Marcus Chibucos, PhD - University of Maryland, Baltimore - Lead Bioinformatics Analyst

Marcus Chibucos

PhD

University of Maryland, Baltimore

Lead Bioinformatics Analyst

Baltimore, Maryland | United States

Main Specialties: Biology, Infectious Disease, Other

Additional Specialties: Genomics, Bioinformatics, Ontology, Fungi, Plant-Microbe Interactions

ORCID logohttps://orcid.org/0000-0001-9586-0780


Top Author

Marcus Chibucos, PhD - University of Maryland, Baltimore - Lead Bioinformatics Analyst

Marcus Chibucos

PhD

Introduction

I am a biologist trained in comparative genomics, bioinformatics, plant pathology, and molecular biology. My research has addressed functional genomics of host-symbiont interactions, phylogenomics of fungi, and genome annotation of diverse taxa. I develop ontological resources to facilitate biological research and data sharing by scientists. I am an advocate for Open Science and STEM education.

Primary Affiliation: University of Maryland, Baltimore - Baltimore, Maryland , United States

Specialties:

Additional Specialties:

Research Interests:

Education

Sep 1997 - Dec 2004
Bowling Green State University
Ph.D.
Biological Sciences
Sep 1991 - Jun 1995
Knox College
B.A.
Biology and Philosophy

Publications

38Publications

1249Reads

358Profile Views

The Gene Ontology Resource: 20 years and still GOing strong.

Authors:
January 2019
35 Reads
9.112 Impact Factor

The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.

Methods Mol Biol 2017 ;1446:245-259

Department of Medicine, Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.

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http://dx.doi.org/10.1007/978-1-4939-3743-1_18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377151PMC
December 2017
6 Reads

Vaginal Candida spp. genomes from women with vulvovaginal candidiasis.

Pathog Dis 2017 08;75(6)

Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201 USA.

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http://dx.doi.org/10.1093/femspd/ftx061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5827580PMC
August 2017
29 Reads

Expansion of the Gene Ontology knowledgebase and resources.

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Nucleic Acids Res 2017 01 29;45(D1):D331-D338. Epub 2016 Nov 29.

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http://dx.doi.org/10.1093/nar/gkw1108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210579PMC
January 2017
3 Reads
9.112 Impact Factor

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

Database (Oxford) 2016 25;2016. Epub 2016 Apr 25.

Department of Biological Sciences, University of Maryland Baltimore County (UMBC), 1000 Hilltop Circle, Baltimore, MD, 21250, USA

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http://dx.doi.org/10.1093/database/baw055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4843526PMC
January 2017
21 Reads
3.372 Impact Factor

Annotated draft genome sequences of three species of Cryptosporidium: Cryptosporidium meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1 and C. hominis isolates TU502_2012 and UKH1.

Pathog Dis 2016 10 12;74(7). Epub 2016 Aug 12.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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http://dx.doi.org/10.1093/femspd/ftw080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5407061PMC
October 2016
13 Reads

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Database (Oxford) 2015 9;2015:bav043. Epub 2015 May 9.

Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley National Lab, 1 Cyclotron Rd., Berkeley, 94720 CA USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland, ETH Zurich, Department of Computer Science, Universitätstr. 19, 8092 Zürich, Switzerland, SIB Swiss Institute of Bioinformatics, Universitätstr. 6, 8092 Zürich, Switzerland and University College London, Gower St, London WC1E 6BT, UK Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland, SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland, Department of Microbiology and Immunology and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, SIB Swiss Institute of Bioinformatics, 1 Rue Michel Servet, 1211 Geneva, Switzerland, Department of Medicine and Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore MD, USA, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, CA 94158, USA, School of Information, University of South Florida, Tampa, FL, 33647, USA, Genomics Division, Lawrence Berkeley Nat

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http://dx.doi.org/10.1093/database/bav043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4425939PMC
December 2015
33 Reads
3.372 Impact Factor

The genome sequence of four isolates from the family Lichtheimiaceae.

Pathog Dis 2015 Jul 9;73(5). Epub 2015 Apr 9.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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http://dx.doi.org/10.1093/femspd/ftv024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4467520PMC
July 2015
9 Reads

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Database (Oxford) 2014 22;2014. Epub 2014 Jul 22.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USAInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1093/database/bau075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105709PMC
February 2015
15 Reads
3.372 Impact Factor

Gene Ontology Consortium: going forward.

Authors:

Nucleic Acids Res 2015 Jan 26;43(Database issue):D1049-56. Epub 2014 Nov 26.

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http://dx.doi.org/10.1093/nar/gku1179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383973PMC
January 2015
6 Reads
9.112 Impact Factor

An ontology for microbial phenotypes.

BMC Microbiol 2014 Nov 30;14:294. Epub 2014 Nov 30.

Institute for Genome Sciences and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, USA.

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http://link.springer.com/content/pdf/10.1186%2Fs12866-014-02
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http://www.biomedcentral.com/1471-2180/14/294
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http://dx.doi.org/10.1186/s12866-014-0294-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287307PMC
November 2014
72 Reads
2.729 Impact Factor

Simultaneous transcriptional profiling of bacteria and their host cells.

PLoS One 2013 4;8(12):e80597. Epub 2013 Dec 4.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080597PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3851178PMC
September 2014
12 Reads
3.234 Impact Factor

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.

BMC Genomics 2014 Sep 12;15:788. Epub 2014 Sep 12.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.

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http://dx.doi.org/10.1186/1471-2164-15-788DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175631PMC
September 2014
35 Reads
3.986 Impact Factor

Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans.

Genome Announc 2013 Dec 19;1(6). Epub 2013 Dec 19.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA.

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http://dx.doi.org/10.1128/genomeA.01045-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3868853PMC
December 2013
65 Reads

Gene Ontology annotations and resources.

January 2013
4 Reads
9.112 Impact Factor

Kinetic and phylogenetic analysis of plant polyamine uptake transporters.

Planta 2012 Oct 19;236(4):1261-73. Epub 2012 Jun 19.

Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.

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http://dx.doi.org/10.1007/s00425-012-1668-0DOI Listing
October 2012
65 Reads
3.263 Impact Factor

The Gene Ontology: enhancements for 2011.

Authors:

Nucleic Acids Res 2012 Jan 18;40(Database issue):D559-64. Epub 2011 Nov 18.

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http://dx.doi.org/10.1093/nar/gkr1028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245151PMC
January 2012
4 Reads
9.112 Impact Factor

The Gene Ontology in 2010: extensions and refinements.

Authors:

Nucleic Acids Res 2010 Jan 17;38(Database issue):D331-5. Epub 2009 Nov 17.

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http://dx.doi.org/10.1093/nar/gkp1018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808930PMC
January 2010
3 Reads
9.112 Impact Factor

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Authors:
Brian J Haas Sophien Kamoun Michael C Zody Rays H Y Jiang Robert E Handsaker Liliana M Cano Manfred Grabherr Chinnappa D Kodira Sylvain Raffaele Trudy Torto-Alalibo Tolga O Bozkurt Audrey M V Ah-Fong Lucia Alvarado Vicky L Anderson Miles R Armstrong Anna Avrova Laura Baxter Jim Beynon Petra C Boevink Stephanie R Bollmann Jorunn I B Bos Vincent Bulone Guohong Cai Cahid Cakir James C Carrington Megan Chawner Lucio Conti Stefano Costanzo Richard Ewan Noah Fahlgren Michael A Fischbach Johanna Fugelstad Eleanor M Gilroy Sante Gnerre Pamela J Green Laura J Grenville-Briggs John Griffith Niklaus J Grünwald Karolyn Horn Neil R Horner Chia-Hui Hu Edgar Huitema Dong-Hoon Jeong Alexandra M E Jones Jonathan D G Jones Richard W Jones Elinor K Karlsson Sridhara G Kunjeti Kurt Lamour Zhenyu Liu Lijun Ma Daniel Maclean Marcus C Chibucos Hayes McDonald Jessica McWalters Harold J G Meijer William Morgan Paul F Morris Carol A Munro Keith O'Neill Manuel Ospina-Giraldo Andrés Pinzón Leighton Pritchard Bernard Ramsahoye Qinghu Ren Silvia Restrepo Sourav Roy Ari Sadanandom Alon Savidor Sebastian Schornack David C Schwartz Ulrike D Schumann Ben Schwessinger Lauren Seyer Ted Sharpe Cristina Silvar Jing Song David J Studholme Sean Sykes Marco Thines Peter J I van de Vondervoort Vipaporn Phuntumart Stephan Wawra Rob Weide Joe Win Carolyn Young Shiguo Zhou William Fry Blake C Meyers Pieter van West Jean Ristaino Francine Govers Paul R J Birch Stephen C Whisson Howard S Judelson Chad Nusbaum

Nature 2009 Sep 9;461(7262):393-8. Epub 2009 Sep 9.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, USA.

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http://dx.doi.org/10.1038/nature08358DOI Listing
September 2009
75 Reads
42.351 Impact Factor

Describing commonalities in microbial effector delivery using the Gene Ontology.

Trends Microbiol 2009 Jul 1;17(7):312-9. Epub 2009 Jul 1.

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

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http://dx.doi.org/10.1016/j.tim.2009.05.001DOI Listing
July 2009
6 Reads
9.186 Impact Factor

Common themes in nutrient acquisition by plant symbiotic microbes, described by the Gene Ontology.

BMC Microbiol 2009 Feb 19;9 Suppl 1:S6. Epub 2009 Feb 19.

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

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http://dx.doi.org/10.1186/1471-2180-9-S1-S6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654666PMC
February 2009
61 Reads
2.729 Impact Factor

Programmed cell death in host-symbiont associations, viewed through the Gene Ontology.

BMC Microbiol 2009 Feb 19;9 Suppl 1:S5. Epub 2009 Feb 19.

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

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http://dx.doi.org/10.1186/1471-2180-9-S1-S5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654665PMC
February 2009
6 Reads
2.729 Impact Factor

Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms.

BMC Microbiol 2009 Feb 19;9 Suppl 1:S7. Epub 2009 Feb 19.

Center for Integrated Fungal Research, North Carolina State University, Raleigh, NC 27695, USA.

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http://dx.doi.org/10.1186/1471-2180-9-S1-S7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2654667PMC
February 2009
5 Reads
2.729 Impact Factor

Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection.

Mol Plant Microbe Interact 2007 Jul;20(7):781-93

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.

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http://dx.doi.org/10.1094/MPMI-20-7-0781DOI Listing
July 2007
14 Reads
3.944 Impact Factor

Levels of polyamines and kinetic characterization of their uptake in the soybean pathogen Phytophthora sojae.

Appl Environ Microbiol 2006 May;72(5):3350-6

Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403, USA.

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http://dx.doi.org/10.1128/AEM.72.5.3350-3356.2006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1472313PMC
May 2006
4 Reads
3.668 Impact Factor

Top co-authors

Joshua Orvis
Joshua Orvis

University of Oklahoma Health Sciences Center

8
Brett M Tyler
Brett M Tyler

Virginia Bioinformatics Institute

6
Claire M Fraser
Claire M Fraser

The Institute for Genomic Research

6
Jonathan Crabtree
Jonathan Crabtree

Institute for Genome Sciences

5
Sean Daugherty
Sean Daugherty

Institute for Genome Sciences

4
Michelle Giglio
Michelle Giglio

Institute for Genome Sciences

4
Vincent M Bruno
Vincent M Bruno

Columbia University

4
Deborah A Siegele
Deborah A Siegele

College Station

3
James C Hu
James C Hu

Texas A&M University

3