Benjamin Good

Benjamin Good

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Benjamin Good

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Applying citizen science to gene, drug and disease relationship extraction from biomedical abstracts.

Bioinformatics 2020 Feb;36(4):1226-1233

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz678DOI Listing
February 2020

Structured reviews for data and knowledge-driven research.

Database (Oxford) 2020 01;2020

Department of Integrative Structural and Computational Biology, Scripps Research, 10550 N Torrey Pines Rd. La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/database/baaa015DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7153956PMC
January 2020

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts.

PLoS Biol 2019 01 23;17(1):e3000102. Epub 2019 Jan 23.

Gladstone Institutes, San Francisco, California, United States of America.

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http://dx.plos.org/10.1371/journal.pbio.3000102
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http://dx.doi.org/10.1371/journal.pbio.3000102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6361464PMC
January 2019

ChlamBase: a curated model organism database for the Chlamydia research community.

Database (Oxford) 2019 01;2019

Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1093/database/baz091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580685PMC
January 2019

Adaptation limits ecological diversification and promotes ecological tinkering during the competition for substitutable resources.

Proc Natl Acad Sci U S A 2018 10 15;115(44):E10407-E10416. Epub 2018 Oct 15.

Department of Physics, University of California, Berkeley, CA 94720.

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http://dx.doi.org/10.1073/pnas.1807530115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6217437PMC
October 2018

Effective models and the search for quantitative principles in microbial evolution.

Curr Opin Microbiol 2018 10 6;45:203-212. Epub 2018 Dec 6.

Department of Physics, University of California, Berkeley, United States; Department of Integrative Biology, University of California, Berkeley, United States.

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http://dx.doi.org/10.1016/j.mib.2018.11.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6599682PMC
October 2018

The Effect of Strong Purifying Selection on Genetic Diversity.

Genetics 2018 08 29;209(4):1235-1278. Epub 2018 May 29.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138 and Harvard University, Cambridge, Massachusetts 02138

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http://dx.doi.org/10.1534/genetics.118.301058DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6063222PMC
August 2018

Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text.

Database (Oxford) 2016 15;2016. Epub 2016 Jun 15.

Research Programme on Biomedical Informatics (GRIB), IMIM, UPF, Barcelona, Spain and

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http://dx.doi.org/10.1093/database/baw094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4908671PMC
November 2017

The dynamics of molecular evolution over 60,000 generations.

Nature 2017 11 18;551(7678):45-50. Epub 2017 Oct 18.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138, USA.

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http://dx.doi.org/10.1038/nature24287DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5788700PMC
November 2017

A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

Database (Oxford) 2016 17;2016. Epub 2016 Apr 17.

Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, CA 92037, USA

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http://dx.doi.org/10.1093/database/baw051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4834205PMC
January 2017

Citizen Science for Mining the Biomedical Literature.

Citiz Sci 2016 31;1(2). Epub 2016 Dec 31.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://theoryandpractice.citizenscienceassociation.org/artic
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http://dx.doi.org/10.5334/cstp.56DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226017PMC
December 2016

Evolution of Mutation Rates in Rapidly Adapting Asexual Populations.

Genetics 2016 11 19;204(3):1249-1266. Epub 2016 Sep 19.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts 02138

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http://dx.doi.org/10.1534/genetics.116.193565DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5105855PMC
November 2016

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes.

Database (Oxford) 2016 28;2016. Epub 2016 Mar 28.

Department of Molecular and Experimental Medicine, the Scripps Research Institute, La Jolla, USA

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http://dx.doi.org/10.1093/database/baw028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4822648PMC
October 2016

Branch: an interactive, web-based tool for testing hypotheses and developing predictive models.

Bioinformatics 2016 07 7;32(13):2072-2074. Epub 2016 Mar 7.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/bioinformatics/btw117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920125PMC
July 2016

Crowdsourcing and mining crowd data.

Pac Symp Biocomput 2015 :267-9

National Center for Biotechnology Information (NCBI), 8600 Rockville Pike, Bethesda, MD 20894, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4376322PMC
April 2016

Microtask crowdsourcing for disease mention annotation in PubMed abstracts.

Pac Symp Biocomput 2015 :282-93

Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA, 92037, USA.

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http://psb.stanford.edu/psb-online/proceedings/psb15/good.pd
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299946PMC
April 2016

Fate of a mutation in a fluctuating environment.

Proc Natl Acad Sci U S A 2015 Sep 24;112(36):E5021-8. Epub 2015 Aug 24.

Department of Organismic and Evolutionary Biology and Faculty of Arts and Sciences Center for Systems Biology, Harvard University, Cambridge, MA 02138; Department of Physics, Harvard University, Cambridge, MA 02138

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http://dx.doi.org/10.1073/pnas.1505406112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568713PMC
September 2015

The evolutionarily stable distribution of fitness effects.

Genetics 2015 May 10;200(1):321-9. Epub 2015 Mar 10.

Department of Organismic and Evolutionary Biology and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138 Department of Physics, Harvard University, Cambridge, Massachusetts 02138

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http://dx.doi.org/10.1534/genetics.114.173815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4423373PMC
May 2015

The impact of macroscopic epistasis on long-term evolutionary dynamics.

Genetics 2015 Jan 12;199(1):177-90. Epub 2014 Nov 12.

Department of Organismic and Evolutionary Biology, Department of Physics, and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138

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http://dx.doi.org/10.1534/genetics.114.172460DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286683PMC
January 2015

Deleterious passengers in adapting populations.

Genetics 2014 Nov 5;198(3):1183-208. Epub 2014 Sep 5.

Department of Organismic and Evolutionary Biology, Department of Physics, and FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts 02138

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http://dx.doi.org/10.1534/genetics.114.170233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224160PMC
November 2014

Dizeez: an online game for human gene-disease annotation.

PLoS One 2013 7;8(8):e71171. Epub 2013 Aug 7.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, United States of America.

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https://www.plos.org/wp-content/uploads/2013/05/pone-08-08-l
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http://dx.plos.org/10.1371/journal.pone.0071171
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071171PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3737187PMC
August 2014

The cure: design and evaluation of a crowdsourcing game for gene selection for breast cancer survival prediction.

JMIR Serious Games 2014 Jul 29;2(2):e7. Epub 2014 Jul 29.

The Scripps Research Institute, Department of Molecular and Experimental Medicine, La Jolla, CA, United States.

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http://dx.doi.org/10.2196/games.3350DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4307816PMC
July 2014

Assessment of the acute psychiatric patient in the emergency department: legal cases and caveats.

West J Emerg Med 2014 May 15;15(3):312-7. Epub 2014 Apr 15.

Madigan Army Medical Center, Department of Emergency Medicine, Tacoma, Washington.

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http://dx.doi.org/10.5811/westjem.2013.8.18378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4025529PMC
May 2014

Ten simple rules for cultivating open science and collaborative R&D.

PLoS Comput Biol 2013 26;9(9):e1003244. Epub 2013 Sep 26.

Waterloo Institute for Complexity and Innovation, Waterloo, Ontario, Canada.

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http://dx.doi.org/10.1371/journal.pcbi.1003244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3784487PMC
April 2014

The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations.

Genetics 2014 Apr 10;196(4):1217-26. Epub 2014 Feb 10.

Program in Biophysics, Harvard University, Cambridge, Massachusetts 02138.

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http://dx.doi.org/10.1534/genetics.113.160069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982683PMC
April 2014

Genetic diversity in the interference selection limit.

PLoS Genet 2014 Mar 27;10(3):e1004222. Epub 2014 Mar 27.

Departments of Organismic and Evolutionary Biology and of Physics, Harvard University, Cambridge, Massachusetts, United States of America; FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3967937PMC
March 2014

Gene Wiki Reviews: marrying crowdsourcing with traditional peer review.

Gene 2013 Dec 5;531(2):125. Epub 2013 Sep 5.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.gene.2013.08.093DOI Listing
December 2013

Crowdsourcing for bioinformatics.

Bioinformatics 2013 Aug 19;29(16):1925-33. Epub 2013 Jun 19.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt333DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3722523PMC
August 2013

Fluctuations in fitness distributions and the effects of weak linked selection on sequence evolution.

Theor Popul Biol 2013 May 18;85:86-102. Epub 2013 Jan 18.

Department of Organismic and Evolutionary Biology, Department of Physics, and FAS Center for Systems Biology, Harvard University, United States.

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http://dx.doi.org/10.1016/j.tpb.2013.01.005DOI Listing
May 2013

A task-based approach for Gene Ontology evaluation.

J Biomed Semantics 2013 Apr 15;4 Suppl 1:S4. Epub 2013 Apr 15.

The Scripps Research Institute, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/2041-1480-4-S1-S4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633003PMC
April 2013

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links.

Database (Oxford) 2012 20;2012:bar060. Epub 2012 Mar 20.

The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/database/bar060DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308151PMC
June 2012

Linking genes to diseases with a SNPedia-Gene Wiki mashup.

J Biomed Semantics 2012 Apr 24;3 Suppl 1:S6. Epub 2012 Apr 24.

The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/2041-1480-3-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337266PMC
April 2012

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations.

Proc Natl Acad Sci U S A 2012 Mar 27;109(13):4950-5. Epub 2012 Feb 27.

Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.

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http://dx.doi.org/10.1073/pnas.1119910109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3323973PMC
March 2012

The Gene Wiki in 2011: community intelligence applied to human gene annotation.

Nucleic Acids Res 2012 Jan 10;40(Database issue):D1255-61. Epub 2011 Nov 10.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/nar/gkr925DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245148PMC
January 2012

Mining the Gene Wiki for functional genomic knowledge.

BMC Genomics 2011 Dec 13;12:603. Epub 2011 Dec 13.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1186/1471-2164-12-603DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3271090PMC
December 2011

Games with a scientific purpose.

Genome Biol 2011 Dec 28;12(12):135. Epub 2011 Dec 28.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1186/gb-2011-12-12-135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334605PMC
December 2011

Performance of modularity maximization in practical contexts.

Phys Rev E Stat Nonlin Soft Matter Phys 2010 Apr 15;81(4 Pt 2):046106. Epub 2010 Apr 15.

Department of Physics, Swarthmore College, Swarthmore, Pennsylvania 19081, USA and Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA.

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http://dx.doi.org/10.1103/PhysRevE.81.046106DOI Listing
April 2010

Social tagging in the life sciences: characterizing a new metadata resource for bioinformatics.

BMC Bioinformatics 2009 Sep 25;10:313. Epub 2009 Sep 25.

Heart + Lung Institute at St, Paul's Hospital, University of British Columbia, Vancouver, Canada.

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http://dx.doi.org/10.1186/1471-2105-10-313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760536PMC
September 2009

Air medical response to traumatic brain injury: a computer learning algorithm analysis.

J Trauma 2008 Apr;64(4):889-97

Divisions of Trauma, University of California, San Diego, California, USA.

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http://dx.doi.org/10.1097/TA.0b013e318148569aDOI Listing
April 2008

Current V3 genotyping algorithms are inadequate for predicting X4 co-receptor usage in clinical isolates.

AIDS 2007 Sep;21(14):F17-24

B.C. Centre for Excellence in HIV/AIDS St. Paul's Hospital, Vancouver, British Columbia, Canada.

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http://dx.doi.org/10.1097/QAD.0b013e3282ef81eaDOI Listing
September 2007

Fast, cheap and out of control: a zero curation model for ontology development.

Pac Symp Biocomput 2006 :128-39

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St. Paul's Hospital, University of British Columbia, Vancouver, British Columbia V6Z1 Y6, Canada.

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January 2007

iHOPerator: user-scripting a personalized bioinformatics Web, starting with the iHOP website.

BMC Bioinformatics 2006 Dec 15;7:534. Epub 2006 Dec 15.

The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Providence Health Care/University of British Columbia, St, Paul's Hospital, Rm, 166, 1081 Burrard St, Vancouver, British Columbia, V6Z 1Y6, Canada.

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http://dx.doi.org/10.1186/1471-2105-7-534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1764905PMC
December 2006

The Life Sciences Semantic Web is full of creeps!

Brief Bioinform 2006 Sep 9;7(3):275-86. Epub 2006 Aug 9.

James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, Vancouver, BC.

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http://dx.doi.org/10.1093/bib/bbl025DOI Listing
September 2006

Genetic attributes of cerebrospinal fluid-derived HIV-1 env.

Brain 2006 Jul 30;129(Pt 7):1872-83. Epub 2006 May 30.

University of California San Diego, Department of Medicine/NCIRE, La Jolla, CA 94121, USA.

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http://dx.doi.org/10.1093/brain/awl136DOI Listing
July 2006

Semen-specific genetic characteristics of human immunodeficiency virus type 1 env.

J Virol 2005 Feb;79(3):1734-42

University of California, San Diego, Division of Biological Sciences, 9500 Gilman Dr., MC 0679, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1128/JVI.79.3.1734-1742.2005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC544119PMC
February 2005

A new perspective on V3 phenotype prediction.

AIDS Res Hum Retroviruses 2003 Feb;19(2):145-9

University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1089/088922203762688658DOI Listing
February 2003