Dr. Jörg Linde
- Analysis of Big Data / High-troughput data / OMICS data
- Next-Generation-Sequencing (Gene Prediction, SNP calling, RNASeq, Splicing)
- Statistics, supervised and unsupervised learning to detect biomarkers
- Modelling of host-pathogen interactions
- Dual RNASeq
|Since 01/2017||Head of Junior Research Group PiDOMICS at the Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena (Germany)|
|2013-2017||Postdoc for the Collaborative Research Center / Transregio 124 Pathogenic fungi and their human host: Networks of Interaction – FungiNet, Jena/Würzburg (Germany)|
|2011-2013||Postdoc at the Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena (Germany)|
|2011||Dr. rer. nat. in Bioinformatics, magna cum laude at the FSU Jena (Gemany)|
|2008-2011||PhD Systemsbiology, supervised by Prof. Dr. Reinhard Guthke at the FSU Jena (Germany)|
|2007-2008||Studies Bioinformatics, masters at the Högskolan Skövde (Sweden)|
|2003-2007||Studies Bioinformatics, diploma at FSU Jena (Germany)|
(2020) Survival strategies of pathogenic Candida species in human blood show independent and specific adaptations. mBio 11(5), e02435-20.
(2019) Comparative genomics of serial Candida glabrata isolates and the rapid acquisition of echinocandin resistance during therapy. Antimicrob Agents Chemother 63(2), e01628-18.
(2019) Phagocytic predation by the fungivorous amoeba Protostelium aurantium targets metal ion and redox homeostasis. bioRxiv 690503, preprint.
(2019) Treatment with etanercept and low monocyte concentration contribute to the risk of invasive aspergillosis in patients post allogeneic stem cell transplantation. Sci Rep 9(1), 17231.
(2018) Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin. BMC Syst Biol 12(1), 88.
(2018) Comparative study on alternative splicing in human fungal pathogens suggests its involvement during host invasion. Front Microbiol 9, 2313.
(2018) Two's company: studying interspecies relationships with dual RNA-seq. Curr Opin Microbiol 42, 7-12. (Review)
(2017) Specific and novel microRNAs are regulated as response to fungal infection in human dendritic cells. Front Microbiol 8, 270.
(2017) LASSIM—A network inference toolbox for genome-wide mechanistic modeling. PLOS Comput Biol 13(6), e1005608.
(2016) Candida albicans infection leads to barrier breakdown and a MAPK/NF-κB mediated stress response in the intestinal epithelial cell line C2BBe1. Cellular Microbiology 18(7), 889-904.
(2016) Krüppel-like Factor 4 modulates interleukin-6 release in human dendritic cells after in vitro stimulation with Aspergillus fumigatus and Candida albicans Sci Rep 6, 27990.
(2016) Genome-wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. Front Microbiol 7, 320.
(2016) Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 22(7), 600-606.
(2016) Smelling the difference: Transcriptome, proteome and volatilome changes after mating. Fungal Genet Biol 112, 2-11.
(2016) A novel hybrid iron regulation network combines features from pathogenic and non-pathogenic yeasts. mBio 7(5), e01782-16.
(2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570.
(2016) Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions. Sci Rep 6, 36055.
(2016) Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells Sci Rep 6, 34589.
(2016) Draft genome sequences of fungus Aspergillus calidoustus. Genome Announc 4(2), e00102-16.
(2016) Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus Front Microbiol 7, 1167.
(2016) How to Predict Molecular Interactions between Species? Front Microbiol 7, 442.
(2015) Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus. PLOS One 10(9), e0136932.
(2015) Dynein Heavy Chain, Encoded by Two Genes in Agaricomycetes, Is Required for Nuclear Migration in Schizophyllum commune. PLOS One 10(8), e0135616.
(2015) Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol 6, 171.
(2015) Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. Genome Announc 3(1), pii: e01439-14.
(2015) Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. Genome Announc 3(5), e00724-15.
(2015) Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. Genome Announc 3(1), pii: e01370-14.
(2015) Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43(3), 1392-1406.
(2015) Data- and knowledge-based modeling of gene regulatory networks: An update EXCLI Journal - Experimental and Clinical Sciences 14, 346-378.
(2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31(3), 445-446.
(2015) Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions Briefings in Functional Genomics 2016, pii: elv064. (Review)
(2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data Front Microbiol 6, 65.
(2015) Tricholoma vaccinum host communication during ectomycorrhiza formation. FEMS Microbiol Ecol 91(11),
(2014) The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93(3), 539-553.
(2014) Draft genome sequence of Streptomyces iranensis. Genome Announc 2(4), e00616-14.
(2014) De Novo Whole-Genome Sequence and Genome Annotation of Lichtheimia ramosa. Genome Announc 2(5), pii: e00888-14.
(2014) Regulatory networks controlling nitrogen sensing and uptake in Candida albicans. PLOS One 9(3), e92734.
(2014) Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial Mucorales (Mucoromycotina). PLOS Genetics 10(8), e1004496.
(2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLOS Genet 10(12), e1004824.
(2013) Global transcriptome sequencing identifies chlamydospore specific markers in Candida albicans and Candida dubliniensis. PLOS One 8(4), e61940.
(2012) Genome-wide scale-free network inference for Candida albicans. Front Microbiol 3, 51.
(2012) Systems biology of microbial infection. Front Microbiol 3, 328.
(2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Syst Biol 6, 6.
(2012) An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front Microbiol 3, 85.
(2012) The extended TILAR approach: a novel tool for dynamic modeling of the transcription factor network regulating the adaption to in vitro cultivation of murine hepatocytes. BMC Syst Biol 6, 147.
(2011) FungiFun: A web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol 48(4), 353-358.
(2010) Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol 4, 148.
(2009) Network Properties for Ranking Predicted miRNA Targets in Breast Cancer. Adv Bioinformatics , 182689-182689.