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Dr. Karsten Hokamp
Senior Experimental Officer - Bioinforma, Genetics

Publications and Further Research Outputs

Peer-Reviewed Publications

Drakeford, C. and Aguila, S. and Roche, F. and Hokamp, K. and Fazavana, J. and Cervantes, M.P. and Curtis, A.M. and Hawerkamp, H.C. and Dhami, S.P.S. and Charles-Messance, H. and Hackett, E.E. and Chion, A. and Ward, S. and Ahmad, A. and Schoen, I. and Breen, E. and Keane, J. and Murphy, R. and Preston, R.J.S. and O†Sullivan, J.M. and Sheedy, F.J. and Fallon, P. and O†Donnell, J.S., von Willebrand factor links primary hemostasis to innate immunity, Nature Communications, 13, (1), 2022 Journal Article, 2022 DOI

Harris NL, Hokamp K, Ménager H, Munoz-Torres M, Unni D, Vasilevsky N, Williams J., BOSC 2022: the first hybrid and 23rd annual Bioinformatics Open Source Conference., F1000Research, 11, 2022, p1034 Journal Article, 2022 DOI

de la Cerda Garcia-Caro, R. and Thompson, G. and Zhang, P. and Hokamp, K. and Roche, F. and Carlin, S. and Vrhovsek, U. and Bond, U., Enhanced flavour profiles through radicicol induced genomic variation in the lager yeasts, Saccharomyces pastorianus, Yeast, 39, (10), 2022, p535-547 Journal Article, 2022 DOI

de la Cerda-Garcia Caro, R. and Hokamp, K. and Roche, F. and Thompson, G. and Timouma, S. and Delneri, D. and Bond, U., Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation, PLoS Genetics, 18, (4), 2022 Journal Article, 2022 DOI TARA - Full Text

Powers TR, Haeberle AL, Predeus AV, Hammarlöf DL, Cundiff JA, Saldaña-Ahuactzi Z, Hokamp K, Hinton JCD, Knodler LA., Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica., PLoS pathogens, 17, (8), 2021, pe1009280 Journal Article, 2021 DOI

Ciara G Doran, Ryoichi Sugisawa, Michael Carty, Fiona Roche, Claire Fergus, Karsten Hokamp, Vincent P Kelly, Andrew G Bowie, CRISPR/Cas9-mediated SARM1 knockout and epitope-tagged mice reveal that SARM1 does not regulate nuclear transcription, but is expressed in macrophages, Journal of Biological Chemistry, 297, (6), 2021 Journal Article, 2021 URL DOI TARA - Full Text

Kenny C, O'Meara E, Ula" M, Hokamp K, O'Sullivan MJ., Global Chromatin Changes Resulting from Single-Gene Inactivation-The Role of SMARCB1 in Malignant Rhabdoid Tumor., Cancers, 13, (11), 2021 Journal Article, 2021 DOI

Palfi, A. and Yesmambetov, A. and Humphries, P. and Hokamp, K. and Farrar, G.J., Non-photoreceptor Expression of Tulp1 May Contribute to Extensive Retinal Degeneration in Tulp1-/- Mice, Frontiers in Neuroscience, 14, (656), 2020 Journal Article, 2020 TARA - Full Text DOI

Bricio-Moreno L, Chaguza C, Yahya R, Shears RK, Cornick JE, Hokamp K, Yang M, Neill DR, French N, Hinton JCD, Everett DB, Kadioglu A., Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes., mBio : Duplicate, marked for deletion, 11, (6), 2020 Journal Article, 2020 DOI

Edwards, S.C. and Sutton, C.E. and Ladell, K. and Grant, E.J. and McLaren, J.E. and Roche, F. and Dash, P. and Apiwattanakul, N. and Awad, W. and Miners, K.L. and Lalor, S.J. and Ribot, J.C. and Baik, S. and Moran, B. and McGinley, A. and Pivorunas, V. and Dowding, L. and Macoritto, M. and Paez-Cortez, J. and Slavin, A. and Anderson, G. and Silva-Santos, B. and Hokamp, K. and Price, D.A. and Thomas, P.G. and McLoughlin, R.M. and Mills, K.H.G., A population of proinflammatory T cells coexpresses αβ and γΎ T cell receptors in mice and humans, Journal of Experimental Medicine, 217, (5), 2020 Journal Article, 2020 DOI TARA - Full Text

Canals R, Hammarlöf DL, Kröger C, Owen SV, Fong WY, Lacharme-Lora L, Zhu X, Wenner N, Carden SE, Honeycutt J, Monack DM, Kingsley RA, Brownridge P, Chaudhuri RR, Rowe WPM, Predeus AV, Hokamp K, Gordon MA, Hinton JCD., Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580., PLoS biology, 17, (1), 2019, pe3000059 Journal Article, 2019 DOI

Sanfeliu, A. and Hokamp, K. and Gill, M. and Tropea, D., Transcriptomic analysis of Mecp2 mutant mice reveals differentially expressed genes and altered mechanisms in both blood and brain, Frontiers in Psychiatry, 10, (278), 2019 Journal Article, 2019 TARA - Full Text DOI

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., Circadian clock protein BMAL1 regulates IL-1ß in macrophages via NRF2., Proceedings of the National Academy of Sciences of the United States of America, 115, (36), 2018, pE8460-E8468 Journal Article, 2018 DOI

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., Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella., Proceedings of the National Academy of Sciences of the United States of America, 2018 Journal Article, 2018 DOI

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., The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978., Nucleic Acids Research, 2018 Journal Article, 2018 DOI

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, Bracken AP., A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities., Molecular Cell, 70, (3), 2018, p408-421 Journal Article, 2018 DOI TARA - Full Text

Kenny, Colin and McDonagh, Naomi and Lazaro, Antonio and O'Meara, Elaine and Klinger, Rut and O'Connor, Darran and Roche, Fiona and Hokamp, Karsten and O'Sullivan, Maureen J, Dysregulated mitogen-activated protein kinase signalling as an oncogenic basis for clear cell sarcoma of the kidney, The Journal of pathology, 244, (3), 2018, p334 - 345 Journal Article, 2018 DOI

O'Reilly J, Pangilinan F, Hokamp K, Ueland PM, Brosnan JT, Brosnan ME, Brody LC, Molloy AM., The impact of common genetic variants in the mitochondrial glycine cleavage system on relevant metabolites., Molecular genetics and metabolism reports, 16, 2018, p20-22 Journal Article, 2018 DOI

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., CD10(-)/ALDH(-) cells are the sole cisplatin-resistant component of a novel ovarian cancer stem cell hierarchy., Cell Death Disease, 19, (8), 2017, pe3128- Journal Article, 2017

Bibollet-Bahena, Olivia and Okafuji, Tatsuya and Hokamp, Karsten and Tear, Guy and Mitchell, Kevin J, A dual-strategy expression screen for candidate connectivity labels in the developing thalamus, PloS one, 12, (5), 2017, pe0177977 Journal Article, 2017 DOI TARA - Full Text

Streubel, G., Fitzpatrick, 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., Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal, EMBO Journal, 36, 2017, p2216 - 2232 Journal Article, 2017 DOI

Young, Conor P and Hillyer, Cory and Hokamp, Karsten and Fitzpatrick, Darren J and Konstantinov, Nikifor K and Welty, Jacqueline S and Ness, Scott A and Werner-Washburne, Margaret and Fleming, Alastair B and Osley, Mary Ann, Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast, BMC genomics, 18, (1), 2017, p107 Journal Article, 2017 DOI

Flanagan PR, Liu NN, Fitzpatrick DJ, Hokamp K, Köhler JR, Moran GP., The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation., mSphere, 2, (6), 2017 Journal Article, 2017 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

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

Colgan AM, Kröger C, Diard M, Hardt WD, Puente JL, Sivasankaran SK, Hokamp K, Hinton JC, The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium., PLoS Genetics, 12, (8), 2016, pe1006258 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

Casey, Maura E and Meade, Kieran G and Nalpas, Nicolas C and Taraktsoglou, Maria and Browne, John A and Killick, Kate E and Park, Stephen D E and Gormley, Eamonn and Hokamp, Karsten and Magee, David A and MacHugh, David E, Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq, Frontiers in immunology, 6, 2015, p23 Journal Article, 2015 DOI

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, Circadian control of innate immunity in macrophages by miR-155 targeting Bmal1., Proceedings of the National Academy of Sciences of the United States of America, 112, (23), 2015, p7231-6 Journal Article, 2015 DOI TARA - Full Text

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., Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients., FEBS J, 282, (18), 2015, p3455 - 3473 Journal Article, 2015 DOI

Salzberg L.I, Botella E, Hokamp K, Antelmann H, Maaà S, Becher D, Noone D, Devine K.M, Genome-wide analysis of phosphorylated PhoP binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis, Journal of Bacteriology, 197, (8), 2015, p1492 - 1506 Journal Article, 2015 URL 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 URL TARA - Full Text Other

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

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

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

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

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 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

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

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

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

Egan CM, Nyman U, Skotte J, Streubel G, Turner S, O'Connell DJ, Rraklli V, Dolan MJ, Chadderton N, Hansen K, Farrar GJ, Helin K, Holmberg J, Bracken AP., 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 TARA - Full Text DOI

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

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

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

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 TARA - Full Text DOI

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, 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

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

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

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, 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

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

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, 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

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

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 DOI URL

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

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

Non-Peer-Reviewed Publications

Harris NL, Cock PJA, Fields CJ, Hokamp K, Maia J, Munoz-Torres M, Sharan M, Williams J., BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference., F1000Research, 10, 2021 Journal Article, 2021 DOI

Harris NL, Cock PJA, Fields CJ, Hokamp K, Maia J, Munoz-Torres M, Taschuk M, Yehudi Y., The 21st annual Bioinformatics Open Source Conference (BOSC 2020, part of BCC2020)., F1000Research, 9, 2020 Journal Article, 2020 DOI

Harris NL, Cock PJA, Fields CJ, Greshake Tzovaras B, Heuer M, Hokamp K, Munoz-Torres M, Peltzer A, Rieck B, Wiencko H, Yehudi Y., BOSC 2019, the 20th annual Bioinformatics Open Source Conference., F1000Research, 8, 2019 Journal Article, 2019 DOI

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