Monday, June 22nd
08:45 - 09:00 am Welcome Remarks
09:00 - 10:00 am Keynote I: Manuela Helmer-Citterich (University of Rome Tor Vergata)
10:00 - 11:00 am Protein Structure and Function - Session Chair: Daisuke Kihara
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 - Session Chair: William Stafford Noble
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 Business meeting
03:00 - 04:20 pm Single-Cell Genomics - Session Chair: Jian Ma
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 Coffee Break
04:40 - 06:20 pm Cancer - Session Chair: Iman Hajirasouliha
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
RL
Tuesday, June 23rd
09:00 - 10:00 am Keynote II: Michal Linial (University of Jerusalem)
10:00 - 11:00 am Phylogenetics - Session Chair: Nadia El-Mabrouk
15. Polynomial-Time Statistical Estimation of Species Trees under Gene Duplication and Loss
Brandon Legried, Erin Molloy, Tandy Warnow and Sebastien Roch
16. Log Transformation Improves Dating of Phylogenies
Uyen Mai and Siavash Mirarab
17. Computing the rearrangement distance of natural genomes
Leonard Bohnenkämper, Marilia Braga, Daniel Doerr and Jens Stoye
11:00 - 11:20 am Coffee Break
11:20 - 12:00 am Molecular Evolution - Session Chair: Teresa Przytycka
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 Poster Session
02:00 - 03:00 pm Keynote III: Satoru Miyano (University of Tokyo)
03:00 - 04:20 pm Networks - Session Chair: Sushmita Roy
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 Coffee Break
04:40 - 06:00 pm Miscellaneous - Session Chair: Leonid Chindelevitch
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
Wednesday, June 24th
09:00 - 10:00 am Keynote IV: Pavel Pevzner
(University of California at San Diego, Howard Hughes Medical Institute, and U.S. National Institutes of Health)
10:00 - 11:00 am Sequencing & Assembly I - Session Chair: Derek Aguiar
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 Coffee Break
11:20 - 12:20 am Panel Discussion: The Future of Algorithms in Biology
Topics centered around the state of research in algorithms for biology in the next 5 years and beyond.
Panelists include:
- Ben Langmead (Johns Hopkins University)
- Olga Troyanskaya (Princeton University/Flatiron Institute)
- Yaron Orenstein (Ben-Gurion University)
- Caroline Uhler (MIT), & Jean-Philippe Vert (Google Brain/Mines ParisTech).
12:20 - 02:20 pm Poster Session
02:20 - 3:40 pm Sequencing & Assembly II - Session Chair: Veli Mäkinen
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 Marçais
34. MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads
Anton Bankevich and Pavel Pevzner
03:40 - 04:00 pm Coffee Break
04:00 - 05:20 pm Epigenetics - Session Chair: Russell Schwartz
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 pm- 05:00 am
Social event: we will have a Gather space (https://gather.town/) just for RECOMB 2020
more information coming soon in Whova
Thursday, June 25th
08:00 - 09:00 pm Keynote V: Eran Segal (Weizmann Institute)
09:00 - 10:00 am Special Session: The DREAM Challenges
10:00 - 10:40 am Nucleic Acids - Session Chair: Ben Raphael
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 Coffee Break
11:00 - 12:00 am Keynote VI: Russ Altman (Stanford University)
12:00 - 02:00 pm Lunch Break
02:00 - 03:20 pm Association Studies - Session Chair: Mukul Bansal
41. PWAS: Proteome-Wide Association Study
Nadav Brandes, Nathan Linial and Michal Linial
42. Potpourri: An Epistasis Test Prioritization Algorithm via DiverseSNP Selection
Gizem Caylak and A. Ercument Cicek
43. Identifying Causal Variants by Fine Mapping Across Multiple Studies
Nathan Lapierre, Kodi Taraszka, Helen Huang, Rosemary He, Farhad Hormozdiari and Eleazar Eskin
44. 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 Coffee Break
03:40 - 04:40 pm Security & Privacy - Session Chair: Cenk Sahinalp
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
06:00 - 08:00pm Special Session: Computational Genomics Summer Institute (CGSI) Session