08:45 - 09:00 am Welcome Remarks

09:00 - 10:00 am Keynote I

10:00 - 11:00 am   Protein Structure and Function

1. Bagging MSA Learning: Enhancing Low-quality PSSM with Deep Learning for Accurate Protein Structure Property Prediction
Yuzhi Guo, Jiaxiang Wu, Hehuan Ma, Sheng Wang and Junzhou Huang

2. MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins
Shuya Li, Fangping Wan, Hantao Shu, Tao Jiang, Dan Zhao and Jianyang Zeng


3. Evolutionary context-integrated deep sequence modeling for protein engineering
Yunan Luo, Lam Vo, Hantian Ding, Yufeng Su, Yang Liu, Wei Qian, Huimin Zhao and Jian Peng ​

11:00 - 11:20 am  Break

11:20 - 12:00 am    Proteomics

4. Multiple competition-based FDR control and its application to peptide detection

Kristen Emery, Syamand Hasam, William Stafford Noble and Uri Keich

5. (Highlight) MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities

Liu Cao, Alexey Gurevich, Kelsey Alexander, Benjamin Naman, Tiago Leão, Evgenia Glukhov, Tal Luzzatto-Knaan, Fernando Vargas, Rob Quinn, Bouslimani Amina, Louis-Félix Nothias, Nitin Singh, Jon Sanders, Rodolfo Benitez, Luke Thompson, Md-Nafiz Hamid, James Morton, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Pieter Dorrestein, Pavel Pevzner and Hosein Mohimanni 

12:00 - 02:00 pm Break

02:00 - 03:00 pm Keynote II

03:00 - 04:20 pm Single-Cell Genomics

6. Supervised Adversarial Alignment of Single-Cell RNA-seq Data

Songwei Ge, Haohan Wang, Amir Alavi, Eric Xing and Ziv Bar-Joseph

7. (Highlight) A comparison of automatic cell identification methods for single-cell RNA sequencing data

Tamim Abdelaal, Lieke Michielsen, Davy Cats, Dylan Hoogduin, Hailiang Mei, Marcel Reinders and Ahmed Mahfouz

8. (Highlight) Understanding phenotypic plasticity by estimating Markov transition rates for cell state transitions

Narendra Suhas Jagannathan, Mario O. Ihsan, Xiao Xuan Kin, Roy E. Welsch, Marie-Veronique Clement and Lisa Tucker-Kellogg

9. Bayesian non-parametric clustering of single-cell mutation profiles

Nico Borgsmueller, Jose Bonet, Francesco Marass, Abel Gonzalez, Nuria Lopez and Niko Beerenwinkel

04:20 - 04:40 pm Break

04:40 - 06:20 pm Cancer

10. (Highlight) Distance Measures for Tumor Evolutionary Trees

Zach DiNardo, Kiran Tomlinson, Anna Ritz and Layla Oesper

11. Single-cell tumor phylogeny inference with copy-number constrained mutation losses

Gryte Satas, Simone Zaccaria, Geoffrey Mon and Ben Raphael

12. (Highlight) Toward Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-Based Convolutional Encoders

Matteo Manica, Ali Oskooei, Jannis Born, Vigneshwari Subramanian, Julio Saez-Rodriguez and Maria Rodriguez Martinez

13. PaccMann     : Designing anticancer drugs from transcriptomic data via reinforcement learning

Jannis Born, Matteo Manica, Ali Oskooei, Joris Cadow and Maria Rodriguez Martinez 

14. (Highlight) PhISCS: A Combinatorial Approach for Sub-perfect Tumor Phylogeny Reconstruction via Integrative use of Single-cell and Bulk Sequencing Data

Salem Malikic, Farid Rashidi Mehrabadi, Simone Ciccolella, Md. Khaledur Rahman, Camir Ricketts, Ehsan Haghshenas, Daniel Seidman, Faraz Hach, Iman Hajirasouliha and S. Cenk Sahinalp


06:30 pm Business Meeting


09:00 - 10:00 am Keynote III

10:00 - 11:00 am   Phylogenetics

15. Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss

Brandon Legried, Erin Molloy, Tandy Warnow and Sebastien Roch

16. Uyen Mai and Siavash Mirarab

Log Transformation Improves Dating of Phylogenies

17. Computing the rearrangement distance of natural genomes

Leonard Bohnenkämper, Marilia Braga, Daniel Doerr and Jens Stoye 

11:00 - 11:20 am   Break

11:20 - 12:00 am    Molecular Evolution

18. A mixture model for signature discovery from sparse mutation data

Itay Sason, Yuexi Chen, Mark Leiserson and Roded Sharan

19. (Highlight) The mutational constraint spectrum quantified from variation in 141,456 humans

Konrad Karczewski, Laurent Francioli, Grace Tiao, Beryl Cummings, Jessica Alfoldi, Qingbo Wang, Benjamin Neale, Mark Daly and Daniel MacArthur

12:00 - 02:00 pm Break

02:00 - 03:00 pm Keynote IV

03:00 - 04:20 pm Networks

20. Deep Large-Scale Multi-Task Learning Network for Gene Expression Inference

Kamran Ghasedi Dizaji, Wei Chen and Heng Huang

21. Reconstruction of Gene Regulatory Networks by integrating biological model and a recommendation system

Yijie Wang, Justin Fear, Isabelle Berger, Hangnoh Lee, Brian Oliver and Teresa Przytycka

22. NetMix: A network-structured mixture model for reduced-bias estimation of altered subnetworks

Matthew Reyna, Uthsav Chitra, Rebecca Elyanow and Benjamin Raphael

23. (Highlight) Assessment of network module identification across complex diseases

Sven Bergmann, Daniel Marbach, Sarvenaz Choobdar, Lenore Cowen and Jake Crawford

04:20 - 04:40 pm Break

04:40 - 06:00 pm Miscellaneous

24. A guided network propagation approach to identify disease genes that combines prior and new information

Borislav Hristov, Bernard Chazelle and Mona Singh

25. Spectral Jaccard Similarity: A new approach to estimating pairwise sequence alignments

Tavor Baharav, Govinda Kamath, David Tse and Ilan Shomorony

26. CluStrat: a structure informed clustering strategy for population stratification

Aritra Bose, Myson Burch, Agniva Chowdhury, Peristera Paschou and Petros Drineas

27. Efficient and accurate inference of microbial trajectories from longitudinal count data

Tyler Joseph, Amey Pasarkar and Itsik Pe'Er


09:00 - 10:00 am Keynote V

10:00 - 11:00 am   Sequencing & Assembly I

28. Strain-aware assembly of genomes from mixed samples using flow variation graphs

Jasmijn Baaijens, Leen Stougie and Alexander Schoenhuth

29. AStarix: Fast and Optimal Sequence-to-Graph Alignment

Pesho Ivanov, Benjamin Bichsel, Harun Mustafa, André Kahles, Gunnar Rätsch, Martin Vechev

30. d-PBWT: dynamic positional Burrows-Wheeler transform

Ahsan Sanaullah, Degui Zhi and Shaojie Zhang

11:00 - 11:20 am Break

11:20 - 12:20 am  Panel Discussion: The Future of Algorithms in Biology

12:20 - 02:20 pm Break

02:20 - 3:40 pm   Sequencing & Assembly II

31. A randomized parallel algorithm for efficiently finding near-optimal universal hitting sets

Baris Ekim, Bonnie Berger and Yaron Orenstein

32. Representation of k-mer sets using spectrum-preserving string sets

Amatur Rahman and Paul Medvedev

33. Lower density selection schemes via small universal hitting sets with short remaining path length

Hongyu Zheng, Carl Kingsford and Guillaume Marcais

34. MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads

Anton Bankevich and Pavel Pevzner

03:40 - 04:00 pm Break

04:00 - 05:20 pm Epigenetics

35. Estimating the rate of cell type degeneration from epigenetic sequencing of cell-free DNA

Christa Caggiano, Barbara Celona, Fleur Garton, Joel Mefford, Brian Black, Catherine Lomen-Hoerth, Andrew Dahl and Noah Zaitlen

36. Probing multi-way chromatin interaction with hypergraph representation learning

Ruochi Zhang and Jian Ma

37. RoboCOP: Multivariate state space model integrating epigenomic accessibility data to elucidate genome-wide chromatin occupancy

Sneha Mitra, Jianling Zhong, David Macalpine and Alexander Hartemink

38. Iterative Refinement of Cellular Identity from Single-Cell Data Using Online Learning

Chao Gao and Joshua Welch


09:00 - 10:00 am Keynote VI

10:00 - 10:40 am   Nucleic Acids

39. Stochastic Sampling of Structural Contexts Improves the Scalability and Accuracy of RNA 3D Module Identification

Roman Sarrazin-Gendron, Hua-Ting Yao, Carlos G. Oliver, Vladimir Reinharz, Yann Ponty and Jérôme Waldispühl

40. (Highlight) Data storage in DNA with fewer synthesis cycles using composite DNA letters

Leon Anavy, Inbal Vaknin, Orna Atar, Roee Amit and Zohar Yakhini

10:40 - 11:00 am    Break

11:00 - 12:00 am    Special Session: The DREAM Challenges

12:00 - 02:00 pm  Break

02:00 - 03:20 pm Association Studies

35. PWAS: Proteome-Wide Association Study

Nadav Brandes, Nathan Linial and Michal Linial

36. Potpourri:  An Epistasis Test Prioritization Algorithm via DiverseSNP Selection

Gizem Caylak and A. Ercument Cicek

37. Identifying Causal Variants by Fine Mapping Across Multiple Studies

Nathan Lapierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari and Eleazar Eskin

38. A scalable method for estimating the regional polygenicity of complex traits

Ruth Johnson, Kathryn S Burch, Kangcheng Hou, Mario Paciuc, Bogdan Pasaniuc and Sriram Sankararaman

03:20 - 03:40 pm Break

03:40 - 04:40 pm Security & Privacy

45. Privacy-preserving biomedical database queries with optimal privacy-utility trade-offs

Hyunghoon Cho, Sean Simmons, Ryan Kim and Bonnie Berger

46. Reconstructing Genotypes in Private Genomic Databases from Genetic Risk Scores

Brooks Paige, James Bell, Aurélien Bellet, Adrià Gascón and Daphne Ezer

47. (Highlight) Better exploration, more security with k-mer analysis of clinical sequencing data and advanced machine learning

William Ritchie

04:40 - 05:30pm Awards Ceremony and Closing

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Organizing Committee

Organizing Secretariat