Evidence map›Paper›PMID 34618807›Full record

ArticlePLoS biology2021

A field guide to cultivating computational biology.

Gregory P Way, Casey S Greene, Piero Carninci, Benilton S Carvalho, Michiel de Hoon, Stacey D Finley, Sara J C Gosline, Kim-Anh Lȇ Cao, Jerry S H Lee, Luigi Marchionni and 6 more

Open access · goldAbstract read
In one paragraph

Article in PLoS biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.

0numbers the graph read from it
0cells of the map it votes in
13citing papers in PubMed
1.1field-weighted citation impact, top 23% of its field
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

13 citing papers in PubMed, 20 citations in OpenAlex.

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  13. Using ChatGPT as a tool for training nonprogrammers to generate genomic sequence analysis code.Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology
    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

16 authors at 14 institutions in 6 countries.

Gregory P WayImaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.ORCID 0000-0002-0503-9348
Casey S GreeneCenter for Health AI, University of Colorado School of Medicine, Aurora, Colorado, United States of America.ORCID 0000-0001-8713-9213
Piero CarninciRIKEN Center for Integrative Medical Sciences Yokohama, Kanagawa, Japan.ORCID 0000-0001-7202-7243
Benilton S CarvalhoDepartment of Statistics, Institute of Mathematics, Statistics and Scientific Computing, University of Campinas, Campinas, Brazil.ORCID 0000-0001-5122-5646
Michiel de HoonRIKEN Center for Integrative Medical Sciences Yokohama, Kanagawa, Japan.ORCID 0000-0003-0489-2352
Stacey D FinleyDepartment of Biomedical Engineering, Quantitative and Computational Biology, and Chemical Engineering & Materials Science, University of Southern California, Los Angeles, California, United States of America.ORCID 0000-0001-6901-3692
Sara J C GoslinePacific Northwest National Laboratory, Seattle, Washington, United States of America.ORCID 0000-0002-6534-4774
Kim-Anh Lȇ CaoMelbourne Integrative Genomics, School of Mathematics and Statistics, The University of Melbourne, Melbourne, Australia.ORCID 0000-0003-3923-1116
Jerry S H LeeEllison Institute and Departments of Medicine/Oncology, Chemical Engineering, and Material Sciences, University of Southern California, Los Angeles, California, United States of America.ORCID 0000-0003-1515-0952
Luigi MarchionniDepartment of Pathology and Laboratory Medicine, Weill-Cornell Medicine, New York, New York, United States of America.
Nicolas RobineComputational Biology Lab, New York Genome Center, New York, New York, United States of America.ORCID 0000-0001-5698-8183
Suzanne S SindiDepartment of Applied Mathematics, University of California Merced, Merced, California, United States of America.
Fabian J TheisInstitute of Computational Biology, Helmholtz Center Munich and Department of Mathematics, Technical University of Munich, Munich, Germany.ORCID 0000-0002-2419-1943
Jean Y H YangCharles Perkins Centre and School of Mathematics and Statistics, The University of Sydney, Australia.ORCID 0000-0002-5271-2603
Anne E CarpenterImaging Platform, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America.ORCID 0000-0003-1555-8261
Elana J FertigConvergence Institute, Departments of Oncology, Biomedical Engineering, and Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, Maryland, United States of America.ORCID 0000-0003-3204-342X
Broad Institute · USUniversity of Southern California · USCornell University · USHelmholtz Zentrum München · DEHuman Technopole · ITJohns Hopkins University · USNew York Genome Center · USPacific Northwest National Laboratory · USRIKEN Center for Integrative Medical Sciences · JPThe University of Melbourne · AUThe University of Sydney · AUUniversidade Estadual de Campinas (UNICAMP) · BRUniversity of California, Merced · USUniversity of Colorado Denver · US

Funding

Extracting rich information from biological imagesR35GM122547 · NIGMS · BROAD INSTITUTE, INC. · PI Anne E. Carpenter · 2017 to 2026
$6.2M
Network-based algorithms for target identification and drug repositioning from genetic associationsR01HG010067 · NHGRI · UNIVERSITY OF PENNSYLVANIA · PI GREENE, CASEY S · 2018 to 2022
$3.2M
Single-cell and imaging data integration software to spatially resolve the tumor microenvironmentU01CA253403 · NCI · JOHNS HOPKINS UNIVERSITY · PI FERTIG, ELANA · 2020 to 2022
$1.2M
Mathematical Strategies to Uncover the Molecular Basis of Prion Transitions R01GM126548 · NIGMS · UNIVERSITY OF CALIFORNIA, MERCED · PI SINDI, SUZANNE · 2017 to 2020
$854k
NCI NIH HHS U01 CA253403NHGRI NIH HHS R01 HG010067NIGMS NIH HHS R01 GM126548NIGMS NIH HHS R35 GM122547
6 · The paper itself

Abstract

Evolving in sync with the computation revolution over the past 30 years, computational biology has emerged as a mature scientific field. While the field has made major contributions toward improving scientific knowledge and human health, individual computational biology practitioners at various institutions often languish in career development. As optimistic biologists passionate about the future of our field, we propose solutions for both eager and reluctant individual scientists, institutions, publishers, funding agencies, and educators to fully embrace computational biology. We believe that in order to pave the way for the next generation of discoveries, we need to improve recognition for computational biologists and better align pathways of career success with pathways of scientific progress. With 10 outlined steps, we call on all adjacent fields to move away from the traditional individual, single-discipline investigator research model and embrace multidisciplinary, data-driven, team science.

Indexed as

Computational BiologyBudgetsCooperative BehaviorHumansInterdisciplinary ResearchMentoringMotivationPublicationsRewardSoftware

Identifiers

PMID34618807
PMCPMC8525744
OpenAlexW3164859410

What OpenQuestion holds

Textmetadata
LicenceCC0
Read underepoch 390

Registered trials

None linked

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.