F1000Research (May 2022)
The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms [version 1; peer review: 1 approved, 2 approved with reservations]
- Fawaz Dabbaghie,
- Divya Kalra,
- Elbay Aliyev,
- Wouter De Coster,
- Kimberley Billingsley,
- Nicolae Sapoval,
- Shangzhe Zhang,
- Gaojianyong Wang,
- Kimberly Walker,
- Deepak Choubey,
- Li Chuin Chong,
- Alejandro R. Gener,
- Yilei Fu,
- Pavel Avdeyev,
- Ben Busby,
- Daniel Paiva Agustinho,
- Sairam Behera,
- Enrico R. Barrozo,
- Luis F Paulin,
- Ahmad Al Khleifat,
- Susanne P. Pfeifer,
- Muhammad Sohail Raza,
- Guangyi Chen,
- Rebecca Lowdon,
- Daniela C. Soto,
- David Molik,
- Anneri Lötter,
- Chunhsuan Lo,
- Suresh Kumar Mendem,
- Sina Majidian,
- Damaris Lattimer,
- Priya Lakra,
- Bai-Wei Lo,
- Chia-Sin Liew,
- Rupesh K. Kesharwani,
- Maria Jose,
- Jędrzej Kubica,
- Sree Rohit Raj Kolora,
- Wolfram Höps,
- David Morgan Henke,
- Michael D. Jochum,
- Anastasia Illarionova,
- Fritz J Sedlazeck,
- Weiyu Zhou,
- Todd Treangen,
- Philippe Sanio,
- Jianzhi Yang,
- Tiancheng Xu,
- Ramanandan Prabhakaran,
- Chi-Lam Poon,
- Aditi Sammi,
- Marie Saitou,
- Hiroko Ohmiya,
- Rajarshi Mondal,
- Najeeb Syed,
- Carolina Peralta,
- Nasrin Parvin,
- Timothy Hefferon,
- Medhat Mahmoud
Affiliations
- Fawaz Dabbaghie
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
- Divya Kalra
- ORCiD
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Elbay Aliyev
- ORCiD
- Research Department, Sidra Medicine, Doha, Qatar
- Wouter De Coster
- Applied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium
- Kimberley Billingsley
- Molecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
- Nicolae Sapoval
- Department of Computer Science, Rice University, Houston, TX, USA
- Shangzhe Zhang
- ORCiD
- School of Biology, University of St Andrews, St Andrews, UK
- Gaojianyong Wang
- Max Planck Institute for Molecular Genetics, Berlin, Germany
- Kimberly Walker
- ORCiD
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Deepak Choubey
- Department of Technology, Savitribai Phule Pune University, Pune, Maharashtra, India
- Li Chuin Chong
- ORCiD
- Beykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Turkey
- Alejandro R. Gener
- ORCiD
- Association of Public Health Labs, Centers for Disease Control and Prevention, Downey, CA, USA
- Yilei Fu
- ORCiD
- Department of Computer Science, Rice University, Houston, TX, USA
- Pavel Avdeyev
- ORCiD
- Computational Biology Institute, The George Washington University, Washington, DC, 20052, USA
- Ben Busby
- DNAnexus, Mountain View, CA, USA
- Daniel Paiva Agustinho
- Department of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
- Sairam Behera
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Enrico R. Barrozo
- ORCiD
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
- Luis F Paulin
- ORCiD
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Ahmad Al Khleifat
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK
- Susanne P. Pfeifer
- ORCiD
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
- Muhammad Sohail Raza
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Beijing, China
- Guangyi Chen
- ORCiD
- Drug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany
- Rebecca Lowdon
- Bayer Crop Science, Chesterfield, MO, 63017, USA
- Daniela C. Soto
- ORCiD
- Biochemistry & Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, Davis, CA, 95616, USA
- David Molik
- Tropical Crop and Commodity Protection Research Unit, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA
- Anneri Lötter
- ORCiD
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa
- Chunhsuan Lo
- Human Genetics Laboratory, National Institute of Genetics, Japan, Mishima City, Japan
- Suresh Kumar Mendem
- ORCiD
- ICAR-NIVEDI, Bangalore, Karnataka, India
- Sina Majidian
- ORCiD
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Damaris Lattimer
- ORCiD
- University of Applied Sciences Upper Austria - FH Hagenberg, Mühlkreis, Austria
- Priya Lakra
- Department of Zoology, University of Delhi, Delhi, India
- Bai-Wei Lo
- Department of Biology, University of Konstanz, Konstanz, Germany
- Chia-Sin Liew
- Center for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA
- Rupesh K. Kesharwani
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Maria Jose
- Centre for Bioinformatics, Pondicherry University, Pondicherry, India
- Jędrzej Kubica
- ORCiD
- University of Warsaw, Warsaw, Poland
- Sree Rohit Raj Kolora
- ORCiD
- University of California Berkeley, Berkeley, CA, USA
- Wolfram Höps
- EMBL Heidelberg, Genome Biology Unit, Heidelberg, Germany
- David Morgan Henke
- ORCiD
- Department Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA
- Michael D. Jochum
- ORCiD
- Department of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA
- Anastasia Illarionova
- German Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany
- Fritz J Sedlazeck
- ORCiD
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Weiyu Zhou
- Department of Statistical Science, George Mason University, Fairfax, Virginia, USA
- Todd Treangen
- Department of Computer Science, Rice University, Houston, TX, USA
- Philippe Sanio
- ORCiD
- University of Applied Sciences Upper Austria - FH Hagenberg, Hagenberg im Mühlkreis, Austria
- Jianzhi Yang
- ORCiD
- Department of Quantitative and Computational Biology,, University of Southern California, Los Angeles, CA, USA
- Tiancheng Xu
- Department of Computer Science, Rice University, Houston, TX, USA
- Ramanandan Prabhakaran
- Hoffmann-La Roche Limited, Regions, Diagnostics & Research (RDR), Mississauga, Canada
- Chi-Lam Poon
- Weill Cornell Medicine, New York, NY, USA
- Aditi Sammi
- School of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India
- Marie Saitou
- Center of Integrative Genetics (CIGENE),Faculty of Biosciences, Norwegian University of Life Sciences, As, Norway
- Hiroko Ohmiya
- Genetic Reagent Development Unit, Medical & Biological Laboratories Co., Ltd., Tokoyo, Japan
- Rajarshi Mondal
- Department of Biotechnology, The University of Burdwan, West Bengal, India
- Najeeb Syed
- Research Department, Sidra Medicine, Doha, Qatar
- Carolina Peralta
- ORCiD
- Max Planck Institute for Evolutionary Biology, Plon, Germany
- Nasrin Parvin
- Department of Biotechnology, The University of Burdwan, West Bengal, India
- Timothy Hefferon
- ORCiD
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA
- Medhat Mahmoud
- ORCiD
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Journal volume & issue
-
Vol. 11
Abstract
In October 2021, 59 scientists from 14 countries and 13 U.S. states collaborated virtually in the Third Annual Baylor College of Medicine & DNANexus Structural Variation hackathon. The goal of the hackathon was to advance research on structural variants (SVs) by prototyping and iterating on open-source software. This led to nine hackathon projects focused on diverse genomics research interests, including various SV discovery and genotyping methods, SV sequence reconstruction, and clinically relevant structural variation, including SARS-CoV-2 variants. Repositories for the projects that participated in the hackathon are available at https://github.com/collaborativebioinformatics.
