Karsten Hokamp

Publications

• BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]
• CRISPR/Cas9-mediated SARM1 knockout and epitope-tagged mice reveal that SARM1 does not regulate nuclear transcription, but is expressed in macrophages
• The impact of common genetic variants in the mitochondrial glycine cleavage system on relevant metabolites
• The Candida albicans TOR-Activating GTPases Gtr1 and Rhb1 Coregulate Starvation Responses and Biofilm Formation
• Dysregulated mitogen-activated protein kinase signalling as an oncogenic basis for clear cell sarcoma of the kidney
• The primary transcriptome, small RNAs and regulation of antimicrobial resistance in Acinetobacter baumannii ATCC 17978
• Role of a single noncoding nucleotide in the evolution of an epidemic African clade of Salmonella
• Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
• Aneuploidy influences the gene expression profiles in Saccharomyces pastorianus group I and II strains during fermentation
• The transcriptional landscape and small RNAs of Salmonella enterica serovar Typhimurium.
• LeuO is a global regulator of gene expression in Salmonella enterica serovar Typhimurium.
• Fam60a defines a variant Sin3a-Hdac complex in embryonic stem cells required for self-renewal.
• Distinct histone methylation and transcription profiles are established during the development of cellular quiescence in yeast.
• The 2016 Bioinformatics Open Source Conference (BOSC).
• The Impact of 18 Ancestral and Horizontally-Acquired Regulatory Proteins upon the Transcriptome and sRNA Landscape of Salmonella enterica serovar Typhimurium.
• microRNA regulatory circuits in a mouse model of inherited retinal degeneration.
• The 2015 Bioinformatics Open Source Conference (BOSC 2015).
• Re-engineering cellular physiology by rewiring high-level global regulatory genes.
• RNA-seq Brings New Insights to the Intra-Macrophage Transcriptome of Salmonella Typhimurium.
• Delineating transcriptional networks of prognostic gene signatures refines treatment recommendations for lymph node-negative breast cancer patients.
• Circadian control of innate immunity in macrophages by miR-155 targeting Bmal1.
• Genome-wide analysis of phosphorylated PhoP binding to chromosomal DNA reveals several novel features of the PhoPR-mediated phosphate limitation response in Bacillus subtilis.
• Analysis of the Bovine Monocyte-Derived Macrophage Response to Mycobacterium avium Subspecies Paratuberculosis Infection Using RNA-seq.
• Gene expression changes during retinal development and rod specification.
• Perl One-Liners: Bridging the Gap Between Large Data Sets and Analysis Tools.
• Telomeric ORFs (TLOs) in Candida spp. Encode mediator subunits that regulate distinct virulence traits.
• Key Hub and Bottleneck Genes Differentiate the Macrophage Response to Virulent and Attenuated Mycobacterium bovis.
• RNA-seq Transcriptional Profiling of Peripheral Blood Leukocytes from Cattle Infected with Mycobacterium bovis.
• A model system for studying the transcriptomic and physiological changes associated with mammalian host-adaptation by Leptospira interrogans serovar Copenhageni.
• A transcription factor network coordinates attraction, repulsion, and adhesion combinatorially to control motor axon pathway selection.
• Complete Genome Sequence of Salmonella enterica Serovar Agona Pulsed-Field Type SAGOXB.0066, Cause of a 2008 Pan-European Outbreak.
• An infection-relevant transcriptomic compendium for Salmonella enterica Serovar Typhimurium.
• Receptor-mediated recognition of mycobacterial pathogens.
• Whole-transcriptome, high-throughput RNA sequence analysis of the bovine macrophage response to Mycobacterium bovis infection in vitro.
• The WalRK (YycFG) and σ(I) RsgI regulators cooperate to control CwlO and LytE expression in exponentially growing and stressed Bacillus subtilis cells.
• A Family of Vertebrate-Specific Polycombs Encoded by the LCOR/LCORL Genes Balance PRC2 Subtype Activities
• CD10-/ALDH- cells are the sole cisplatin-resistant component of a novel ovarian cancer stem cell hierarchy
• A dual-strategy expression screen for candidate connectivity labels in the developing thalamus
• BOSC 2022: the first hybrid and 23rd annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]
• Enhanced flavour profiles through radicicol induced genomic variation in the lager yeasts, Saccharomyces pastorianus
• 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
• von Willebrand factor links primary hemostasis to innate immunity
• Global analysis of the RNA-RNA interactome inAcinetobacter baumanniiAB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO
• The 2017 Bioinformatics Open Source Conference (BOSC) [version 1; referees: not peer reviewed]
• The 2018 Bioinformatics Open Source Conference (GCCBOSC 2018) [version 1; referees: not peer reviewed]
• The 2016 Bioinformatics Open Source Conference (BOSC)
• BOSC 2019, the 20th annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]
• The 21st annual Bioinformatics Open Source Conference (BOSC 2020, part of BCC2020) [version 1; peer review: not peer reviewed]
• Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
• Global Chromatin Changes Resulting from Single-Gene Inactivation—The Role of SMARCB1 in Malignant Rhabdoid Tumor
• ArrayPipe: a flexible processing pipeline for microarray data.
• Proteome-wide analysis of functional divergence in bacteria: exploring a host of ecological adaptations.
• Pan-genomic analysis of bovine monocyte-derived macrophage gene expression in response to in vitro infection with Mycobacterium avium subspecies paratuberculosis.
• Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis.
• Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes.
• Cell envelope gene expression in phosphate-limited Bacillus subtilis cells.
• PubCrawler: keeping up comfortably with PubMed and GenBank.
• Wrapping up BLAST and other applications for use on Unix clusters.
• A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome.
• The 2R hypothesis and the human genome sequence.
• Extensive genomic duplication during early chordate evolution.
• Characterization of protein C receptor expression in monocytes.
• Initial sequencing and analysis of the human genome.
• What's new in the library? What's new in GenBank? let PubCrawler tell you.
• Genome-wide analysis of the H-NS and Sfh regulatory networks in Salmonella Typhimurium identifies a plasmid-encoded transcription silencing mechanism.
• Comparative transcript profiling of Candida albicans and Candida dubliniensis identifies SFL2, a C. albicans gene required for virulence in a reconstituted epithelial infection model.
• G-protein-coupled receptor independent, immunomodulatory properties of chemokine CXCL9.
• Compensatory evolution of gene regulation in response to stress by Escherichia coli lacking RpoS.
• The extracellular Leucine-Rich Repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns.
• The complex relationship of gene duplication and essentiality.
• Transcriptome studies on Streptococcus pneumoniae, illustration of early response genes to THP-1 human macrophages.
• The growth phase-dependent regulation of the pilus locus genes by two-component system TCS08 in Streptococcus pneumoniae.
• A common microRNA signature in mouse models of retinal degeneration.
• InnateDB: facilitating systems-level analyses of the mammalian innate immune response.
• Streptococcus pneumoniae early response genes to human lung epithelial cells.
• Microarray analysis of Streptococcus pneumoniae gene expression changes to human lung epithelial cells.
• The extracellular leucine-rich repeat superfamily; a comparative survey and analysis of evolutionary relationships and expression patterns.
• Altered retinal microRNA expression profile in a mouse model of retinitis pigmentosa.
• Bovine and human cathelicidin cationic host defense peptides similarly suppress transcriptional responses to bacterial lipopolysaccharide.
• Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37.
• Effect of stress on viral-bacterial synergy in bovine respiratory disease: novel mechanisms to regulate inflammation.
• ProbeLynx: a tool for updating the association of microarray probes to genes.
• BOSC 2023, the 24th annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]
• Plasminogen activator inhibitor 1 is associated with high-grade serous ovarian cancer metastasis and is reduced in patients who have received neoadjuvant chemotherapy.
• Targeting the NLRP3 inflammasome reduces inflammation in hidradenitis suppurativa skin.
• Salmonella entericaserovar Typhimurium ST313 sublineage 2.2 has emerged in Malawi with a characteristic gene expression signature and a fitness advantage
• Mechanically activated mesenchymal-derived bone cells drive vessel formation via an extracellular vesicle mediated mechanism.
• The human tRNA-guanine transglycosylase displays promiscuous nucleobase preference but strict tRNA specificity.
• Lower Density and Shorter Duration of Nasopharyngeal Carriage by Pneumococcal Serotype 1 (ST217) May Explain Its Increased Invasiveness over Other Serotypes.
• Non-photoreceptor Expression of Tulp1 May Contribute to Extensive Retinal Degeneration in Tulp1-/- Mice.
• A population of proinflammatory T cells coexpresses αβ and γδ T cell receptors in mice and humans.
• Transcriptomic Analysis of Mecp2 Mutant Mice Reveals Differentially Expressed Genes and Altered Mechanisms in Both Blood and Brain.
• Adding function to the genome of African Salmonella Typhimurium ST313 strain D23580.
• Circadian clock protein BMAL1 regulates IL-1β in macrophages via NRF2.
• High-throughput fitness experiments reveal specific vulnerabilities of human-adapted Salmonella during stress and infection
• Global analysis of the RNA-RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO
• Niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle ofSalmonella enterica
• Global analysis of the RNA–RNA interactome in Acinetobacter baumannii AB5075 uncovers a small regulatory RNA repressing the virulence-related outer membrane protein CarO
• 25 Years of BOSC, the Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]