Dr. Karsten Hokamp
Senior Experimental Officer - Bioinforma, Genetics
Publications and Further Research Outputs
Peer-Reviewed Publications
Hamrock FJ, Ryan D, Shaibah A, Ershova AS, Mogre A, Sulimani AA, Ben Taarit S, Reichardt S, Hokamp K, Westermann AJ and Kröger C, Global analysis of the RNA"RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO, Nucleic Acids Research, 2024
Kumwenda B, Canals R, Predeus AV, Zhu X, Kröger C, Pulford C, Wenner N, Lora LL, Li Y, Owen SV, Everett D, Hokamp K, Heyderman RS, Ashton PM, Hinton JCD, Salmonella entericaserovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage, 2023
Kelly TE, Spillane CL, Ward MP, Hokamp K, Huang Y, Tewari P, Martin CM, Norris LA, Mohamed BM, Bates M, Brooks R, Selemidis S, Brooks DA, Kamran W, Saadeh FA, O'Toole SA, O'Leary JJ., Plasminogen activator inhibitor 1 is associated with high-grade serous ovarian cancer metastasis and is reduced in patients who have received neoadjuvant chemotherapy., Frontiers in cell and developmental biology, 11, 2023, p1150991
Shen N, Maggio M, Woods I, C Lowry M, Almasri R, Gorgun C, Eichholz KF, Stavenschi E, Hokamp K, Roche FM, O'Driscoll L, Hoey DA., Mechanically activated mesenchymal-derived bone cells drive vessel formation via an extracellular vesicle mediated mechanism., Journal of tissue engineering, 14, 2023, p20417314231186918
Lee B, Church M, Hokamp K, Alhussain MM, Bamagoos AA, Fleming AB., Systematic analysis of tup1 and cyc8 mutants reveals distinct roles for TUP1 and CYC8 and offers new insight into the regulation of gene transcription by the yeast Tup1-Cyc8 complex., PLoS genetics, 19, (8), 2023, pe1010876
Moran, B. and Smith, C.M. and Zaborowski, A. and Ryan, M. and Karman, J. and Dunstan, R.W. and Smith, K.M. and Hambly, R. and Musilova, J. and Petrasca, A. and Fabre, A. and O'Donnell, M. and Hokamp, K. and Mills, K.H.G. and Housley, W.J. and Winter, D.C. and Kirby, B. and Fletcher, J.M., Targeting the NLRP3 inflammasome reduces inflammation in hidradenitis suppurativa skin, The British journal of dermatology, 189, (4), 2023, p447-458
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 Oâ Sullivan, J.M. and Sheedy, F.J. and Fallon, P. and Oâ Donnell, J.S., von Willebrand factor links primary hemostasis to innate immunity, Nature Communications, 13, (1), 2022
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
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
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
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
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
TuShun R. Powers, Amanda L. Haeberle, Disa L. Hammarlöf, Jennifer A. Cundiff, Alexander V. Predeus, Karsten Hokamp, Jay C.D. Hinton, Leigh A. Knodler, Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica, 2021
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
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
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
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
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
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
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
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
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
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
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
, The impact of common genetic variants in the mitochondrial glycine cleavage system on relevant metabolites, Molecular genetics and metabolism reports, 2018
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
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-
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
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
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
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
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
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
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
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
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
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
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
Mansergh FC, Carrigan M, Hokamp K, Farrar GJ, Gene expression changes during retinal development and rod specification, Molecular Vision, 21, 2015, p61 - 87
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
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
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
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
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
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
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
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
Killick, K.E., Ní Cheallaigh, C., O'Farrelly, C., (...), Machugh, D.E., Harris, J., Receptor-mediated recognition of mycobacterial pathogens, Cellular Microbiology, 15, (9), 2013, p1484-1495
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 -
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
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
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
, Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis., Veterinary research, 2012
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
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
Dillon SC, Espinosa E, Hokamp K, Ussery DW, Casadesús J, Dorman CJ, LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium., Molecular microbiology, 85, (6), 2012, p1072-89
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, The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium., Proceedings of the National Academy of Sciences of the United States of America, 109, (20), 2012, pE1277-86
Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, et al., Proteome-Wide Analysis of Functional Divergence in Bacteria: Exploring a Host of Ecological Adaptations, PLoS ONE, 7, (4), 2012, pe35659
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
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
, G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9., Cellular immunology, 2010
Dillon SC, Cameron ADS, Hokamp K, Lucchini S, Hinton JCD, Dorman CJ, Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism, Molecular Microbiology, 76, (5), 2010, p1250 - 1265
, Comparative transcript profiling of Candida albicans and Candida dubliniensis identifies SFL2, a C. albicans gene required for virulence in a reconstituted epithelial infection model., Eukaryotic cell, 2010
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
Makino, T, Hokamp, K, McLysaght, A, The complex relationship of gene duplication and essentiality., Trends in genetics, 25, (4), 2009, p152 - 155
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
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
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
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
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
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
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-
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-
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
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
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
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
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
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
Hokamp, K., Wolfe, K.H., PubCrawler: keeping up comfortably with PubMed and GenBank, Nucleic Acids Res, 32, 2004, pW16-W19
Hokamp K, Wolfe KH., PubCrawler: keeping up comfortably with PubMed and GenBank., Nucleic Acids Research, 32, (Web Server Issue), 2004, pW16 - W19
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
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
Blanc, G, Hokamp, K, Wolfe, KH, A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome., Genome research, 13, (2), 2003
McLysaght, A., Hokamp K, and Wolfe, K.H., Extensive genomic duplication during early chordate evolution, Nature Genetics, 31, (2), 2002, p200 - 204
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
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
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
Non-Peer-Reviewed Publications
Debruyne C,Hodge L, Hokamp K, Ershova AS, Kröger C, Salcedo SP, Differential roles of the type I and II secretion systems for the intracellular ABC141 Acinetobacter baumannii infection, which elicits an atypical hypoxia response in endothelial cells, bioRxiv, 2025
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
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
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
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
Arpad Palfi; Sophia Millington-Ward; Naomi Chadderton; Karsten Hokamp; Stefanie M Hauck; Marius Ueffing; Sebastian Vencken; Catherine Greene; Paul Kenna; Jane Farrar, MiR-182 and miR-96 co-regulate Rac1 expression in the mouse retina, Investigative Ophthalmology and Visual Science (IOVS), ARVO 2015, 57, (12), 2015