8:00 – 8:15 Welcome Remarks

8:15 – 9:15 Keynote Talk

Bing Ren, Single-cell analysis of epigenome in health and disease

9:15 – 10:15 Talks (Single-cell Multiomics)

Session chair: Jingyi Jessica Li

[PT] Pinar Demetci, Rebecca Santorella, Bjorn Sandstede and Ritambhara Singh, Unsupervised integration of single-cell multi-omics datasets with disparities in cell-type representation

[PT] Ran Zhang, Laetitia Meng-Papaxanthos, Jean-Philippe Vert and William Noble, Semi-supervised single-cell cross-modality translation using Polarbear

[PT] Chen Li, Maria Virgilio, Kathleen Collins and Joshua Welch, Single-cell multi-omic velocity infers dynamic and decoupled gene regulation

10:15 – 10:25 Coffee Break

10:25 – 11:20 Talks (3D Omics)

Session chair: Fengzhu Sun

[PT] Ruochi Zhang, Tianming Zhou and Jian Ma, Ultrafast and Interpretable Single-cell 3D Genome Analysis with Fast-Higashi

[HT] Yue Qin, Edward Huttlin, Casper Winsnes, Maya Gosztyla, Ludivine Wacheul, Marcus Kelly, Steven Blue, Fan Zheng, Michael Chen, Leah Schaffer, Katherine Licon, Anna Bäckström, Laura Pontano Vaites, John Lee, Wei Ouyang, Sophie Liu, Tian Zhang, Erica Silva, Jisoo Park, Adriana Pitea, Jason Kreisberg, Steven Gygi, Jianzhu Ma, J. Wade Harper, Gene Yeo, Denis Lafontaine, Emma Lundberg and Trey Ideker, A multi-scale map of cell structure fusing protein images and interactions

[PT] Dunming Hua, Ming Gu, Yanyi Du, Li Qi, Xiangjun Du, Zhidong Bai, Xiaopeng Zhu and Dechao Tian, DiffDomain enables identification of structurally reorganized topologically associating domains

11:20 – 12:15 Talks (Statistics)

Session chair: Leah Schaffer

[HT] Jacob Schreiber, Sean Whalen, William Noble and Katherine Pollard, Navigating the pitfalls of applying machine learning in genomics

[HT] Fengzhu Sun, DeepLINK: Deep learning inference using knockoffs with applications to genomics

[HT] Nicasia Beebe-Wang, Safiye Celik, Ethan Weinberger, Pascal Sturmfels, Philip L. De Jager, Sara Mostafavi and Su-In Lee, Unified AI framework to uncover deep interrelationships between gene expression and Alzheimer’s disease neuropathologies

12:15 – 13:30 Lunch Break (on your own)

13:30 – 14:30 Keynote Talk

Howard Chang, Personal regulome navigation

14:30 – 15:10 Talks (Cancer I)

Session chair: Mohammed El-Kebir

[PT] Xiang Ge Luo, Jack Kuipers and Niko Beerenwinkel, Joint inference of repeated evolutionary trajectories and patterns of clonal exclusivity or co-occurrence from tumor mutation trees

[PT] Jingkang Zhao, Vincentius Martin and Raluca Gordan, Transcription Factor-Centric Approach to Identify Non-Recurring Putative Regulatory Drivers in Cancer

15:10 – 15:20 Coffee Break

15:20 – 16:40 Talks (Metagenomics)

Session chair: Iman Hajirasouliha

[PT] Pesho Ivanov, Benjamin Bichsel and Martin Vechev, Fast and Optimal Sequence-to-Graph Alignment Guided by Seeds

[PT] Quang Minh Hoang, Hongyu Zheng and Carl Kingsford, DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes

[PT] Vijini Mallawaarachchi and Yu Lin, MetaCoAG: Binning Metagenomic Contigs via Composition, Coverage and Assembly Graphs

[PT] Pengfei Zhang, Zhengyuan Jiang, Yixuan Wang and Yu Li, CLMB: deep contrastive learning for robust metagenomic binning

16:40 – 18:40 Business Meeting

8:00 – 8:55 Talks (Single-cell Transcriptomics I)

Session chair: Joshua Welch

[PT] Dongshunyi Li, Jun Ding and Ziv Bar-Joseph, Unsupervised cell functional annotation for single-cell RNA-Seq

[HT] Mohammad Lotfollahi, Mapping single-cell data to reference atlases by transfer learning
Speaker: Malte Lücken

[PT] Kun Qian, Shiwei Fu, Li Hongwei and Wei Vivian Li, A novel matrix factorization model for interpreting single-cell gene expression from biologically heterogeneous data

8:55 – 9:05 Coffee Break

9:05 – 10:15 Talks (Genetics)

Session chair: Eran Halperin

[HT] Sai Zhang, Johnathan Cooper-Knock, Annika Weimer, Minyi Shi, Tobias Moll, Jack Marshall, Calum Harvey, Helia Ghahremani Nezhad, John Franklin, Cleide dos Santos Souza, Ke Ning, Cheng Wang, Jingjing Li, Allison Dilliott, Sali Farhan, Eran Elhaik, Iris Pasniceanu, Matthew Livesey, Chen Eitan, Eran Hornstein, Kevin Kenna, Jan Veldink, Laura Ferraiuolo, Pamela Shaw and Michael Snyder, Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis

[HT] Zachary R. McCaw, Thomas Colthurst, Taedong Yun, Nicholas A. Furlotte, Andrew Carroll, Babak Alipanahi, Cory Y. McLean and Farhad Hormozdiari, DeepNull models non-linear covariate effects to improve phenotypic prediction and association power

[PT] Meihua Dang, Anji Liu, Xinzhu Wei, Sriram Sankararaman and Guy Van den Broeck, Tractable and expressive generative models of genetic variation data

[PT] Agniva Chowdhury, Aritra Bose, Samson Zhou, David P. Woodruff and Petros Drineas, A Fast, Provably Accurate Approximation Algorithm for Sparse Principal Component Analysis Reveals Human Genetic Variation Across the World

10:15 – 10:25 Coffee Break

10:25 – 11:00 Talks (Networks)

Session chair: Ritambhara Singh

[PT] Haohan Wang, Oscar Lopez, Wei Wu and Eric Xing, Gene Set Prioritization Guided by Regulatory Networks with p-values through Kernel Mixed Model

[HT] Xiaojun Ma, Ashwin Somasundaram, Zengbiao Qi, Douglas Hartman, Harinder Singh and Hatice Osmanbeyoglu, SPaRTAN, a computational framework for linking cell-surface receptors to transcriptional regulators

11:00 – 12:00 Keynote Talk

Lenore Cowen, Pathways for Learning from Structure and Organization of Protein Interaction Networks

12:00 – 13:30 Lunch Break (on your own)

13:30 – 14:30 Talks (Annotation)

Session chair: Serghei Mangul

[PT] Yang Yang, Yuchuan Wang, Yang Zhang and Jian Ma, CONCERT: Genome-wide prediction of sequence elements that modulate DNA replication timing

[PT] Chuanyi Zhang, Palash Sashittal and Mohammed El-Kebir, CORSID enables de novo identification of transcription regulatory sequences and genes in coronaviruses

[PT] Joshua Wetzel, Kaiqian Zhang and Mona Singh, Learning probabilistic protein-DNA recognition codes from DNA-binding specificities using structural mappings

14:30 – 16:20 Poster Session I: odd-numbered posters (poster list)

16:20 – 17:10 Talks (Covid)

Session chair: Louxin Zhang

[HT] Serghei Mangul, Sergey Knyazev, Karishma Chhugani, Ram Ayyala, Varuni Sarwal, Harman Singh, Dhrithi Deshpande, Angela Lu, Smruthi Karthikeyan, Alex Zelikovsky, Rob Knight and Keith Crandall, Unlocking capacities of genomics for the COVID-19 response and future pandemics

[PT] Seyran Saeedi, Myrna Serrano, Dennis Yang, Paul Brooks, Gregory Buck and Tomasz Arodz, Real-valued Group Testing for Quantitative Molecular Assays

[HT] Juncheng Wu, Anushka Rajesh, Yu-Ning Huang, Karishma Chhugani, Rajesh Acharya, Kerui Peng, Ruth D. Johnson, Andrada Fiscutean, Carla Daniela Robles-Espinoza, Francisco M. De La Vega, Riyue Bao and Serghei Mangul, Virtual meetings promise to eliminate geographical and administrative barriers and increase accessibility, diversity and inclusivity

17:10 – 18:10 Keynote Talk

John Chodera, The COVID Moonshot: Open science discovery of a novel oral SARS-CoV-2 antiviral

8:00 – 9:20 Talks (Phylogenomics)

Session chair: Lingling Jin

[PT] Max Hill and Sebastien Roch, On the Effect of Intralocus Recombination on Triplet-Based Species Tree Estimation

[PT] Eleonora Rachtman, Shahab Sarmashghi, Vineet Bafna and Siavash Mirarab, Uncertainty quantification using subsampling for assembly-free estimates of genomic distance and phylogenetic relationships

[PT] Sazan Mahbub, Shashata Sawmya, Arpita Saha, Rezwana Reaz, M. Sohel Rahman and Md Shamsuzzoha Bayzid, QT-GILD: Quartet based gene tree imputation using deep learning improves phylogenomic analyses despite missing data

[PT] Pavel Skums, Fatemeh Mohebbi, Viachaslau Tsyvina, Pelin Burcak Icer, Sumathi Ramachandran and Yury Khudyakov, SOPHIE: viral outbreak investigation and transmission history reconstruction in a joint phylogenetic and network theory framework

9:20 – 9:30 Coffee Break

9:30 – 10:30 Keynote Talk

John Marioni, Computational challenges in single-cell genomics

10:30 – 11:10 Talks (Single-cell Transcriptomics II)

Session chair: Wei Vivian Li

[PT] Elior Rahmani, Michael Jordan and Nir Yosef, Identifying systematic variation at the single-cell level by leveraging low-resolution population-level data

[PT] Cong Ma, Uthsav Chitra, Shirley Zhang and Benjamin Raphael, Belayer: Modeling discrete and continuous spatial variation in gene expression from spatially resolved transcriptomics

11:10 – 13:00 Poster Session II: even-numbered posters (poster list)

13:00 – 14:30 Lunch Break (on your own)

14:30 – 15:30 Talks (Assembly I)

Session chair: Benjamin Langmead

[PT] Mikhail Karasikov, Harun Mustafa, Gunnar Ratsch and Andre Kahles, Lossless Indexing with Counting de Bruijn Graphs

[PT] Shahbaz Khan, Milla Kortelainen, Manuel Ariel Cáceres Reyes, Lucia Williams and Alexandru I. Tomescu, Safety and Completeness in Flow Decompositions for RNA Assembly

[PT] Amatur Rahman and Paul Medvedev, Uncovering hidden assembly artifacts: when unitigs are not safe and bidirected graphs are not helpful

15:30 – 15:40 Coffee Break

15:40 – 16:40 Privacy and Security Workshop

Session chair: Gamze Gürsoy

18:00 – 21:30 Social Event (at the Scripps Aquarium)

18:00 – 19:15 Charter buses pick up at Marriott

21:30 – 21:45 Return buses pick up at Aquarium (with an early return bus 20:30).

8:00 – 9:00 Keynote Talk

Wenyi Wang, Deciphering cancer cell evolution and ecology

9:00 – 9:40 Talks (Cancer II)

Session chair: Salem Malikic

[PT] Uthsav Chitra, Tae Yoon Park and Ben Raphael, NetMix2: Unifying network propagation and altered subnetworks

[PT] Pedro F. Ferreira, Jack Kuipers and Niko Beerenwinkel, Mapping single-cell transcriptomes to copy number evolutionary trees

9:40 – 9:50 Coffee Break

9:50 – 10:50 Talks (Genotype Phenotype)

Session chair: Yun William Yu

[PT] Alireza Ganjdanesh, Jipeng Zhang, Wei Chen and Heng Huang, Multi-Modal Genotype and Phenotype Mutual Learning to Enhance Single-Modal Input Based Longitudinal Outcome Prediction

[PT] Michael Ford, Ananth Hari, Oscar Rodriguez, Junyan Xu, Justin Lack, Cihan Oguz, Yu Zhang, Sarah Weber, Mary Magliocco, Jason Barnett, Sandhya Xirasagar, Smilee Samuel, Luisa Imberti, Paolo Bonfanti, Andrea Biondi, Clifton Dalgard, Stephen Chanock, Lindsey Rosen, Steven Holland, Helen Su, Luigi Notarangelo, Uzi Vishkin, Corey Watson and S. Cenk Sahinalp, ImmunoTyper-SR: A Novel Computational Approach for Genotyping Immunoglobulin Heavy Chain Variable Genes using Short Read Data

[PT] Ulzee An, Na Cai, Andy Dahl and Sriram Sankararaman, AutoComplete: Deep Learning-based Phenotype Imputation for Large-scale Biomedical Data

10:50 – 11:00 Coffee Break

11:00 – 12:00 Talks (Assembly II)

Session chair: Faraz Hach

[PT] Fernando Hugo Cunha Dias, Lucia Williams, Brendan Mumey and Alexandru I. Tomescu, Fast, Flexible, and Exact Minimum Flow Decompositions via ILP

[PT] Chirag Jain, Daniel Gibney and Sharma V. Thankachan, Co-linear Chaining with Overlaps and Gap Costs

[PT] Daniel Gibney, Sharma V. Thankachan and Srinivas Aluru, The Complexity of Approximate Pattern Matching on De Bruijn Graphs

12:00 – 13:30 Lunch Break (on your own)

13:30 – 14:30 Talks (Molecular structure)

Session chair: Helena Gomes Dos Santos

[PT] Nathan Guerin, Teresa Kaserer and Bruce Donald, Resistor: an Algorithm for Predicting Resistance Mutations using Pareto Optimization over Multistate Protein Design and Mutational Signatures

[PT] Zheng Dai, Sachit Saksena, Geraldine Horny, Christine Banholzer, Stefan Ewert and David Gifford, Ultra high diversity factorizable libraries for efficient therapeutic discovery

[PT] Hanwen Xu and Sheng Wang, ProTranslator: zero-shot protein function prediction using textual description

14:30 – 15:30 Keynote Talk

Regina Barzilay, Infusing Biology into Molecular Models for Drug Discovery

15:30pm – 15:50pm Awards Ceremony & Closing Remarks