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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, 628
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.

Haas BJ, Kamoun S, Zody MC, et al. [Chibucos MC, 53rd out of 96 authors]. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 461: 393-398. doi:10.1038/nature08358.

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 [Chibucos MC, 78th out of 130 authors]. (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Research. 38(Database issue):D331-335.

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).

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 [Chibucos M, 92nd out of 147 authors]. (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Research. 40(Database issue):D559-64. doi: 10.1093/nar/gkr1028.

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 [Chibucos MC, 85th out of 136 authors]. (2013) Gene Ontology annotations and resources. Nucleic Acids Research. 41(Database issue): D530-5. doi: 10.1093/nar/gks1050.

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.

Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG. (2014) An ontology for microbial phenotypes. BMC Microbiology. 2014 Nov 30;14(1):294. doi:10.1186/s12866-014-0294-3

Gene Ontology Consortium [Chibucos MC, 47th of 159 authors]. (2015) Gene Ontology Consortium: going forward. Nucleic Acids Research. 43(Database issue):D1049-56. doi: 10.1093/nar/gku1179.

Chibucos MC, Etienne KA, Orvis J, Lee H, Daugherty S, Lockhart SR, Ibrahim AS, Bruno VM. (2015) The genome sequence of four isolates from the family Lichtheimiaceae. Pathogens and Disease. 73(5): pii: ftv024. doi: 10.1093/femspd/ftv024.

Bastian FB, Chibucos MC, Gaudet P, Giglio M, Holliday GL, Huang H, Lewis SE, Niknejad A, Orchard S, Poux S, Skunca N, Robinson-Rechavi M. (2015) The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations. Database (Oxford). 2015:bav043. doi: 10.1093/database/bav043.

Conference Proceedings

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.

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.