RECOMB 2019 materials is avaliable here.

Saturday, May 4


8:00 AM - 6:00 PM
Venue: Marvin Center, Lobby

Sunday, May 5


8:00 AM - 8:45 AM
Venue: Lisner Auditorium

Opening and Welcome Remarks

8:45 AM - 9:00 AM
Venue: Lisner Auditorium


The Landscape of Disease Comorbidities

Alfonso Valencia

9:00 AM - 10:00 AM

Chair: Martin Vingron (Max Planck Institute for Molecular Genetics)


10:00 AM - 11:00 AM
Chair: Itsik Pe'er

Interpretable deep learning modeling embedding gene regulatory network for understanding functional genomics in neuropsychiatric disorders [Highlight]

Authors: Daifeng Wang, Shuang Liu, Jonathan Warrell, Hyejung Won, Xu Shi, Fabio Navarro, Declan Clarke, Mengting Gu, Prashant Emani, Daniel Geschwind, James Knowles and Mark Gerstein

Scalable multi-component linear mixed models with application to SNP heritability estimation

Authors: Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Bogdan Pasaniuc and Sriram Sankararaman

Fast estimation of genetic correlation for Biobank-scale data

Authors: Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, and Sriram Sankararaman

Coffee Break

11:00 AM - 11:20 AM
Venue: Lisner Auditorium


11:20 AM - 12:00 PM
Chair: Paul Medvedev

Efficient Construction of a Complete Index for Pan-Genomics Read Alignment

Authors: Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead and Giovanni Manzini

Assembly of a pan-genome from deep sequencing of 910 humans of African descent [Highlight]

Authors: Rachel M. Sherman, Juliet Forman, Valentin Antonescu, Daniela Puiu, Michelle Daya, Nicholas Rafaels, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E. Ortega, Albert M. Levin, Celeste Eng, Maria Yazdanbakhsh, James G. Wilson, Javier Marrugo, Leslie A. Lange, L. Keoki Williams, Harold Watson, Lorraine B. Ware, Christopher O. Olopade, Olufunmilayo Olopade, Ricardo R. Oliveira, Carole Ober, Dan L. Nicolae, Deborah A. Meyers, Alvaro Mayorga, Jennifer Knight-Madden, Tina Hartert, Nadia N. Hansel, Marilyn G. Foreman, Jean G. Ford, Mezbah U. Faruque, Georgia M. Dunston, Luis Caraballo, Esteban G. Burchard, Eugene R. Bleecker, Maria I. Araujo, Edwin F. Herrera-Paz, Monica Campbell Cassandra Foster, Margaret A. Taub, Terri H. Beaty, Ingo Ruczinski, Rasika A. Mathias, Kathleen C. Barnes and Steven L. Salzberg

Lunch Break

12:00 PM - 1:30 PM


Evolutionary mathematical modeling enables optimization of glioblastoma treatment strategies

Franziska Michor

1:30 PM - 2:30 PM

Chair: Teresa Przytycka (NIH)


2:30 PM - 3:10 PM
Chair: Russell Schwartz

Inferring tumor evolution from longitudinal samples

Authors: Matthew Myers, Gryte Satas and Benjamin Raphael

A sticky multinomial mixture model of strand-coordinated mutational processes in cancer

Authors: Ali Itay Sason, Damian Wojtowicz, Welles Robinson, Mark Leiserson, Teresa Przytycka and Roded Sharan

Coffee Break

3:10 PM - 3:30 PM
Venue: Lisner Auditorium


3:30 PM - 4:30 PM
Chair: Manolis Kellis

FOCS: a novel method for analyzing enhancer and gene activity patterns infers an extensive enhancer–promoter map [Highlight]

Authors: Tom Aharon Hait, David Amar, Ron Shamir and Ran Elkon

MethCP: Differentially Methylated Region Detection with Change Point Models

Authors: Boying Gong and Elizabeth Purdom

Distinguishing biological from technical sources of variation by leveraging multiple methylation datasets

Authors: Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani and Eran Halperin


4:30 PM - 5:50 PM
Chair: Simon Gravel

AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing [Highlight]

Authors: Martin Zhang, Fei Xia and James Zou

A Note on Computing Interval Overlap Statistics

Authors: Shahab Sarmashghi and Vineet Bafna

Efficient estimation and applications of cross-validated genetic predictions

Authors: Joel Mefford, Danny Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Paivi Pajukanta, Jian Yang, John Witte and Noah Zaitlen

How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories

Authors: Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel and Govind Ramnarayan

RECOMB Business Meeting

6:00 PM
Venue: Lisner Auditorium

Monday, May 6


Harnessing genetic interactions to advance whole-exome precision cancer treatment

Eytan Ruppin

9:00 AM - 10:00 AM

Chair: Cenk Sahinalp (Indiana University)

Venue: Lisner Auditorium


10:00 AM - 10:40 AM
Chair: Max Leiserson

Mutational interactions define novel cancer subgroups [Highlight]

Authors: Jack Kuipers, Thomas Thurnherr, Giusi Moffa, Polina Suter, Jonas Behr, Ryan Goosen, Gerhard Christofori and Niko Beerenwinkel

Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data

Authors: Haoyun Lei, Bochuan Lyu, E. Michael Gertz, Alejandro A. Schaffer, Xulian Shi, Kui Wu, Guibo Li, Liquin Xu, Yong Hu, Michael Dean and Russell Schwartz

Coffee Break

10:40 AM - 11:00 AM
Venue: Lisner Auditorium


11:00 AM - 12:00 PM
Chair: Ben Raphael

Geometric sketching of single-cell data preserves transcriptional structure

Authors: Brian Hie, Hyunghoon Cho, Benjamin DeMeo, Bryan Bryson and Bonnie Berger

Dynamic pseudo-time warping of complex single-cell trajectories

Authors: Van Hoan Do, Mislav Blažević, Pablo Monteagudo, Luka Borozan, Khaled Elbassioni, Soeren Laue, Francisca Rojas Ringeling, Domagoj Matijevic and Stefan Canzar

Accurate sub-population detection and mapping across single cell experiments with PopCorn

Authors: Yijie Wang, Jan Hoinka and Teresa M. Przytycka

Lunch Break

12:00 PM - 1:30 PM


Evolution-CSI: hunting for evidence in the protein universe

Rachel Kolodny

1:30 PM - 2:30 PM

Chair: Lenore Cowen (Tufts University)

Venue: Lisner Auditorium


2:30 PM - 3:30 PM
Chair: Dario Ghersi

Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning

Authors: Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker and Jian Peng

Distance-based Protein Folding Powered by Deep Learning

Authors: Jinbo Xu

Minimization-Aware Recursive K* (MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the Energy Landscape

Authors: Jonathan Jou, Graham Holt, Anna Lowegard and Bruce Donald

Coffee Break

3:30 PM - 3:50 PM
Venue: Lisner Auditorium


3:50 PM - 4:50 PM
Chair: Fabio Vandin

netNMF: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

Authors: Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, and Benjamin J. Raphael

Disentangled Representations of Cellular Identity

Authors: Ziheng Wang, Grace Ht Yeo, Richard Sherwood and David Gifford

Towards a post-clustering test for differential expression

Authors: Jesse Zhang, Govinda Kamath and David Tse


4:50 PM - 5:30 PM
Chair: Roded Sharan

RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature

Authors: Ye Wu, Ruibang Luo, Henry C.M. Leung, Hing-Fung Ting and Tak-Wah Lam

Identifying clinical terms in free-text notes using ontology-guided machine learning

Authors: Aryan Arbabi, David Adams, Sanja Fidler and Michael Brudno


5:30 PM - 6:00 PM

Poster Session and Reception

6:00 PM - 8:00 PM

Venue: Marvin Center, Grand Ballroom

Tuesday, May 7


Innovating in Biomedical Data Science for Precision Health

Carlos Bustamante

9:00 AM - 10:00 AM

Chair: Bonnie Berger (MIT)

Venue: Lisner Auditorium


10:00 AM - 11:00 AM
Chair: Cenk Sahinalp

Identity inference of genomic data using long-range familial searches [Highlight]

Authors: Yaniv Erlich, Tal Shor, Itsik Pe'Er and Shai Carmi

Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave

Authors: Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, Oguzhan Kulekci, David Woodruff and Cenk Sahinalp

Realizing private and practical pharmacological collaboration [Highlight]

Authors: Brian Hie, Hyunghoon Cho and Bonnie Berger

Coffee Break

11:00 AM - 11:20 AM
Venue: Lisner Auditorium

Special Panel Session on Genomic Privacy

11:20 AM - 12:30 PM

Chair: Bonnie Berger

Lunch Break

12:30 PM - 2:00 PM


2:00 PM - 2:40 PM
Chair: Knut Reinert

Venue: Lisner Auditorium

De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments

Authors: Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne and Pavel A. Pevzner

Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry [Highlight]

Authors: Ngoc-Hieu Tran, Rui Qiao, Lei Xin, Xin Chen, Chuyi Liu, Xianglilan Zhang, Baozhen Shan, Ali Ghodsi and Ming Li


2:40 PM - 3:20 PM
Chair: Vineet Bafna

Comparing 3D Genome Organization in Multiple Species using Phylo-HMRF

Authors: Yang Yang, Yang Zhang, Bing Ren, Jesse Dixon and Jian Ma

ModHMM: A modular supra-Bayesian genome segmentation method

Authors: Philipp Benner and Martin Vingron

Coffee Break

3:20 PM - 3:40 PM
Venue: Lisner Auditorium


3:40 PM - 5:00 PM
Chair: Pavel Avdeyev

An Efficient and Scalable Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search

Authors: Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson and Rob Patro

Sparse Binary Relation Representations for Genome Graph Annotation

Authors: Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh No, Gunnar Rätsch and André Kahles

De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm

Authors: Kristoffer Sahlin and Paul Medvedev

OMGS: Optical Map-based Genome Scaffolding

Authors: Weihua Pan, Tao Jiang and Stefano Lonardi

Depart for Social Event

5:00 PM

Wednesday, May 8


Uncovering heterogeneity in microbial communities

Mihai Pop

9:00 AM - 10:00 AM

Chair: Tandy Warnow (UIUC)

Venue: Lisner Auditorium


10:00 AM - 10:40 AM
Chair: Alex Zelikovsky

Minerva: An Alignment and Reference Free Approach to Deconvolve Linked-Reads for Metagenomics [Highlight]

Authors: David Danko, Dmitrii Meleshko, Daniela Bezdan, Christopher Mason and Iman Hajirasouliha

Fast Approximation of Frequent k-mers and Applications to Metagenomics

Authors: Leonardo Pellegrina, Cinzia Pizzi and Fabio Vandin

Coffee Break

10:40 AM - 11:00 AM
Venue: Lisner Auditorium


11:00 AM - 12:00 PM

Lunch Break

12:00 PM - 1:30 PM


1:30 PM - 2:30 PM
Chair: Carl Kingsford

Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data [Highlight]

Authors: Ali Sinan Köksal, Kirsten Beck, Dylan R Cronin, Aaron McKenna, Nathan D Camp, Saurabh Srivastava, Matthew E MacGilvray, Rastislav Bodík, Alejandro Wolf-Yadlin, Ernest Fraenkel, Jasmin Fisher and Anthony Gitter

GRep: Gene Set Representation via Gaussian Embedding

Authors: Sheng Wang, Emily Flynn and Russ Altman

The Distance Precision Matrix: computing networks from non-linear relationships [Highlight]

Authors: Mahsa Ghanbari, Julia Lasserre and Martin Vingron

Coffee Break

2:30 PM - 2:50 PM
Venue: Lisner Auditorium


2:50 PM - 3:30 PM
Chair: Yann Ponty

APPLES: Fast Distance Based Phylogenetic Placement

Authors: Metin Balaban, Shahab Sarmashghi and Siavash Mirarab

On the Complexity of Sequence to Graph Alignment

Authors: Chirag Jain, Haowen Zhang, Yu Gao and Srinivas Aluru


3:30 PM - 4:10 PM
Chair: Damian Wojtowicz

Learning Robust Multi-Label Sample Specific Distances for Identifying HIV-1 Drug Resistance

Authors: Lodewijk Brand, Xue Yang, Liu Kai, Saad Elbeleidy, Hua Wang and Hao Zhang

Biological Sequence Modeling with Convolutional Kernel Networks

Authors: Dexiong Chen, Laurent Jacob and Julien Mairal


4:10 PM - 5:00 PM