CONFERENCE
PROGRAM
PRELIMINARY PROGRAM
Saturday
06:30 - 08:30 pm Welcome Party @ Caffè Pedrocchi
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Sunday
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
06:30 - 08:30 pm Poster session and Reception
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
05:30 pm Depart for Social Event
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
