curtis, Mark J. Dunning, Helen Bardwell, Nicola Johnson, Sarah Doyle, Gulisa Turashvili, Elen Provenzano, Sam Aparicio, Carlos Caldas and Florian Markowetz (highlight talk)
Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling
  15:00-15:20 Sheng Zhong (highlight talk)
Comparative Epigenomics
  15:20-15:40 Tea Break
  15:40-17:00 Session 13: Proteomics
Co-Chairs: Simin He (Chinese Academy of Sciences, China) and Sungroh Yoon (Seoul National University, Korea)
  15:40-16:00 Kyowon Jeong, Sangtae Kim and Pavel Pevzner
UniNovo: a Universal Tool for De Novo Peptide Sequencing
  16:00-16:20 Sergey Nurk, Anton Bankevich, Dmitry Antipov, Alexey Gurevich, Anton Korobeynikov, Alla Lapidus, Andrey Prjibelsky, Alexey Pyshkin, Alexander Sirotkin, Yakov Sirotkin, Ramunas Stepanauskas, Jeffrey McLean, Roger Lasken, Scott R. Clingenpeel, Tanja Woyke, Glenn Tesler, Max A. Alekseyev, and Pavel A. Pevzner
Assembling Genomes and Mini-metagenomes from Highly Chimeric Reads
  16:20-16:40 Mingxun Wang and Nuno Bandeira
Spectral Library Generating Function for Assessing Spectrum-Spectrum Match Significance
  16:40-17:00 Xiaowen Liu, Shawna Hengel, Si Wu, Nikola Tolic, Ljiljana Pasa-Tolic and Pavel Pevzner
Identification of Proteins with Multiple Post-Translational Modifications Using Top-Down Tandem Mass Spectra
  17:00-17:10 Closing Ceremony
  17:10-18:00 RECOMB-Seq 2013 On-site Registration

  bottom banner  
Home Program Travel Registration Committees Contact Accommodation Travel & Visa Program About RECOMB Accommodation Key Dates General Information Conference Venue Keynote Speakers Registration Committees Submission Call for Posters Call for Papers Travel Fellowships About Beijing Sponsors Contact Stellite Workshop