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Items: 35

1.

BINDER: computationally inferring a gene regulatory network for Mycobacterium abscessus.

Staunton PM, Miranda-CasoLuengo AA, Loftus BJ, Gormley IC.

BMC Bioinformatics. 2019 Sep 10;20(1):466. doi: 10.1186/s12859-019-3042-8.

2.
3.

High-throughput transcriptomics reveals common and strain-specific responses of human macrophages to infection with Mycobacterium abscessus Smooth and Rough variants.

Aulicino A, Dinan AM, Miranda-CasoLuengo AA, Browne JA, Rue-Albrecht K, MacHugh DE, Loftus BJ.

BMC Genomics. 2015 Dec 9;16:1046. doi: 10.1186/s12864-015-2246-1.

4.

Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle.

Park SD, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE.

Genome Biol. 2015 Oct 26;16:234. doi: 10.1186/s13059-015-0790-2.

5.

Fertility and genomics: comparison of gene expression in contrasting reproductive tissues of female cattle.

McGettigan PA, Browne JA, Carrington SD, Crowe MA, Fair T, Forde N, Loftus BJ, Lohan A, Lonergan P, Pluta K, Mamo S, Murphy A, Roche J, Walsh SW, Creevey CJ, Earley B, Keady S, Kenny DA, Matthews D, McCabe M, Morris D, O'Loughlin A, Waters S, Diskin MG, Evans AC.

Reprod Fertil Dev. 2016;28(1-2):11-24. doi: 10.1071/RD15354.

PMID:
27062871
6.

Relaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.

Dinan AM, Tong P, Lohan AJ, Conlon KM, Miranda-CasoLuengo AA, Malone KM, Gordon SV, Loftus BJ.

MBio. 2014 Aug 5;5(4):e01169-14. doi: 10.1128/mBio.01169-14.

7.

(Non-)translational medicine: targeting bacterial RNA.

Dinan AM, Loftus BJ.

Front Genet. 2013 Nov 8;4:230. doi: 10.3389/fgene.2013.00230. eCollection 2013.

8.

Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro.

Nalpas NC, Park SD, Magee DA, Taraktsoglou M, Browne JA, Conlon KM, Rue-Albrecht K, Killick KE, Hokamp K, Lohan AJ, Loftus BJ, Gormley E, Gordon SV, MacHugh DE.

BMC Genomics. 2013 Apr 8;14:230. doi: 10.1186/1471-2164-14-230.

9.

Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling.

Clarke M, Lohan AJ, Liu B, Lagkouvardos I, Roy S, Zafar N, Bertelli C, Schilde C, Kianianmomeni A, B├╝rglin TR, Frech C, Turcotte B, Kopec KO, Synnott JM, Choo C, Paponov I, Finkler A, Heng Tan CS, Hutchins AP, Weinmeier T, Rattei T, Chu JS, Gimenez G, Irimia M, Rigden DJ, Fitzpatrick DA, Lorenzo-Morales J, Bateman A, Chiu CH, Tang P, Hegemann P, Fromm H, Raoult D, Greub G, Miranda-Saavedra D, Chen N, Nash P, Ginger ML, Horn M, Schaap P, Caler L, Loftus BJ.

Genome Biol. 2013 Feb 1;14(2):R11. doi: 10.1186/gb-2013-14-2-r11.

10.

Polycomb PHF19 binds H3K36me3 and recruits PRC2 and demethylase NO66 to embryonic stem cell genes during differentiation.

Brien GL, Gambero G, O'Connell DJ, Jerman E, Turner SA, Egan CM, Dunne EJ, Jurgens MC, Wynne K, Piao L, Lohan AJ, Ferguson N, Shi X, Sinha KM, Loftus BJ, Cagney G, Bracken AP.

Nat Struct Mol Biol. 2012 Dec;19(12):1273-81. doi: 10.1038/nsmb.2449. Epub 2012 Nov 18.

PMID:
23160351
11.

Molecular aspects of mucin biosynthesis and mucus formation in the bovine cervix during the periestrous period.

Pluta K, McGettigan PA, Reid CJ, Browne JA, Irwin JA, Tharmalingam T, Corfield A, Baird A, Loftus BJ, Evans AC, Carrington SD.

Physiol Genomics. 2012 Dec 18;44(24):1165-78. doi: 10.1152/physiolgenomics.00088.2012. Epub 2012 Oct 23.

PMID:
23092952
12.

Evidence for an early endometrial response to pregnancy in cattle: both dependent upon and independent of interferon tau.

Forde N, Duffy GB, McGettigan PA, Browne JA, Mehta JP, Kelly AK, Mansouri-Attia N, Sandra O, Loftus BJ, Crowe MA, Fair T, Roche JF, Lonergan P, Evans AC.

Physiol Genomics. 2012 Aug 17;44(16):799-810. doi: 10.1152/physiolgenomics.00067.2012. Epub 2012 Jul 3.

PMID:
22759920
13.

Methicillin resistance alters the biofilm phenotype and attenuates virulence in Staphylococcus aureus device-associated infections.

Pozzi C, Waters EM, Rudkin JK, Schaeffer CR, Lohan AJ, Tong P, Loftus BJ, Pier GB, Fey PD, Massey RC, O'Gara JP.

PLoS Pathog. 2012;8(4):e1002626. doi: 10.1371/journal.ppat.1002626. Epub 2012 Apr 5.

14.

Sequencing illustrates the transcriptional response of Legionella pneumophila during infection and identifies seventy novel small non-coding RNAs.

Weissenmayer BA, Prendergast JG, Lohan AJ, Loftus BJ.

PLoS One. 2011 Mar 3;6(3):e17570. doi: 10.1371/journal.pone.0017570.

15.

Characterization of the equine skeletal muscle transcriptome identifies novel functional responses to exercise training.

McGivney BA, McGettigan PA, Browne JA, Evans AC, Fonseca RG, Loftus BJ, Lohan A, MacHugh DE, Murphy BA, Katz LM, Hill EW.

BMC Genomics. 2010 Jun 23;11:398. doi: 10.1186/1471-2164-11-398.

16.

A complete mitochondrial genome sequence from a mesolithic wild aurochs (Bos primigenius).

Edwards CJ, Magee DA, Park SD, McGettigan PA, Lohan AJ, Murphy A, Finlay EK, Shapiro B, Chamberlain AT, Richards MB, Bradley DG, Loftus BJ, MacHugh DE.

PLoS One. 2010 Feb 17;5(2):e9255. doi: 10.1371/journal.pone.0009255.

17.

The Aedes aegypti glutathione transferase family.

Lumjuan N, Stevenson BJ, Prapanthadara LA, Somboon P, Brophy PM, Loftus BJ, Severson DW, Ranson H.

Insect Biochem Mol Biol. 2007 Oct;37(10):1026-35. Epub 2007 Jun 13.

PMID:
17785190
18.

Analysis of 14 BAC sequences from the Aedes aegypti genome: a benchmark for genome annotation and assembly.

Lobo NF, Campbell KS, Thaner D, Debruyn B, Koo H, Gelbart WM, Loftus BJ, Severson DW, Collins FH.

Genome Biol. 2007;8(5):R88.

19.

Unique organisation of tRNA genes in Entamoeba histolytica.

Clark CG, Ali IK, Zaki M, Loftus BJ, Hall N.

Mol Biochem Parasitol. 2006 Mar;146(1):24-9. Epub 2005 Oct 28.

PMID:
16307803
20.

Gene discovery in the Acanthamoeba castellanii genome.

Anderson IJ, Watkins RF, Samuelson J, Spencer DF, Majoros WH, Gray MW, Loftus BJ.

Protist. 2005 Aug;156(2):203-14.

PMID:
16171187
21.

Entamoeba: still more to be learned from the genome.

Loftus BJ, Hall N.

Trends Parasitol. 2005 Oct;21(10):453. No abstract available.

PMID:
16099723
22.

The diversity of Rab GTPases in Entamoeba histolytica.

Saito-Nakano Y, Loftus BJ, Hall N, Nozaki T.

Exp Parasitol. 2005 Jul;110(3):244-52. Epub 2005 Apr 7.

PMID:
15955319
23.

Entamoeba histolytica: observations on metabolism based on the genome sequence.

Anderson IJ, Loftus BJ.

Exp Parasitol. 2005 Jul;110(3):173-7. Epub 2005 Apr 14.

PMID:
15955308
24.

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.

Loftus BJ, Fung E, Roncaglia P, Rowley D, Amedeo P, Bruno D, Vamathevan J, Miranda M, Anderson IJ, Fraser JA, Allen JE, Bosdet IE, Brent MR, Chiu R, Doering TL, Donlin MJ, D'Souza CA, Fox DS, Grinberg V, Fu J, Fukushima M, Haas BJ, Huang JC, Janbon G, Jones SJ, Koo HL, Krzywinski MI, Kwon-Chung JK, Lengeler KB, Maiti R, Marra MA, Marra RE, Mathewson CA, Mitchell TG, Pertea M, Riggs FR, Salzberg SL, Schein JE, Shvartsbeyn A, Shin H, Shumway M, Specht CA, Suh BB, Tenney A, Utterback TR, Wickes BL, Wortman JR, Wye NH, Kronstad JW, Lodge JK, Heitman J, Davis RW, Fraser CM, Hyman RW.

Science. 2005 Feb 25;307(5713):1321-4. Epub 2005 Jan 13.

25.

Aedes aegypti genomics.

Severson DW, Knudson DL, Soares MB, Loftus BJ.

Insect Biochem Mol Biol. 2004 Jul;34(7):715-21. Review.

PMID:
15242713
27.

Construction of a BAC library and generation of BAC end sequence-tagged connectors for genome sequencing of the African malaria mosquito Anopheles gambiae.

Hong YS, Hogan JR, Wang X, Sarkar A, Sim C, Loftus BJ, Ren C, Huff ER, Carlile JL, Black K, Zhang HB, Gardner MJ, Collins FH.

Mol Genet Genomics. 2003 Mar;268(6):720-8. Epub 2003 Feb 20.

PMID:
12655398
28.

Iron-dependent hydrogenases of Entamoeba histolytica and Giardia lamblia: activity of the recombinant entamoebic enzyme and evidence for lateral gene transfer.

Nixon JE, Field J, McArthur AG, Sogin ML, Yarlett N, Loftus BJ, Samuelson J.

Biol Bull. 2003 Feb;204(1):1-9.

PMID:
12588739
29.
30.

A spliceosomal intron in Giardia lamblia.

Nixon JE, Wang A, Morrison HG, McArthur AG, Sogin ML, Loftus BJ, Samuelson J.

Proc Natl Acad Sci U S A. 2002 Mar 19;99(6):3701-5. Epub 2002 Feb 19.

31.

Complete genome sequence of a virulent isolate of Streptococcus pneumoniae.

Tettelin H, Nelson KE, Paulsen IT, Eisen JA, Read TD, Peterson S, Heidelberg J, DeBoy RT, Haft DH, Dodson RJ, Durkin AS, Gwinn M, Kolonay JF, Nelson WC, Peterson JD, Umayam LA, White O, Salzberg SL, Lewis MR, Radune D, Holtzapple E, Khouri H, Wolf AM, Utterback TR, Hansen CL, McDonald LA, Feldblyum TV, Angiuoli S, Dickinson T, Hickey EK, Holt IE, Loftus BJ, Yang F, Smith HO, Venter JC, Dougherty BA, Morrison DA, Hollingshead SK, Fraser CM.

Science. 2001 Jul 20;293(5529):498-506.

32.

Mutation screening of the TNFRSF11A gene encoding receptor activator of NF kappa B (RANK) in familial and sporadic Paget's disease of bone and osteosarcoma.

Sparks AB, Peterson SN, Bell C, Loftus BJ, Hocking L, Cahill DP, Frassica FJ, Streeten EA, Levine MA, Fraser CM, Adams MD, Broder S, Venter JC, Kinzler KW, Vogelstein B, Ralston SH.

Calcif Tissue Int. 2001 Mar;68(3):151-5.

PMID:
11351498
33.

TIGRFAMs: a protein family resource for the functional identification of proteins.

Haft DH, Loftus BJ, Richardson DL, Yang F, Eisen JA, Paulsen IT, White O.

Nucleic Acids Res. 2001 Jan 1;29(1):41-3.

34.

Molecular structure and evolution of an alpha satellite/non-alpha satellite junction at 16p11.

Horvath JE, Viggiano L, Loftus BJ, Adams MD, Archidiacono N, Rocchi M, Eichler EE.

Hum Mol Genet. 2000 Jan 1;9(1):113-23.

PMID:
10587586
35.

Genome duplications and other features in 12 Mb of DNA sequence from human chromosome 16p and 16q.

Loftus BJ, Kim UJ, Sneddon VP, Kalush F, Brandon R, Fuhrmann J, Mason T, Crosby ML, Barnstead M, Cronin L, Deslattes Mays A, Cao Y, Xu RX, Kang HL, Mitchell S, Eichler EE, Harris PC, Venter JC, Adams MD.

Genomics. 1999 Sep 15;60(3):295-308.

PMID:
10493829

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