Karsten Hokamp
Research Fellow, Genetics

Publications and Further Research Outputs

Peer-Reviewed Publications

Palfi A, Hokamp K, Hauck SM, Vencken S, Millington-Ward S, Chadderton N, Carrigan M, Kortvely E, Greene CM, Kenna PF, Farrar GJ, microRNA regulatory circuits in a mouse model of inherited retinal degeneration., Scientific reports, 6, 2016, p31431 Journal Article, 2016 DOI

Harris NL, Cock PJ, Lapp H, Chapman B, Davey R, Fields C, Hokamp K, Munoz-Torres M, The 2015 Bioinformatics Open Source Conference (BOSC 2015)., PLoS computational biology, 12, (2), 2016, pe1004691 Journal Article, 2016 DOI

Srikumar S, Kröger C, Hébrard M, Colgan A, Owen SV, Sivasankaran SK, Cameron AD, Hokamp K, Hinton JC, RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium., PLoS pathogens, 11, (11), 2015, pe1005262 Journal Article, 2015 DOI

Mansergh FC, Carrigan M, Hokamp K, Farrar GJ, Gene expression changes during retinal development and rod specification, Molecular Vision, 21, 2015, p61 - 87 Journal Article, 2015 Other URL TARA - Full Text

Hokamp K, Perl One-Liners: Bridging the Gap Between Large Data Sets and Analysis Tools., Methods in molecular biology (Clifton, N.J.), 1326, 2015, p177-191 Journal Article, 2015 DOI

Fitzgerald S, Dillon SC, Chao TC, Wiencko HL, Hokamp K, Cameron AD, Dorman CJ, Re-engineering cellular physiology by rewiring high-level global regulatory genes., Scientific reports, 5, 2015, p17653 Journal Article, 2015 DOI

Caimano MJ, Sivasankaran SK, Allard A, Hurley D, Hokamp K, Grassmann AA, Hinton JC, Nally JE, A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni., PLoS pathogens, 10, (3), 2014, pe1004004 Journal Article, 2014 TARA - Full Text DOI

Haran J, Boyle H, Hokamp K, Yeomans T, Liu Z, Church M, Fleming AB, Anderson MZ, Berman J, Myers LC, Sullivan DJ, Moran GP, Telomeric ORFs (TLOs) in Candida spp. Encode mediator subunits that regulate distinct virulence traits., PLoS genetics, 10, (10), 2014, pe1004658 Journal Article, 2014 DOI TARA - Full Text URL

Zarin AA, Asadzadeh J, Hokamp K, McCartney D, Yang L, Bashaw GJ, Labrador JP, A transcription factor network coordinates attraction, repulsion, and adhesion combinatorially to control motor axon pathway selection., Neuron, 81, (6), 2014, p1297-311 Journal Article, 2014 TARA - Full Text DOI

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, RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis., Frontiers in immunology, 5, 2014, p396 Journal Article, 2014 DOI TARA - Full Text

Killick KE, Magee DA, Park SD, Taraktsoglou M, Browne JA, Conlon KM, Nalpas NC, Gormley E, Gordon SV, MacHugh DE, Hokamp K, Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis., Frontiers in immunology, 5, 2014, p422 Journal Article, 2014

McCusker MP, Hokamp K, Buckley JF, Wall PG, Martins M, Fanning S, Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak., Genome announcements, 2, (1), 2014 Journal Article, 2014

Egan,Chris M. C.M., Nyman,Ulrika U., Skotte,Julie J., Streubel,Gundula G., Turner,Siobhán A. S.A., O'Connell,David J. D.J., Rraklli,Vilma V., Dolan,Michael J. M.J., Chadderton,Naomi S. N.S., Hansen,Klaus H. K.H., Farrar,Gwyneth Jane G.J., Helin,Kristian K., Holmberg,Johan T. J.T., Bracken,Adrian P. A.P., CHD5 is required for neurogenesis and has a dual role in facilitating gene expression and polycomb gene repression, Developmental Cell, 26, (3), 2013, p223-236 Journal Article, 2013 DOI TARA - Full Text

Kröger C, Colgan A, Srikumar S, Händler K, Sivasankaran SK, Hammarlöf DL, Canals R, Grissom JE, Conway T, Hokamp K, Hinton JC, An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium., Cell host & microbe, 14, (6), 2013, p683-95 Journal Article, 2013 TARA - Full Text DOI

Salzberg, L.I., Powell, L., Hokamp, K., Botella, E., Noone, D., Devine, K.M. 2013, The WalRK (YycFG) and σI RsgI regulators cooperate to control CwlO and LytE expression in exponentially growing and stressed Bacillus subtilis cells, Molecular Microbiology, 87, (1), 2013, p180-195 Journal Article, 2013 DOI

Nalpas, Nicolas C Park, Stephen DE Magee, David A Taraktsoglou, Maria Browne, John A Conlon, Kevin M Rue-Albrecht, Kévin Killick, Kate E Hokamp, Karsten Lohan, Amanda J , Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro , BMC genomics , 14 , (1 ), 2013, p230 - Journal Article, 2013 TARA - Full Text

David A. Magee, Maria Taraktsoglou, Kate E. Killick, Nicolas C. Nalpas, John A. Browne, Stephen D. E. Park, Kevin M. Conlon, David J. Lynn, Karsten Hokamp, Stephen V. Gordon, Eamonn Gormley, David E. MacHugh, Global Gene Expression and Systems Biology Analysis of Bovine Monocyte-Derived Macrophages in Response to In Vitro Challenge with Mycobacterium bovis, PLoS ONE, 7, (2, e32034), 2012 Journal Article, 2012 TARA - Full Text

Botella, E., Noone, D., Salzberg, L.I., Hokamp, K., Devine, S.K., Fogg, M., Wilkinson, A.J., Devine, K.M., High-resolution temporal analysis of global promoter activity in Bacillus subtilis, Methods in Microbiology, 39, 2012, p1-26 Journal Article, 2012 DOI

Botella E, Hübner S, Hokamp K, Hansen A, Bisicchia P, Noone D, Powell L, Salzberg LI, Devine KM, Cell envelope gene expression in phosphate-limited Bacillus subtilis cells., Microbiology (Reading, England), 157, (Pt 9), 2011, p2470-2484 Journal Article, 2011 DOI TARA - Full Text

Kate E Killick, John A Browne, Stephen DE Park, David A Magee, Irene Martin, Kieran G Meade, Stephen V Gordon, Eamonn Gormley, Cliona O'Farrelly, Karsten Hokamp and David E MacHugh, Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes, BMC Genomics , 12, (611), 2011 Journal Article, 2011 TARA - Full Text

Stoebel DM, Hokamp K, Last MS, Dorman CJ, Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS., PLoS Genetics, 5, (10), 2009, pe1000671 Journal Article, 2009 DOI TARA - Full Text

Song, XM, Connor, W, Hokamp, K, Babiuk, LA, Potter, AA, The growth phase-dependent regulation of the pilus locus genes by two-component system TCS08 in Streptococcus pneumoniae., Microbial pathogenesis, 46, (1), 2009, p28 - 35 Journal Article, 2009 DOI

Makino, T, Hokamp, K, McLysaght, A, The complex relationship of gene duplication and essentiality., Trends in genetics, 25, (4), 2009, p152 - 155 Journal Article, 2009 DOI TARA - Full Text

Song, XM, Connor, W, Hokamp, K, Babiuk, LA, Potter, AA, Transcriptome studies on Streptococcus pneumoniae, illustration of early response genes to THP-1 human macrophages., Genomics, 93, (1), 2009, p72 - 82 Journal Article, 2009 DOI

Song, XM, Connor, W, Hokamp, K, Babiuk, LA, Potter, AA, Streptococcus pneumoniae early response genes to human lung epithelial cells., BMC research notes, 1, 2008 Journal Article, 2008 URL DOI

Lynn, DJ, Winsor, GL, Chan, C, Richard, N, Laird, MR, Barsky, A, Gardy, JL, Roche, FM, Chan, TH, Shah, N, Lo, R, Naseer, M, Que, J, Yau, M, Acab, M, Tulpan, D, Whiteside, MD, Chikatamarla, A, Mah, B, Munzner, T, Hokamp, K, Hancock, RE, Brinkman, FS, InnateDB: facilitating systems-level analyses of the mammalian innate immune response., Molecular systems biology, 4, 2008 Journal Article, 2008 URL DOI

Loscher, CJ, Hokamp, K, Wilson, JH, Li, T, Humphries, P, Farrar, GJ, Palfi, A, A common microRNA signature in mouse models of retinal degeneration., Experimental eye research, 87, (6), 2008, p529 - 534 Journal Article, 2008 DOI

Song, XM, Connor, W, Jalal, S, Hokamp, K, Potter, AA, Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells., Canadian journal of microbiology, 54, (3), 2008, p189 - 200 Journal Article, 2008 DOI

Loscher CJ, Hokamp K, Kenna PF, Ivens AC, Humphries P, Palfi A, Farrar GJ., Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa., Genome Biology, 8, (11), 2007, pR248- Journal Article, 2007

Dolan, J, Walshe, K, Alsbury, S, Hokamp, K, O'Keeffe, S, Okafuji, T, Miller, SF, Tear, G, Mitchell, KJ, The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns., BMC Genomics, 8, (320), 2007 Journal Article, 2007 TARA - Full Text DOI

Dolan J, Walshe K, Alsbury S, Hokamp K, O'Keeffe S, Okafuji T, Miller SF, Tear G, Mitchell KJ., The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns., BMC Genomics, 14, (8), 2007, p320- Journal Article, 2007

Mookherjee N, Brown KL, Bowdish DM, Doria S, Falsafi R, Hokamp K, Roche FM, Mu R, Doho GH, Pistolic J, Powers JP, Bryan J, Brinkman FS, Hancock RE, Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37, Journal of Immunology, 176, (4), 2006, p2455 - 2464 Journal Article, 2006

Mookherjee N, Wilson HL, Doria S, Popowych Y, Falsafi R, Yu JJ, Li Y, Veatch S, Roche FM, Brown KL, Brinkman FS, Hokamp K, Potter A, Babiuk LA, Griebel PJ, Hancock RE., Bovine and human cathelicidin cationic host defense peptides similarly suppress transcriptional responses to bacterial lipopolysaccharide., Journal of Leukocyte Biology, 80, (6), 2006, p1563 - 1574 Journal Article, 2006

Hodgson PD, Aich P, Manuja A, Hokamp K, Roche FM, Brinkman FSL, Potter A, Babiuk LA, Griebel PJ, Effect of stress on viral-bacterial synergy in bovine respiratory disease: novel mechanisms to regulate inflammation, Comparative and Functional Genomics, 6, (4), 2005, p244 - 250 Journal Article, 2005

Roche FM, Hokamp K, Acab M, Babiuk LA, Hancock RE, Brinkman FS, ProbeLynx: a tool for updating the association of microarray probes to genes., Nucleic Acids Research, 32, (Web Server Issue), 2004, pW471 - W474 Journal Article, 2004

Hokamp K, Wolfe KH., PubCrawler: keeping up comfortably with PubMed and GenBank., Nucleic Acids Research, 32, (Web Server Issue), 2004, pW16 - W19 Journal Article, 2004

Hokamp, K., Wolfe, K.H., PubCrawler: keeping up comfortably with PubMed and GenBank, Nucleic Acids Res, 32, 2004, pW16-W19 Journal Article, 2004 TARA - Full Text

Hokamp K, Roche FM, Acab M, Rousseau ME, Kuo B, Goode D, Aeschliman D, Bryan J, Babiuk LA, Hancock RE, Brinkman FS., ArrayPipe: a flexible processing pipeline for microarray data., Nucleic Acids Research, 32, (Web Server Issue), 2004, pW457 - W459 Journal Article, 2004

Hokamp, K., McLysaght, A. and Wolfe, K. H., The 2R hypothesis and the human genome sequence., Journal of Structural and Functional Genomics, 3, (1-4), 2003, p95 - 110 Journal Article, 2003 URL DOI

Hokamp, K, Shields, DC, Wolfe, KH, Caffrey, DR, Wrapping up BLAST and other applications for use on Unix clusters., Bioinformatics , 19, (3), 2003, p441-442 Journal Article, 2003 DOI

Blanc, G, Hokamp, K, Wolfe, KH, A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome., Genome research, 13, (2), 2003 Journal Article, 2003 DOI

McLysaght, A., Hokamp K, and Wolfe, K.H., Extensive genomic duplication during early chordate evolution, Nature Genetics, 31, (2), 2002, p200 - 204 Journal Article, 2002 URL DOI

Lander, ES, Linton, LM, Birren, B, Nusbaum, C, Zody, MC, Baldwin, J, Devon, K, Dewar, K, Doyle, M, FitzHugh, W, Funke, R, Gage, D, Harris, K, Heaford, A, Howland, J, Kann, L, Lehoczky, J, LeVine, R, McEwan, P, McKernan, K, Meldrim, J, Mesirov, JP, Miranda, C, Morris, W, Naylor, J, Raymond, C, Rosetti, M, Santos, R, Sheridan, A, Sougnez, C, Stange-Thomann, N, Stojanovic, N, Subramanian, A, Wyman, D, Rogers, J, Sulston, J, Ainscough, R, Beck, S, Bentley, D, Burton, J, Clee, C, Carter, N, Coulson, A, Deadman, R, Deloukas, P, Dunham, A, Dunham, I, Durbin, R, French, L, Grafham, D, Gregory, S, Hubbard, T, Humphray, S, Hunt, A, Jones, M, Lloyd, C, McMurray, A, Matthews, L, Mercer, S, Milne, S, Mullikin, JC, Mungall, A, Plumb, R, Ross, M, Shownkeen, R, Sims, S, Waterston, RH, Wilson, RK, Hillier, LW, McPherson, JD, Marra, MA, Mardis, ER, Fulton, LA, Chinwalla, AT, Pepin, KH, Gish, WR, Chissoe, SL, Wendl, MC, Delehaunty, KD, Miner, TL, Delehaunty, A, Kramer, JB, Cook, LL, Fulton, RS, Johnson, DL, Minx, PJ, Clifton, SW, Hawkins, T, Branscomb, E, Predki, P, Richardson, P, Wenning, S, Slezak, T, Doggett, N, Cheng, JF, Olsen, A, Lucas, S, Elkin, C, Uberbacher, E, Frazier, M, Gibbs, RA, Muzny, DM, Scherer, SE, Bouck, JB, Sodergren, EJ, Worley, KC, Rives, CM, Gorrell, JH, Metzker, ML, Naylor, SL, Kucherlapati, RS, Nelson, DL, Weinstock, GM, Sakaki, Y, Fujiyama, A, Hattori, M, Yada, T, Toyoda, A, Itoh, T, Kawagoe, C, Watanabe, H, Totoki, Y, Taylor, T, Weissenbach, J, Heilig, R, Saurin, W, Artiguenave, F, Brottier, P, Bruls, T, Pelletier, E, Robert, C, Wincker, P, Smith, DR, Doucette-Stamm, L, Rubenfield, M, Weinstock, K, Lee, HM, Dubois, J, Rosenthal, A, Platzer, M, Nyakatura, G, Taudien, S, Rump, A, Yang, H, Yu, J, Wang, J, Huang, G, Gu, J, Hood, L, Rowen, L, Madan, A, Qin, S, Davis, RW, Federspiel, NA, Abola, AP, Proctor, MJ, Myers, RM, Schmutz, J, Dickson, M, Grimwood, J, Cox, DR, Olson, MV, Kaul, R, Raymond, C, Shimizu, N, Kawasaki, K, Minoshima, S, Evans, GA, Athanasiou, M, Schultz, R, Roe, BA, Chen, F, Pan, H, Ramser, J, Lehrach, H, Reinhardt, R, McCombie, WR, de la Bastide, M, Dedhia, N, Blöcker, H, Hornischer, K, Nordsiek, G, Agarwala, R, Aravind, L, Bailey, JA, Bateman, A, Batzoglou, S, Birney, E, Bork, P, Brown, DG, Burge, CB, Cerutti, L, Chen, HC, Church, D, Clamp, M, Copley, RR, Doerks, T, Eddy, SR, Eichler, EE, Furey, TS, Galagan, J, Gilbert, JG, Harmon, C, Hayashizaki, Y, Haussler, D, Hermjakob, H, Hokamp, K, Jang, W, Johnson, LS, Jones, TA, Kasif, S, Kaspryzk, A, Kennedy, S, Kent, WJ, Kitts, P, Koonin, EV, Korf, I, Kulp, D, Lancet, D, Lowe, TM, McLysaght, A, Mikkelsen, T, Moran, JV, Mulder, N, Pollara, VJ, Ponting, CP, Schuler, G, Schultz, J, Slater, G, Smit, AF, Stupka, E, Szustakowski, J, Thierry-Mieg, D, Thierry-Mieg, J, Wagner, L, Wallis, J, Wheeler, R, Williams, A, Wolf, YI, Wolfe, KH, Yang, SP, Yeh, RF, Collins, F, Guyer, MS, Peterson, J, Felsenfeld, A, Wetterstrand, KA, Patrinos, A, Morgan, MJ, de Jong, P, Catanese, JJ, Osoegawa, K, Shizuya, H, Choi, S, Chen, YJ, Szustakowki, J, Initial sequencing and analysis of the human genome., Nature, 409, (6822), 2001 Journal Article, 2001 DOI

Galligan, L, Livingstone, W, Volkov, Y, Hokamp, K, Murphy, C, Lawler, M, Fukudome, K, Smith, O, Characterization of protein C receptor expression in monocytes., British journal of haematology, 115, (2), 2001 Journal Article, 2001

Hokamp, K, Wolfe, K, What's new in the library? What's new in GenBank? let PubCrawler tell you., Trends in genetics : TIG, 15, (11), 1999 Journal Article, 1999