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Marcus C Chibucos
 

Marcus C Chibucos Ph.D.

Academic Title: Research Associate
Primary Appointment: Microbiology and Immunology
mchibucos@som.umaryland.edu
Location: BIO PARK II, 549
Phone: 410-706-0885

Personal History:

Dr. Chibucos received his B.A. in Biology & Philosophy from Knox College in Galesburg, Illinois and his Ph.D. in Biological Sciences from Bowling Green State University in Ohio, where he studied enzyme kinetics of plant pathogenic oomycetes. During his two and a half years as a Postdoctoral Associate at the Virginia Bioinformatics Institute in Blacksburg, Virginia he developed the Gene Ontology to describe host-microbe interactions and did comparative genomics of plant pathogens. In 2008 he joined the staff of the Institute for Genome Sciences at the University of Maryland School of Medicine as a Bioinformatics Analyst. He became a Research Associate within the Department of Microbiology & Immunology in 2012.

Research Interests:

His research at the University of Maryland involves genome annotation, comparative genomics, and transcriptomics of a wide range of animal and plant pathogens. Dr. Chibucos has structurally and functionally annotated the genomes of bacteria, fungi, apicomplexans, and oomycetes. He conducts both primary research into the function and structure of genes involved in microbial pathogenesis, primarily by pathogenic fungi, as well developing community resources to make possible such research by others.

Dr. Chibucos develops biomedical ontologies and annotation methods to facilitate biological research. He has worked on the Gene Ontology and the Ontology for Biomedical Investigations, and is currently lead developer of the Evidence Ontology and Ontology of Microbial Phenotypes.


Publications:

Chibucos MC and Morris PF. (2006) Levels of polyamines and kinetic characterization of their uptake in the soybean pathogen Phytophthora sojae. Applied and Environmental Microbiology. 72(5): 3350-3356.

Torto-Alalibo TA, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H, Chibucos MC, Qutob D, Gijzen M, Mao C, Sobral BWS, Waugh ME, Mitchell TK, Dean RA, and Tyler BM. (2007) Expressed sequence tags from Phytophthora sojae reveal genes specific to development and infection. Molecular Plant-Microbe Interactions. 20(7): 781-793.

Chibucos MC, Collmer C, Torto-Alalibo T, Gwinn-Giglio M, Lindberg M, Li D, and Tyler BM. (2009) Programmed cell death in host-symbiont associations, viewed through the Gene Ontology. BMC Microbiology. 9(Suppl 1):S5.

Chibucos MC and Tyler BM. (2009) Common themes in nutrient acquisition by plant symbiotic microbes, described by the Gene Ontology. BMC Microbiology. 9(Suppl 1):S6.

Meng S, Torto-Alalibo T, Chibucos MC, Tyler BM, and Dean R. (2009) Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms. BMC Microbiology. 9(Suppl 1): S7.

Chibucos MC, Tseng T-T, and Setubal JC. (2009) Describing commonalities in microbial effector delivery using the Gene Ontology. Trends in Microbiology. 17(7): 312-319. Epub 2009 Jul. 1.

Giglio M, Mungall C, Uetz P, Yin L, Goll J, Siegele D, Chibucos M, Hu J. (2009) Development of an Ontology of Microbial Phenotypes (OMP). Nature Precedings.

Haas BJ, Kamoun S, Zody MC, et al. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 461: 393-398 (17 September 2009).

Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, and Sherlock G. (2010) The Aspergillus Genome Database (AspGD), a curated comparative genomics resource for gene, protein, and sequence information for the Aspergillus research community. Nucleic Acids Research. 38(Database issue):D420-427. Epub 2009 Sep 22.

Gene Ontology Consortium (Berardini TZ, Li D, Huala E, et al.). (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Research. 38(Database issue):D331-335. Epub 2009 Nov 17.

Torto-Alalibo T, Collmer CW, Gwinn-Giglio M, Lindeberg M, Meng S, Chibucos MC, Tseng TT, Lomax J, Biehl B, Ireland A, Bird D, Dean RA, Glasner JD, Perna N, Setubal JC, Collmer A, and Tyler BM. (2010) Unifying themes in microbial associations with animal and plant hosts described using the Gene Ontology. Microbiology and Molecular Biology Reviews. 74(4):479-503.

Baxter L, Tripathy S, Ishaque N, Boot N, Cabral A, Kemen E, Thines M, Ah-Fong A, Anderson R, Badejoko W, Bittner-Eddy P, Boore JL, Chibucos MC, Coates M, Dehal P, Delehaunty K, Dong S, Downton P, Dumas B, Fabro G, Fronick C, Fuerstenberg SI, Fulton L, Gaulin E, Govers F, Hughes L, Humphray S, Jiang RH, Judelson H, Kamoun S, Kyung K, Meijer H, Minx P, Morris P, Nelson J, Phuntumart V, Qutob D, Rehmany A, Rougon-Cardoso A, Ryden P, Torto-Alalibo T, Studholme D, Wang Y, Win J, Wood J, Clifton SW, Rogers J, Van den Ackerveken G, Jones JD, McDowell JM, Beynon J, and Tyler BM. (2010) Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science. 330(6010):1549-1551 (December 10).

Chibucos M, Zweifel A, Siegele D, Uetz P, Giglio M, Hu JC. (2011) The Ontology of Microbial Phenotypes (OMP): A Precomposed Ontology Based on Cross Products from Multiple External Ontologies that is Used for Guiding Microbial Phenotype Annotation. In proceeding of: 2nd International Conference on Biomedical Ontology, Buffalo, NY.

Arnaud MB, Cerqueira GC, Inglis DO, Skrzypek MS, Binkley J, Chibucos MC, Crabtree J, Howarth C, Orvis J, Shah P, Wymore F, Binkley G, Miyasato SR, Simison M, Sherlock G, Wortman JR. (2012) The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Research. Advanced Access published November 12, 2011, doi:10.1093/nar/gkr875.

Gene Ontology Consortium (Blake JA, Dolan M, Drabkin H, et al.) The Gene Ontology: enhancements for 2011. (2012) Nucleic Acids Res. 40(Database issue):D559-64.

Hazen TH, Sahl JW, Redman JC, Morris CR, Daugherty SC, Chibucos MC, Sengamalay NA, Fraser-Liggett CM, Steinsland H, Whittam TS, Whittam B, Manning SD, Rasko DA. (2012) Draft genome sequences of the diarrheagenic Escherichia coli collection. J Bacteriol. 194(11):3026-7.

Mulangi V, Chibucos MC, Phuntumart V, Morris P. (2012) Kinetic and phylogenetic analysis of plant polyamine uptake transporters. Planta. Jun 19. [Epub ahead of print]: DOI 10.1007/s00425-012-1668-0.

Gene Ontology Consortium (Blake JA, et al.) (2013) Gene Ontology annotation and resources. Nucleic Acids Res. 41(Database issue):D530-5.

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengalamay N, Ott S, Shou H, Bavoil PM, Mahurkar A, Myers GSA. (2013) Simultaneous transcriptional profiling of bacteria and their host cells. PLOS ONE. Dec. 4;8(12):e80597. doi: 10.1371/journal.pone.0080597.

Chibucos MC, Crabtree J, Nagaraj S, Chaturvedi S, Chaturvedi V. (2013) Draft genome sequences of human pathogenic fungus Geomyces pannorum sensu lato and bat White Nose Syndrome pathogen Geomyces (Pseudogymnoascus) destructans. Genome Announcements. Nov./Dec.;1(6):e01045-13.

Etienne KA, Chibucos MC, Su Q, Orvis J, Daugherty S, Ott S, Sengamalay NA, Fraser CM, Lockhart SR, Bruno VM. (2014) Draft genome sequence of Mortierella alpina isolate CDC-B6842. Genome Announcements. Jan./Feb.;2(1): e01180-13.

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database. Vol. 2014: article ID bau066; doi:10.1093/database/bau075.

Ioannidis P, Lu Y, Kumar N, Creasy T, Daugherty S, Chibucos MC, Orvis J, Shetty A, Ott S, Flowers M, Sengamalay N, Tallon LJ, Pick L, Hotopp JC. (2014) Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. BMC Genomics. 15(1):738. doi:10.1186/1471-2164-15-738.

Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC. (2014) Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis. BMC Genomics. 2014 Sep 12;15(1):788.