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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 | 'Theatrum Orbis Terrarum' of Urban Metagenomes and Anti-Microbial Resistance | 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 | Janet Piñero, 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 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. |
11:20 | ISMB/ECCB Proceeding talk: Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology | Gregor Sturm, Technical University of Munich, Germany |
12:00 | ISMB/ECCB Proceeding talk: PRECISE: A domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors | Soufiane Mourragui, The Netherlands Cancer Institute / Delft University of Technology, Netherlands |
12:40 | Lunch break | |
14:00 | Evaluation of Connectivity Map shows limited reproducibility in drug repositioning | Nathaniel Lim, The University of British Columbia, Canada |
14:40 | A systematic analysis of multiple cancer studies within a novel enhanced framework for semantic data integration | Maciej Kańduła, Boku University Vienna, Austria |
15:00 | Contest voting and summary | |
15:10 | Retrospective and Outlook: Metagenomic Forensic Challenge | Paweł P Łabaj, MCB Jagiellonian University, Poland |
15:30 | Retrospective and Discussion: Read-level Data Anonymization | Andre Kahles, ETH Zurich, Switzerland |
16:00 | 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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