The scientific program includes keynotes by leading researchers in the field (Rita R. Colwell and Gunnar Rätsch) and selected presentations of contest dataset analyses. The two-day meeting will also feature a social dinner with and opportunities for informal discussions.

Tentative Program

Wednesday, 24 July 2019

08:15 ISMB/ECCB Welcome
08:30 ISCB 2019 Overton Prize Award: Challenges and rewards of benchmarking – how to cope with a biased, incomplete, or even entirely missing ground truth Christophe Dessimoz, University of Lausanne, Switzerland
09:30 Coffee break
10:15 CAMDA Welcome David P Kreil, Boku University Vienna, Austria
10:20 CAMDA Keynote Rita Colwell, University of Maryland College Park, U.S.A.
11:20 Data Analysis Challenges of the CAMDA Contest 2019 Wenzhong Xiao, Stanford and Harvard Medical School, U.S.A.
11:40 A Machine Learning Framework to Determine Geolocations from Metagenomics Profiling Lihong Huang, Xiamen University, China
12:00 Metagenomic sequence classification to search for the origin of samples Jolanta Kawulok, Silesian University of Technology, Poland
12:20 Comparison between functional profiles derived from whole genome sequencing and inferred from 16S sequencing Carlos Loucera Clinical Bioinformatics Area, Fundacion Progreso y Salud, Spain
12:40 Lunch break
14:00 Systematic evaluation of microbial abundance from amplicon and shotgun sequencing for machine learning prediction of sample origin Julie Chih-yu Chen, Public Health Agency of Canada - National Microbiology Laboratory, Canada
14:40 MetaSUB: A Global Atlas of the Urban Microbiome David Danko, MetaSUB International Consortium / Weill Cornell Medicine, U.S.A.
15:00 Integration of human cell lines gene expression and chemical properties of drugs for Drug Induced Liver Injury prediction Witold R. Rudnicki, Institute of Informatics, University of Białystok / ICM University of Warsaw, Poland
15:40 An ensemble learning approach for modeling the systems biology of drug-induced injury in human liver Joaquim Aguirre-Plans, GRIB (IMIM-UPF), Spain
16:00 Coffee break
16:40 Steps towards predictive models for DILI based on chemical structure and gene expression signatures and their interpretation Anika Liu, University of Cambridge, U.K.
17:00 Flash talks
Prediction of human clinical drug-induced liver injury: cell-line responses versus chemical structures Thin Nguyen, Deakin University, Australia
A Novel Gene Selection Method for Gene Expression Data for the Task of Cancer Type Classification Nuriye Özlem ÖZCAN ŞİMŞEK, Boğaziçi Unversity, Turkey
mi-faser based partition of the CAMDA 2019 mystery samples in the Metagenomic Forensics Challenge Maximilian Miller / Yannick Mahlich, Rutgers University, U.S.A.
CAMDA Forensics Challenge: An Evaluation of Mass-Transit, Microbiome Profiles Scott Lewis, Saint Louis University, U.S.A.
Constructing microbial fingerprint for unraveling city-specific signature and identifying sample origin locations Susmita Datta, University of Florida, U.S.A.
18:00 CAMDA@ISMB/ECCB Poster Presentations
19:30 CAMDA Dinner, joint departure from lobby

Thursday, 25 July 2019

8:30 CAMDA Welcome Joaquin Dopazo, Fundacion Progreso y Salud, Sevilla, Spain
8:40 CAMDA Keynote Gunnar Rätsch, ETH Zurich, Switzerland
9:40 Coffee break
10:15 Data Analysis Challenges of the CAMDA Contest 2019 (II) Paweł P Łabaj, MCB Jagiellonian University, Poland
10:20 Analyzing cancer through Hipathia: a new insight on cancer signaling pathways Marta R. Hidalgo, Centro de Investigación Príncipe Felipe, Spain
10:40 A systematic analysis of multiple cancer studies within a novel enhanced framework for semantic data integration Maciej Kańduła, Boku University Vienna, Austria
11:00 A sparse Bayesian factor model for the construction of gene co-expression networks from single-cell RNA sequencing count data Susmita Datta, University of Florida, U.S.A.
11:40 Benchmarking scRNA-seq clustering methods using multi-parameter ensembles of simulated data and workflows Xianing Zheng, University of Michigan, U.S.A.
12:00 Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology Gregor Sturm, Technical University of Munich, Germany
12:40 Lunch break
14:00 PRECISE: A domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors Soufiane Mourragui, Delft University of Technology, Netherlands
14:40 Evaluation of Connectivity Map shows limited reproducibility in drug repositioning Nathaniel Lim, The University of British Columbia, Canada
15:20 Contest voting and summary
15:25 Retrospective and Outlook: Metagenomic Forensic Challenge Paweł P Łabaj, MCB Jagiellonian University, Poland
15:40 Retrospective and Discussion: Read-level Data Anonymization Andre Kahles, ETH Zurich, Switzerland
16:10 Discussion & outlook Wenzhong Xiao, Stanford and Harvard Medical School, U.S.A.
16:30 Awards and Closing Julia E Vogt, ETH Zurich, Switzerland, and David P. Kreil, Boku University Vienna, Austria
16:40 Break (Grab and Go beverages)
17:00 ISCB Accomplishments by a Senior Scientist Award Keynote Bonnie Berger, Massachusetts Institute of Technology, U.S.A.

Keynotes

Rita Colwell, PhD

Distinguished University Professor, University of Maryland College Park and
Johns Hopkins University Bloomberg School of Public Health
President and Chairman, CosmosID, Inc.
Senior Advisor and Chairman Emeritus, Canon U. S. Life Sciences

TBP – Keynote

About the speaker: Dr. Rita Colwell’s interests are focused on global infectious diseases, water, and health and Dr. Colwell developed an international network to address emerging infectious diseases and water issues, including safe drinking water for both the developed and developing world, in collaboration with Safe Water Network, headquartered in New York City.
Dr. Colwell served as the 11 th Director of the National Science Foundation, 1998-2004. In her capacity as NSF Director, she served as Co-chair of the Committee on Science of the National Science and Technology Council. One of her major interests includes K-12 science and mathematics education, graduate science and engineering education, and increased participation of women and minorities in science and engineering.
Dr. Colwell served as President of the University of Maryland Biotechnology Institute and Professor of Microbiology and Biotechnology at the University Maryland. She was also a member of the National Science Board from 1984 to 1990.
Dr. Colwell has been awarded 63 honorary degrees from institutions of higher education, including her Alma Mater, Purdue University and is the recipient of the 2005 Order of the Rising Sun, Gold and Silver Star, bestowed by the Emperor of Japan, the 2006 National Medal of Science awarded by the President of the United States, the 2010 Stockholm Water Prize awarded by the King of Sweden, the 2017 Vannevar Bush Award from the National Science Foundation, the 2017 International Prize for Biology from the Japan Society for the Promotion of Science, and the 2018 Lee Kuan Yew Water Prize of Singapore. Dr. Colwell is an honorary member of the microbiological societies of the UK, Australia, France, India, Israel, Bangladesh, and the U.S. and has held several honorary professorships, including the University of Queensland, Australia. A geological site in Antarctica, Colwell Massif, has been named in recognition of her work in the Polar Regions.
Dr. Colwell has held many advisory positions in the U.S. Government, nonprofit science policy organizations, and private foundations, as well as in the international scientific research community. She is a nationally-respected scientist and educator, and has authored or co-authored 19 books and more than 800 scientific publications. She produced the award-winning film, Invisible Seas, and has served on editorial boards of numerous scientific journals.
Dr. Colwell has previously served as Chairman of the Board of Governors of the American Academy of Microbiology and also as President of the American Association for the Advancement of Science, the Washington Academy of Sciences, the American Society for Microbiology, the Sigma Xi National Science Honorary Society, the International Union of Microbiological Societies, and the American Institute of Biological Sciences (AIBS). Dr. Colwell is a member of the U.S. National Academy of Sciences, the Royal Swedish Academy of Sciences, Stockholm, the Royal Society of Canada, the Royal Irish Academy, the Bangladesh Academy of Science, the Indian Academy of Science, the American Academy of Arts and Sciences, and the American Philosophical Society.
Born in Beverly, Massachusetts, Dr. Colwell holds a B.S. in Bacteriology and an M.S. in Genetics, from Purdue University, and a Ph.D. in Oceanography from the University of Washington.

Gunnar Rätsch, PhD

Head of Biomedical Informatics at ETH Zurich, Switzerland
TBP – Keynote

About the speaker: Gunnar Rätsch leads the Biomedical Informatics group at the Institute of Machine Learning at ETH Zurich since May 2016. Before, he was an Associate Professor at Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College in New York City, where he will continue to hold adjunct positions for the coming years.
Gunnar Rätsch studied computer science and physics and obtained his Ph.D. degree in Machine Learning in 2001 at the National Institute for Data Analysis in Berlin. As a postdoctoral fellow he was at the Research School of Information Sciences and Engineering of the Australian National University in Canberra (Australia) and at the Max Planck Institute for Biological Cybernetics in Tübingen (Germany). Between 2005 and 2011 he also led a research group at the Friedrich Miescher Laboratory of the Max Planck Society in Tübingen (Germany).
His group’s research at ETH lies at the interface between methods research in machine learning & sequence analysis and relevant application areas in biology & medicine. In interdisciplinary collaborations, his group has significantly contributed to the understanding of several RNA- dependent processes including RNA splicing and translation.
Current research focuses include large-scale Machine Learning, accurate transcriptome reconstruction, identification of RNA-processing regulators, developing clinical decision support systems (analysis of electronic health records (EHR)) and developing methods and resources for international data sharing of genomic and clinical data. He is leading multiple international working groups, including the RNA analysis group of the International Cancer Genome Consortium. He is an active contributor to the Global Alliance of Genomics and Health (GA4GH), an international organization that promotes and technically supports data sharing across institutional and country boundaries. He leads the data group of the BRCA Challenge project, a driver project of GA4GH.


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PAST KEYNOTE SPEAKERS

Atul Butte, MD, PhD
Atul Butte, MD, PhD
Stanford University School of Medicine

Nikolaus Rajewsky, PhD
Nikolaus Rajewsky, PhD
Max-Delbrück-Center for Molecular Medicine

Terry Speed, PhD
Terry Speed, PhD
The Walter and Eliza Hall Institute of Medical Research

Sandrine Dupoit, PhD
Sandrine Dudoit, PhD
University of California, Berkeley

John Quackenbush, PhD
John Quackenbush, PhD
Harvard School of Public Health

Eran Segal, PhD
Eran Segal, PhD
Weizmann Institute of Science

John Storey, PhD
John Storey, PhD
Princeton University

Chris Sander, PhD
Chris Sander, PhD
Memorial Sloan Kettering Cancer Center

Temple F. Smith, PhD
Temple F. Smith, PhD
Boston University

Curtis Huttenhower, PhD
Curtis Huttenhower, PhD
Harvard School of Public Health

Christopher E. Mason, PhD
Christopher E. Mason, PhD
Weill Cornell Medicine

Lodewyk Wessels, PhD
Lodewyk Wessels, PhD
Netherlands Cancer Institute

Cesare Furlanello, PhD
Cesare Furlanello, PhD
Fondazione Bruno Kessler

IMPORTANT DATES
Extended Abstract Proposals due12 May 2019
Notification of Accepted Contributions23 May 2019
Early Registration Closes20 Jun 2019
CAMDA2019 Conference24-25 Jul 2019
ISMB/ECCB 2019 Conference21–25 Jul 2019
Full Paper Submission 24 Sep 2019
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