Chair of Bioinformatics

    Publications

    Publications 2017

    Transcriptomic buffering of cryptic genetic variation contributes to meningococcal virulence.
    Ampattu BJ, Hagmann L, Liang C, Dittrich M, Schlüter A, Blom J, Krol E, Goesmann A, Becker A, Dandekar T, Müller T, Schoen C (2017) BMC Genomics. 2017 Apr 7;18(1):282. doi: 10.1186/s12864-017-3616-7. PubMed PMID: 28388876; PubMed Central PMCID: PMC5383966.

    A Systems Biology Methodology Combining Transcriptome and Interactome Datasets to Assess the Implications of Cytokinin Signaling for Plant Immune Networks.
    Kunz M, Dandekar T, Naseem M (2017) Methods Mol Biol. 2017;1569:165-173. doi:10.1007/978-1-4939-6831-2_14. PubMed PMID: 28265997. 

    Reconstruction of an Immune Dynamic Model to Simulate the Contrasting Role of Auxin and Cytokinin in Plant Immunity.
    Kaltdorf M, Dandekar T, Naseem M (2017) Methods Mol Biol. 2017;1569:83-92. doi: 10.1007/978-1-4939-6831-2_6. PubMed PMID: 28265989.

    Optimality principles reveal a complex interplay of intermediate toxicity and kinetic efficiency in the regulation of prokaryotic metabolism.
    Ewald J, Bartl M, Dandekar T, Kaleta C (2017) PLoS Comput Biol. 2017 Feb 17;13(2):e1005371. doi: 10.1371/journal.pcbi.1005371. eCollection 2017 Feb. PubMed PMID: 28212377; PubMed Central PMCID: PMC5315294.

    Frequency of regulatory T cells determines the outcome of the T-cell-engaging antibody blinatumomab in patients with B-precursor ALL.
    Duell J, Dittrich M, Bedke T, Mueller T, Eisele F, Rosenwald A, Rasche L, Hartmann E, Dandekar T, Einsele H, Topp MS (2017) Leukemia. 2017 Feb 24. doi: 10.1038/leu.2017.41. [Epub ahead of print] PubMed PMID: 28119525.

    FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms.
    Kaltdorf KV, Schulze K, Helmprobst F, Kollmannsberger P, Dandekar T, Stigloher C (2017) PLoS Comput Biol. 2017 Jan 5;13(1):e1005317. doi: 10.1371/journal.pcbi.1005317. eCollection 2017 Jan. PubMed PMID: 28056033; PubMed Central PMCID: PMC5289597.

    Non-Coding RNAs in Lung Cancer: Contribution of Bioinformatics Analysis to the Development of Non-Invasive Diagnostic Tools.
    Kunz M, Wolf B, Schulze H, Atlan D, Walles T, Walles H, Dandekar T (2017) Genes (Basel). 2016 Dec 26;8(1). pii: E8. doi: 10.3390/genes8010008. Review. PubMed PMID: 28035947; PubMed Central PMCID: PMC5295003.

    The Plant Hormone Cytokinin Confers Protection against Oxidative Stress in Mammalian Cells.
    Othman EM, Naseem M, Awad E, Dandekar T, Stopper H (2017) PLoS One. 2016 Dec 22;11(12):e0168386. doi: 10.1371/journal.pone.0168386. eCollection 2016. PubMed PMID: 28005918; PubMed Central PMCID: PMC5179003.

    Oxime Ethers of (E)-11-Isonitrosostrychnine as Highly Potent Glycine Receptor Antagonists.
    Mohsen AM, Mandour YM, Sarukhanyan E, Breitinger U, Villmann C, Banoub MM, Breitinger HG, Dandekar T, Holzgrabe U, Sotriffer C, Jensen AA, Zlotos DP (2017) J Nat Prod. 2016 Dec 23;79(12):2997-3005. doi: 10.1021/acs.jnatprod.6b00479. Epub 2016 Dec 14. PubMed PMID: 27966945.

    Influence of Platelet-rich Plasma on the immune response of human monocyte-derived dendritic cells and macrophages stimulated with Aspergillus fumigatus.
    Czakai K, Dittrich M, Kaltdorf M, Müller T, Krappmann S, Schedler A, Bonin M, Dühring S, Schuster S, Speth C, Rambach G, Einsele H, Dandekar T, Löffler J (2017) Int J Med Microbiol. 2017 Feb;307(2):95-107. doi: 10.1016/j.ijmm.2016.11.010. Epub 2016 Dec 9. PubMed PMID: 27965080.

    Publications 2016

    Revisiting adult neurogenesis and the role of erythropoietin for neuronal and oligodendroglial differentiation in the hippocampus.
    Hassouna I, Ott C, Wüstefeld L, Offen N, Neher RA, Mitkovski M, Winkler D, Sperling S, Fries L, Goebbels S, Vreja IC, Hagemeyer N, Dittrich M, Rossetti MF, Kröhnert K, Hannke K, Boretius S, Zeug A, Höschen C, Dandekar T, Dere E, Neher E, Rizzoli SO, Nave KA, Sirén AL, Ehrenreich H (2016) Mol Psychiatry. 2016 Jan 26. doi: 10.1038/mp.2015.212.

    Long noncoding RNA Chast promotes cardiac remodeling.
    Viereck J, Kumarswamy R, Foinquinos A, Xiao K, Avramopoulos P, Kunz M, Dittrich M, Maetzig T, Zimmer K, Remke J, Just A, Fendrich J, Scherf K, Bolesani  E, Schambach A, Weidemann F, Zweigerdt R, de Windt LJ, Engelhardt S, Dandekar T,  Batkai S, Thum T (2016)  Sci Transl Med. 2016 Feb 17;8(326):326ra22. doi: 10.1126/scitranslmed.aaf1475. PubMed PMID: 26888430.

    The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development.
    Kunz M, Liang C, Nilla S, Cecil A, Dandekar T (2016) Database (Oxford). 2016 Apr 7;2016. pii: baw041. doi: 10.1093/database/baw041. Print 2016. PubMed PMID: 27055828; PubMed Central PMCID: PMC4823820.

    A Combined 3D Tissue Engineered In Vitro/In Silico Lung Tumor Model for Predicting Drug Effectiveness in Specific Mutational Backgrounds.
    Göttlich C, Müller LC, Kunz M, Schmitt F, Walles H, Walles T, Dandekar T, Dandekar G, Nietzer SL (2016) J Vis Exp. 2016 Apr 6;(110). doi: 10.3791/53885. PubMed PMID: 27077967.

    A Staphylococcus aureus Proteome Overview: Shared and Specific Proteins and Protein Complexes from Representative Strains of All Three Clades.
    Liang, C.; Schaack, D.; Srivastava, M.; Gupta, S.K.; Sarukhanyan, E.; Giese, A.; Pagels, M.; Romanov, N.; Pané-Farré, J.; Fuchs, S.; Dandekar, T (2016) Proteomes 2016, 4, 8.

    Analyzing ERK ½ signalling and targets.
    Brietz A, Schuch KV, Wangorsch G, Lorenz K, Dandekar T (2016)  Mol Biosyst. 2016 Jul 19;12(8):2436-46. doi: 10.1039/c6mb00255b.

    Systematic identification of anti-fungal drug targets by a metabolic network approach.
    Kaltdorf M, Srivastava M, Gupta SK, Liang C, Binder J, Dietl AM, Meir Z, Haas H, Osherov N, Krappmann S, Dandekar T (2016) Frontiers Molecular Bioscience 3: 22.

    An antibiotic target ranking and prioritization pipeline combining sequence, structure and network-based approaches exemplified for Serratia marcescens.
    Gupta SK, Gross R, Dandekar T (2016)  Gene. 2016 Oct 10;591(1):268-78. doi:10.1016/j.gene.2016.07.030. Epub 2016 Jul 16. PubMed PMID: 27425866.

    Mining biomedical images towards valuable information retrieval in biomedical and life sciences.
    Ahmed Z, Zeeshan S, Dandekar T (2016) Database (Oxford). 2016 Sep 6;2016. pii: baw134. doi: 10.1093/database/baw134. Print 2016.  

    Application of Proteomic Biomarkers in Livestock Disease Management. (Chapter)
    Oskoueian E, Eckersall PD, Bencurova E, Dandekar T (2016) Agricultural Proteomics
    Vol. 2 DOI 10.1007/978-3-319-43278-6_14 G.H. Salekdeh (ed.), Springer

    Publications 2015

    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.

    Publications Dr. Frank Förster

    Publications Dr. Tobias Müller

    Publications Prof. Jörg Schultz

    Publications Dr. Matthias Wolf

    Publications 2014

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

    Bioinformatics of cardiovascular miRNA biology.
    Kunz M, Xiao K, Liang C, Viereck J, Pachel C, Frantz S, Thum T, Dandekar T.  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.

    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, and Dandekar T. (2014)  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]

    Hormone Signaling Networks Open Multiple Routes for Immunity and Disease in 
    Plants.

    Kunz M, Ahmed N, Dandekar T, Naseem M (2013). Biohelikon: Immunity and Diseases, 2013 1:2.

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

    Inhibition of the SR Protein-Phosphorylating CLK Kinases of Plasmodium falciparum
    Impairs Blood Stage Replication and Malaria Transmission.
    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. PLoS One. 2014 Sep 4;9(9):e105732. doi: 10.1371/journal.pone.0105732. eCollection 2014. 
    PubMed PMID: 25188378; PubMed Central PMCID: PMC4154858.

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

    Antigen profiling analysis of vaccinia virus injected canine tumors: Oncolytic virus
    efficiency predicted by boolean models.

    Cecil A, Gentschev I, Adelfinger M, Nolte I, Dandekar T, Szalay AA.  Bioengineered. 2014 Jul 31;5(5). [Epub ahead of print] PubMed PMID: 25078897; PubMed Central PMCID: PMC4156493.

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

    A comparative analysis of the bistability switch for platelet aggregation by
    logic ODE based dynamical modeling.

    Mischnik M, Gambaryan S, Subramanian H, Geiger J, Schütz C, Timmer J, Dandekar T. Mol Biosyst. 2014 Aug;10(8):2082-9. doi: 10.1039/c4mb00170b. PubMed PMID: 24852796.

    Functional module search in protein networks based on semantic similarity improves the
    analysis of proteomics data.

    Boyanova D, Nilla S, Klau GW, Dandekar T, Müller T, Dittrich M. 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.

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

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

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

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

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

    Establishment of a human 3D lung cancer model based on a biological tissue matrix combined with a Boolean in silico model.
    Stratmann AT, Fecher D, Wangorsch G, Göttlich C, Walles T, Walles H, Dandekar T, Dandekar G, Nietzer SL. Mol Oncol. 2014 Mar;8(2):351-65. doi: 10.1016/j.molonc.2013.11.009. Epub 2013 Dec 18.

    Publications 2013

    'Isotopo' a database application for facile analysis and management of mass isotopomer data.
    (Oxford, Database (2014).

    A Boolean view separates platelet activatory and inhibitory signalling as verified by phosphorylation monitoring including threshold behaviour and integrin modulation.
    Mischnik, Marcel; Boyanova, Desislava; Hubertus, Katharina; Geiger, Jorg; Philippi, Nicole; Dittrich, Marcus; Wangorsch, Gaby; Timmer, Jens; Dandekar, Thomas in Mol. BioSyst. (2013). 9(6) 1326-1339.

    A semi-quantitative model of Quorum-Sensing in Staphylococcus aureus, approved by microarray meta-analyses and tested by mutation studies.
    Audretsch, Christof; Lopez, Daniel; Srivastava, Mugdha; Wolz, Christiane; Dandekar, Thomas in Mol. BioSyst. (2013). 9(11) 2665-2680.

    Analysing molecular polar surface descriptors to predict blood-brain barrier permeation.
    Shityakov, Sergey; Neuhaus, Winfried; Dandekar, Thomas; Förster, Carola in International Journal of Computational Biology and Drug Design (2013). 6(1/2) 146.

    Dynamical modelling of prostaglandin signalling in platelets reveals individual receptor contributions and feedback properties.
    Mischnik, Marcel; Hubertus, Katharina; Geiger, Jorg; Dandekar, Thomas; Timmer, Jens in Mol. BioSyst. (2013). 9(10) 2520-2529.

    GoSynthetic database tool to analyse natural and engineered molecular processes.
    Liang, C.; Kruger, B.; Dandekar, T. in Database (2013). 2013 bat043-bat043.

    Hormone Signaling Networks Open Multiple Routes for Immunity and Disease in Plants.
    Immunity, Biohelikon:; Diseases, (2013).

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

    Integration of boolean models on hormonal interactions and prospects of cytokinin-auxin crosstalk in plant immunity.
    Naseem, Muhammad; Kunz, Meik; Ahmed, Nazeer; Dandekar, Thomas in Plant Signaling & Behavior (2013). 8(4) e23890.

    Jimena: efficient computing and system state identification for genetic regulatory networks.
    Karl, Stefan; Dandekar, Thomas in BMC Bioinformatics (2013). 14 306.

    Metabolic Adaptation and Protein Complexes in Prokaryotes.
    Krüger, Beate; Liang, Chunguang; Prell, Florian; Fieselmann, Astrid; Moya, Andres; Schuster, Stefan; Völker, Uwe; Dandekar, Thomas in Metabolites (2012). 2(4) 940-958.

    PlanktoVision - an automated analysis system for the identification of phytoplankton.
    Schulze, Katja; Tillich, Ulrich M.; Dandekar, Thomas; Frohme, Marcus in BMC Bioinformatics (2013). 14 115.

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

    The ITS2 Database.
    Merget, B.; Koetschan, C.; Hackl, T.; Forster, F.; Dandekar, T.; Muller, T.; Schultz, J.; Wolf, M. in J Vis Exp (2012). (61)

    Wall teichoic acid structure governs horizontal gene transfer between major bacterial pathogens.
    Winstel, Volker; Liang, Chunguang; Sanchez-Carballo, Patricia; Steglich, Matthias; Munar, Marta; Bröker, Barbara M.; Penadés, Jose R.; Nübel, Ulrich; Holst, Otto; Dandekar, Thomas; Peschel, Andreas; Xia, Guoqing in Nat Commun (2013). 4 Naseem M, Kaldorf M, Hussain A, Dandekar T (2013).

    The impact of cytokinin on jasmonate-salicylate antagonism in Arabidopsis immunity against infection with Pst DC3000. Plant Signal Behav.,
    9(1). doi: pii: e26791 [Epub ahead of print]

    Publications 2012

    Metabolic Adaption and Protein Complexes in Prokaryotes Metabolites 2(4), 
    Krüger B, Liang C, Prell F, Fieselmann A, Moya A, Schuster S, Voelker U, Dandekar T (2012) 940-958; doi:10.3390/metabo2040940

    Analyzing Thiol-Dependent Redox Networks in the Presence of Methylene Blue and Other Antimalarial Agents with RT-PCR-Supported in silico Modeling. Bioinform Biol Insights. Zirkel J, Cecil A, Schäfer F, Rahlfs S, Ouedraogo A, Xiao K, Sawadogo S, Coulibaly B, Becker K, Dandekar T. 2012;6:287-302. doi: 10.4137/BBI.S10193. Epub 2012 Dec 3. PubMed PMID:  23236254; PubMed Central PMCID: PMC3516044.

    The role of auxin-cytokinin antagonism in plant-pathogen interactions. 
    Naseem M, Dandekar T. , PLoS Pathog. 2012;8(11):e1003026. doi: 10.1371/journal.ppat.1003026. Epub 2012 Nov 29. PubMed PMID: 23209407; PubMed Central PMCID: PMC3510258.

    Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform. Dandekar T, Fieselmann A, Majeed S, Ahmed Z. 2012 Nov 9. [Epub ahead of print] PubMed PMID: 23142828.

    Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state.
    Schokraie E, Warnken U, Hotz-Wagenblatt A, Grohme MA, Hengherr S, Förster F, Schill RO, Frohme M, Dandekar T, Schnölzer M. PLoS One. 2012;7(9):e45682.

    Molecular characterization of antimicrobial peptide genes of the carpenter ant Camponotus floridanus.
    Ratzka C, Förster F, Liang C, Kupper M, Dandekar T, Feldhaar H, Gross R. PLoS One. 2012;7(8):e43036. doi: 10.1371/journal.pone.0043036. Epub 2012 Aug 9. PubMed PMID: 22912782; PubMed Central PMCID: PMC3415428.

    Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum.
    Beisser D, Grohme MA, Kopka J, Frohme M, Schill RO, Hengherr S, Dandekar T, Klau GW, Dittrich M, Müller T. I BMC Syst Biol. 2012 Jun 19;6:72. doi: 10.1186/1752-0509-6-72. PubMed PMID: 22713133; PubMed Central PMCID: PMC3534414.

    Integrated systems view on networking by hormones in Arabidopsis immunity reveals multiple crosstalk for cytokinin.
    Naseem M, Philippi N, Hussain A, Wangorsch G, Ahmed N, Dandekar T. Plant Cell. 2012 May;24(5):1793-814. doi: 10.1105/tpc.112.098335. Epub 2012 May 29. PubMed PMID: 22643121; PubMed Central PMCID: PMC3442570.

    Different evolutionary modifications as a guide to rewire two-component systems. Bioinform Biol Insights.
    Krueger B, Friedrich T, Förster F, Bernhardt J, Gross R, Dandekar T. Bioinform Biol Insights. 37/BBI.S9356. Epub 2012 May 3. PubMed PMID: 22586357; PubMed Central PMCID: PMC3348925.

    Robustness and accuracy of functional modules in integrated network analysis.
    Bioinformatics.

    Beisser D, Brunkhorst S, Dandekar T, Klau GW, Dittrich MT, Müller T. 2012 Jul 15;28(14):1887-94. doi: 10.1093/bioinformatics/bts265.  Epub 2012 May 11. PubMed PMID: 22581175.

    Salmonella enterica: a surprisingly well-adapted intracellular lifestyle. Front Microbiol.
    Dandekar T, Astrid F, Jasmin P, Hensel M.  2012;3:164. doi: 10.3389/fmicb.2012.00164. Epub 2012 May 3. PubMed PMID: 22563326; PubMed Central PMCID: PMC3342586.

    T. Transcriptome analysis in tardigrade species reveals specific molecular
    pathways for stress adaptations. Bioinform Biol Insights.

    Förster F, Beisser D, Grohme MA, Liang C, Mali B, Siegl AM, Engelmann JC, Shkumatov AV, Schokraie E, Müller T, Schnölzer M, Schill RO, Frohme M, Dandekar 2012;6:69-96.

    Toward a Systemic Understanding of Listeria monocytogenes Metabolism during Infection. Front Microbiol.
    Fuchs TM, Eisenreich W, Kern T, Dandekar T.  2012;3:23. doi: 10.3389/fmicb.2012.00023. Epub 2012 Feb 3. PubMed PMID: 22347216; PubMed Central PMCID: PMC3271275.

    PlateletWeb: a systems biologic analysis of signaling networks in human platelets. Blood. 2012
    Boyanova D, Nilla S, Birschmann I, Dandekar T, Dittrich M. Jan 19;119(3):e22-34. doi: 10.1182/blood-2011-10-387308. Epub 2011 Nov 28. PubMed PMID: 22123846.

    Publications 2011

    Immune response of the ant Camponotus floridanus against pathogens and its obligate mutualistic endosymbiont. Insect Biochem Mol Biol.
    Ratzka C, Liang C, Dandekar T, Gross R, Feldhaar H. 2011 Mar 23. [Epub ahead of print] PubMed PMID: 21440063.

    Modeling antibiotic and cytotoxic effects of the dimeric isoquinoline IQ-143 on metabolism and its regulation in Staphylococcus aureus, Staphylococcus epidermidis and human cells. Genome Biol.
    Cecil A, Rikanovic C, Ohlsen K, Liang C, Bernhardt J, Oelschlaeger TA, Gulder T, Bringmann G, Holzgrabe U, Unger M, Dandekar T. 2011 Mar 21;12(3):R24. [Epub ahead of print] PubMed PMID: 21418624.

    A metabolomics and proteomics study of the adaptation of Staphylococcus aureus to glucose starvation. Mol Biosyst.
    Liebeke M, Dörries K, Zühlke D, Bernhardt J, Fuchs S, Pané-Farré J, Engelmann S, Völker U, Bode R, Dandekar T, Lindequist U, Hecker M, Lalk M. 2011 Apr 1;7(4):1241-53. Epub 2011 Feb 16. PubMed PMID: 21327190.

    Two nucleus-localized CDK-like kinases with crucial roles for malaria parasite erythrocytic replication are involved in phosphorylation of splicing factor. J Cell Biochem.
    Agarwal S, Kern S, Halbert J, Przyborski JM, Baumeister S, Dandekar T, Doerig C, Pradel G. 2011 Feb 10. doi: 10.1002/jcb.23034. [Epub ahead of print] PubMed PMID: 21312235.

    Tardigrade bioinformatics: Molecular adapations, DNA j-family and dynamical modeling. Journal of Zoological Systematics and Evolutionary
    Förster F, Beisser D, Frohme M, Schill RO und Dandekar T (2011). Research 49 (1), 120-126.

    Staphylococcus aureus physiological growth limitations: Insights from flux calculations built on proteomics and external metabolite data. Proteomics.
    Liang C, Liebeke M, Schwarz R, Zühlke D, Fuchs S, Menschner L, Engelmann S, Wolz C, Jaglitz S, Bernhardt J, Hecker M, Lalk M, Dandekar T. 2011 May;11(10):1915-35.

    Integrated Platelet Networks for the Analysis of Different System States. Current Proteomics
    8, in press  Dittrich M, Birschmann I, Dandekar T (2011)

    Integration of Boolean models exemplified on hepatocyte signal transduction. Briefings in Bioinformatics
    Schlatter R, Philippi N, Wangorsch G, Pick R, Sawodny O, Borner C, Timmer J, Ederer M and Dandekar T. BIB-11-0103.R1, in press

    Time-resolved in silico modeling of fine-tuned cAMP signaling in platelets: feedback loops, titrated phosphorylations and pharmacological modulation. BMC Syst Biol.
    Wangorsch G, Butt E, Mark R, Hubertus K, Geiger J, Dandekar T, Dittrich M. 2011 Oct 28;5:178.PMID:22034949.

    Publications 2010

    Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL. Proteomics.
    Fuchs S, Mehlan H, Kusch H, Teumer A, Zühlke D, Berth M, Wolf C, Dandekar T, Hecker M, Engelmann S, Bernhardt J. 2010 Aug;10(16):2982-3000. PubMed PMID: 20662099.

    Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges.
    Siegl A, Kamke J, Hochmuth T, Piel J, Richter M, Liang C, Dandekar T, Hentschel U. ISME J. 2010 Jul 8. [Epub ahead of print] PubMed PMID: 20613790.

    Developmental profiling by mass spectrometry of phosphocholine containing phospholipids in the rat nervous system reveals temporo-spatial gradients. J Neurochem.
    Löhmann C, Schachmann E, Dandekar T, Villmann C, Becker CM. 2010 Aug;114(4):1119-34. Epub 2010 May 28. PubMed PMID: 20524967.

    Carbon metabolism of intracellular bacterial pathogens and possible links to virulence. Nat Rev Microbiol.
    Eisenreich W, Dandekar T, Heesemann J, Goebel W. 2010 Jun;8(6):401-12. Epub 2010 May 10. Review. PubMed PMID: 20453875.

    G244E in the canine factor IX gene leads to severe haemophilia B in Rhodesian Ridgebacks.
    Mischke R, Kühnlein P, Kehl A, Langbein-Detsch I, Steudle F, Schmid A, Dandekar T, Czwalinna A, Müller E. Vet J. 2010 Mar 17. [Epub ahead of print] PubMed PMID: 20303304.

    Transcriptome survey of the anhydrobiotic tardigrade Milnesium tardigradum in comparison with Hypsibius dujardini and Richtersius coronifer. BMC Genomics.
    Mali B, Grohme MA, Förster F, Dandekar T, Schnölzer M, Reuter D, We?nicz W, Schill RO, Frohme M. 2010 Mar 12;11:168. PubMed PMID: 20226016; PubMed Central PMCID: PMC2848246.

    Proteomic analysis of tardigrades: towards a better understanding of molecular mechanisms by anhydrobiotic organisms. PLoS One.
    Schokraie E, Hotz-Wagenblatt A, Warnken U, Mali B, Frohme M, Förster F, Dandekar T, Hengherr S, Schill RO, Schnölzer M. 2010 Mar 3;5(3):e9502. PubMed PMID: 20224743; PubMed Central PMCID: PMC2835947.

    The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays. BMC Bioinformatics.
    Vainshtein Y, Sanchez M, Brazma A, Hentze MW, Dandekar T, Muckenthaler MU. 2010 Mar 1;11:112. PubMed PMID: 20193060; PubMed Central PMCID: PMC2838865.

    BioNet: an R-Package for the functional analysis of biological networks. Bioinformatics.
    Beisser D, Klau GW, Dandekar T, Müller T, Dittrich MT.  2010 Apr 15;26(8):1129-30. Epub 2010 Feb 25. PubMed PMID: 20189939.

    Characterization of a novel interaction between vasodilator-stimulated phosphoprotein and Abelson interactor 1 in human platelets: a concerted computational and experimental approach. Arterioscler Thromb Vasc Biol.
    Dittrich M, Strassberger V, Fackler M, Tas P, Lewandrowski U, Sickmann A, Walter U, Dandekar T, Birschmann I. 2010 Apr;30(4):843-50. Epub 2010 Jan 28. PubMed PMID: 20110575.

    Using compensatory base change analysis of internal transcribed spacer 2 secondary structures to identify three new species in Paramacrobiotus (Tardigrada). Organisms Diversity and Evolution (in press).
    Schill RO, Förster F, Dandekar T, Wolf M (2010)

    Ribosomal RNA phylogenetics: the third dimension.
    Keller A, Wolf M, Dandekar T (2010) Biologia 3:388-391.

    Microevolution and speciation in Thalassiosira weissflogii.
    Sorhannus U, Ortiz JD, Wolf M, Fox MG (2010) Protist 161:237-249.

    ITS2 sequence-structure phylogeny in Scenedesmaceae with special reference on Coelastrum (Chlorophyta, Chlorophyceae). Phycologia (in press).
    Hegewald E, Wolf M, Keller A, Friedl T, Krienitz L (2010)

    The ITS2 Database III – sequences and structures for phylogeny.
    Koetschan C, Förster F, Keller A, Schleicher T, Ruderisch B, Schwarz R, Müller T, Wolf M, Schultz J (2010) Nucleic Acids Research 38:D275-D279.

    Including RNA secondary structures improve accuracy and robustness in reconstruction of phylogenetic trees.
    Keller A, Förster F, Müller T, Schultz J, Dandekar T, Wolf M (2010) Biology Direct 5:4.

    Compensatory base changes illuminate morphologically difficult taxonomy. Molecular Phylogenetics and Evolution
    Ruhl M, Wolf M, Jenkins TM (2010) 54:664-669.

    Publications 2009

    Bioinformatical approaches to detect and analyze protein interactions.
    Krüger,B. Dandekar,T. (2009) In: Proteomics: Methods and Protocols (Ed.s: Reinders, J. and Sickmann, A). Humana Press Inc. Totowa, NJ, USA in press.

    ITS2 secondary structure improves phylogeny estimation in a radiation of blue butterflies (Lepidoptera: Lycaenidae: Polyommatus).
    Wiemers M, Keller A, Wolf M (2009) BMC Evolutionary Biology 9:300.

    rRNA interaction and HMM based ITS2-annotation. Gene 430:50-57.
    Keller A, Schleicher T, Schultz J, Müller T, Dandekar T, Wolf M (2009) 5.8S-28S

    New molecular data for tardigrade phylogeny, with the erection of Paramacrobiotus gen. nov. Journal of Zoological Systematics and Evolutionary
    Guidetti R, Schill R, Bertolani R, Dandekar T, Wolf M (2009) Research 47:315-321.

    Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.
    Engelmann JC, Rahmann S, Wolf M, Schultz J, Fritzilas E, Kneitz S, Dandekar T, Müller T (2009) Molecular Ecology Resources 9:83-93.

    Evolutionary Diversification Indicated by Compensatory Base Changes in ITS2 Secondary Structures in a Complex Fungal Species
    Ahvenniemi P, Wolf M, Lehtonen MJ, Wilson P, German-Kinnari M, Valkonen JPT (2009) Rhizoctonia solani. Journal of Molecular Evolution 69:150-163.

    ITS2 Sequence-Structure Analysis in Phylogenetics: A How-to Manual for Molecular Systematics.
    Schultz J, Wolf M (2009) Molecular Phylogenetics and Evolution 52:520-523.

    A probabilistic model of cell size reduction in Pseudo-nitzschia delicatissima (Bacillariophyta).
    Schwarz R, Wolf M, Müller T (2009) Journal of Theoretical Biology 258:316-322.

    ITS better than its reputation.
    Wolf M, Schultz J (2009)  Science (E-Letter, 10 December 2009)
    http://www.sciencemag.org/cgi/eletters/325/5941/682#12692.

    Publications 2008

    Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in Neisseria meningitidis.
    Christoph Schoen, Jochen Blom, Heike Claus, Anja Schramm-Glück, Petra Brandt, Tobias Müller, Alexander Goesmann, Biju Joseph, Sebastian Konietzny, Oliver Kurzai, Corinna Schmitt, Torben Friedrich, Burkhard Linke, Ulrich Vogel, Matthias Frosch (2008) Proc Natl Acad Sci U S A 105: 9.3473-3478 Mar

    The ITS2 Database II: homology modelling RNA structure for molecular systematics.
    Selig C, Wolf M, Muller T, Dandekar T, Schultz J. (2008) Nucleic Acids Res. Nucleic Acids Res. 36(Database issue):D377-80.

    Use of functional highly purified human platelets for the identification of new proteins of the IPP signaling pathway.
    Birschmann I, Mietner S, Dittrich M, Pfrang J, Dandekar T, Walter U. (2008) Thromb Res. 122, 59-68

    Interactions of methylene blue with human disulfide reductases and their orthologues from Plasmodium falciparum.

    Buchholz K, Schirmer RH, Eubel JK, Akoachere MB, Dandekar, T., Becker K, Gromer S. (2008) Antimicrob Agents Chemother. 52, 183-191.

    From Sanger to ultrafast DNA sequencing. Feature article.
    Dandekar, G., Dandekar, T. (2008) Chemtracts ? Biochemistry and Molecular Biology in press

    Platelet protein interactions: map, signaling components and phosphorylation groundstate, Arteriosclerosis, Thrombosis, and Vascular

    Dittrich,M., Birschmann,I., Mietner,S., Sickmann, A., Walter,U. und Dandekar,T. (2008) Biology 28, 1326-1331 (is an Editorial highlight: Cagney G, McRedmond J.; Arterioscler Thromb Vasc Biol. 2008;28:1214-1215) (chosen as faculty of 1000 paper)

    Explorative data analysis of MCL reveals gene expression networks implicated in survival and prognosis supported by explorative CGH analysis,

    Blenk,S., Engelmann, J.C., Pinkert,S., Weniger, M., Schultz, J., Rosenwald, A., Müller-Hermelink, H.-K., Müller,T., und Dandekar,T. (2008) BMC Cancer 8, 106 (10 pp.).

    Identifying functional modules in protein-protein interaction networks: an integrated exact approach.
    Dittrich, M., Klau, G., Rosenwald, A., Dandekar, T., Müller, T. (2008) Bioinformatics 24, i223-31. (paper bekam den ISMB best paper award)

    Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation.
    Engelmann,J., Schwarz,S., Blenk,S., Friedrich,T., Seibel,P., Dandekar,T., Müller, T. Bioinformatics and Biological Insights 2, 271-286

    Modeling cross-hybridization on phylogenetic DNA microarrays increases the detection power of closely related species.
    Engelmann,J.C., Rahmann,S., Wolf,M., Schultz,J., Fritzilas, E., Kneitz,S., Dandekar,T., Müller,T. (2008) Molecular Ecology Resources, in press

    Publications 2007

    Deep metazoan phylogeny.
    Gerlach D, Wolf M, Dandekar T, Muller T, Pokorny A, Rahmann S. (2007) In Silico Biol. 7, 151-154.

    Germinal center B cell-like (GCB) and activated B cell-like (ABC) type of diffuse large B cell lymphoma (DLBCL): Analysis of molecular predictors, signatures, cell cycle state and patient survival.
    Blenk, S., Engelmann, J., Weniger, M., Schultz, J., Dittrich, M., Rosenwald, A., Müller-Hermelink, H. K., Müller, T. und Dandekar, T. (2007) Cancer Informatics 3, 409-430.

    Exonization of active mouse L1s: a driver of transcriptome evolution?
    Zemojtel, T., Penzkofer, T., Schultz, J., Dandekar, T., Badge, R. und Vingron, M. (2007) BMC Genomics 8, 392.

    Placozoa: at least two. Biologia, Section Cellular and Molecular Biology,
    Matthias Wolf, Christian Selig, Tobias Mueller, Nicole Philippi, Thomas Dandekar & Jörg Schultz. (2007) Bratislava, 62/6: 1?5, 2007

    Use of pathway analysis and genome context methods for functional genomics of Mycoplasma pneumoniae nucleotide metabolism.
    Pachkov, M., Dandekar, T., Korbel, J., Bork, P. und Schuster, S. (2007) Gene 396, 215-225.

    Integrated network reconstruction, visualization and analysis using YANAsquare.
    Schwarz,R., Liang,C., Kaleta, C., Kuhnel, M., Hoffmann, E., Kuznetsov, S., Hecker, M., Griffith, G., Schuster, S. und Dandekar, T. (2007) BMC Bioinformatics 8, 313 (10 pp.)

    Distinguishing species.

    Müller T, Philippi N, Dandekar T, Schultz J, Wolf M. RNA 13, 1469-1472.

    Publications 2006

    An Integrated View of Gene Expression and Solute Profiles of Arabidopsis Tumors: A Genome-Wide Approach.
    Rosalia Deeken, Julia C. Engelmann, Marina Efetova, Tina Czirjak, Tobias Müller, Werner M. Kaiser, Olaf Tietz, Markus Krischke, Martin J. Mueller, Klaus Palme, Thomas Dandekar, and Rainer Hedrich (2006). The Plant Cell, in press.

    RIP death domain structural interactions implicated in TNF-mediated proliferation and survival.
    Thakar,J., Schleinkofer,K., Borner, C and Dandekar,T. (2006) Proteins, Structure, Function and Bioinformatics 63, 413-423.

    Function predictions for conserved hypothetical proteins and proteins with putative function in Blochmannia floridanus.

    Gaudermann, P., Vogl, I., Zientz, E., Silva, F.J., Moya, A., Gross, R. und Dandekar, T. (2006) BMC Microbiology 6, 1 (15 pp.).

    13C Isotopolog perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator
    Eisenreich,W., Slaghuis,J., Laupitz,R., Bussemer,J., Stritzker,J., Schwarz,C., Schwarz,R., Dandekar,T., Goebel,W. und Bacher,A. (2006) PrfA. Proc. Natl. Acad. Sci. USA 103, 2040-2045.

    Analysis of SAGE data in the platelet: Features of active translation and regulation.
    Dittrich, M., Smolenski, A., Herterich, S., Birschmann, I., Walter, U. and Dandekar, T. (2006) Thromb Haemost. 95, 643-651.

    Genome-wide mapping of foamy virus vector integrations into a human cell line.
    Nowrouzi,A., Dittrich, M., Klanke, C., Heinkelein,M., Rammling,R., Dandekar, T., von Kalle,C. und Rethwilm,A. (2006)  J. General Virology 87,1339-1347.

    Efficient and robust analysis of large phylogenetic datasets. Advanced Data Mining Technologies in Bioinformatics.
    Rahmann, S., Müller, T., Dandekar, T. und Wolf,M. (2006) In: Hui-Huang Hsu (ed.), Idea Group, Inc., Hershey, PA. in press

    Lysosomal, cytoskeletal, and metabolic alterations in cardiomyopathy of cathepsin L knockout mice.
    Petermann, I., Mayer, C., Stypmann, J., Biniossek, M.L., Tobin, D.J., Engelen, M.A., Dandekar, T., Grune, T., Schild, L., Peters, C. und Reinheckel, T. (2006) FASEB J. 20, 1266-8.

    Iron regulation and the cell cycle: Identification of an iron-responsive element in the 3' untranslated region of human cell division cycle 14A mRNA by a refined microarray-based screening strategy.
    Sanchez M, Galy B, Dandekar, T., Bengert P, Vainshtein Y, Stollte J, Muckenthaler MU, Hentze MW. (2006) J Biol Chem. 2006 Jun 7; [Epub ahead of print]

    The internal transcribed spacer 2 database--a web server for (not only) low level phylogenetic analyses
    .
    Schultz, J., Müller, T., Achtziger, M., Seibel, P.N., Dandekar, T., Wolf, M.  Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W704-7.

    Whole genome sequence of Listeria welshimeri reveals common steps in genome reduction with Listeria innocua as compared to Listeria monocytogenes.
    Hain T, Steinweg C, Kuenne CT, Billion A, Ghai R, Chatterjee SS, Domann E, Karst U, Goesmann A, Bekel T, Bartels D, Kaiser O, Meyer F, Puhler A, Weisshaar B, Wehland J, Liang C, Dandekar, T., Lampidis R, Kreft J, Goebel W, Chakraborty T. (2006) J Bacteriol. 2006 Aug 25; [Epub ahead of print]

    A java applet for exploring the new higher level classification of eukaryotes with emphasis on the taxonomy of protists.
    Wolf M, Seibel PN, Dandekar, T. und Lynn DH. (2006) J Eukaryot Microbiol. 53, 315.

    Modelling interaction sites in protein domains with interaction profile hidden Markov models.
    Friedrich T, Pils B, Dandekar T, Schultz J, Muller T. Bioinformatics. 2006 Sep 25;

    inGeno - an integrated genome and ortholog viewer for improved genome to genome comparisons.
    Liang, C. und Dandekar, T. (2006) BMC Bioinformatics, in press.

    Publications 2005

    Clues from 3-dimensional structure analysis and molecular modelling: new insights into cytochrome P450 mechanisms/functions.
    Schleinkofer, K. und Dandekar, T. (2005) Buchkapitel, pp 1-10. In: Eisenhaber, F. (Hrgb.) Discovering Biomolecular Mechanisms with Computational Biology. Springer Verlag Heidelberg.

    Homology modeling revealed more than 20,000 rRNA internal transcribed spacer 2 (ITS2) secondary structures.
    Wolf, M., Achtziger, M., Schultz, J., Dandekar, T. & Müller, T. (2005) RNA 11: 1616-1623. [ supplementary material ] [ PubMed ]

     CBCAnalyzer: inferring phylogenies based on compensatory base changes in RNA secondary structures.
    Wolf , M., J. Friedrich, T. Dandekar & T. Müller (2005): In Silico Biology 5: 0027. [ PubMed ]

    A tool for the construction of large phylogenetic trees based on profile distances.
    Friedrich, J., T. Dandekar, M. Wolf & T., Müller (2005): ProfDist, Bioinformatics 21: 2108-2109. [ PubMed ]

    Phylogeny of the Hydrodictyaceae (Chlorophyta, Sphaeropleales): Inferrences from rDNA data.
    Buchheim, M.A., Buchheim, J. A., Carlson, T., Braband, A., Hepperle, D., Krienitz, L., Wolf , M. & Hegewald, E. (2005), J. Phycol. 41: 1039-1054.

    A common core of secondary structure of the internal transcribed spacer 2 (ITS2) throughout the Eukaryota.
    Schultz, J., Maisel, S., Gerlach, D., Müller, T. & M. Wolf (2005), RNA 11: 361-364. [ supplementary material ] [ PubMed ]

    ITS2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).
    Schmitt, S., Hentschel, U., Zea, S., Dandekar, T. & M. Wolf (2005), J. Mol. Evol. 60: 327-336. [ PubMed ]

    Erratum for: J. Mol. Evol. 60: 327-326 (2005) ITS-2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).

    Schmitt, S., Hentschel, U., Zea, S., Dandekar, T. & M. Wolf (2005), J. Mol. Evol. 61: 148-150. [ PubMed ]

    Efficent and robust analysis of large phylogenetic datasets. In: Hui-Huang Hsu (ed.): Advanced Data Mining Technologies in Bioinformatics.
    Rahmann, S., T. Müller, T. Dandekar & M. Wolf (2005), Idea Group, Inc., Hershey, PA, USA, pp. (in press).

    Modelling cellular networks. (Condensation and Commentary)
    Dandekar, T. (2005), Chemtracts – Biochemistry and Molecular Biology, in press.

    B-Raf and C-Raf signaling investigated in a simplified model of the mitogenic kinase cascade. Biol.
    Robubi, A., Mueller. T., Fueller,J., Hekman,M., Rapp,U.R. und Dandekar, T. (2005), Chemistry, in press.

    Understanding platelets: Lessons from proteomics and promises from network analysis.
    Dittrich, M., Birschmann, I., Stuhlfelder, C., Sickmann, A., Herterich, S., Nieswandt, B., Walter, U. und Dandekar, T. (2005), Thrombosis & Haemostasis, in press.

    YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.
    Schwarz, R., Musch, P., v.Kamp, A., Engels, B., Schirmer, H., Schuster, S. und Dandekar, T. (2005),  BMC Bioinformatics 6, 135-146.

    Current efforts in the analysis of RNAi and RNAi target genes.
    P. Bengert und T. Dandekar (2005). Brief. Bioinformatics, in press.

    L1Base: from functional annotation to prediction of active LINE-1 elements.
    T. Penzkofer, T. Dandekar, T. Zemojtel (2005), Nucleic Acids Res 33 (Database Issue) D498-500.

    Publications 2004

    Riboswitch finder - a tool for identification of riboswitch RNAs.
    P. Bengert und T. Dandekar (2004). Nucleic Acids Research 31, 3441-3445.

    Related Articles, Links Yeast Kre1p is GPI-anchored and involved in both cell wall assembly and architecture.

    F. Breinig , K. Schleinkofer, MJ. Schmitt (2004), Microbiology. 150(Pt 10):3209-18. PMID: 15470101 [PubMed - in process]

    The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources.
    T. Crass, I. Antes, R. Basekow, et al. (2004), BIOINFORMATICS 20 (2): 268-270

    Molekular- und Evolutionsbiologische Aspekte des Alterns.
    T. Dandekar (2004), In: „Enzyklopädie der Gerontologie“ (Herausgeber: A.Kruse, M.Martin), Seiten 151-166, Hans Huber Verlag, Bern, Göttingen, Toronto.

    Metabolites and Pathway flexibility.
    T. Dandekar und S. Schmidt (2004), In Silico Biology, 5 (No. 0012), pp. 1-13.

    Targets of the cyclin-dependent kinase Cdk1. (Condensation and Commentary)
    M. Dittrich und T. Dandekar (2004), Chemtracts – Biochemistry and Molecular Biology 17, 1-5.

    Integration of Data in Pathogenomics: Three Layers of cellular complexity and an XML-based Framework.
    M. Dünßer, R. Lampidis, S. Schmidt, D. Seipel and T. Dandekar (2004), J. of Integrative Bioinformatics, in press.

    Related Articles, Links Solution structure of the pore-forming protein of Entamoeba histolytica.
    O. Hecht, N.A. Van Nuland, K. Schleinkofer, A.J. Dingley, H. Bruhn, M. Leippe, Grotzinger J. (2004), J Biol Chem. 23;279(17):17834-41. Epub 2004 Feb 17. PMID: 14970207 [PubMed - indexed for MEDLINE]

    Shared components of protein complexes—versatile building blocks or biochemical artefacts?

    R. Krause, C. v.Mering, P. Bork und T. Dandekar (2004), BioEssays 26, 1333-1343

    Phylogenetic relationship of Chlorella and Parachlorella nov. gen. (Chlorophyta, Trebouxiophyceae).
    Krienitz, L., E. Hegewald, D. Hepperle, V.A.R. Huss, T. Rohr & M. Wolf (2004), Phycologia 43: 529-542.

    SMART 4.0: towards genomic data integration.
    I. Letunic, Copley RR, Schmidt S, Ciccarelli FD, Doerks T, Schultz J, Ponting CP and P. Bork (2004), Nucleic Acids Res. (2004), 32, D142-4

    Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta)
    T. Müller, S. Rahmann, T. Dandekar und M. Wolf (2004), BMC Evolutionary Biology 4, 20-26.

    Robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta).
    T. Müller, S. Rahmann, T. Dandekar und M. Wolf (2004), BMC Evolutionary Biology 4: 20.

    Inactive Enzyme-Homologues find new Function in Regulatory Processes.
    B. Pils, Schultz J. (2004), J Mol Biol, 340, 399-404

    Evolution of the multifunctional protein tyrosine phosphatase family.
    B. Pils and J. Schultz, Mol Biol Evol (2004), Epub ahead of print

    Non-unique probe selection by matrix condition optimization. In Currents in Computational Molecular Biology.
    S. Rahmann, T. Müller, and M. Vingron (2004), San Diego, USA, 2004.

    The embedding problem for evolutionary Markov processes.
    S. Rahmann and T. Müller (2004), In Proceedings of the Karlsruher Stochastik-Tage.

    Annotating significant pairs of transcription factor binding sites in regulatory DNA.
    K. Rateitschak, T. Müller and M. Vingron (2004), In Silico Biology 4, 0040.

    Related Articles, Links Comparative Structural and Energetic Analysis of WW Domain-Peptide Interactions.
    K. Schleinkofer, U. Wiedemann, L. Otte, T. Wang, G. Krause, H. Oschkinat, R.C. Wade (2004), J Mol Biol.;344(3):865-81. PMID: 15533451 [PubMed - in process]

    ITS2 and 18S rRNA gene phylogeny of Aplysinidae (Verongida, Demospongiae).
    S. Schmitt, U. Hentschel, S. Zea, T. Dandekar & M. Wolf (2004), J. Mol. Evol. (in press).

    HTTM, a horizontally transferred transmembrane domain.
    J. Schultz, Trends Biochem Sci (2004),29, 4-7.

    HMM Logos for Visualization of Protein Families.
    B. Schuster-Boeckler, J. Schultz, S. Rahmann (2004), BMC Bioinformatics, 5, 7

    Phylogeny of Firmicutes with special reference to Mycoplasma (Mollicutes) as inferred from phosphoglycerate kinase amino acid sequence data.

    M. Wolf, T. Müller, T. Dandekar & J.D. Pollack (2004), Int. J. Syst. Evol. Microbiol. (IJSEM) 54: 871-875.

    The secondary structure of the ITS2 transcript in Cyclotella and Stephanodiscus (Thalassiosiraceae, Bacillariophyta).
    M. Wolf (2004), Diatom Res. 19: 135-142.

    Verweisstichwort: Sphaeroplea.
    M. Wolf (2004), In: Lexikon der Biologie, Spektrum Akademischer Verlag, Heidelberg, Bd. 14: 79. M. Wolf (2004): Stichwort: Sphaeropleales. In: Lexikon der Biologie, Spektrum Akademischer Verlag, Heidelberg, Bd. 14: 79.

    Stichwort: Sphaeropleaceae.

    M. Wolf (2004), In: Lexikon der Biologie, Spektrum Akademischer Verlag, Heidelberg, Bd. 14: 79.

    A novel conserved family of nitric oxide synthase?
    T. Zemojtel, T. Penzkofer, T. Dandekar, J. Schultz (2004), Trends Biochem Sci, 29, 224-6

    NO bound Myoglobin: Structural diversity and dynamics of the NO ligand.
    T. Zemojtel, M. Rini, K. Heyne, T. Dandekar, E. T. J. Nibbering, P.M. Kozlowski (2004), J.Am.Chem.Soc. 126, 1930-1931.

    Pharmacogenomic strategies against resistance development in microbial infections.
    R. W. Ziebuhr, K. Xiao, B. Coulibaly, R. Schwarz und T. Dandekar (2004), Pharmacogenomics 5, 361-379.

    Metabolic interdependence of obligate intracellular bacteria and their insect hosts.
    E. Zientz, T. Dandekar and R. Gross (2004), Microbial and Molecular Biology Reviews 68, 745-777.

    Book:
    Genetik des Alterns.
    T. Dandekar (2004), Book chapter in „Lehrbuch der Gerontologie“ (Herausgeber: A.Kruse, M.Martin) Huber Verlag, in press

    Publications 2003

    Deep-sea heterotrophic nanofauna of the Eastern Mediterranean Sea: qualitative and quantitative aspects of their pelalgic and benthic occurence.
    H Arndt, K. Hausmann, M. Wolf (2003), Mar. Ecol. Prog. Ser. (MEPS) 256: 45-56.

    A software tool-box for analysis of regulatory RNA elements.
    P. Bengert and T. Dandekar (2003). Nucleic Acids Research 31, 3441-3445.

    On the Track of Pathogenicity and Bacteria.
    H. Bertram, S. Balthasar and T. Dandekar (2003), BIOforum Europe 3, 2-4.

    A single motif responsible for ubiquitin recognition and monoubiquitination in endocytic proteins (Condensation and Commentary)
    G. Dandekar and T. Dandekar (2003), Chemtracts – Biochemistry and Molecular Biology 16, 632-637.

    A method or classifying metabolites in topological pathway analyses based on minimization of pathway number.
    T. Dandekar, F. Moldenhauer, S. Bulik, H. Bertram and S. Schuster (2003), BioSystems 70, 255-270.

    A protein gel documentation system for the analysis of gene knockouts.
    D. Faller, T. Reinheckel, D. Wenzler, S. Hagemann, K. Xiao, J. Honerkamp, C. Peters, T. Dandekar und J. Timmer (2003), J.Chem.Inf. and Comp.Sci. 44, 168-169.

    Phylogenetic relationships of Scenedesmus and Acutodesmus (Chlorophyta, Chlorophyceae) as inferred from 18S rDNA and ITS-2 sequence comparisons.
    E. Hegewald, M. Wolf (2003), Plant Syst. Evol., in press

    Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Metabolic Network. (Condensation and Commentary)
    S. Kneitz und T. Dandekar (2003), Chemtracts – Biochemistry and Molecular Biology 16, 806-809.

    Systematics of coccoid green algae: morphology versus 18S rRNA gene phylogeny
    L. Krienitz, E. Hegewald, D. Hepperle, M. Wolf (2003), Biologia 58., 437-446

    Toward Computer Based Cleavage Site Prediction of Cysteine Endopeptidases.
    T. Lohmüller, D.Wenzler, S. Hagemann, W. Kieß, C. Peters, T. Dandekar and T. Reinheckel (2003), Biological Chemistry 384, 899-909.

    Robust estimation of the phylogeny of Chlorophyceae (Chlorophyta) based on profile distances.
    T. Müller, S. Rahmann, T. Dandekar, and M. Wolf. (2003), In H.-W. Mewes, D. Frishman, V. Heun, and S. Kramer, editors, Proceedings of the German Conference on Bioinformatics (GCB'03), volume 1, pages 97-101, Munich, . belleville.

    On the power of profiles for transcription factor binding site detection.
    S. Rahmann, T. Müller, and M. Vingron. (2003), Statistical Applications in Genetics and Molecular Biology, 2(1): Article 7.

    Measuring the quality of profiles for transcription factor binding site detection.
    S. Rahmann, T. Müller, and M. Vingron (2003), In Rainer Spang, Patricia Béziat, and Martin Vingron, editors, Currents in Computational Molecular Biology. Berlin, Germany

    The SLIMSEARCH world wide web server for the detection of transmembrane proteins.
    S. Rahmann, H. Luz, and T. Müller. (2003), http://slimsearch.molgen.mpg.de.

    Developing a protein-interactions ontology.
    E. Ratsch, Schultz J, Saric J, Lavin PC, Wittig U, Reyle U and Rojas I., Comparative and Functional Genomics (2003), 4, 85-89

    Metabolites: A key for enzyme flexibility and pathway evolution?
    S. Schmidt, S. Sunyaev, P. Bork and T. Dandekar (2003). Trends in Biochemical Sciences 28, 336-341.

    Gaussian Mixture Density Estimation Applied to Microarray Data Lect. Notes Comp.
    C. Steinhoff*, T. Müller* (*equal contribution), U. A. Nuber and M. Vingron. (2003), Sci. 2810, 418-429

    On the phylogeny of Radiococcus, Planktosphaeria and Schizochlamydella (Radiococcaceae, Chlorophyta).

    M. Wolf, L. Krienitz & D. Hepperle (2003), Biologia 58: 759-765.

    Phylogenetic position of the Golenkiniaceae (Chlorophyta) as inferred from 18S rDNA sequence data.

    M. Wolf., E. Hegewald, D. Hepperle & L. Krienitz (2003), Biologia 58: 433-436.

    In search for the prototype of Nitric Oxide Synthase.
    T. Zemojtel, R. Wade and T. Dandekar (2003), FEBS, in press

    Publications 2002

    A 'periodic table' for protein structure. Chemtracts.
    H. Bertram and T. Dandekar (2002), Biochemistry and Molecular Biology 15, 735-739.

    Comparative genome analysis and pathway reconstruction.
    T. Dandekar and R. Sauerborn (2002) Pharmacogenomics 3, 245-256.

    Comparative genome analysis of the Mollicutes, pp.255-278.
    T. Dandekar, B. Snel, S. Schmidt, W. Lathe, M. Suyama, M. Huynen and P. Bork (2002). In: The Mollicutes (Hgb.: S.Razin and R.Herrmann; Kluver Academic / Plenum Publishers, New York, 2002.

    Initial sequencing and comparative analysis of the mouse genome.

    Mouse Genome Sequencing Consortium. Nature (2002), 420, 520-562

    Suspected utility of enzymes with multiple activities in the small genome Mycoplasma species: The replacement of the missing “household” nucleoside diphosphate kinase gene and activity by glycolytic kinases.

    J.D. Pollack, M.A.. Myers, T. Dandekar and R Herrmann (2002). Omics (a journal of integrative biology) 6, 247-258.

    Metabolic Pathways (bookchapter, pp. 251-272 in: ”gene regulation and metabolism: post genomic computational approaches”, (ed. J.Collado-Vides and R.Hofestädt) MIT Press,
    S. Schmidt and T.Dandekar (2002) Massachusettes ISBN 0-262-03297-X

    Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to Mycoplasma pneumoniae.
    S. Schuster, T. Pfeiffer, F. Moldenhauer, I. Koch and T. Dandekar (2002). Bioinformatics 18, 351-361.

    A versatile structural domain server using profile weight matrices.

    S. Schmidt, P. Bork and T. Dandekar (2002). Journal of Chemical Information and Computer Sciences 42, 405-407.

    Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method.
    T. Müller, R. Spang and M. Vingron (2002) Mol Biol Evol 19(1): 8-13.

    A new formulation of evolutionary models.
    S. Rahmann and T. Müller (2002) In Liliana Florea, Brian Walenz, and Sridhar Hannenhalli, editors, Currents in Computational Molecular Biology 2002, pages 156-157. Washington D.C., USA

    Related Articles, Links The matrix metalloproteinase 9 (mmp-9) hemopexin domain is a novel gelatin binding domain and acts as an antagonist.

    E. Roeb, K. Schleinkofer, T. Kernebeck, S. Potsch, B. Jansen, I. Behrmann, S. Matern, J. Grotzinger (2002) J Biol Chem. 2002 Dec 27;277(52):50326-32. Epub. PMID: 12384502 [PubMed - indexed for MEDLINE]

    Prediction of structure and functional residues for O-GlcNAcase, a divergent homologue of Acetyltransferases.
    J. Schultz and B. Pils (2002) FEBS Letters 529, 179-182.

    Book:

    RNA motifs and regulatory elements. Monographie.
    T. Dandekar (2002; Editor) Springer Verlag, Berlin, Heidelberg, New York (new, completely revised edition, 233pp.). ISBN 3-540-41701-X

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