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Hire Dr. Marcus C.

United States

USD 75 /hr

Biologist, Researcher, Writer. Expert in genomics, bioinformatiics, ontologies, big data, host-microbe interactions.

Profile Summary

Subject Matter Expertise

Services

Writing
Research
Consulting
Data & AI
Product Development

Writing Technical Writing

Research Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Work Experience

Biomedical Ontology Specialist (Consultant)

ProPharma Group Holdings LLC

February 2022 - Present

Bioinformatics Associate (Contractor)

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

Group 4 Biomedical Research Support Personnel

CITI Program
https://www.citiprogram.org/verify/?w145382be-45cd-4d7a-8c26-2d669852a60e-434153703415370
July 2021 - Present
Responsible Conduct of Research Refresher for Biomedical Researchers

CITI Program
https://www.citiprogram.org/verify/?wc933da0d-93ca-41b2-8aac-9811f06d03c1-43415406
July 2021 - Present

Publications

JOURNAL ARTICLE

Marcus Chibucos, Marcus C. Chibucos, Shilpa Hakre, Evelyn Y. Lam, Irina Maljkovic-Berry, Jun Hang, Luis A. Pow Sang, Elizabeth J. Bianchi, Christian Fung, Jay Gandhi, et al.(2022). Investigation of an outbreak of COVID-19 among U.S. military personnel and beneficiaries stationed in the Republic of Korea, June-July 2021 . PLOS Global Public Health. 2. (5). p. e0000236. Public Library of Science ({PLoS})

ECO: the Evidence and Conclusion Ontology, an update for 2022 @article{2021, doi = {10.1093/nar/gkab1025}, url = {https://doi.org/10.1093%2Fnar%2Fgkab1025}, year = 2021, publisher = {Oxford University Press ({OUP})}, title = {{OUP} accepted manuscript}, journal = {Nucleic Acids Research} } . Nucleic Acids Research.

Nadendla, S., Jackson, R., Munro, J., Quaglia, F., Mészáros, B., Olley, D., Hobbs, E.T., Goralski, S.M., Chibucos, M., Mungall, C.J., et al.(2022). ECO: The Evidence and Conclusion Ontology, an update for 2022 . Nucleic Acids Research. 50. (D1). p. D1515-D1521.

Maljkovic Berry, I., Hang, J., Fung, C., Yang, Y., Chibucos, M., Pollio, A., Gandhi, J., Li, T., Conte, M.A., Lidl, G.M., et al.(2022). Genomic surveillance of SARS-CoV-2 in US military compounds in Afghanistan reveals multiple introductions and outbreaks of Alpha and Delta variants . BMC Genomics. 23. (1).

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.

Vita, R., Zheng, J., Jackson, R., Dooley, D., Overton, J.A., Miller, M.A., Berrios, D.C., Scheuermann, R.H., He, Y., Mcginty, H.K., et al.(2021). Standardization of assay representation in the Ontology for Biomedical Investigations . Database. 2021.

Carbon, S., Douglass, E., Good, B.M., Unni, D.R., Harris, N.L., Mungall, C.J., Basu, S., Chisholm, R.L., Dodson, R.J., Hartline, E., et al.(2021). The Gene Ontology resource: Enriching a GOld mine . Nucleic Acids Research. 49. (D1). p. D325-D334.

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.

C. Silva, M., Chibucos, M., Munro, J.B., Daugherty, S., Coelho, M.M., 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. 10. (1).

(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.

Siegele, D.A., Labonte, S.A., Wu, P.I.-F., Chibucos, M.C., Nandendla, S., Giglio, M.G., Hu, J.C.(2019). Phenotype annotation with the ontology of microbial phenotypes (OMP) . Journal of Biomedical Semantics. 10. (1).

Giglio, M., Tauber, R., Nadendla, S., Munro, J., Olley, D., Ball, S., Mitraka, E., Schriml, L.M., Gaudet, P., Hobbs, E.T., et al.(2019). Eco, the evidence & conclusion ontology: Community standard for evidence information . Nucleic Acids Research. 47. (D1). p. D1186-D1194.

Carbon, S., Douglass, E., Dunn, N., Good, B., Harris, N.L., Lewis, S.E., Mungall, C.J., Basu, S., Chisholm, R.L., Dodson, R.J., et al.(2019). The Gene Ontology Resource: 20 years and still GOing strong . Nucleic Acids Research. 47. (D1). p. D330-D338.

Attrill, H., Gaudet, P., Huntley, R.P., Lovering, R.C., Engel, S.R., Poux, S., Van Auken, K.M., Georghiou, G., Chibucos, M.C., Berardini, T.Z., et al.(2019). Annotation of gene product function from high-throughput studies using the Gene Ontology . Database. 2019.

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.

Carbon, S., Dietze, H., Lewis, S.E., Mungall, C.J., Munoz-Torres, M.C., Basu, S., Chisholm, R.L., Dodson, R.J., Fey, P., Thomas, P.D., et al.(2017). Expansion of the gene ontology knowledgebase and resources: The gene ontology consortium . Nucleic Acids Research. 45. (D1). p. D331-D338.

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).

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})

Kiliç, S., Sagitova, D.M., Wolfish, S., Bely, B., Courtot, M., Ciufo, S., Tatusova, T., O'Donovan, C., Chibucos, M.C., Martin, M.J., et al.(2016). From data repositories to submission portals: Rethinking the role of domain-specific databases in CollecTF . Database. 2016.

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.

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 . Scientific Reports. 6.

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 .

Bandrowski, A., Brinkman, R., Brochhausen, M., Brush, M.H., Bug, B., Chibucos, M.C., Clancy, K., Courtot, M., Derom, D., Dumontier, M., et al.(2016). The Ontology for Biomedical Investigations . PLoS ONE. 11. (4).

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 . Scientific Reports. 6.

Chibucos, M.C., Soliman, S., Gebremariam, T., Lee, H., Daugherty, S., Orvis, J., Shetty, A.C., Crabtree, J., Hazen, T.H., Etienne, K.A., et al.(2016). An integrated genomic and transcriptomic survey of mucormycosis-causing fungi . Nature Communications. 7.

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. 2015.

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).

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 . Pathogens and Disease. 73. (5).

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.

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).

Blake, J.A., Christie, K.R., Dolan, M.E., Drabkin, H.J., Hill, D.P., Ni, L., Sitnikov, D., Burgess, S., Buza, T., Gresham, C., et al.(2015). Gene ontology consortium: Going forward . Nucleic Acids Research. 43. (D1). p. D1049-D1056.

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.

Gene Ontology Consortium(2015). Gene Ontology Consortium: going forward . Nucleic Acids Res. 43. (Database issue). p. D1049-56.

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.

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. (1).

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.

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 Microbiology. 14. (1).

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.

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. 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).

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. (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., 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. 2014.

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.

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.

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).

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 Announcements. 1. (6).

Blake, J.A., Dolan, M., Drabkin, H., Hill, D.P., Ni, L., Sitnikov, D., Bridges, S., Burgess, S., Buza, T., McCarthy, F., et al.(2013). Gene ontology annotations and resources . Nucleic Acids Research. 41. (D1).

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.

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).

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.

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 . Journal of Bacteriology. 194. (11). p. 3026-3027.

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.

Mulangi, V., Chibucos, M.C., Phuntumart, V., Morris, P.F.(2012). Kinetic and phylogenetic analysis of plant polyamine uptake transporters . Planta. 236. (4). p. 1261-1273.

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 Research. 40. (D1).

Gene Ontology Consortium(2012). The Gene Ontology: enhancements for 2011 . Nucleic Acids Res. 40. (Database issue). p. D559-64.

Blake, J.A., Dolan, M., Drabkin, H., Hill, D.P., Ni, L., Sitnikov, D., Burgess, S., Buza, T., Gresham, C., McCarthy, F., et al.(2012). The Gene Ontology: Enhancements for 2011 . Nucleic Acids Research. 40. (D1).

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. 1261-1273.

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. 1549-1551.

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.

Berardini, T.Z., Li, D., Huala, E., Bridges, S., Burgess, S., McCarthy, F., Carbon, S., Lewis, S.E., Mungall, C.J., Abdulla, A., et al.(2010). The Gene Ontology in 2010: Extensions and refinements . Nucleic Acids Research. 38. (SUPPL.1).

Gene Ontology Consortium(2010). The Gene Ontology in 2010: extensions and refinements . Nucleic Acids Res. 38. (Database issue). p. D331-5.

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 . Microbiology and Molecular Biology Reviews. 74. (4). p. 479-503.

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.

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., Tseng, T.-T., Setubal, J.C.(2009). Describing commonalities in microbial effector delivery using the Gene Ontology . Trends in Microbiology. 17. (7). p. 312-319.

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.(2009). The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community . Nucleic Acids Research. 38. (SUPPL.1).

Haas, B.J., Kamoun, S., Zody, M.C., Jiang, R.H.Y., 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. 393-398.

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).

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).

Chibucos, M.C., Tseng, T.-T., Setubal, J.C.(2009). Describing commonalities in microbial effector delivery using the Gene Ontology . Trends in Microbiology. 17. (7). p. 312-319.

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.

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.

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 . Molecular Plant-Microbe Interactions. 20. (7). p. 781-793.

Chibucos, M.C., Morris, P.F.(2006). Levels of polyamines and kinetic characterization of their uptake in the soybean pathogen Phytophthora sojae . Applied and Environmental Microbiology. 72. (5). p. 3350-3356.

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.

CONFERENCE PAPER

Tauber, R., Munro, J.B., Nadendla, S., Chibucos, M.C., Giglio, M.(2018). Current development in the Evidence and Conclusion Ontology (ECO) . CEUR Workshop Proceedings. 2285.

Tauber R, Munro JB, Nadendla S, Chunara B, Chibucos MC, and Giglio M. (2018) Current development in the Evidence and Conclusion Ontology (ECO), in Proc. of the 9th International Conference on Biological Ontology (ICBO 2018), August 7-10, 2018, Corvalis, Oregon, USA. Edited by: Pankaj Jaiswal, Laurel Cooper, Melissa A. Haendel, Christopher J. Mungall .

Tauber R and Chibucos MC. (2017) Logical axiomatization of the Evidence & Conclusion Ontology (ECO) by integrating external ontology classes, in Proc. of the 8th International Conference on Biomedical Ontology (ICBO 2017), September 13-15, 2017, Newcastle-upon-Tyne, United Kingdom. Edited by: Matthew Horridge, Phillip Lord, Jennifer D. Warrender .

Tauber, R., Chibucos, M.C.(2017). Logical axiomatization of the evidence and conclusion ontology (ECO) by integrating external ontology classes . CEUR Workshop Proceedings. 2137.

Chibucos, Marcus C., Nadendla, Suvarna, Munro , James B., Mitraka, Elvira, Olley, Dustin, Vasilevsky, Nicole A., Brush, Matthew H., Giglio, Michelle(2016). Supporting database annotations and beyond with the Evidence and Conclusion Ontology (ECO) . ICBO-BioCreative 2016: Food, Nutrition, Health and Environment for the 9 Billion. 1747.

Chibucos, M.C., Nadendla, S., Munro, J.B., Mitraka, E., Olley, D., Vasilevsky, N.A., Brush, M.H., Giglio, M.(2016). Supporting database annotations and beyond with the Evidence & Conclusion Ontology (ECO) . CEUR Workshop Proceedings. 1747.

Chibucos, M., Zweifel, A., Siegele, D., Uetz, P., Giglio, M., Hu, J.(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 . CEUR Workshop Proceedings. 833. p. 237-239.

BOOK CHAPTER

Chibucos, M.C., Siegele, D.A., Hu, J.C., Giglio, M.(2017). The evidence and conclusion ontology (ECO): Supporting GO annotations . Methods in Molecular Biology. 1446. p. 245-259.

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 .

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University of Maryland School of Medicine

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Virginia Polytechnic Institute and State University

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