CONFERENCE

PROGRAM

PRELIMINARY PROGRAM

DATE TO BE UPDATED

Saturday

06:30 - 08:30 pm Welcome Party @ Caffè Pedrocchi

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Sunday

IMPORTANT:

THE CONFERENCE WILL BE RESCHEDULED

see message here

08:45 - 09:00 am Welcome Remarks

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09:00 - 10:00 am Keynote I: Manuela Helmer-Citterich

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

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1. 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 Bagging

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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 Coffee Break

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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

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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 Lunch Break

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02:00 - 03:00 pm Keynote II: Eran Segal

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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

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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

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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

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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

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04:40 - 06:20 pm Cancer

10. (Highlight) Distance Measures for Tumor Evolutionary Trees

Zach DiNardo, Kiran Tomlinson, Anna Ritz and Layla Oesper

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

Gryte Satas, Simone Zaccaria, Geoffrey Mon and Ben Raphael

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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

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

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

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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

06:30 pm Business Meeting

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Monday

09:00 - 10:00 am Keynote III: Marie-France Sagot

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10:00 - 11:00 am   Phylogenetics

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

Brandon Legried, Erin Molloy, Tandy Warnow and Sebastien Roch

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16. Uyen Mai and Siavash Mirarab

Log Transformation Improves Dating of Phylogenies

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17. Computing the rearrangement distance of natural genomes

Leonard Bohnenkämper, Marilia Braga, Daniel Doerr and Jens Stoye 

11:00 - 11:20 am Coffee Break

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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

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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 Lunch Break

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02:00 - 03:00 pm Keynote IV: Satoru Miyano

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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

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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

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

Matthew Reyna, Uthsav Chitra, Rebecca Elyanow and Benjamin Raphael

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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

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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

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

Tavor Baharav, Govinda Kamath, David Tse and Ilan Shomorony

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

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

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

Tyler Joseph, Amey Pasarkar and Itsik Pe'Er

Tuesday

09:00 - 10:00 am Keynote V: Pavel Pevzner

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

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

Jasmijn Baaijens, Leen Stougie and Alexander Schoenhuth

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

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

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

Ahsan Sanaullah, Degui Zhi and Shaojie Zhang

11:00 - 11:20 am Coffee Break

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

12:20 - 02:20 pm Lunch Break

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

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

Baris Ekim, Bonnie Berger and Yaron Orenstein

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

Amatur Rahman and Paul Medvedev

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

Hongyu Zheng, Carl Kingsford and Guillaume Marcais

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34. MosaicFlye: Resolving Long Mosaic Repeats Using Long Reads

Anton Bankevich and Pavel Pevzner

03:40 - 04:00 pm Coffee Break

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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

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

Ruochi Zhang and Jian Ma

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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

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

Chao Gao and Joshua Welch

Wednesday

09:00 - 10:00 am Keynote VI: Maurizio Corbetta

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10:00 - 10:40 am   Nucleic Acids

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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

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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

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

12:00 - 02:00 pm Lunch Break

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02:00 - 03:20 pm Association Studies

35. PWAS: Proteome-Wide Association Study

Nadav Brandes, Nathan Linial and Michal Linial

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

Gizem Caylak and A. Ercument Cicek

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37. Identifying Causal Variants by Fine Mapping Across Multiple Studies

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

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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 Coffee Break

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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

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

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

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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

© 2020 - 2021 Sistema Congressi srl

Organizing Committee organizingcommittee@recomb2020.org

Organizing Secretariat info@recomb2020.org

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