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Results: 1 to 20 of 88

1.

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project.

Andersson L, Archibald AL, Bottema CD, Brauning R, Burgess SC, Burt DW, Casas E, Cheng HH, Clarke L, Couldrey C, Dalrymple BP, Elsik CG, Foissac S, Giuffra E, Groenen MA, Hayes BJ, Huang LS, Khatib H, Kijas JW, Kim H, Lunney JK, McCarthy FM, McEwan JC, Moore S, Nanduri B, Notredame C, Palti Y, Plastow GS, Reecy JM, Rohrer GA, Sarropoulou E, Schmidt CJ, Silverstein J, Tellam RL, Tixier-Boichard M, Tosser-Klopp G, Tuggle CK, Vilkki J, White SN, Zhao S, Zhou H; FAANG Consortium.

Genome Biol. 2015 Mar 25;16:57. doi: 10.1186/s13059-015-0622-4.

2.

Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

Green RE, Braun EL, Armstrong J, Earl D, Nguyen N, Hickey G, Vandewege MW, St John JA, Capella-Gutiérrez S, Castoe TA, Kern C, Fujita MK, Opazo JC, Jurka J, Kojima KK, Caballero J, Hubley RM, Smit AF, Platt RN, Lavoie CA, Ramakodi MP, Finger JW Jr, Suh A, Isberg SR, Miles L, Chong AY, Jaratlerdsiri W, Gongora J, Moran C, Iriarte A, McCormack J, Burgess SC, Edwards SV, Lyons E, Williams C, Breen M, Howard JT, Gresham CR, Peterson DG, Schmitz J, Pollock DD, Haussler D, Triplett EW, Zhang G, Irie N, Jarvis ED, Brochu CA, Schmidt CJ, McCarthy FM, Faircloth BC, Hoffmann FG, Glenn TC, Gabaldón T, Paten B, Ray DA.

Science. 2014 Dec 12;346(6215):1254449. doi: 10.1126/science.1254449. Epub 2014 Dec 11.

PMID:
25504731
3.

Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC.

Jaratlerdsiri W, Deakin J, Godinez RM, Shan X, Peterson DG, Marthey S, Lyons E, McCarthy FM, Isberg SR, Higgins DP, Chong AY, John JS, Glenn TC, Ray DA, Gongora J.

PLoS One. 2014 Dec 11;9(12):e114631. doi: 10.1371/journal.pone.0114631. eCollection 2014.

4.

Schistosoma mansoni infection after three years of mass drug administration in Sierra Leone.

Sesay S, Paye J, Bah MS, McCarthy FM, Conteh A, Sonnie M, Hodges MH, Zhang Y.

Parasit Vectors. 2014 Jan 9;7:14. doi: 10.1186/1756-3305-7-14.

5.

From data to function: functional modeling of poultry genomics data.

McCarthy FM, Lyons E.

Poult Sci. 2013 Sep;92(9):2519-29. doi: 10.3382/ps.2012-02808.

PMID:
23960137
6.

Developing a biocuration workflow for AgBase, a non-model organism database.

Pillai L, Chouvarine P, Tudor CO, Schmidt CJ, Vijay-Shanker K, McCarthy FM.

Database (Oxford). 2012 Nov 17;2012:bas038. doi: 10.1093/database/bas038. Print 2012.

7.

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes.

St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ Jr, Glenn TC, Green RE, Ray DA.

Genome Biol. 2012 Jan 31;13(1):415. doi: 10.1186/gb-2012-13-1-415.

8.

Transcriptome-based differentiation of closely-related Miscanthus lines.

Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, Baldwin BS, Burgess SC, Peterson DG.

PLoS One. 2012;7(1):e29850. doi: 10.1371/journal.pone.0029850. Epub 2012 Jan 10.

9.

Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences.

Bright LA, Mujahid N, Nanduri B, McCarthy FM, Costa LR, Burgess SC, Swiderski CE.

Anim Genet. 2011 Aug;42(4):395-405. doi: 10.1111/j.1365-2052.2010.02158.x. Epub 2011 Feb 6.

PMID:
21749422
10.

Systemic response to Campylobacter jejuni infection by profiling gene transcription in the spleens of two genetic lines of chickens.

Li X, Swaggerty CL, Kogut MH, Chiang HI, Wang Y, Genovese KJ, He H, McCarthy FM, Burgess SC, Pevzner IY, Zhou H.

Immunogenetics. 2012 Jan;64(1):59-69. doi: 10.1007/s00251-011-0557-1. Epub 2011 Jul 7.

PMID:
21748442
11.

The proteogenomic mapping tool.

Sanders WS, Wang N, Bridges SM, Malone BM, Dandass YS, McCarthy FM, Nanduri B, Lawrence ML, Burgess SC.

BMC Bioinformatics. 2011 Apr 22;12:115. doi: 10.1186/1471-2105-12-115.

12.

Tibial dyschondroplasia-associated proteomic changes in chicken growth plate cartilage.

Rasaputra KS, Liyanage AB, Lay JO Jr, McCarthy FM, Rath NC.

Avian Dis. 2010 Dec;54(4):1166-71.

PMID:
21313835
13.

AgBase: supporting functional modeling in agricultural organisms.

McCarthy FM, Gresham CR, Buza TJ, Chouvarine P, Pillai LR, Kumar R, Ozkan S, Wang H, Manda P, Arick T, Bridges SM, Burgess SC.

Nucleic Acids Res. 2011 Jan;39(Database issue):D497-506. doi: 10.1093/nar/gkq1115. Epub 2010 Nov 12.

14.

Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences.

Ammari M, McCarthy FM, Nanduri B, Pinchuk LM.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S9. doi: 10.1186/1471-2105-11-S6-S9.

15.

GOModeler--a tool for hypothesis-testing of functional genomics datasets.

Manda P, Freeman MG, Bridges SM, Jankun-Kelly TJ, Nanduri B, McCarthy FM, Burgess SC.

BMC Bioinformatics. 2010 Oct 7;11 Suppl 6:S29. doi: 10.1186/1471-2105-11-S6-S29.

16.

Proteome profile of the developing maize (Zea mays L.) rachis.

Pechanova O, Pechan T, Ozkan S, McCarthy FM, Williams WP, Luthe DS.

Proteomics. 2010 Aug;10(16):3051-5. doi: 10.1002/pmic.200900833.

PMID:
20662101
17.

Re-annotation is an essential step in systems biology modeling of functional genomics data.

van den Berg BH, McCarthy FM, Lamont SJ, Burgess SC.

PLoS One. 2010 May 14;5(5):e10642. doi: 10.1371/journal.pone.0010642.

18.

Structural and functional-annotation of an equine whole genome oligoarray.

Bright LA, Burgess SC, Chowdhary B, Swiderski CE, McCarthy FM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S8. doi: 10.1186/1471-2105-10-S11-S8.

19.

Facilitating functional annotation of chicken microarray data.

Buza TJ, Kumar R, Gresham CR, Burgess SC, McCarthy FM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S2. doi: 10.1186/1471-2105-10-S11-S2.

20.

The Chicken Gene Nomenclature Committee report.

Burt DW, Carrë W, Fell M, Law AS, Antin PB, Maglott DR, Weber JA, Schmidt CJ, Burgess SC, McCarthy FM.

BMC Genomics. 2009 Jul 14;10 Suppl 2:S5. doi: 10.1186/1471-2164-10-S2-S5.

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