Sunday, August 29


10:00am - 10:30am WELCOME REMARKS


10:30am - 11:30am  KEYNOTE TALK

Design for Inference and the Power of Random Experiments in Biology

Aviv Regev


11:30am - 12:30pm  TALKS (Single-cell data integration)


Strain Level Microbial Detection and Quantification with Applications to Single Cell Metagenomics

Kaiyuan Zhu, Welles Robinson, Alejandro Schaffer, Junyan Xu, Eytan Ruppin, Funda Ergun, Yuzhen Ye and S. Cenk Sahinalp.


scAdapt: Virtual adversarial domain adaptation network for single cell RNA-seq data classification across platforms and species

Xiang Zhou, Hua Chai, Yuansong Zeng, Huiying Zhao, Ching-Hsing Luo and Yuedong Yang

SPICEMIX: Integrative single-cell spatial modeling for inferring cell identity

Benjamin Chidester, Tianming Zhou and Jian Ma

12:30pm - 12:40pm  SHORT BREAK


12:40pm - 1:20pm TALKS (Single-cell data integration)


Gromov-Wasserstein optimal transport to align single-cell multi-omics data

Pinar Demetci, Rebecca Santorella, Bjorn Sandstede, William Stafford Noble and Ritambhara Singh


Alignment and Integration of Spatial Transcriptomics Data

Ron Zeira, Max Land and Ben Raphael


1:20pm - 2:30pm LONG BREAKS


2:30pm - 3:30pm  KEYNOTE TALK

Trey Ideker


3:30pm - 4:30pm TALKS (Network biology)

VeRNAl: Mining RNA Structures for Fuzzy Base Pairing Network Motifs

Carlos Oliver, Vincent Mallet, Pericles Philippopoulos, William L. Hamilton and Jerome Waldispuhl

MoTSE: an interpretable task similarity estimator for small molecular property prediction tasks

Han Li, Xinyi Zhao, Shuya Li, Fangping Wan, Jianyang Zeng and Dan Zhao

Towards the prediction of higher-order genetic interactions

Ruochi Zhang, Jianzhu Ma and Jian Ma



4:30pm - 4:40pm SHORT BREAK


4:40pm - 6:00pm TALKS (Network biology + Highlights)

DrugOrchestra: Jointly predicting drug response, targets, and side effects via deep multi-task learning

Yuepeng Jiang, Stefano Rensi, Sheng Wang and Russ Altman


Robust Inference of Kinase Activity Using Functional Networks

Serhan Yılmaz, Marzieh Ayati, Daniela Schlatzer, A. Ercument Cicek, Mark Chance and Mehmet Koyuturk


(Highlight) A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data

Wennan Chang, Norah Alghamdi, Pengtao Dang, Xiaoyu Lu, Changlin Wan, Silpa Gampala, Yong Zang, Melissa Fishel, Sha Cao and Chi Zhang.


(Highlight) Learning a genome-wide score of human-mouse conservation from large-scale functional genomic annotations

Soo Bin Kwon and Jason Ernst.

6:00pm – Business meeting



Monday, August 30


10:00am - 11:00am KEYNOTE TALK

Ming Li


11:00am - 12:00pm TALKS (Cancer genomics)

Deep unfolding for non-negative matrix factorization with application to mutational signature analysis

Rami Nasser, Yonina Eldar and Roded Sharan


ScalpelSig: Automated Design of Genomic Panels to Expand Clinical Access to Mutational Signature Analysis

Nicholas Franzese, Jason Fan, Roded Sharan and Mark D.M. Leiserson

RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer

Damian Wójtowicz, Jan Hoinka, Bayarbaatar Amgalan, Yoo-Ah Kim and Teresa M. Przytycka



12:00pm - 12:10pm SHORT BREAK


12:10pm - 1:10pm TALKS (Cancer genomics + Highlights)

DeCiFering the Elusive Cancer Cell Fraction in Tumor Heterogeneity and Evolution

Gryte Satas, Simone Zaccaria, Mohammed El-Kebir and Benjamin J Raphael

(Highlights) ASHIC: hierarchical Bayesian modeling of diploid chromatin contacts and structures

Tiantian Ye and Wenxiu Ma


(Highlights) CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells

Shadi Darvish Shafighi, Szymon Kielbasa, Julieta Sepúlveda-Yáñez, Ramin Monajemi, Davy Cats, Hailiang Mei, Roberta Menafra, Susan Kloet, Hendrik Veelken, Cornelis A.M. Van Bergen and Ewa Szczurek.

1:10pm - 2:00pm LONG BREAKS


2:00pm - 3:20pm TALKS (Transcriptome analysis)

Deriving Ranges of Optimal Estimated Transcript Expression due to Non-identifiability

Hongyu Zheng, Cong Ma and Carl Kingsford


scDesign2: an interpretable simulator that generates high-fidelity single-cell gene expression count data with gene correlations captured

Tianyi Sun, Dongyuan Song, Wei Vivian Li and Jingyi Jessica Li


An Unrolled Deep Learning Framework for Single Cell Gene Regulatory Networks

Harsh Shrivastava, Xiuwei Zhang, Le Song and Srinivas Aluru

Freddie: Annotation-independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms

Baraa Orabi, Brian McConeghy, Cedric Chauve and Faraz Hach


3:20pm - 3:30pm SHORT BREAK


3:30pm - 5:10pm TALKS (Transcriptome analysis + Highlights)

scLink: Inferring Sparse Gene Co-expression Networks from Single-cell Expression Data

Wei Vivian Li and Yanzeng Li

(Highlight) Assessing single-cell transcriptomic variability through density-preserving data visualization

Ashwin Narayan, Bonnie Berger and Hyunghoon Cho

(Highlight) BABEL enables translation between multi-omic profiles at single-cell resolution

Kevin Wu, Kathryn Yost, Howard Chang and James Zou

(Highlight) Conserved regions of mRNA secondary structure strength regulate protein translation across the tree of life

Michael Peeri, Yonatan Chemla, Mathias Luidor Heltberg, Jerry Eichler, Mogens Høgh Jensen, Lital Alfonta and Tamir Tuller

(Highlight) Accelerating Genome Analysis: A Primer on an Ongoing Journey

Mohammed Alser, Zulal Bingol, Damla Senol Cali, Jeremie Kim, Saugata Ghose, Can Alkan and Onur Mutlu.


5:10pm - 7:00pm POSTER SESSION



Tuesday, August 31, 2021


10:00am - 11:00am KEYNOTE TALK

Precision tango

Marie-France Sagot


11:00am - 12:20pm TALKS (Genomic data analysis)


Estimating repeat spectra and genome length from low-coverage genome skims with RESPECT

Shahab Sarmashghi, Metin Balaban, Eleonora Rachtman, Behrouz Touri, Siavash Mirarab and Vineet Bafna

FaNDOM: Fast Nested Distance-based seeding of Optical Maps

Siavash Raeisi Dehkordi, Jens Luebeck and Vineet Bafna

HiCzin Normalizing metagenomic Hi-C data and detecting spurious contacts using zero-inflated negative binomial regression

Yuxuan Du, Sarah Laperriere, Jed Fuhrman and Fengzhu Sun

Privacy-Preserving Genotype Imputation in a Trusted Execution Environment

Natnatee Dokmai, Can Kockan, Kaiyuan Zhu, Xiaofeng Wang, S. Cenk Sahinalp and Hyunghoon Cho


12:20pm - 12:30pm LONG BREAKS


12:30pm - 1:10pm TALKS (Genome assembly)

Practical probabilistic and graphical formulations of long-read polyploid haplotype phasing

Jim Shaw and Yun William Yu

Assembling Long Accurate Reads Using de Bruijn Graphs

Anton Bankevich, Andrey Bzikadze, Mikhail Kolmogorov and Pavel Pevzner



1:10pm - 2:00pm LONG BREAKS


2:00pm - 3:00pm KEYNOTE TALK

Katie Pollard


3:00pm - 4:00pm TALKS (Genome assembly + Efficient sequence analysis)

Minimizer-space de Bruijn Graphs

Barış Ekim, Bonnie Berger and Rayan Chikhi

The statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches

Antonio Blanca, Robert Harris, David Koslicki and Paul Medvedev

Raptor: A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences

Enrico Seiler, Svenja Mehringer, Mitra Darvish, Etienne Turc and Knut Reinert


4:00pm - 4:10pm SHORT BREAK


4:10pm - 5:30pm TALKS (Efficient sequence analysis)

Set-Min sketch: a probabilistic map for power-law distributions with application to k-mer annotation

Yoshihiro Shibuya and Gregory Kucherov

SPRISS: Approximating Frequent k-mers by Sampling Reads, and Applications

Diego Santoro, Leonardo Pellegrina and Fabio Vandin

Fast Alignment-Free Similarity Estimation By TensorSketching

Amir Joudaki, Gunnar Ratsch and Andre Kahles


MONI: A Pangenomics Index for Finding MEMs

Massimiliano Rossi, Marco Oliva, Ben Langmead, Travis Gagie and Christina Boucher


5:30pm - 7:00pm POSTER SESSION



Wednesday, September 1


10:00am - 11:00am KEYNOTE TALK

Mona Singh


11:00pm - 12:20pm TALKS (Structural biology)


Sequence-based prediction of protein-protein interactions: a structure-aware interpretable deep learning model

Samuel Sledzieski, Rohit Singh, Lenore Cowen and Bonnie Berger


Study of Real-Valued Distance Prediction For Protein Structure Prediction with Deep Learning

Jin Li and Jinbo Xu

Taming Disruptive Base Pairs to Reconcile Positive and Negative Structural Design of RNA

Hua-Ting Yao, Jerome Waldispuhl, Yann Ponty and Sebastian Will

ProALIGN: directly learning alignments for protein structure prediction via exploiting context-specific alignment motifs

Lupeng Kong, Fusong Ju, Wei-Mou Zheng, Siwei Sun, Jinbo Xu and Dongbo Bu


12:20pm - 12:30pm SHORT BREAK


12:30pm - 1:50pm TALKS (Phylogenomics and population genetics)

Re-evaluating deep neural networks for phylogeny estimation: the issue of taxon sampling

Martin Grosshauser, Paul Zaharias and Tandy Warnow

DEPP: Deep Learning Enables Extending Species Trees using Single Genes

Yueyu Jiang, Metin Balaban and Siavash Mirarab


Variational Inference Using Approximate Likelihood Under the Coalescent With Recombination

Xinhao Liu, Huw A. Ogilvie and Luay Nakhleh.


Biobank-scale estimation of the proportion of trait variance explained by gene-environment interactions

Ali Pazokitoroudi, Andy Dahl, Noah Zaitlen, Saharon Rosset and Sriram Sankararaman


1:50pm  - 2.00pm CLOSING REMARKS

2:10pm - 4:00pm CGSI SESSION (Hosts: Eleazar Eskin & Eran Halperin)


Methods for genome-wide analysis of short tandem repeats

Melissa Gymrek


Extrachromosomal DNA in cancer

Vineet Bafna


Scaling statistical models to millions of human genomes

Sriram Sankararaman