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Items: 1 to 50 of 68

1.

The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018).

Harris NL, Wiencko H, Chapman B, Cock PJA, Hokamp K, Lapp H, Fields C, Greshake Tzovaras B.

F1000Res. 2018 Aug 17;7. pii: ISCB Comm J-1309. doi: 10.12688/f1000research.15936.1. eCollection 2018.

2.

Circadian clock protein BMAL1 regulates IL-1β in macrophages via NRF2.

Early JO, Menon D, Wyse CA, Cervantes-Silva MP, Zaslona Z, Carroll RG, Palsson-McDermott EM, Angiari S, Ryan DG, Corcoran SE, Timmons G, Geiger SS, Fitzpatrick DJ, O'Connell D, Xavier RJ, Hokamp K, O'Neill LAJ, Curtis AM.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):E8460-E8468. doi: 10.1073/pnas.1800431115. Epub 2018 Aug 20.

3.

The impact of common genetic variants in the mitochondrial glycine cleavage system on relevant metabolites.

O'Reilly J, Pangilinan F, Hokamp K, Ueland PM, Brosnan JT, Brosnan ME, Brody LC, Molloy AM.

Mol Genet Metab Rep. 2018 Jun 11;16:20-22. doi: 10.1016/j.ymgmr.2018.05.006. eCollection 2018 Sep.

4.

The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978.

Kröger C, MacKenzie KD, Alshabib EY, Kirzinger MWB, Suchan DM, Chao TC, Akulova V, Miranda-CasoLuengo AA, Monzon VA, Conway T, Sivasankaran SK, Hinton JCD, Hokamp K, Cameron ADS.

Nucleic Acids Res. 2018 Oct 12;46(18):9684-9698. doi: 10.1093/nar/gky603.

5.

A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities.

Conway E, Jerman E, Healy E, Ito S, Holoch D, Oliviero G, Deevy O, Glancy E, Fitzpatrick DJ, Mucha M, Watson A, Rice AM, Chammas P, Huang C, Pratt-Kelly I, Koseki Y, Nakayama M, Ishikura T, Streubel G, Wynne K, Hokamp K, McLysaght A, Ciferri C, Di Croce L, Cagney G, Margueron R, Koseki H, Bracken AP.

Mol Cell. 2018 May 3;70(3):408-421.e8. doi: 10.1016/j.molcel.2018.03.005. Epub 2018 Apr 5.

PMID:
29628311
6.

Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella.

Hammarlöf DL, Kröger C, Owen SV, Canals R, Lacharme-Lora L, Wenner N, Schager AE, Wells TJ, Henderson IR, Wigley P, Hokamp K, Feasey NA, Gordon MA, Hinton JCD.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):E2614-E2623. doi: 10.1073/pnas.1714718115. Epub 2018 Feb 27.

7.

Dysregulated mitogen-activated protein kinase signalling as an oncogenic basis for clear cell sarcoma of the kidney.

Kenny C, McDonagh N, Lazaro A, O'Meara E, Klinger R, O'Connor D, Roche F, Hokamp K, O'Sullivan MJ.

J Pathol. 2018 Mar;244(3):334-345. doi: 10.1002/path.5020. Epub 2018 Jan 23.

PMID:
29243812
8.

The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation.

Flanagan PR, Liu NN, Fitzpatrick DJ, Hokamp K, Köhler JR, Moran GP.

mSphere. 2017 Nov 15;2(6). pii: e00477-17. doi: 10.1128/mSphere.00477-17. eCollection 2017 Nov-Dec.

9.

The 2017 Bioinformatics Open Source Conference (BOSC).

Harris NL, Cock PJA, Chapman B, Fields CJ, Hokamp K, Lapp H, Munoz-Torres M, Tzovaras BG, Wiencko H.

F1000Res. 2017 Oct 19;6. pii: ISCB Comm J-1858. doi: 10.12688/f1000research.12929.1. eCollection 2017.

10.

CD10-/ALDH- cells are the sole cisplatin-resistant component of a novel ovarian cancer stem cell hierarchy.

Ffrench B, Gasch C, Hokamp K, Spillane C, Blackshields G, Mahgoub TM, Bates M, Kehoe L, Mooney A, Doyle R, Doyle B, O'Donnell D, Gleeson N, Hennessy BT, Stordal B, O'Riain C, Lambkin H, O'Toole S, O'Leary JJ, Gallagher MF.

Cell Death Dis. 2017 Oct 19;8(10):e3128. doi: 10.1038/cddis.2017.379.

11.

A dual-strategy expression screen for candidate connectivity labels in the developing thalamus.

Bibollet-Bahena O, Okafuji T, Hokamp K, Tear G, Mitchell KJ.

PLoS One. 2017 May 30;12(5):e0177977. doi: 10.1371/journal.pone.0177977. eCollection 2017.

12.

Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal.

Streubel G, Fitzpatrick DJ, Oliviero G, Scelfo A, Moran B, Das S, Munawar N, Watson A, Wynne K, Negri GL, Dillon ET, Jammula S, Hokamp K, O'Connor DP, Pasini D, Cagney G, Bracken AP.

EMBO J. 2017 Aug 1;36(15):2216-2232. doi: 10.15252/embj.201696307. Epub 2017 May 29.

13.

Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast.

Young CP, Hillyer C, Hokamp K, Fitzpatrick DJ, Konstantinov NK, Welty JS, Ness SA, Werner-Washburne M, Fleming AB, Osley MA.

BMC Genomics. 2017 Jan 26;18(1):107. doi: 10.1186/s12864-017-3509-9.

14.

The 2016 Bioinformatics Open Source Conference (BOSC).

Harris NL, Cock PJ, Chapman B, Fields CJ, Hokamp K, Lapp H, Muñoz-Torres M, Wiencko H.

F1000Res. 2016 Oct 6;5. pii: ISCB Comm J-2464. eCollection 2016.

15.

The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium.

Colgan AM, Kröger C, Diard M, Hardt WD, Puente JL, Sivasankaran SK, Hokamp K, Hinton JC.

PLoS Genet. 2016 Aug 26;12(8):e1006258. doi: 10.1371/journal.pgen.1006258. eCollection 2016 Aug.

16.

microRNA regulatory circuits in a mouse model of inherited retinal degeneration.

Palfi A, Hokamp K, Hauck SM, Vencken S, Millington-Ward S, Chadderton N, Carrigan M, Kortvely E, Greene CM, Kenna PF, Farrar GJ.

Sci Rep. 2016 Aug 16;6:31431. doi: 10.1038/srep31431.

17.

The 2015 Bioinformatics Open Source Conference (BOSC 2015).

Harris NL, Cock PJ, Lapp H, Chapman B, Davey R, Fields C, Hokamp K, Munoz-Torres M.

PLoS Comput Biol. 2016 Feb 25;12(2):e1004691. doi: 10.1371/journal.pcbi.1004691. eCollection 2016 Feb.

18.

Re-engineering cellular physiology by rewiring high-level global regulatory genes.

Fitzgerald S, Dillon SC, Chao TC, Wiencko HL, Hokamp K, Cameron AD, Dorman CJ.

Sci Rep. 2015 Dec 3;5:17653. doi: 10.1038/srep17653.

19.

RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium.

Srikumar S, Kröger C, Hébrard M, Colgan A, Owen SV, Sivasankaran SK, Cameron AD, Hokamp K, Hinton JC.

PLoS Pathog. 2015 Nov 12;11(11):e1005262. doi: 10.1371/journal.ppat.1005262. eCollection 2015.

20.

Perl One-Liners: Bridging the Gap Between Large Data Sets and Analysis Tools.

Hokamp K.

Methods Mol Biol. 2015;1326:177-91. doi: 10.1007/978-1-4939-2839-2_15.

PMID:
26498621
21.

Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients.

Lanigan F, Brien GL, Fan Y, Madden SF, Jerman E, Maratha A, Aloraifi F, Hokamp K, Dunne EJ, Lohan AJ, Flanagan L, Garbe JC, Stampfer MR, Fridberg M, Jirstrom K, Quinn CM, Loftus B, Gallagher WM, Geraghty J, Bracken AP.

FEBS J. 2015 Sep;282(18):3455-73. doi: 10.1111/febs.13354. Epub 2015 Jul 14.

22.

Circadian control of innate immunity in macrophages by miR-155 targeting Bmal1.

Curtis AM, Fagundes CT, Yang G, Palsson-McDermott EM, Wochal P, McGettrick AF, Foley NH, Early JO, Chen L, Zhang H, Xue C, Geiger SS, Hokamp K, Reilly MP, Coogan AN, Vigorito E, FitzGerald GA, O'Neill LA.

Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7231-6. doi: 10.1073/pnas.1501327112. Epub 2015 May 20.

23.

Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.

Casey ME, Meade KG, Nalpas NC, Taraktsoglou M, Browne JA, Killick KE, Park SD, Gormley E, Hokamp K, Magee DA, MacHugh DE.

Front Immunol. 2015 Feb 4;6:23. doi: 10.3389/fimmu.2015.00023. eCollection 2015.

24.

Gene expression changes during retinal development and rod specification.

Mansergh FC, Carrigan M, Hokamp K, Farrar GJ.

Mol Vis. 2015 Jan 20;21:61-87. eCollection 2015.

25.

Genome-wide analysis of phosphorylated PhoP binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis.

Salzberg LI, Botella E, Hokamp K, Antelmann H, Maaß S, Becher D, Noone D, Devine KM.

J Bacteriol. 2015 Apr;197(8):1492-506. doi: 10.1128/JB.02570-14. Epub 2015 Feb 9.

26.

Telomeric ORFs (TLOs) in Candida spp. Encode mediator subunits that regulate distinct virulence traits.

Haran J, Boyle H, Hokamp K, Yeomans T, Liu Z, Church M, Fleming AB, Anderson MZ, Berman J, Myers LC, Sullivan DJ, Moran GP.

PLoS Genet. 2014 Oct 30;10(10):e1004658. doi: 10.1371/journal.pgen.1004658. eCollection 2014 Oct.

27.

Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis.

Killick KE, Magee DA, Park SD, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K.

Front Immunol. 2014 Oct 1;5:422. doi: 10.3389/fimmu.2014.00422. eCollection 2014.

28.

RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.

McLoughlin KE, Nalpas NC, Rue-Albrecht K, Browne JA, Magee DA, Killick KE, Park SD, Hokamp K, Meade KG, O'Farrelly C, Gormley E, Gordon SV, MacHugh DE.

Front Immunol. 2014 Aug 26;5:396. doi: 10.3389/fimmu.2014.00396. eCollection 2014.

29.

A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni.

Caimano MJ, Sivasankaran SK, Allard A, Hurley D, Hokamp K, Grassmann AA, Hinton JC, Nally JE.

PLoS Pathog. 2014 Mar 13;10(3):e1004004. doi: 10.1371/journal.ppat.1004004. eCollection 2014 Mar.

30.

A transcription factor network coordinates attraction, repulsion, and adhesion combinatorially to control motor axon pathway selection.

Zarin AA, Asadzadeh J, Hokamp K, McCartney D, Yang L, Bashaw GJ, Labrador JP.

Neuron. 2014 Mar 19;81(6):1297-1311. doi: 10.1016/j.neuron.2014.01.038. Epub 2014 Feb 20.

31.

Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak.

McCusker MP, Hokamp K, Buckley JF, Wall PG, Martins M, Fanning S.

Genome Announc. 2014 Jan 23;2(1). pii: e01219-13. doi: 10.1128/genomeA.01219-13.

32.

An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.

Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JC.

Cell Host Microbe. 2013 Dec 11;14(6):683-95. doi: 10.1016/j.chom.2013.11.010.

33.

Receptor-mediated recognition of mycobacterial pathogens.

Killick KE, Ní Cheallaigh C, O'Farrelly C, Hokamp K, MacHugh DE, Harris J.

Cell Microbiol. 2013 Sep;15(9):1484-95. doi: 10.1111/cmi.12161. Epub 2013 Jul 29. Review.

PMID:
23795683
34.

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.

35.

The WalRK (YycFG) and σ(I) RsgI regulators cooperate to control CwlO and LytE expression in exponentially growing and stressed Bacillus subtilis cells.

Salzberg LI, Powell L, Hokamp K, Botella E, Noone D, Devine KM.

Mol Microbiol. 2013 Jan;87(1):180-95. doi: 10.1111/mmi.12092. Epub 2012 Nov 30.

36.

LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium.

Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ.

Mol Microbiol. 2012 Sep;85(6):1072-89. doi: 10.1111/j.1365-2958.2012.08162.x. Epub 2012 Jul 23.

37.

Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations.

Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA.

PLoS One. 2012;7(4):e35659. doi: 10.1371/journal.pone.0035659. Epub 2012 Apr 26.

38.

The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.

Kröger C, Dillon SC, Cameron AD, Papenfort K, Sivasankaran SK, Hokamp K, Chao Y, Sittka A, Hébrard M, Händler K, Colgan A, Leekitcharoenphon P, Langridge GC, Lohan AJ, Loftus B, Lucchini S, Ussery DW, Dorman CJ, Thomson NR, Vogel J, Hinton JC.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):E1277-86. doi: 10.1073/pnas.1201061109. Epub 2012 Apr 25.

39.

Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis.

Machugh DE, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, DE Park S, Hokamp K, Gormley E, Magee DA.

Vet Res. 2012 Mar 28;43:25. doi: 10.1186/1297-9716-43-25.

40.

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis.

Magee DA, Taraktsoglou M, Killick KE, Nalpas NC, Browne JA, Park SD, Conlon KM, Lynn DJ, Hokamp K, Gordon SV, Gormley E, MacHugh DE.

PLoS One. 2012;7(2):e32034. doi: 10.1371/journal.pone.0032034. Epub 2012 Feb 22.

41.

Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes.

Killick KE, Browne JA, Park SD, Magee DA, Martin I, Meade KG, Gordon SV, Gormley E, O'Farrelly C, Hokamp K, MacHugh DE.

BMC Genomics. 2011 Dec 19;12:611. doi: 10.1186/1471-2164-12-611.

42.

Cell envelope gene expression in phosphate-limited Bacillus subtilis cells.

Botella E, Hübner S, Hokamp K, Hansen A, Bisicchia P, Noone D, Powell L, Salzberg LI, Devine KM.

Microbiology. 2011 Sep;157(Pt 9):2470-84. doi: 10.1099/mic.0.049205-0. Epub 2011 Jun 2.

PMID:
21636651
43.

Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism.

Dillon SC, Cameron AD, Hokamp K, Lucchini S, Hinton JC, Dorman CJ.

Mol Microbiol. 2010 Jun 1;76(5):1250-65. doi: 10.1111/j.1365-2958.2010.07173.x. Epub 2010 Apr 27.

44.

G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9.

Gong JH, Nicholls EF, Elliott MR, Brown KL, Hokamp K, Roche FM, Cheung CY, Falsafi R, Brinkman FS, Bowdish DM, Hancock RE.

Cell Immunol. 2010;261(2):105-13. doi: 10.1016/j.cellimm.2009.11.007. Epub 2009 Dec 3.

PMID:
20038462
45.

Comparative transcript profiling of Candida albicans and Candida dubliniensis identifies SFL2, a C. albicans gene required for virulence in a reconstituted epithelial infection model.

Spiering MJ, Moran GP, Chauvel M, Maccallum DM, Higgins J, Hokamp K, Yeomans T, d'Enfert C, Coleman DC, Sullivan DJ.

Eukaryot Cell. 2010 Feb;9(2):251-65. doi: 10.1128/EC.00291-09. Epub 2009 Dec 18.

46.

Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS.

Stoebel DM, Hokamp K, Last MS, Dorman CJ.

PLoS Genet. 2009 Oct;5(10):e1000671. doi: 10.1371/journal.pgen.1000671. Epub 2009 Oct 2.

47.

The complex relationship of gene duplication and essentiality.

Makino T, Hokamp K, McLysaght A.

Trends Genet. 2009 Apr;25(4):152-5. doi: 10.1016/j.tig.2009.03.001. Epub 2009 Mar 13.

PMID:
19285746
48.

The growth phase-dependent regulation of the pilus locus genes by two-component system TCS08 in Streptococcus pneumoniae.

Song XM, Connor W, Hokamp K, Babiuk LA, Potter AA.

Microb Pathog. 2009 Jan;46(1):28-35. doi: 10.1016/j.micpath.2008.10.006. Epub 2008 Oct 17.

PMID:
18983906
49.

Transcriptome studies on Streptococcus pneumoniae, illustration of early response genes to THP-1 human macrophages.

Song XM, Connor W, Hokamp K, Babiuk LA, Potter AA.

Genomics. 2009 Jan;93(1):72-82. doi: 10.1016/j.ygeno.2008.09.008. Epub 2008 Oct 29.

50.

A common microRNA signature in mouse models of retinal degeneration.

Loscher CJ, Hokamp K, Wilson JH, Li T, Humphries P, Farrar GJ, Palfi A.

Exp Eye Res. 2008 Dec;87(6):529-34. doi: 10.1016/j.exer.2008.08.016. Epub 2008 Sep 13.

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