Jörg Linde

Dr. Jörg Linde

Systems Biology and Bioinformatics

Phone: +49 3641 532-1290 Fax: +49 3641 532-2290 Email: joerg.linde@leibniz-hki.de

Main Research Areas
  • 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
Topics
Curriculum vitae

Professional Career

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)
Publications

Dix A, Czakai K, Leonhardt I, Schäferhoff K, Bonin M, Einsele H, Guthke R, Kurzai O, Löffler J, Linde J (2017) Specific and novel microRNAs are regulated as response to fungal infection in human dendritic cells Front. Microbiol. 8, Details Open Access

Böhringer M, Pohlers S, Schulze S, Albrecht-Eckardt D, Piegsa J, Weber M, Martin R, Hünniger K, Linde J, Guthke R, Kurzai O (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. Details PubMed

Czakai K, Leonhardt I, Dix A, Bonin M, Linde J, Einsele H, Kurzai O, Löffler J (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. Details PubMed Open Access

Dix A, Czakai K, Springer J, Fliesser M, Bonin M, Guthke R, Schmitt AL, Einsele H, Linde J, Löffler J (2016) Genome-wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. Frontiers in Microbiology 7, 320. Details PubMed PDF

Dix A, Vlaic S, Guthke R, Linde J (2016) Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers. Clin Microbiol Infect 22(7), 600-606. Details PubMed Open Access

Freihorst D, Brunsch M, Wirth S, Krause K, Kniemeyer O, Linde J, Kunert M, Boland W, Kothe E (2016) Smelling the difference: Transcriptome, proteome and volatilome changes after mating. Fungal Genet Biol , Details PubMed

Gerwien F, Safyan A, Wisgott S, Hille F, Kämmer P, Linde J, Brunke S, Kasper L, Hube B (2016) A novel hybrid iron regulation network combines features from pathogenic and non-pathogenic yeasts. mBio 7(5), e01782-16. Details PubMed Open Access

Guthke R, Gerber S, Conrad T, Vlaic S, Durmus S, Cakir T, Sevilgen E, Shelest E, Linde J (2016) Data-based reconstruction of gene regulatory networks of fungal pathogens. Front Microbiol 7, 570. Details PubMed Open Access

Hebecker B, Vlaic S, Conrad T, Bauer M, Brunke S, Kapitan M, Linde J, Hube B, Jacobsen ID (2016) Dual-species transcriptional profiling during systemic candidiasis reveals organ-specific host-pathogen interactions. Sci Rep 6, 36055. Details PubMed Open Access PDF

Hölzer M, Krähling V, Amman F, Barth E, Bernhart SH, Carmelo VAO, Collatz M, Doose G, Fallmann F, Feldhahn LM, Fricke M, Eggenhofer F, Ewald J, Linde J, Gebauer J, Gruber AJ, Hufsky F, Indrischek H, Mostajo NB, Ochsenreiter R, Riege K, Kanton S, Rivarola-Duarte L, Sahyoun AH, Saunders SJ, Seemann SE, Tanzer A, Vogel B, Wehner S, Wolfinger MT, Backofen R, Gorodkin J, Grosse I, Hofacker I, Hoffmann S, Kaleta C, Stadler PF, Becker S, Marz M (2016) Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells Sci Rep. 6, 34589. Details PubMed Open Access

Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Scherlach K, Martin K, Brakhage AA, Petzke L, Valiante V (2016) Draft genome sequences of fungus Aspergillus calidoustus. Genome Announc 4(2), e00102-16. Details PubMed

Manchanda H, Seidel N, Blaess MF, Claus RA, Linde J, Slevogt H, Sauerbrei A, Guthke R, Schmidtke M (2016) Differential Biphasic Transcriptional Host Response Associated with Coevolution of Hemagglutinin Quasispecies of Influenza A Virus Front Microbiol 7, 1167. Details PubMed

Schulze S, Schleicher J, Guthke R, Linde J (2016) How to Predict Molecular Interactions between Species? Front Microbiol 7, 442. Details PubMed

Altwasser R, Baldin C, Weber J, Guthke R, Kniemeyer O, Brakhage AA, Linde J, Valiante V (2015) Network Modeling Reveals Cross Talk of MAP Kinases during Adaptation to Caspofungin Stress in Aspergillus fumigatus. PLoS One 10(9), e0136932. Details PubMed Open Access

Brunsch M, Schubert D, Gube M, Ring C, Hanisch L, Linde J, Krause K, Kothe E (2015) Dynein Heavy Chain, Encoded by Two Genes in Agaricomycetes, Is Required for Nuclear Migration in Schizophyllum commune. PLoS One 10(8), e0135616. Details PubMed

Dix A, Hünniger K, Weber M, Guthke R, Kurzai O, Linde J (2015) Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. Front Microbiol 6, 171. Details PubMed Open Access

Horn F, Habel A, Scharf DH, Dworschak J, Brakhage AA, Guthke R, Hertweck C, Linde J (2015) Draft Genome Sequence and Gene Annotation of the Entomopathogenic Fungus Verticillium hemipterigenum. Genome Announc 3(1), pii: e01439-14. Details PubMed Open Access

Horn F, Linde J, Mattern DJ, Walther G, Guthke R, Brakhage AA, Valiante V (2015) Draft Genome Sequence of the Fungus Penicillium brasilianum MG11. Genome Announc 3(5), e00724-15. Details PubMed

Horn F, Üzüm Z, Möbius N, Guthke R, Linde J, Hertweck C (2015) Draft Genome Sequences of Symbiotic and Nonsymbiotic Rhizopus microsporus Strains CBS 344.29 and ATCC 62417. Genome Announc 3(1), pii: e01370-14. Details PubMed Open Access

Linde J, Duggan S, Weber M, Horn F, Sieber P, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O (2015) Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res 43(3), 1392-1406. Details PubMed Open Access

Linde J, Schulze S, Henkel SG, Guthke R (2015) Data- and knowledge-based modeling of gene regulatory networks: An update EXCLI Journal - Experimental and Clinical Sciences 14, 346-378. Details PDF

Priebe S, Kreisel C, Horn F, Guthke R, Linde J (2015) FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. Bioinformatics 31(3), 445-446. Details PubMed

Schleicher J(+), Conrad T(+), Gustafsson M, Cedersund G, Guthke R, Linde J (2015) Facing the challenges of multiscale modelling of bacterial and fungal pathogen-host interactions Briefings in Functional Genomics 2016, pii: elv064. (Review) Details PubMed Open Access

Schulze S, Henkel SG, Driesch D, Guthke R, Linde J (2015) Computational prediction of molecular pathogen-host interactions based on dual transcriptome data Front Microbiol 6, 65. Details PubMed Open Access

Wagner K, Linde J, Krause K, Gube M, Koestler T, Sammer D, Kniemeyer O, Kothe E (2015) Tricholoma vaccinum host communication during ectomycorrhiza formation. FEMS Microbiol Ecol 91(11), Details PubMed

Hillmann F, Linde J, Beckmann N, Cyrulies M, Strassburger M, Heinekamp T, Haas H, Guthke R, Kniemeyer O, Brakhage AA (2014) The novel globin protein fungoglobin is involved in low oxygen adaptation of Aspergillus fumigatus. Mol Microbiol 93(3), 539-553. Details PubMed

Horn F, Schroeckh V, Netzker T, Guthke R, Brakhage AA, Linde J (2014) Draft genome sequence of Streptomyces iranensis. Genome Announc 2(4), e00616-14. Details PubMed

Linde J, Schwartze V, Binder U, Lass-Flörl C, Voigt K, Horn F (2014) De Novo Whole-Genome Sequence and Genome Annotation of Lichtheimia ramosa. Genome Announc 2(5), pii: e00888-14. Details PubMed Open Access

Ramachandra S, Linde J, Brock M, Guthke R, Hube B, Brunke S (2014) Regulatory networks controlling nitrogen sensing and uptake in Candida albicans. PLoS One 9(3), e92734. Details PubMed Open Access

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K (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. Details PubMed Open Access

Wartenberg A, Linde J, Martin R, Schreiner M, Horn F, Jacobsen ID, Jenull S, Wolf T, Kuchler K, Guthke R, Kurzai O, Forche A, d'Enfert C, Brunke S, Hube B (2014) Microevolution of Candida albicans in macrophages restores filamentation in a nonfilamentous mutant. PLoS Genet 10(12), e1004824. Details PubMed Open Access

Palige K, Linde J, Martin R, Böttcher B, Citiulo F, Sullivan DJ, Weber J, Staib C, Rupp S, Hube B, Morschhäuser J, Staib P (2013) Global transcriptome sequencing identifies chlamydospore specific markers in Candida albicans and Candida dubliniensis. PLoS One 8(4), e61940. Details PubMed

Altwasser R, Linde J, Buyko E, Hahn U, Guthke R (2012) Genome-wide scale-free network inference for Candida albicans. Front Microbiol 3, 51. Details PubMed

Guthke R, Linde J, Mech F, Figge MT (2012) Systems biology of microbial infection. Front Microbiol 3, 328. Details PubMed Open Access

Linde J, Hortschansky P, Fazius E, Brakhage AA, Guthke R, Haas H (2012) Regulatory interactions for iron homeostasis in Aspergillus fumigatus inferred by a Systems Biology approach. BMC Syst Biol 6, 6. Details PubMed

Tierney L, Linde J, Müller S, Brunke S, Molina JC, Hube B, Schöck U, Guthke R, Kuchler K (2012) An interspecies regulatory network inferred from simultaneous RNA-seq of Candida albicans invading innate immune cells. Front Microbiol 3, 85. Details PubMed

Vlaic S, Schmidt-Heck W, Matz-Soja M, Marbach E, Linde J, Meyer-Baese A, Zellmer S, Guthke R, Gebhardt R (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. Details PubMed

Priebe S, Linde J, Albrecht D, Guthke R, Brakhage AA (2011) FungiFun: A web-based application for functional categorization of fungal genes and proteins. Fungal Genet Biol 48(4), 353-358. Details PubMed

Linde J, Wilson D, Hube B, Guthke R (2010) Regulatory network modelling of iron acquisition by a fungal pathogen in contact with epithelial cells. BMC Syst Biol 4, 148. Details PubMed

Linde J, Olsson B, Lubovac Z (2009) Network Properties for Ranking Predicted miRNA Targets in Breast Cancer. Adv Bioinformatics , 182689-182689. Details PubMed

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