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Items: 32

1.

Phenotype annotation with the ontology of microbial phenotypes (OMP).

Siegele DA, LaBonte SA, Wu PI, Chibucos MC, Nandendla S, Giglio MG, Hu JC.

J Biomed Semantics. 2019 Jul 15;10(1):13. doi: 10.1186/s13326-019-0205-5.

2.

Annotation of gene product function from high-throughput studies using the Gene Ontology.

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, Reiser L, Tauber R, Toro S; Gene Ontology Consortium.

Database (Oxford). 2019 Jan 1;2019. doi: 10.1093/database/baz007.

3.

ECO, the Evidence & Conclusion Ontology: community standard for evidence information.

Giglio M, 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, Chibucos MC.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1186-D1194. doi: 10.1093/nar/gky1036.

4.

Vaginal Candida spp. genomes from women with vulvovaginal candidiasis.

Bradford LL, Chibucos MC, Ma B, Bruno V, Ravel J.

Pathog Dis. 2017 Aug 31;75(6). doi: 10.1093/femspd/ftx061.

5.

The Evidence and Conclusion Ontology (ECO): Supporting GO Annotations.

Chibucos MC, Siegele DA, Hu JC, Giglio M.

Methods Mol Biol. 2017;1446:245-259.

6.

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.

Ifeonu OO, Chibucos MC, Orvis J, Su Q, Elwin K, Guo F, Zhang H, Xiao L, Sun M, Chalmers RM, Fraser CM, Zhu G, Kissinger JC, Widmer G, Silva JC.

Pathog Dis. 2016 Oct;74(7). pii: ftw080. Epub 2016 Aug 12.

7.

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi.

Chibucos MC, Soliman S, Gebremariam 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 SR, Skory CD, Ibrahim AS, Bruno VM.

Nat Commun. 2016 Jul 22;7:12218. doi: 10.1038/ncomms12218.

8.

The 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 CJ Jr, Taylor CF, Torniai C, Turner JA, Vita R, Whetzel PL, Zheng J.

PLoS One. 2016 Apr 29;11(4):e0154556. doi: 10.1371/journal.pone.0154556. eCollection 2016.

9.

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

Kılıç S, Sagitova DM, Wolfish S, Bely B, Courtot M, Ciufo S, Tatusova T, O'Donovan C, Chibucos MC, Martin MJ, Erill I.

Database (Oxford). 2016 Apr 25;2016. pii: baw055. doi: 10.1093/database/baw055. Print 2016.

10.

Implementation of a Pan-Genomic Approach to Investigate Holobiont-Infecting Microbe Interaction: A Case Report of a Leukemic Patient with Invasive Mucormycosis.

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, Kontoyiannis DP.

PLoS One. 2015 Nov 10;10(11):e0139851. doi: 10.1371/journal.pone.0139851. eCollection 2015.

11.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

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.

Database (Oxford). 2015 May 9;2015:bav043. doi: 10.1093/database/bav043. Print 2015.

12.

The genome sequence of four isolates from the family Lichtheimiaceae.

Chibucos MC, Etienne KA, Orvis J, Lee H, Daugherty S, Lockhart SR, Ibrahim AS, Bruno VM.

Pathog Dis. 2015 Jul;73(5). pii: ftv024. doi: 10.1093/femspd/ftv024. Epub 2015 Apr 9.

13.

An ontology for microbial phenotypes.

Chibucos MC, Zweifel AE, Herrera JC, Meza W, Eslamfam S, Uetz P, Siegele DA, Hu JC, Giglio MG.

BMC Microbiol. 2014 Nov 30;14:294. doi: 10.1186/s12866-014-0294-3.

14.

Single molecule sequencing and genome assembly of a clinical specimen of Loa loa, the causative agent of loiasis.

Tallon LJ, Liu X, Bennuru S, Chibucos MC, Godinez A, Ott S, Zhao X, Sadzewicz L, Fraser CM, Nutman TB, Dunning Hotopp JC.

BMC Genomics. 2014 Sep 12;15:788. doi: 10.1186/1471-2164-15-788.

15.

Rapid transcriptome sequencing of an invasive pest, the brown marmorated stink bug Halyomorpha halys.

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, Dunning Hotopp JC.

BMC Genomics. 2014 Aug 29;15:738. doi: 10.1186/1471-2164-15-738.

16.

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M.

Database (Oxford). 2014 Jul 22;2014. pii: bau075. doi: 10.1093/database/bau075. Print 2014.

17.

Draft Genome Sequence of Mortierella alpina Isolate CDC-B6842.

Etienne KA, Chibucos MC, Su Q, Orvis J, Daugherty S, Ott S, Sengamalay NA, Fraser CM, Lockhart SR, Bruno VM.

Genome Announc. 2014 Jan 23;2(1). pii: e01180-13. doi: 10.1128/genomeA.01180-13.

18.

Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans.

Chibucos MC, Crabtree J, Nagaraj S, Chaturvedi S, Chaturvedi V.

Genome Announc. 2013 Dec 19;1(6). pii: e01045-13. doi: 10.1128/genomeA.01045-13.

19.

Simultaneous transcriptional profiling of bacteria and their host cells.

Humphrys MS, Creasy T, Sun Y, Shetty AC, Chibucos MC, Drabek EF, Fraser CM, Farooq U, Sengamalay N, Ott S, Shou H, Bavoil PM, Mahurkar A, Myers GS.

PLoS One. 2013 Dec 4;8(12):e80597. doi: 10.1371/journal.pone.0080597. eCollection 2013.

20.

Kinetic and phylogenetic analysis of plant polyamine uptake transporters.

Mulangi V, Chibucos MC, Phuntumart V, Morris PF.

Planta. 2012 Oct;236(4):1261-73. Epub 2012 Jun 19.

PMID:
22711282
21.

Draft genome sequences of the diarrheagenic Escherichia coli collection.

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.

J Bacteriol. 2012 Jun;194(11):3026-7. doi: 10.1128/JB.00426-12.

22.

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources.

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.

Nucleic Acids Res. 2012 Jan;40(Database issue):D653-9. doi: 10.1093/nar/gkr875. Epub 2011 Nov 12.

23.

Signatures of adaptation to obligate biotrophy in the Hyaloperonospora arabidopsidis genome.

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, Tyler BM.

Science. 2010 Dec 10;330(6010):1549-1551. doi: 10.1126/science.1195203.

24.

Unifying themes in microbial associations with animal and plant hosts described using the 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, Tyler BM.

Microbiol Mol Biol Rev. 2010 Dec;74(4):479-503. doi: 10.1128/MMBR.00017-10. Review.

25.

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community.

Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G.

Nucleic Acids Res. 2010 Jan;38(Database issue):D420-7. doi: 10.1093/nar/gkp751. Epub 2009 Sep 22.

26.

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, 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 AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, 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 PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C.

Nature. 2009 Sep 17;461(7262):393-8. doi: 10.1038/nature08358. Epub 2009 Sep 9.

PMID:
19741609
27.

Describing commonalities in microbial effector delivery using the Gene Ontology.

Chibucos MC, Tseng TT, Setubal JC.

Trends Microbiol. 2009 Jul;17(7):312-9. doi: 10.1016/j.tim.2009.05.001. Epub 2009 Jul 1. Review.

PMID:
19576779
28.

Common processes in pathogenesis by fungal and oomycete plant pathogens, described with Gene Ontology terms.

Meng S, Torto-Alalibo T, Chibucos MC, Tyler BM, Dean RA.

BMC Microbiol. 2009 Feb 19;9 Suppl 1:S7. doi: 10.1186/1471-2180-9-S1-S7. Review.

29.

Common themes in nutrient acquisition by plant symbiotic microbes, described by the Gene Ontology.

Chibucos MC, Tyler BM.

BMC Microbiol. 2009 Feb 19;9 Suppl 1:S6. doi: 10.1186/1471-2180-9-S1-S6. Review.

30.

Programmed cell death in host-symbiont associations, viewed through the Gene Ontology.

Chibucos MC, Collmer CW, Torto-Alalibo T, Gwinn-Giglio M, Lindeberg M, Li D, Tyler BM.

BMC Microbiol. 2009 Feb 19;9 Suppl 1:S5. doi: 10.1186/1471-2180-9-S1-S5. Review.

31.

Expressed sequence tags from phytophthora sojae reveal genes specific to development and infection.

Torto-Alalibo TA, Tripathy S, Smith BM, Arredondo FD, Zhou L, Li H, Chibucos MC, Qutob D, Gijzen M, Mao C, Sobral BW, Waugh ME, Mitchell TK, Dean RA, Tyler BM.

Mol Plant Microbe Interact. 2007 Jul;20(7):781-93.

32.

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