Program

Program

  • Schedule
  • Accepted Papers

 

 

SCHEDULE

 

 

  • Saturday, May 4
  • Sunday, May 5
  • Monday, May 6
  • Tuesday, May 7
  • Wednesday, May 8
Saturday, May 4
Registration

8:00 AM – 6:00 PM
Venue: Mavrin Center
Sunday, May 5
Registration

8:00 AM – 8:45 AM
Venue: Lisner Auditorium
Opening and Welcome Remarks

8:45 AM – 9:00 AM
Venue: Lisner Auditorium
Keynote

Alfonso Valencia

9:00 AM – 10:00 AM

Chair: Martin Vingron (Max Planck Institute for Molecular Genetics)
GENETICS AND ASSOCIATION STUDIES

10:00 AM – 11:00 AM

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
SEQUENCING I

11:20 AM – 12:00 PM

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
Keynote

Franziska Michor

1:30 PM – 2:30 PM

Chair: Teresa Przytycka (NIH)
CANCER I

2:30 PM – 3:10 PM

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
REGULATORY GENOMICS

3:30 PM – 4:30 PM

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
STATISTICAL FOUNDATIONS

4:30 PM – 5:50 PM

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: TBA
Monday, May 6
Keynote

Eytan Ruppin

9:00 AM – 10:00 AM

Chair: Cenk Sahinalp (Indiana University)

Venue: Lisner Auditorium
CANCER II

10:00 AM – 10:40 AM

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
SINGLE CELL I

11:00 AM – 12:00 PM

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
Keynote

Rachel Kolodny

1:30 PM – 2:30 PM

Chair: Lenore Cowen (Tufts University)

Venue: Lisner Auditorium
PROTEIN STRUCTURE

2:30 PM – 3:30 PM

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
SINGLE CELL II

3:50 PM – 4:50 PM

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
TEXT MINING

4:50 PM – 5:30 PM

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
Break

5:30 PM – 6:00 PM
Poster Session

6:00 PM – 8:00 PM

Venue: Mavrin Center
Tuesday, May 7
Keynote

Carlos Bustamante

9:00 AM – 10:00 AM

Chair: Bonnie Berger (MIT)

Venue: Lisner Auditorium
GENOMIC PRIVACY

10:00 AM – 11:00 AM

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
Lunch Break

12:00 PM – 1:30 PM
PROTEOMICS

2:00 PM – 2:40 PM
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
GENOME ORGANIZATION

2:40 PM – 3:20 PM

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
SEQUENCING II

3:40 PM – 5:00 PM

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
Keynote

Mihai Pop

9:00 AM – 10:00 AM

Chair: Tandy Warnow (UIUC)

Venue: Lisner Auditorium
METAGENOMICS

10:00 AM – 10:40 AM

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
PANEL WITH NSF AND NIH PROGRAM DIRECTORS

11:00 AM – 12:00 PM
Lunch Break

12:00 PM – 1:30 PM
NETWORKS AND PATHWAY ANALYSIS

1:30 PM – 2:30 PM

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 – 3:50 PM
Venue: Lisner Auditorium
ALGORITHMIC FOUNDATIONS

3:50 PM – 4:30 PM

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
SEQUENCE LEARNING

4:30 PM – 5:10 PM

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
CONFERENCE CLOSING AND AWARDS CEREMONY

5:10 PM – 6:00 PM

 

 

ACCEPTED PAPERS

 

 

  1. Fatemeh Almodaresi, Prashant Pandey, Michael Ferdman, Rob Johnson and Rob Patro.An Efficient and Scalable Representation of High-Dimensional Color Information Enabled via de Bruijn Graph Search
  2. Aryan Arbabi, David Adams, Sanja Fidler and Michael Brudno.Identifying clinical terms in free-text notes using ontology-guided machine learning
  3. Metin Balaban, Shahab Sarmashghi and Siavash Mirarab.APPLES: Fast Distance Based Phylogenetic Placement
  4. Bahar Behsaz, Hosein Mohimani, Alexey Gurevich, Andrey Prjibelski, Mark F Fisher, Larry Smarr, Pieter C. Dorrestein, Joshua S. Mylne and Pavel A. Pevzner.De Novo Peptide Sequencing Reveals a Vast Cyclopeptidome in Human Gut and Other Environments
  5. Philipp Benner and Martin Vingron.ModHMM: A modular supra-Bayesian genome segmentation method
  6. Lodewijk Brand, Xue Yang, Liu Kai, Saad Elbeleidy, Hua Wang and Hao Zhang.Learning Robust Multi-Label Sample Specific Distances for Identifying HIV-1 Drug Resistance
  7. Dexiong Chen, Laurent Jacob and Julien Mairal.Biological Sequence Modeling with Convolutional Kernel Networks
  8. Van Hoan Do, Mislav Blažević, Pablo Monteagudo, Luka Borozan, Khaled Elbassioni, Soeren Laue, Francisca Rojas Ringeling, Domagoj Matijevic and Stefan Canzar.Dynamic pseudo-time warping of complex single-cell trajectories
  9. Rebecca Elyanow, Bianca Dumitrascu, Barbara E. Engelhardt, and Benjamin J. Raphael.netNMF: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data
  10. Boying Gong and Elizabeth Purdom.MethCP: Differentially Methylated Region Detection with Change Point Models
  11. Brian Hie, Hyunghoon Cho, Benjamin DeMeo, Bryan Bryson and Bonnie Berger.Geometric sketching of single-cell data preserves transcriptional structure
  12. Chirag Jain, Haowen Zhang, Yu Gao and Srinivas Aluru.On the Complexity of Sequence to Graph Alignment
  13. Jonathan Jou, Graham Holt, Anna Lowegard and Bruce Donald.Minimization-Aware Recursive K* (MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the Energy Landscape
  14. Mikhail Karasikov, Harun Mustafa, Amir Joudaki, Sara Javadzadeh No, Gunnar Rätsch and André Kahles.Sparse Binary Relation Representations for Genome Graph Annotation
  15. Younhun Kim, Frederic Koehler, Ankur Moitra, Elchanan Mossel and Govind Ramnarayan.How Many Subpopulations is Too Many? Exponential Lower Bounds for Inferring Population Histories
  16. Can Kockan, Kaiyuan Zhu, Natnatee Dokmai, Nikolai Karpov, Oguzhan Kulekci, David Woodruff and Cenk Sahinalp.Sketching Algorithms for Genomic Data Analysis and Querying in a Secure Enclave
  17. Alan Kuhnle, Taher Mun, Christina Boucher, Travis Gagie, Ben Langmead and Giovanni Manzini.Efficient Construction of a Complete Index for Pan-Genomics Read Alignment
  18. 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.Tumor Copy Number Deconvolution Integrating Bulk and Single-Cell Sequencing Data
  19. Yunan Luo, Jianzhu Ma, Xiaoming Zhao, Yufeng Su, Yang Liu, Trey Ideker and Jian Peng.Mitigating Data Scarcity in Protein Binding Prediction Using Meta-Learning
  20. Joel Mefford, Danny Park, Zhili Zheng, Arthur Ko, Mika Ala-Korpela, Markku Laakso, Paivi Pajukanta, Jian Yang, John Witte and Noah Zaitlen.Efficient estimation and applications of cross-validated genetic predictions
  21. Matthew Myers, Gryte Satas and Benjamin Raphael.Inferring tumor evolution from longitudinal samples
  22. Weihua Pan, Tao Jiang and Stefano Lonardi.OMGS: Optical Map-based Genome Scaffolding
  23. Ali Pazokitoroudi, Yue Wu, Kathryn S. Burch, Kangcheng Hou, Bogdan Pasaniuc and Sriram Sankararaman.Scalable multi-component linear mixed models with application to SNP heritability estimation
  24. Leonardo Pellegrina, Cinzia Pizzi and Fabio Vandin.Fast Approximation of Frequent k-mers and Applications to Metagenomics
  25. Kristoffer Sahlin and Paul Medvedev.De novo clustering of long-read transcriptome data using a greedy, quality-value based algorithm
  26. Shahab Sarmashghi and Vineet Bafna.A Note on Computing Interval Overlap Statistics
  27. Itay Sason, Damian Wojtowicz, Welles Robinson, Mark Leiserson, Teresa Przytycka and Roded Sharan.A sticky multinomial mixture model of strand-coordinated mutational processes in cancer
  28. Mike Thompson, Zeyuan Johnson Chen, Elior Rahmani and Eran Halperin.Recovery of cell-type composition in methylation data using canonical correlation analysis
  29. Sheng Wang, Emily Flynn and Russ Altman.GRep: Gene Set Representation via Gaussian Embedding
  30. Yijie Wang, Jan Hoinka and Teresa M. Przytycka.Accurate sub-population detection and mapping across single cell experiments with PopCorn
  31. Ziheng Wang, Grace Ht Yeo, Richard Sherwood and David Gifford.Disentangled Representations of Cellular Identity
  32. Ye Wu, Ruibang Luo, Henry C.M. Leung, Hing-Fung Ting and Tak-Wah Lam.RENET: A Deep Learning Approach for Extracting Gene-Disease Associations from Literature
  33. Yue Wu, Anna Yaschenko, Mohammadreza Hajy Heydary, and Sriram Sankararaman.Fast estimation of genetic correlation for Biobank-scale data
  34. Jinbo Xu.Distance-based Protein Folding Powered by Deep Learning
  35. Yang Yang, Yang Zhang, Bing Ren, Jesse Dixon and Jian Ma.Comparing 3D Genome Organization in Multiple Species using Phylo-HMRF
  36. Jesse Zhang, Govinda Kamath and David Tse.Towards a post-clustering test for differential expression
  37. Martin Zhang, Fei Xia and James Zou.AdaFDR: a Fast, Powerful and Covariate-Adaptive Approach for Multiple Hypothesis Testing