Dolan, Jackie, Walshe, Karen, Alsbury, Samantha, Hokamp, Karsten, O'Keeffe, Sean, Okafuji, Tatsuya, ...
Abstract Correction to 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...
Streptococcus pneumoniaeearly response genes to human lung epithelial cells (2008)
Song, Xin-Ming, Connor, Wayne, Hokamp, Karsten, Babiuk, Lorne A, Potter, Andrew A
Abstract Background Streptococcus pneumoniae infection starts from colonization of the host respiratory tract where interaction with host respiratory tract epithelial cells occurs. To investigate...
Journal of Structural and Functional Genomics 3: 95–110, 2003. (2008)
Karsten Hokamp, Aoife Mclysaght, Kenneth H. Wolfe
† These authors contributed equally to this work. Received 02.04.2002; accepted in final form 29.08.2002
Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa (2007)
Loscher, Carol J, Hokamp, Karsten, Kenna, Paul F, Ivens, Alasdair C, Humphries, Peter, Palfi, Arpad, ...
Abstract Background The role played by microRNAs (miRs) as common regulators in physiologic processes such as development and various disease states was recently highlighted. Retinitis pigmentosa...
Dolan, Jackie, Walshe, Karen, Alsbury, Samantha, Hokamp, Karsten, O'Keeffe, Sean, Okafuji, Tatsuya, ...
Abstract Background Leucine-rich repeats (LRRs) are highly versatile and evolvable protein-ligand interaction motifs found in a large number of proteins with diverse functions, including innate...
PubCrawler: keeping up comfortably with (2004)
Karsten Hokamp, Kenneth H. Wolfe
The free PubCrawler web service
ArrayPipe: a flexible processing pipeline for microarray data (2004)
Karsten Hokamp, Fiona M. Roche, Michael Acab, Marc-etienne Rousseau, Byron Kuo, David Goode, ...
A number of microarray analysis software packages exist already; however, none combines the userfriendly features of a web-based interface with potential ability to analyse multiple arrays at once...
microarray probes to genes (2004)
Fiona M. Roche, Karsten Hokamp, Michael Acab, Lorne A. Babiuk
ProbeLynx: a tool for updating the association of
PubCrawler: keeping up comfortably with PubMed and GenBank (2004)
Hokamp, Karsten, Wolfe, Kenneth H.
The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on...
ArrayPipe: a flexible processing pipeline for microarray data (2004)
Hokamp, Karsten, Roche, Fiona M., Acab, Michael, Rousseau, Marc-Etienne, Kuo, Byron, Goode, David, ...
A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once...
ProbeLynx: a tool for updating the association of microarray probes to genes (2004)
Roche, Fiona M., Hokamp, Karsten, Acab, Michael, Babiuk, Lorne A., Hancock, Robert E. W., Brinkman, Fiona S. L.
As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes....
Wrapping up BLAST and other applications for use on Unix clusters (2003)
Karsten Hokamp, Denis C. Shields, Kenneth H. Wolfe, Daniel R
Summary: We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster. 1) BLAST.pm is a new module for the 'MOLLUSC ' package that...
Wrapping up BLAST and other applications for use on Unix clusters (2003)
Hokamp, Karsten, Shields, Denis C., Wolfe, Kenneth H., Caffrey, Daniel R.
Summary: We have developed two programs that speed up common bioinformatic applications by spreading them across a UNIX cluster.(1) BLAST.pm, a new module for the ‘MOLLUSC’ package. (2) WRAPID, a...
A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome (2003)
Blanc, Guillaume, Hokamp, Karsten, Wolfe, Kenneth H.
The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing...
A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
Blanc, Guillaume, Hokamp, Karsten, Wolfe, Kenneth H.
The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing...
ArrayPipe: a flexible processing pipeline for microarray data
Hokamp, Karsten, Roche, Fiona M., Acab, Michael, Rousseau, Marc-Etienne, Kuo, Byron, Goode, David, ...
A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once...
ProbeLynx: a tool for updating the association of microarray probes to genes
Roche, Fiona M., Hokamp, Karsten, Acab, Michael, Babiuk, Lorne A., Hancock, Robert E. W., Brinkman, Fiona S. L.
As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes....
PubCrawler: keeping up comfortably with PubMed and GenBank
Hokamp, Karsten, Wolfe, Kenneth H.
The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on...
A Recent Polyploidy Superimposed on Older Large-Scale Duplications in the Arabidopsis Genome
Blanc, Guillaume, Hokamp, Karsten, Wolfe, Kenneth H.
The Arabidopsis genome contains numerous large duplicated chromosomal segments, but the different approaches used in previous analyses led to different interpretations regarding the number and timing...
ArrayPipe: a flexible processing pipeline for microarray data
Hokamp, Karsten, Roche, Fiona M., Acab, Michael, Rousseau, Marc-Etienne, Kuo, Byron, Goode, David, ...
A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once...
ProbeLynx: a tool for updating the association of microarray probes to genes
Roche, Fiona M., Hokamp, Karsten, Acab, Michael, Babiuk, Lorne A., Hancock, Robert E. W., Brinkman, Fiona S. L.
As genome sequence data and gene prediction improve, probes developed for a given microarray experiment should be continuously re-evaluated for their specificity for given genes....
PubCrawler: keeping up comfortably with PubMed and GenBank
Hokamp, Karsten, Wolfe, Kenneth H.
The free PubCrawler web service (http://www.pubcrawler.ie) has been operating for five years and so far has brought literature and sequence updates to over 22 000 users. It provides information on...
Dolan, Jackie, Walshe, Karen, Alsbury, Samantha, Hokamp, Karsten, O'Keeffe, Sean, Okafuji, Tatsuya, ...
Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa
Loscher, Carol J, Hokamp, Karsten, Kenna, Paul F, Ivens, Alasdair C, Humphries, Peter, Palfi, Arpad, ...
MicroRNA expression profiling showed that the retina of mice carrying a rhodopsin mutation that leads to retinitis pigmentosa have notably different microRNA profiles from wildtype mice; further in...
Streptococcus pneumoniae early response genes to human lung epithelial cells
Song, Xin-Ming, Connor, Wayne, Hokamp, Karsten, Babiuk, Lorne A, Potter, Andrew A
InnateDB: facilitating systems-level analyses of the mammalian innate immune response
Lynn, David J, Winsor, Geoffrey L, Chan, Calvin, Richard, Nicolas, Laird, Matthew R, Barsky, Aaron, ...
Although considerable progress has been made in dissecting the signaling pathways involved in the innate immune response, it is now apparent that this response can no longer be productively thought...
Dolan, Jackie, Walshe, Karen, Alsbury, Samantha, Hokamp, Karsten, O'Keeffe, Sean, Okafuji, Tatsuya, ...
Correction to 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...
Compensatory Evolution of Gene Regulation in Response to Stress by Escherichia coli Lacking RpoS
Stoebel, Daniel M., Hokamp, Karsten, Last, Michael S., Dorman, Charles J.
The RpoS sigma factor protein of Escherichia coli RNA polymerase is the master transcriptional regulator of physiological responses to a variety of stresses. This stress response comes at the expense...