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Hire Dr. Marcus Chibucos
United States
USD 50 /hr

Genome biologist, writer, ontologist. Experienced with writing, collaborating, bioinformatics, and laboratory.

Profile Summary
Subject Matter Expertise
Services
Work Experience

Bioinformatics Associate

Cherokee Nation Technology Solutions

October 2020 - October 2021

Lead Bioinformatics Analyst

University of Maryland School of Medicine

November 2017 - February 2020

Research Associate

University of Maryland School of Medicine

January 2012 - September 2017

Bioinformatics Analyst II

University of Maryland School of Medicine

2008 - 2011

Postdoctoral Associate

Virginia Polytechnic Institute and State University

2006 - 2008

Education

Ph.D. (Biological Sciences)

Bowling Green State University

September 1997 - December 2004

B.A. (Biology and Philosophy)

Knox College

September 1991 - June 1995

Certifications
  • Certification details not provided.
Publications
JOURNAL ARTICLE
Vita R, Zheng J, Jackson R, Dooley D, Overton JA, Miller MA, Berrios DC, Scheuermann RH, He Y, McGinty HK, et al.(2021). Standardization of assay representation in the Ontology for Biomedical Investigations . Database : the journal of biological databases and curation.
Gene Ontology Consortium (2020). The Gene Ontology resource: enriching a GOld mine . Nucleic acids research.
C Silva M, Chibucos M, Munro JB, Daugherty S, Coelho MM, C Silva J(2020). Signature of adaptive evolution in olfactory receptor genes in Cory's Shearwater supports molecular basis for smell in procellariiform seabirds . Scientific reports.
(2019). Phenotype annotation with the ontology of microbial phenotypes (OMP) . Journal of biomedical semantics.
Annotation of gene product function from high-throughput studies using the Gene Ontology @article{2019, doi = {10.1093/database/baz007}, url = {https://doi.org/10.1093%2Fdatabase%2Fbaz007}, year = 2019, publisher = {Oxford University Press ({OUP})}, title = {{OUP} accepted manuscript}, journal = {Database} } . Database.
Michelle Giglio, Rebecca Tauber, Suvarna Nadendla, James Munro, Dustin Olley, Shoshannah Ball, Elvira Mitraka, Lynn M Schriml, Pascale Gaudet, Elizabeth T Hobbs, et al.(2018). ECO, the Evidence & Conclusion Ontology: community standard for evidence information . Nucleic Acids Research. Oxford University Press ({OUP})
The Gene Ontology Resource: 20 years and still GOing strong @article{2018,doi = {10.1093/nar/gky1055},url = {https://doi.org/10.1093%2Fnar%2Fgky1055},year = 2018,month = {nov},publisher = {Oxford University Press ({OUP})},author = {and S Carbon and E Douglass and N Dunn and B Good and N L Harris and S E Lewis and C J Mungall and S Basu and R L Chisholm and R J Dodson and E Hartline and P Fey and P D Thomas and L P Albou and D Ebert and M J Kesling and H Mi and A Muruganujan and X Huang and S Poudel and T Mushayahama and J C Hu and S A LaBonte and D A Siegele and G Antonazzo and H Attrill and N H Brown and S Fexova and P Garapati and T E M Jones and S J Marygold and G H Millburn and A J Rey and V Trovisco and G dos Santos and D B Emmert and K Falls and P Zhou and J L Goodman and V B Strelets and J Thurmond and M Courtot and D Osumi-Sutherland and H Parkinson and P Roncaglia and M L Acencio and M Kuiper and A L{\ae}greid and C Logie and R C Lovering and R P Huntley and P Denny and N H Campbell and B Kramarz and V Acquaah and S H Ahmad and H Chen and J H Rawson and M C Chibucos and M Giglio and S Nadendla and R Tauber and M J Duesbury and N Del-Toro and B H M Meldal and L Perfetto and P Porras and S Orchard and A Shrivastava and Z Xie and H Y Chang and R D Finn and A L Mitchell and N D Rawlings and L Richardson and A Sangrador-Vegas and J A Blake and K R Christie and M E Dolan and H J Drabkin and D P Hill and L Ni and D Sitnikov and M A Harris and S G Oliver and K Rutherford and V Wood and J Bahler and A Lock and E R Bolton and J De Pons and M Dwinell and G T Hayman and S J F Laulederkind and M Shimoyama and M Tutaj and S-J Wang and P D'Eustachio and L Matthews and J P Balhoff and S A Aleksander and G Binkley and B L Dunn and J M Cherry and S R Engel and F Gondwe and K Karra and K A MacPherson and S R Miyasato and R S Nash and P C Ng and T K Sheppard and A Shrivatsav VP and M Simison and M S Skrzypek and S Weng and E D Wong and M Feuermann and P Gaudet and E Bakker and T Z Berardini and L Reiser and S Subramaniam and E Huala and C Arighi and A Auchincloss and K Axelsen and G Argoud-Puy and A Bateman and B Bely and M-C Blatter and E Boutet and L Breuza and A Bridge and R Britto and H Bye-A-Jee and C Casals-Casas and E Coudert and A Estreicher and L Famiglietti and P Garmiri and G Georghiou and A Gos and N Gruaz-Gumowski and E Hatton-Ellis and U Hinz and C Hulo and A Ignatchenko and F Jungo and G Keller and K Laiho and P Lemercier and D Lieberherr and Y Lussi and A MacDougall and M Magrane and M J Martin and P Masson and D A Natale and N Hyka-Nouspikel and I Pedruzzi and K Pichler and S Poux and C Rivoire and M Rodr{\'{\i}}guez-L{\'{o}}pez and T Sawford and E Speretta and A Shypitsyna and A Stutz and S Sundaram and M Tognolli and N Tyagi and K Warner and R Zaru and C Wu and A D Diehl and J Chan and J Cho and S Gao and C Grove and M C Harrison and K Howe and R Lee and J Mendel and H-M Muller and D Raciti and K Van Auken and M Berriman and L Stein and P W Sternberg and D Howe and S Toro and M Westerfield},title = {The Gene Ontology Resource: 20 years and still {GOing} strong},journal = {Nucleic Acids Research}} . Nucleic Acids Research.
The Gene Ontology Consortium(2017). Expansion of the Gene Ontology knowledgebase and resources . Nucleic Acids Res. 45. (D1). p. D331-D338.
Bradford, L.L., Chibucos, M.C., Ma, B., Bruno, V., Ravel, J.(2017). Vaginal Candida spp. genomes from women with vulvovaginal candidiasis . Pathogens and Disease. 75. (6).
Marcus C. Chibucos, Sameh Soliman, Teclegiorgis Gebremariam, Hongkyu Lee, Sean Daugherty, Joshua Orvis, Amol C. Shetty, Jonathan Crabtree, Tracy H. Hazen, Kizee A. Etienne, et al.(2016). An integrated genomic and transcriptomic survey of mucormycosis-causing fungi . Nature Communications. 7. (1). Springer Nature
Ifeonu, O.O., Chibucos, M.C., Orvis, J., Su, Q., Elwin, K., Guo, F., Zhang, H., Xiao, L., Sun, M., Chalmers, R.M., et al.(2016). 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 . Pathogens and Disease. 74. (7).
Silva, J. C., Cornillot, E., McCracken, C., Usmani-Brown, S., Dwivedi, A., Ifeonu, O. O., Crabtree, J., Gotia, H. T., Virji, A. Z., Reynes, C., et al.(2016). Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions . Sci Rep. 6. p. 35284.
Sefa Kılıç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely, Mélanie Courtot, Stacy Ciufo, Tatiana Tatusova, Claire O’Donovan, Marcus C. Chibucos, Maria J. Martin, et al.(2016). From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF . Database. 2016. p. baw055. Oxford University Press ({OUP})
Bandrowski A, Brinkman R, Brochhausen M, Brush MH, Bug B, Chibucos MC, Clancy K, Courtot M, Derom D, Dumontier M, Fan L, Fostel J, Fragoso G, Gibson F, Gonzalez-Beltran A, Haendel MA, He Y, Heiskanen M, Hernandez-Boussard T, Jensen M, PloS one, 2016, vol. 11, no. 4, pp. e0154556, 2016 .
Gene Ontology Consortium(2015). Gene Ontology Consortium: going forward . Nucleic Acids Res. 43. (Database issue). p. D1049-56.
Shelburne, S. A., Ajami, N. J., Chibucos, M. C., Beird, H. C., Tarrand, J., Galloway-Peña, J., Albert, N., Chemaly, R. F., Ghantoji, S. S., Marsh, L., et al.(2015). Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis . PLoS One. 10. (11). p. e0139851.
Bastian, F. B., Chibucos, M. C., Gaudet, P., Giglio, M., Holliday, G. L., Huang, H., Lewis, S. E., Niknejad, A., Orchard, S., Poux, S., et al.(2015). The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations . Database (Oxford). 2015. p. bav043.
Chibucos, M. C., Etienne, K. A., Orvis, J., Lee, H., Daugherty, S., Lockhart, S. R., Ibrahim, A. S., Bruno, V. M.(2015). The genome sequence of four isolates from the family Lichtheimiaceae . Pathog Dis. 73. (5).
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.
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.
Tallon, L. J., Liu, X., Bennuru, S., Chibucos, M. C., Godinez, A., Ott, S., Zhao, X., Sadzewicz, L., Fraser, C. M., Nutman, T. B., et al.(2014). Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis . BMC Genomics. 15. p. 788.
Chibucos, M. C., Mungall, C. J., Balakrishnan, R., Christie, K. R., Huntley, R. P., White, O., Blake, J. A., Lewis, S. E., Giglio, M.(2014). Standardized description of scientific evidence using the Evidence Ontology (ECO) . Database (Oxford). 2014.
Etienne, K.A., Chibucos, M.C., Su, Q., Orvis, J., Daugherty, S., Ott, S., Sengamalay, N.A., Fraser, C.M., Lockhart, S.R., Bruno, V.M.(2014). Draft genome sequence of Mortierella alpina isolate CDC-B6842 . Genome Announcements. 2. (1).
Ioannidis, P., Lu, Y., Kumar, N., Creasy, T., Daugherty, S., Chibucos, M. C., Orvis, J., Shetty, A., Ott, S., Flowers, M., et al.(2014). Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys . BMC Genomics. 15. p. 738.
Chibucos, M. C., Zweifel, A. E., Herrera, J. C., Meza, W., Eslamfam, S., Uetz, P., Siegele, D. A., Hu, J. C., Giglio, M. G.(2014). An ontology for microbial phenotypes . BMC Microbiol. 14. (1). p. 294.
Blake, J. A., Dolan, M., Drabkin, H., Hill, D. P., Li, N., Sitnikov, D., Bridges, S., Burgess, S., Buza, T., McCarthy, F., et al.(2013). Gene Ontology annotations and resources . Nucleic Acids Res. 41. (Database issue). p. D530-5.
Chibucos, M. C., 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 Announc. 1. (6).
Humphrys, M. S., Creasy, T., Sun, Y., Shetty, A. C., Chibucos, M. C., Drabek, E. F., Fraser, C. M., Farooq, U., Sengamalay, N., Ott, S., et al.(2013). Simultaneous transcriptional profiling of bacteria and their host cells . PLoS One. 8. (12). p. e80597.
Hazen, T. H., Sahl, J. W., Redman, J. C., Morris, C. R., Daugherty, S. C., Chibucos, M. C., Sengamalay, N. A., Fraser-Liggett, C. M., Steinsland, H., Whittam, T. S., et al.(2012). Draft genome sequences of the diarrheagenic Escherichia coli collection . J Bacteriol. 194. (11). p. 3026-7.
Gene Ontology Consortium(2012). The Gene Ontology: enhancements for 2011 . Nucleic Acids Res. 40. (Database issue). p. D559-64.
Arnaud, M. B., Cerqueira, G. C., Inglis, D. O., Skrzypek, M. S., Binkley, J., Chibucos, M. C., Crabtree, J., Howarth, C., Orvis, J., Shah, P., et al.(2012). The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources . Nucleic Acids Res. 40. (Database issue). p. D653-9.
Mulangi, V., Chibucos, M. C., Phuntumart, V., Morris, P. F.(2012). Kinetic and phylogenetic analysis of plant polyamine uptake transporters . Planta. 236. (4). p. 1261-73.
Torto-Alalibo, T., Collmer, C. W., Gwinn-Giglio, M., Lindeberg, M., Meng, S., Chibucos, M. C., Tseng, T. T., Lomax, J., Biehl, B., Ireland, A., et al.(2010). Unifying themes in microbial associations with animal and plant hosts described using the gene ontology . Microbiol Mol Biol Rev. 74. (4). p. 479-503.
Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E., Thines, M., Ah-Fong, A., Anderson, R., Badejoko, W., et al.(2010). Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome . Science. 330. (6010). p. 1549-51.
Arnaud, M. B., Chibucos, M. C., Costanzo, M. C., Crabtree, J., Inglis, D. O., Lotia, A., Orvis, J., Shah, P., Skrzypek, M. S., Binkley, G., et al.(2010). The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community . Nucleic Acids Res. 38. (Database issue). p. D420-7.
Gene Ontology Consortium(2010). The Gene Ontology in 2010: extensions and refinements . Nucleic Acids Res. 38. (Database issue). p. D331-5.
Marcus Chibucos, Michelle Giglio, Chris Mungall, Peter Uetz, Lanlan Yin, Johannes Goll, Deborah Siegele, James Hu(2009). Development of an Ontology of Microbial Phenotypes (OMP) . Nature Precedings. Nature Publishing Group
Chibucos, M.C., Tyler, B.M.(2009). Common themes in nutrient acquisition by plant symbiotic microbes, described by the Gene Ontology . BMC microbiology. 9 Suppl 1.
Chibucos, M. C., Tseng, T. T., Setubal, J. C.(2009). Describing commonalities in microbial effector delivery using the Gene Ontology . Trends Microbiol. 17. (7). p. 312-9.
Chibucos, M.C., Collmer, C.W., Torto-Alalibo, T., Gwinn-Giglio, M., Lindeberg, M., Li, D., Tyler, B.M.(2009). Programmed cell death in host-symbiont associations, viewed through the Gene Ontology . BMC Microbiology. 9. (SUPPL. 1).
Haas, B. J., Kamoun, S., Zody, M. C., Jiang, R. H., Handsaker, R. E., Cano, L. M., Grabherr, M., Kodira, C. D., Raffaele, S., Torto-Alalibo, T., et al.(2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans . Nature. 461. (7262). p. 393-8.
Meng, S., Torto-Alalibo, T., Chibucos, M.C., Tyler, B.M., Dean, R.A.(2009). Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms . BMC Microbiology. 9. (SUPPL. 1).
Torto-Alalibo, T. A., Tripathy, S., Smith, B. M., Arredondo, F. D., Zhou, L., Li, H., Chibucos, M. C., Qutob, D., Gijzen, M., Mao, C., et al.(2007). Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection . Mol Plant Microbe Interact. 20. (7). p. 781-93.
Chibucos, M. C., Morris, P. F.(2006). Levels of polyamines and kinetic characterization of their uptake in the soybean pathogen Phytophthora sojae . Appl Environ Microbiol. 72. (5). p. 3350-6.
OTHER
Marcus C. Chibucos, Deborah A. Siegele, James C. Hu, Michelle Giglio(2016). The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations . The Gene Ontology Handbook. p. 245--259. Springer New York
CONFERENCE POSTER
Marcus Chibucos and Michelle Giglio and Chris Mungall and Peter Uetz and Lanlan Yin and Johannes Goll and Deborah Siegele and Marcus Chibucos and James Hu(2009). Development of an Ontology of Microbial Phenotypes (OMP) . Nature Precedings. Nature Publishing Group
Chibucos MC (2000) Reproductive output differences as a function of population size in the oak savanna perennial plant Lupinus perennis. Ohio Journal of Science. 100(1):7-44 .
CONFERENCE ABSTRACT
Collmer, CW and Torto-Alalibo, T and Lindeberg, M and Chibucos, M and Gwinn-Giglio, M and Biehl, B and Ireland, A and Lomax, J and Bird, D and Collmer, A and others(2008). Using the universal language of Gene Ontology to annotate gene products involved in the interactions between microbes and their hosts . Phytopathology. 98. (6). p. S40--S41.
Chibucos, M.C., & Morris, P.F. (2003). Polyamines in Phytophthora sojae-soybean interactions. Fungal Genetics Newsletter, 50(Supplement), abstract #38 .