“I have studied microbe-host interactions using laboratory and computational tools. I also build computational resources to facilitate biology research. I love working on plants and fungi, in particular.”


Read My Work | Continue Intro Below 

MY BIOLOGY RESEARCH

I have studied host-microbe interactions using laboratory, computational, and field approaches & tools. I love working on plants and fungi, in particular. I also build bioinformatics resources to facilitate biology research, such as ontologies & genome annotation pipelines.

When you take a look at my papers, you may notice that I have: (i) annotated & analyzed genomes from across the tree of life; (ii) frequently studied oomycetes and fungi; (iii) worked on multiple ontologies; (iv) performed both laboratory and computational research; (v) collaborated on diverse projects, large and small, sometimes as lead author and sometimes in the middle of the pack; and (vi) published the vast majority of my work as open access—so that anyone can read it and learn from it.

I hope you enjoy reading my work!

 

Marcus takes photos of natural things on his nature walks

I Love Biology


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JOURNAL ARTICLES (39)    BOOK CHAPTERS (1)          ICBO PAPERS (4)        DOCTORAL WORK (1)

 

                

Peer-Reviewed Journal Articles


 

39. Adaptive Evolution of Olfaction Genes

Silva MC, Chibucos M, Munro JB, Daugherty S, Coelho MM, and Silva JC. (2020) Signature of adaptive evolution in olfactory receptor genes in Cory’s Shearwater supports molecular basis for smell in procellariiform seabird. Scientific Reports. 10(1):543.

17 January 2020

38. Ontology of Microbial Phenotypes

Siegele DA, LaBonte SA, Wu PI, Chibucos MC, Nadendla S, Giglio MG, and Hu JC. (2019) Phenotype annotation with the Ontology of Microbial Phenotypes (OMP). Journal of Biomedical Semantics. 10(1):13.

15 July 2019

37. High-Throughput Gene Annotation

Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Tauber R, Toro S, and the Gene Ontology Consortium. (2019) Annotation of gene product function from high throughput studies using the Gene Ontology. Database (Oxford). v.2019:baz007.

1 February 2019

36. Evidence and Conclusion Ontology

Giglio MG, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, and Chibucos MC. (2018) ECO, the Evidence and Conclusion Ontology: Community Standard for Evidence Information. Nucleic Acids Research. gky1036.

8 November 2018

35. Gene Ontology Consortium

The Gene Ontology Consortium (Chibucos MC, 59th of 192 authors). (2018) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research. gky1055.

5 November 2018

34. Four Vaginal Candida Genomes (Fungi)

Bradford LL, Chibucos MC, Ma B, Bruno V, and Ravel J. (2017) Vaginal Candida spp. genomes from women with vulvovaginal candidiasis. Pathogens and Disease. 75(6):ftx061.

4 June 2017

33. Gene Ontology Consortium

The Gene Ontology Consortium (Chibucos MC, 51st of 186 authors). (2017) Expansion of the Gene Ontology knowledgebase and resources. Nucleic Acids Research. 45(D1):D331-D338.

28 November 2016

32. Genomics of Babesia microti (Apicomplexan)

Silva JC, Cornillot E, McCracken C, Usmani-Brown S, Dwivedi A, Ifeonu OO, Crabtree J, Gotia HT, Virji AZ, Reynes C, Colinge J, Kumar V, Lawres L, Pazzi JE, Pablo JV, Hung C, Brancato J, Kumari P, Orvis J, Tretina K, Chibucos M, Ott S, Sadzewicz L, Sengamalay N, Shetty AC, Su Q, Tallon L, Fraser CM, Frutos R, Molina DM, Krause PJ, and Mamoun CB. (2016) Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions. Scientific Reports. 6:35284.

18 October 2016

31. Three Genomes of Cryptosporidium (Apicomplexan)

Ifeonu OO, Chibucos M, Orvis J, Su Q, Elwin K, Guo F, Zhang H, Xiao L, Sun M, Chalmers R, Fraser CM, Zhu G, Kissinger JC, Widmer G, and Silva JC. (2016) Annotated draft genome sequences of three species of Cryptosporidium: C. meleagridis isolate UKMEL1, C. baileyi isolate TAMU-09Q1, and C. hominis isolates TU502_2012 and UKH1. Pathogens and Disease. 74(7):ftw080.

12 August 2016

30. Phylogenomics & Transcriptomics: Comparison of 41 Mucorales Genomes (Fungi)

Chibucos MC, Soliman S, Ghebremarimam T, Lee H, Daugherty S, Orvis J, Shetty AC, Crabtree J, Hazen TH, Etienne KA, Kumari P, O’Connor TD, Rasko DA, Filler SG, Fraser CM, Lockhart S, Skory CD, Ibrahim AS, and Bruno VM. (2016) An integrated genomic and transcriptomic survey of mucormycosis-causing fungi. Nature Communications. 7:12218.

22 July 2016

29. Ontology for Biomedical Investigations

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, Lin Y, Lister AL, Lord P, Malone J, Manduchi E, McGee M, Morrison N, Overton JA, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Schober D, Smith B, Soldatova LN, Stoeckert Jr. CJ, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, and Zheng J. (2016) The Ontology for Biomedical Investigations. PLoS One. 11(4):e0154556.

29 April 2016

28. CollecTF Transcription Factor Database

Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O’Donovan C, Chibucos MC, Martin MJ, and Erill I. (2016) From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. Database (Oxford). v.2016:baw055.

25 April 2016

27. Genomics of Mucor velutinosus (Fungus) in a Patient

Shelburne SA, Ajami NJ, Chibucos MC, Beird HC, Tarrand J, Galloway-Peña J, Albert N, Chemaly RF, Ghantoji SS, Marsh L, Pemmaraju N, Andreeff M, Shpall EJ, Wargo JA, Rezvani K, Alousi A, Bruno VM, Futreal PA, Petrosino JF, and Kontoyiannis DP. (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):e0139851. equal contribution

10 November 2015

26. Confidence Information Ontology

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

9 May 2015

25. Lichtheimiaceae: Four Genomes (Fungi)

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

9 April 2015

24. Ontology of Microbial Phenotypes

Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, and Giglio MG. (2014) An ontology for microbial phenotypes. BMC Microbiology. 14(1):294. corresponding

30 November 2014

23. Gene Ontology Consortium

Gene Ontology Consortium (Chibucos MC, 45th of 156 authors). (2015) Gene Ontology Consortium: going forward. Nucleic Acids Research. 43(Database issue):D1049-1056.

26 November 2014

22. Genomics of Loa loa (Filarial Nematode)

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

12 September 2014

21. Genomics of Halyomorpha halys (Insect)

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, and Dunning Hotopp JC. (2014) Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys. BMC Genomics. 15(1):738.

29 August 2014

20. Evidence and Conclusion Ontology

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, and Giglio M. (2014) Standardized description of scientific evidence using the Evidence Ontology (ECO). Database (Oxford). v.2014:bau075. corresponding

21 July 2014

19. Mortierella alpina Genome (Fungus)

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

23 January 2014

18. Bat White Nose Syndrome: Pseudogymnoascus destructans & P. pannorum Genomes (Fungi)

Chibucos MC, Crabtree J, Nagaraj S, Chaturvedi S, and 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):e01045-13. corresponding

19 December 2013

17. Host-Microbe Transcriptomics in Chlamydia trachomatis (Bacteria)

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengalamay N, Ott S, Shou H, Bavoli PM, Mahurkar A, and Myers GSA. (2013) Simultaneous transcriptional profiling of bacteria and their host cells. PLoS One. 8(12):e80597.

4 December 2013

16. Gene Ontology Consortium

Gene Ontology Consortium (Chibucos MC, 85th of 136 authors). (2013) Gene Ontology annotations and resources. Nucleic Acids Research. 41(Database issue):D530-D535.

17 November 2012

15. Polyamine Transporter Phylogeny & Kinetics (Plants)

Mulangi V, Chibucos MC, Phuntumart V, and Morris PF. (2012) Kinetic and phylogenetic analysis of plant polyamine uptake transporters. Planta. 236(4):1261-1273.

19 June 2012

14. Escherichia coli Genome Collection (Bacteria)

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, and Rasko DA. (2012) Draft genome sequences of the diarrheagenic Escherichia coli collection. Journal of Bacteriology. 194(11):3026-3027.

10 May 2012

13. Gene Ontology Consortium

Gene Ontology Consortium (Chibucos M, 92nd of 147 authors). (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Research. 40(Database issue):D559-D564.

17 November 2011

12. Aspergillus Genome Database (Fungi)

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, and Wortman JR. (2012) The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources. Nucleic Acids Research. 40(Database issue):D653-D659.

12 November 2011

11. Genome of Hyaloperonospora arabidopsidis (Oomycete)

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 RHY, 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 JDG, McDowell JM, Beynon J, and Tyler BM. (2010) Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome. Science. 330(6010):1549-1551 (10 December).

10 December 2010

10. Plant-Associated Microbe Gene Ontology

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.

30 November 2010

9. Gene Ontology Consortium

Gene Ontology Consortium (Chibucos M, 78th of 130 authors). (2010) The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Research. 38(Database issue):D331-D335.

22 October 2009

8. Aspergillus Genome Database (Fungi)

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-D427.

22 September 2009

7. Phytophthora infestans Genome (Oomycete)

Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AMV, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JIB, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AME, Jones JDG, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, MacLean D, Chibucos MC, McDonald H, McWalters J, Meijer HJG, Morgan W, Morris PF, Munro CA, O’Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJI, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PRJ, Whisson SC, Judelson HS, and Nusbaum C. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature. 461:393-398 (17 September).

9 September 2009

6. Plant-Microbe Interactions Review: Effectors

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. equal contribution

2 July 2009

5. Plant-Microbe Interactions Review: Fungi Vs. Oomycetes

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

19 February 2009

4. Plant-Microbe Interactions Review: Nutrition

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.

19 February 2009

3. Plant-Microbe Interactions Review: Programmed Cell Death

Chibucos MC, Collmer CW, 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.

19 February 2009

2. Life Stage- & Growth Condition-Specific Transcriptomics in Phytophthora sojae (Oomycete)

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.

18 June 2007

1. Phytophthora sojae: Polyamine Nutrition & Transporter Kinetics (Oomycete)

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.

May 2006

            

Peer-Reviewed Book Chapters


 

Evidence and Conclusion Ontology & Gene Ontology

Chibucos MC, Hu JC, Siegele DA, and Giglio M. (2016) The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations. In Christophe Dessimoz & Nives Škunca (eds.), The Gene Ontology Handbook, Methods in Molecular Biology, vol. 1446, pp. 245-259. New York City: Humana Press (Springer). ISBN 978-1-4939-3743-1. corresponding.

4 November 2016

            

Peer-Reviewed Conference Proceedings


 

Evidence and Conclusion Ontology

Tauber R, Munro JB, Nadendla S, Chunara B, Chibucos MC, and Giglio M. (2018) Current development in the Evidence and Conclusion Ontology (ECO), in Proceedings 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.

20 December 2018

Harmonization & Logic in Biological Ontologies

Tauber R and Chibucos MC. (2017) Logical axiomatization of the Evidence & Conclusion Ontology (ECO) by integrating external ontology classes, in Proceedings 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.

11 July 2018

Database Annotations with Evidence and Conclusion Ontology

Chibucos MC, Nadendla S, Munro JB, Mitraka E, Olley D, Vasilevsky NA, Brush MH, and Giglio M. (2016) Supporting database annotations and beyond with the Evidence & Conclusion Ontology (ECO), in Proceedings of the Joint International Conference on Biological Ontology and BioCreative, August 1-4, 2016, Corvalis, OR, USA. Edited by: Pankaj Jaiswal, Robert Hoehndorf, Cecilia Arighi, Austin Meier.

29 November 2016

Ontology of Microbial Phenotypes

Chibucos M, Zweifel A, Siegele D, Uetz P, Giglio M, and 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, in Proceedings of the 2nd International Conference on Biomedical Ontology, July 26-30, 2011, Buffalo, NY, USA. Edited by: Olivier Bodenreider, Maryann E. Martone, Alan Ruttenberg.

26 February 2012

            

My Doctoral Dissertation


 

Phytophthora sojae Transporter Kinetics & Nutrition (Oomycete)

Chibucos MC. (2004) Biogenic polyamines in the plant-pathogenic oomycete Phytophthora sojae: First functional analysis of polyamine transport. Doctoral dissertation.

December 2004

 

Thank you for reading My Journal Articles/Other Science Publications.

Marcus Chibucos, Ph.D. Professional Science, Personal Blog