Publications

Draft genome sequence of the moderately heat-tolerant Lactococcus lactis subsp. lactis bv. diacetylactis strain GL2 from Algerian dromedary milk
Gabed N, Yang M, Bey Baba Hamed M, Drici H, Gross R, Dandekar T, Liang C (2015) Genome Announc 3(6):e01334-15. doi:10.1128/genomeA.01334-15.

LONELY-GUY Knocks Every Door: Crosskingdom Microbial Pathogenesis
Naseem M, Sarukhanyan E, Dandekar T (2015) TRPLSC 1363; doi:10.1016/j.tplants.2015.10.017

Development of Long Noncoding RNA-Based Strategies to Modulate Tissue Vascularization
Fiedler J, Breckwoldt K, Remmele CW, Hartmann D, Dittrich M, Pfanne A, Just A, Xiao K, Kunz M, Müller T, Hansen A, Geffers R, Dandekar T, Eschenhagen T, Thum T (2015) J Am Coll Cardiol. 66(18):2005-15. doi:10.1016/j.jacc.2015.07.081. PMID: 26516004 [PubMed - in process]

Integrated inference and evaluation of host-fungi interaction networks.
Remmele CW, Luther CH, Balkenhol J,n Dandekar T, Müller T, Dittrich MT (2015) Front Microbiol. 2015 Aug 4;6:764.

Scrutinizing the immune defence inventory of Camponotus floridanus applying total transcriptome sequencing.
Gupta SK, Kupper M, Ratzka C, Feldhaar H, Vilcinskas A, Gross R, Dandekar T, Förster F. (2015) BMC Genomics. 2015 Jul 22;16:540.

Host-pathogen interactions between the human innate immune system and Candida albicans-understanding and modeling defense and evasion strategies.
Dühring S, Germerodt S, Skerka C, Zipfel PF, Dandekar T, Schuster S. Front Microbiol. 2015 Jun 30;6:625. doi: 10.3389/fmicb.2015.00625.

DNAseq Workflow in a Diagnostic Context and an Example of a User Friendly Implementation.
Wolf B, Kuonen P, Dandekar T, Atlan D. (2015) Biomed Res Int. 2015;2015:403497. doi: 10.1155/2015/403497. Epub 2015 Jun 7. PubMed PMID: 26137478; PubMed Central PMCID: PMC4475531.

The nexus between growth and defence signalling: auxin and cytokinin modulate plant immune response pathways.
Naseem M, Kaltdorf M, Dandekar T. (2015) J Exp Bot. 2015 Jun 24. pii: erv297. [Epub ahead of print] Review. PubMed PMID: 26109575.

Convergence behaviour and Control in Non-Linear Biological Networks.
Karl S, Dandekar T. (2015) Sci Rep. (Nature Publ.) 2015 Jun 11;5:9746. doi: 10.1038/srep09746. PubMed PMID:26068060; PubMed Central PMCID: PMC4464179.

Diagnostic value of preoperative CT scan to stratify colon cancer for neoadjuvant therapy.
Wiegering A, Kunz M, Hussein M, Klein I, Wiegering V, Uthe FW, Dietz UA, Jurowich C, Bley T, Dandekar T, Germer CT, Ritter C. (2015) Int J Colorectal Dis. 2015 May 22. [Epub ahead of print] PubMed PMID: 25997602.

Host-adapted metabolism and its regulation in bacterial pathogens.
Dandekar T, Eisenreich W. Front Cell Infect Microbiol. 2015 Mar 27; 5:28. doi: 10.3389/fcimb. 2015.00028. eCollection 2015. PubMed PMID: 25870851;  

Salmonella-how a metabolic generalist adopts an intracellular lifestyle during infection.
Dandekar T, Fieselmann A, Fischer E, Popp J, Hensel M, Noster J. Front Cell Infect Microbiol. 2015 Jan 29;4:191. doi: 10.3389/fcimb.2014.00191. eCollection 2014. PubMed PMID: 25688337; PubMed CentralPMCID: PMC4310325.

Modelling antibiotic and cytotoxic Isoquinoline effects in Staphylococcus aureus, Staphylococcus epidermidis and mammalian cells.
Cecil A, Ohlsen K, Menzel T, François P, Schrenzel J, Fischer A, Dörries K, Selle M, Lalk M, Hantzschmann J, Dittrich M, Liang C, Bernhardt J, Ölschläger TA, Bringmann G, Bruhn H, Unger M, Ponte-Sucre A, Lehmann L, Dandekar T. (2015) International Journal of Medical Microbiology. 305(1):96-109.

Stratmann AT, Fecher D, Wangorsch G, Göttlich C, Walles T, Walles H, Dandekar T, Dandekar G, Nietzer SL (2014). Establishment of a human 3D lung cancer model based on a biological tissue matrix combined with a Boolean in silico model. Molecular Oncology 8(2):351-365.

Kunz M, Ahmed N, Dandekar T, Naseem M (2013). Hormone Signaling Networks Open Multiple Routes for Immunity and Disease in Plants. Biohelikon: Immunity and Diseases, 2013 1:2.

Hemer S, Konrad C, Spiliotis M, Koziol U, Schaack D, Förster S, Gelmedin V, Stadelmann B, Dandekar T, Hemphill A, Brehm K. Host insulin stimulates Echinococcus multilocularis insulin signalling pathways and larval development. BMC Biol. 2014 Jan 27;12:5. doi: 10.1186/1741-7007-12-5.

Cecil A, Ohlsen K, Menzel T, François P, Schrenzel J, Fischer A, Dörries K, Selle M, Lalk M, Hantzschmann J, Dittrich M, Liang C, Bernhardt J, Ölschläger TA, Bringmann G, Bruhn H, Unger M, Ponte-Sucre A, Lehmann L, and Dandekar T. (2014) Modelling antibiotic and cytotoxic Isoquinoline effects in Staphylococcus aureus, Staphylococcus epidermidis and mammalian cells. International Journal of Medical Microbiology 2014 Nov 27. pii: S1438-4221(14)00154-4. doi:10.1016/j.ijmm.2014.11.006. [Epub ahead of print]

Kunz M, Xiao K, Liang C, Viereck J, Pachel C, Frantz S, Thum T, Dandekar T. Bioinformatics of cardiovascular miRNA biology. J Mol Cell Cardiol. 2014 Dec 5. pii: S0022-2828(14)00387-3. doi:10.1016/j.yjmcc.2014.11.027. [Epub ahead of print] Review. PubMed PMID: 25486579.

Ahmed Z, Mayr M, Zeeshan S, Dandekar T, Mueller MJ, Fekete A. Lipid-Pro: A computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms. Bioinformatics. 2014 Nov 29. pii: btu796.

Ahmed Z, Zeeshan S, Huber C, Hensel M, Schomburg D, Münch R, Eylert E, Eisenreich W, Dandekar T. 'Isotopo' a database application for facile analysis and management of mass isotopomer data. Database (Oxford). 2014 Sep 9;2014. pii: bau077. doi: 10.1093/database/bau077. Print 2014. PubMed PMID: 25204646; PubMed Central PMCID: PMC4158277.

Kern S, Agarwal S, Huber K, Gehring AP, Strödke B, Wirth CC, Brügl T, Abodo LO, Dandekar T, Doerig C, Fischer R, Tobin AB, Alam MM, Bracher F, Pradel G. Inhibition of the SR Protein-Phosphorylating CLK Kinases of Plasmodium falciparum Impairs Blood Stage Replication and Malaria Transmission. PLoS One. 2014 Sep 4;9(9):e105732. doi:10.1371/journal.pone.0105732. eCollection 2014. PubMed PMID: 25188378; PubMed Central PMCID: PMC4154858.

Reister M, Hoffmeier K, Krezdorn N, Rotter B, Liang C, Rund S, Dandekar T, Sonnenborn U, Oelschlaeger TA. Complete genome sequence of the Gram-negative probiotic Escherichia coli strain Nissle 1917. J Biotechnol. 2014 Aug 2;187C:106-107. doi: 10.1016/j.jbiotec.2014.07.442. [Epub ahead of print] PubMed PMID: 25093936.

Cecil A, Gentschev I, Adelfinger M, Nolte I, Dandekar T, Szalay AA. Antigen profiling analysis of vaccinia virus injected canine tumors: Oncolytic virus efficiency predicted by boolean models. Bioengineered. 2014 Jul 31;5(5). [Epub ahead of print] PubMed PMID: 25078897; PubMed Central PMCID: PMC4156493.

Shityakov S, Förster C, Rethwilm A, Dandekar T. Evaluation and prediction of the HIV-1 central polypurine tract influence on foamy viral vectors to transduce dividing and growth-arrested cells. ScientificWorldJournal. 2014;2014:487969. doi: 10.1155/2014/487969. Epub 2014 Jun 9. PubMed PMID: 25009830; PubMed Central PMCID: PMC4070436.

Mischnik M, Gambaryan S, Subramanian H, Geiger J, Schütz C, Timmer J, Dandekar T. A comparative analysis of the bistability switch for platelet aggregation by logic ODE based dynamical modeling. Mol Biosyst. 2014 Aug;10(8):2082-9. doi: 10.1039/c4mb00170b. PubMed PMID: 24852796.

Boyanova D, Nilla S, Klau GW, Dandekar T, Müller T, Dittrich M. Functional module search in protein networks based on semantic similarity improves the analysis of proteomics data. Mol Cell Proteomics. 2014 Jul;13(7):1877-89. doi:10.1074/mcp.M113.032839. Epub 2014 May 7. PubMed PMID: 24807868; PubMed Central PMCID: PMC4083122.

Naseem M, Wölfling M, Dandekar T. Cytokinins for immunity beyond growth, galls and green islands. Trends Plant Sci. 2014 Aug;19(8):481-4. doi: 10.1016/j.tplants.2014.04.001. Epub 2014 May 1. PubMed PMID: 24794463.

Wirth CC, Glushakova S, Scheuermayer M, Repnik U, Garg S, Schaack D, Kachman MM, Weißbach T, Zimmerberg J, Dandekar T, Griffiths G, Chitnis CE, Singh S, Fischer R, Pradel G. Perforin-like protein PPLP2 permeabilizes the red blood cell membrane during egress of Plasmodium falciparum gametocytes. Cell Microbiol. 2014 May;16(5):709-33. doi: 10.1111/cmi.12288. Epub 2014 Apr 4. PubMed PMID: 24602217.

Naseem M, Kunz M, Dandekar T. Probing the unknowns in cytokinin-mediated immune defense in Arabidopsis with systems biology approaches. Bioinform Biol Insights. 2014 Feb 13;8:35-44. doi: 10.4137/BBI.S13462.. eCollection 2014. PubMed PMID: 24558299; PubMed Central PMCID: PMC3929428.

Fricke F, Malkusch S, Wangorsch G, Greiner JF, Kaltschmidt B, Kaltschmidt C, Widera D, Dandekar T, Heilemann M. Quantitative single-molecule localization microscopy combined with rule-based modeling reveals ligand-induced TNF-R1 reorganization toward higher-order oligomers. Histochem Cell Biol. 2014 Jul;142(1):91-101. doi: 10.1007/s00418-014-1195-0. Epub 2014 Feb 12. PubMed PMID: 24519400.

Hormone Signaling Networks Open Multiple Routes for Immunity and Disease in Plants. In Biohelikon: Immunity, und Diseases (Hrsg.), 2013. [BibSonomy: test]

Dandekar T Naseem M, Kunz M. Probing the unknowns in cytokinin mediated immune defense in Arabidopsis with systems biology approaches. In Bioinformatics, und Biology insights (Hrsg.), 2014. [BibSonomy: test]

Muhammad Naseem, Meik Kunz, Nazeer Ahmed, und Thomas Dandekar. Integration of boolean models on hormonal interactions and prospects of cytokinin-auxin crosstalk in plant immunity. Plant Signaling & Behavior, (8)4:e23890, Landes Bioscience, April 2013. [BibSonomy: test] URL

Sergey Shityakov, Winfried Neuhaus, Thomas Dandekar, und Carola Förster. Analysing molecular polar surface descriptors to predict blood-brain barrier permeation. International Journal of Computational Biology and Drug Design, (6)1/2:146, Inderscience Enterprises Ltd., 2013. [BibSonomy: test] URL

Marcel Mischnik, Desislava Boyanova, Katharina Hubertus, Jorg Geiger, Nicole Philippi, Marcus Dittrich, Gaby Wangorsch, Jens Timmer, und Thomas Dandekar. A Boolean view separates platelet activatory and inhibitory signalling as verified by phosphorylation monitoring including threshold behaviour and integrin modulation. Mol. BioSyst., (9)6:1326-1339, The Royal Society of Chemistry, 2013. [BibSonomy: test] URL

Volker Winstel, Chunguang Liang, Patricia Sanchez-Carballo, Matthias Steglich, Marta Munar, Barbara M. Bröker, Jose R. Penadés, Ulrich Nübel, Otto Holst, Thomas Dandekar, Andreas Peschel, und Guoqing Xia. Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens. Nat Commun, (4)Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved., August 2013. [BibSonomy: test] URL

Christof Audretsch, Daniel Lopez, Mugdha Srivastava, Christiane Wolz, und Thomas Dandekar. A semi-quantitative model of Quorum-Sensing in Staphylococcus aureus, approved by microarray meta-analyses and tested by mutation studies. Mol. BioSyst., (9)11:2665-2680, The Royal Society of Chemistry, 2013. [BibSonomy: test] URL

Marcel Mischnik, Katharina Hubertus, Jorg Geiger, Thomas Dandekar, und Jens Timmer. Dynamical modelling of prostaglandin signalling in platelets reveals individual receptor contributions and feedback properties. Mol. BioSyst., (9)10:2520-2529, The Royal Society of Chemistry, 2013. [BibSonomy: test] URL

Beate Krüger, Chunguang Liang, Florian Prell, Astrid Fieselmann, Andres Moya, Stefan Schuster, Uwe Völker, und Thomas Dandekar. Metabolic Adaptation and Protein Complexes in Prokaryotes. Metabolites, (2)4:940-958, MDPI AG, Dezember 2012. [BibSonomy: test] URL

C. Liang, B. Kruger, und T. Dandekar. GoSynthetic database tool to analyse natural and engineered molecular processes. Database, (2013)0:bat043-bat043, Oxford University Press, Januar 2013. [BibSonomy: test] URL

Ana-Maria Buga, Claus Jürgen Scholz, Senthil Kumar, James G. Herndon, Dragos Alexandru, Gabriel Radu Cojocaru, Thomas Dandekar, und Aurel Popa-Wagner. Identification of New Therapeutic Targets by Genome-Wide Analysis of Gene Expression in the Ipsilateral Cortex of Aged Rats after Stroke. PLoS ONE, (7)12:e50985, Public Library of Science, Dezember 2012. [BibSonomy: test] URL

B. Merget, C. Koetschan, T. Hackl, F. Forster, T. Dandekar, T. Muller, J. Schultz, und M. Wolf. The ITS2 Database. J Vis Exp, 612012. [BibSonomy: test]

Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Wolfgang Eisenreich, und Thomas Dandekar. Software LS-MIDA for efficient mass isotopomer distribution analysis in metabolic modelling.. BMC Bioinformatics, (14):218, 2013. [BibSonomy: test] URL

Stefan Karl, und Thomas Dandekar. Jimena: efficient computing and system state identification for genetic regulatory networks.. BMC Bioinformatics, (14):306, 2013. [BibSonomy: test] URL

Katja Schulze, Ulrich M. Tillich, Thomas Dandekar, und Marcus Frohme. PlanktoVision - an automated analysis system for the identification of phytoplankton.. BMC Bioinformatics, (14):115, 2013. [BibSonomy: test] URL