Evidence map›Paper›PMID 36262335›Full record

ArticleF1000Research2022

The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms.

Kimberly Walker, Divya Kalra, Rebecca Lowdon, Guangyi Chen, David Molik, Daniela C Soto, Fawaz Dabbaghie, Ahmad Al Khleifat, Medhat Mahmoud, Luis F Paulin and 49 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in F1000Research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. EvANI benchmarking workflow for evolutionary distance estimation.bioRxiv : the preprint server for biology · 2025
    Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

59 authors.

Kimberly WalkerHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0001-9686-5217
Divya KalraHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0001-6580-3785
Rebecca LowdonBayer Crop Science, Chesterfield, MO, 63017, USA.
Guangyi ChenDrug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.ORCID 0000-0001-6614-5315
David MolikTropical Crop and Commodity Protection Research Unit, Pacific Basin Agricultural Research Center, Hilo, HI, 96720, USA.
Daniela C SotoBiochemistry & Molecular Medicine, Genome Center, MIND Institute, University of California, Davis, Davis, CA, 95616, USA.ORCID 0000-0002-6292-655X
Fawaz DabbaghieDrug Bioinformatics, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Saarbrücken, Germany.
Ahmad Al KhleifatInstitute of Psychiatry, Psychology & Neuroscience, King's College London, London, UK.
Medhat MahmoudHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0002-2553-4231
Luis F PaulinHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0003-2567-3773
Muhammad Sohail RazaCAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Beijing, China.
Susanne P PfeiferCenter for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.ORCID 0000-0003-1378-2913
Daniel Paiva AgustinhoDepartment of Molecular Microbiology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA.
Elbay AliyevResearch Department, Sidra Medicine, Doha, Qatar.ORCID 0000-0002-6469-1854
Pavel AvdeyevComputational Biology Institute, The George Washington University, Washington, DC, 20052, USA.ORCID 0000-0002-7953-6259
Enrico R BarrozoDepartment of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0002-6335-4354
Sairam BeheraHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Kimberley BillingsleyMolecular Genetics Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
Li Chuin ChongBeykoz Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Beykoz, Istanbul, Turkey.ORCID 0000-0002-3574-1365
Deepak ChoubeyDepartment of Technology, Savitribai Phule Pune University, Pune, Maharashtra, India.
Wouter De CosterApplied and Translational Neurogenomics Group, VIB Center for Molecular Neurology, Antwerp, Belgium.
Yilei FuDepartment of Computer Science, Rice University, Houston, TX, USA.ORCID 0000-0002-7721-7027
Alejandro R GenerAssociation of Public Health Labs, Centers for Disease Control and Prevention, Downey, CA, USA.ORCID 0000-0001-7875-2358
Timothy HefferonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.ORCID 0000-0003-0980-1413
David Morgan HenkeDepartment Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0003-2911-2834
Wolfram HöpsEMBL Heidelberg, Genome Biology Unit, Heidelberg, Germany.
Anastasia IllarionovaGerman Center for Neurodegenerative Diseases (DZNE), Tübingen, Germany.
Michael D JochumDepartment of Obstetrics & Gynecology, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0002-2398-356X
Maria JoseCentre for Bioinformatics, Pondicherry University, Pondicherry, India.
Rupesh K KesharwaniHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.
Sree Rohit Raj KoloraUniversity of California Berkeley, Berkeley, CA, USA.ORCID 0000-0001-7839-735X
Jędrzej KubicaUniversity of Warsaw, Warsaw, Poland.ORCID 0000-0001-7037-3900
Priya LakraDepartment of Zoology, University of Delhi, Delhi, India.
Damaris LattimerUniversity of Applied Sciences Upper Austria - FH Hagenberg, Mühlkreis, Austria.ORCID 0000-0003-1534-9291
Chia-Sin LiewCenter for Biotechnology, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, USA.
Bai-Wei LoDepartment of Biology, University of Konstanz, Konstanz, Germany.
Chunhsuan LoHuman Genetics Laboratory, National Institute of Genetics, Japan, Mishima City, Japan.
Anneri LötterDepartment of Biochemistry, University of Pretoria, Pretoria, South Africa.ORCID 0000-0003-4502-7234
Sina MajidianDepartment of Computational Biology, University of Lausanne, Lausanne, Switzerland.ORCID 0000-0001-5345-6982
Suresh Kumar MendemICAR-NIVEDI, Bangalore, Karnataka, India.ORCID 0000-0003-0767-8626
Rajarshi MondalDepartment of Biotechnology, The University of Burdwan, West Bengal, India.
Hiroko OhmiyaGenetic Reagent Development Unit, Medical & Biological Laboratories Co., Ltd., Tokoyo, Japan.
Nasrin ParvinDepartment of Biotechnology, The University of Burdwan, West Bengal, India.
Carolina PeraltaMax Planck Institute for Evolutionary Biology, Plon, Germany.ORCID 0000-0002-8058-4952
Chi-Lam PoonWeill Cornell Medicine, New York, NY, USA.
Ramanandan PrabhakaranHoffmann-La Roche Limited, Regions, Diagnostics & Research (RDR), Mississauga, Canada.
Marie SaitouCenter of Integrative Genetics (CIGENE),Faculty of Biosciences, Norwegian University of Life Sciences, As, Norway.
Aditi SammiSchool of Biochemical Engineering, Indian Institute of Technology (BHU), Varanasi, Uttar Pradesh, India.
Philippe SanioUniversity of Applied Sciences Upper Austria - FH Hagenberg, Hagenberg im Mühlkreis, Austria.ORCID 0000-0002-2884-7268
Nicolae SapovalDepartment of Computer Science, Rice University, Houston, TX, USA.
Najeeb SyedResearch Department, Sidra Medicine, Doha, Qatar.
Todd TreangenDepartment of Computer Science, Rice University, Houston, TX, USA.
Gaojianyong WangMax Planck Institute for Molecular Genetics, Berlin, Germany.
Tiancheng XuDepartment of Computer Science, Rice University, Houston, TX, USA.
Jianzhi YangDepartment of Quantitative and Computational Biology,, University of Southern California, Los Angeles, CA, USA.ORCID 0000-0001-8270-5052
Shangzhe ZhangSchool of Biology, University of St Andrews, St Andrews, UK.ORCID 0000-0003-2064-4287
Weiyu ZhouDepartment of Statistical Science, George Mason University, Fairfax, Virginia, USA.
Fritz J SedlazeckHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA.ORCID 0000-0001-6040-2691
Ben BusbyDNAnexus, Mountain View, CA, USA.

Funding

Comprehensive Mechanisms in Reproductive SciencesT32HD098068 · NICHD · BAYLOR COLLEGE OF MEDICINE · PI STEPHANIE A. PANGAS · 2020 to 2026
$2.4M
Department of Health
6 · The paper itself

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.

Indexed as

COVID-19SARS-CoV-2GenomicsHumansSoftwareCancerCovid-19Hackathonk-merLong-readsNGSStructural variantsTomatoesViral integration

Identifiers

PMID36262335
PMCPMC9557141

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.