Publications

Simplified urinary steroid profiling by LC-MS as diagnostic tool for malignancy in adrenocortical tumors.
Vogg N, Müller T, Floren A, Dandekar T, Riester A, Dischinger U, Kurlbaum M, Kroiss M, Fassnacht M. Clin Chim Acta. 2023 Mar 15;543:117301. doi: 10.1016/j.cca.2023.117301. Epub 2023 Mar 21. PMID: 36948238

Minimal Collagen-Binding Epitope of Glycoprotein VI in Human and Mouse Platelets.
Han C, Ren P, Mamtimin M, Kruk L, Sarukhanyan E, Li C, Anders HJ, Dandekar T, Krueger I, Elvers M, Goebel S, Adler K, Münch G, Gudermann T, Braun A, Mammadova-Bach E. Biomedicines. 2023 Feb 1;11(2):423. doi: 10.3390/biomedicines11020423. PMID: 36830959

DNA storage-from natural biology to synthetic biology.
Bencurova E, Akash A, Dobson RCJ, Dandekar T. Comput Struct Biotechnol J. 2023 Feb 2;21:1227-1235. doi: 10.1016/j.csbj.2023.01.045. eCollection 2023. PMID: 36817961

Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis.
Kaltdorf M, Breitenbach T, Karl S, Fuchs M, Kessie DK, Psota E, Prelog M, Sarukhanyan E, Ebert R, Jakob F, Dandekar G, Naseem M, Liang C, Dandekar T. Sci Rep. 2023 Feb 1;13(1):1855. doi: 10.1038/s41598-022-27098-7. PMID: 36725967

The β-cell primary cilium is an autonomous Ca2+ compartment for paracrine GABA signaling.
Sanchez GM, Incedal TC, Prada J, O'Callaghan P, Dyachok O, Echeverry S, Dumral Ö, Nguyen PM, Xie B, Barg S, Kreuger J, Dandekar T, Idevall-Hagren O. J Cell Biol. 2023 Jan 2;222(1):e202108101. doi: 10.1083/jcb.202108101. Epub 2022 Nov 9. PMID: 36350286; PMCID: PMC9813980.

Oxidative DNA Damage in Reconstituting T-cells is Associated with Relapse and Inferior Survival Following Allo-SCT.
Karl F, Liang C, Boettcher-Loschinski R, Stoll A, Flamann CS, Richter S, Lischer C, Völkl S, Jacobs B, Böttcher M, Jitschin R, Bruns H, Fischer T, Holler E, Roesler W, Dandekar T, Mackensen A, Mougiakakos D. Blood. 2022 Dec 23:blood.2022017267. doi: 10.1182/blood.2022017267. Online ahead of print. PMID: 36564029

Author Correction: Estimation of R0 for the spread of SARS-CoV-2 in Germany from excess mortality.
Prada JP, Maag LE, Siegmund L, Bencurova E, Liang C, Koutsilieri E, Dandekar T, Scheller C. Sci Rep. 2022 Dec 21;12(1):22071. doi: 10.1038/s41598-022-26627-8. PMID: 36543859 Free PMC article. No abstract available.

Genome-wide scan for potential CD4+ T-cell vaccine candidates in Candida auris by exploiting reverse vaccinology and evolutionary information.
Gupta SK, Osmanoglu Ö, Minocha R, Bandi SR, Bencurova E, Srivastava M, Dandekar T. Front Med (Lausanne). 2022 Nov 3;9:1008527. doi: 10.3389/fmed.2022.1008527. eCollection 2022. PMID: 36405591 Free PMC article.

About the Analysis of 18S rDNA Sequence Data from Trypanosomes in Barcoding and Phylogenetics: Tracing a Continuation Error Occurring in the Literature.
Rackevei AS, Borges A, Engstler M, Dandekar T, Wolf M. Biology (Basel). 2022 Nov 4;11(11):1612. doi: 10.3390/biology11111612. PMID: 36358313 Free PMC article.

In silico designed microtubule-stabilizer drugs against tauopathy in Alzheimer's disease.
Sarukhanyan E, Dandekar T. J Biomol Struct Dyn. 2022 Nov 4:1-21. doi: 10.1080/07391102.2022.2139760. Online ahead of print. PMID: 36331069

Progeria and Aging-Omics Based Comparative Analysis.
Caliskan A, Crouch SAW, Giddins S, Dandekar T, Dangwal S. Biomedicines. 2022 Sep 29;10(10):2440. doi: 10.3390/biomedicines10102440. PMID: 36289702 Free PMC article.

Motif and conserved module analysis in DNA (promoters, enhancers) and RNA (lncRNA, mRNA) using AlModules.
Aydinli M, Liang C, Dandekar T. Sci Rep. 2022 Oct 20;12(1):17588. doi: 10.1038/s41598-022-21732-0. PMID: 36266399 Free PMC article.

Estimation of R0 for the spread of SARS-CoV-2 in Germany from excess mortality.
Prada JP, Maag LE, Siegmund L, Bencurova E, Liang C, Koutsilieri E, Dandekar T, Scheller C. Sci Rep. 2022 Oct 14;12(1):17221. doi: 10.1038/s41598-022-22101-7. PMID: 36241688 Free PMC article.

In silico investigation of nonsynonymous single nucleotide polymorphisms in BCL2 apoptosis regulator gene to design novel protein-based drugs against cancer.
Fareed MM, Dutta K, Dandekar T, Tarabonda H, Skorb EV, Shityakov S. J Cell Biochem. 2022 Dec;123(12):2044-2056. doi: 10.1002/jcb.30330. Epub 2022 Sep 22. PMID: 36146908

In Silico Studies Reveal Peramivir and Zanamivir as an Optimal Drug Treatment Even If H7N9 Avian Type Influenza Virus Acquires Further Resistance.
Sarukhanyan E, Shanmugam TA, Dandekar T. Molecules. 2022 Sep 12;27(18):5920. doi: 10.3390/molecules27185920. PMID: 36144655 Free PMC article.

Nephroprotective potential of eugenol in a rat experimental model of chronic kidney injury; targeting NOX, TGF-β, and Akt signaling.
Fathy M, Abdel-Latif R, Abdelgwad YM, Othman OA, Abdel-Razik AH, Dandekar T, Othman EM. Life Sci. 2022 Nov 1;308:120957. doi: 10.1016/j.lfs.2022.120957. Epub 2022 Sep 14. PMID: 36113730

Nanocellulose Composites as Smart Devices With Chassis, Light-Directed DNA Storage, Engineered Electronic Properties, and Chip Integration.
Bencurova E, Shityakov S, Schaack D, Kaltdorf M, Sarukhanyan E, Hilgarth A, Rath C, Montenegro S, Roth G, Lopez D, Dandekar T. Front Bioeng Biotechnol. 2022 Aug 8;10:869111. doi: 10.3389/fbioe.2022.869111. eCollection 2022. PMID: 36105598 Free PMC article.

Prediction and validation of host-pathogen interactions by a versatile inference approach using Aspergillus fumigatus as a case study.
Balkenhol J, Bencurova E, Gupta SK, Schmidt H, Heinekamp T, Brakhage A, Pottikkadavath A, Dandekar T. Comput Struct Biotechnol J. 2022 Aug 5;20:4225-4237. doi: 10.1016/j.csbj.2022.07.050. eCollection 2022. PMID: 36051885 Free PMC article.

Role of the Pangolin in Origin of SARS-CoV-2: An Evolutionary Perspective.
Gupta SK, Minocha R, Thapa PJ, Srivastava M, Dandekar T. Int J Mol Sci. 2022 Aug 14;23(16):9115. doi: 10.3390/ijms23169115. PMID: 36012377 Free PMC article.

Targeted metabolic profiling of urinary steroids with a focus on analytical accuracy and sample stability.
Vogg N, Müller T, Floren A, Dandekar T, Scherf-Clavel O, Fassnacht M, Kroiss M, Kurlbaum M. J Mass Spectrom Adv Clin Lab. 2022 Jul 25;25:44-52. doi: 10.1016/j.jmsacl.2022.07.006. eCollection 2022 Aug. PMID: 35910411 Free PMC article.

Kinetin Ameliorates Cisplatin-Induced Hepatotoxicity and Lymphotoxicity via Attenuating Oxidative Damage, Cell Apoptosis and Inflammation in Rats.
Fathy M, Darwish MA, Abdelhamid AM, Alrashedy GM, Othman OA, Naseem M, Dandekar T, Othman EM. Biomedicines. 2022 Jul 6;10(7):1620. doi: 10.3390/biomedicines10071620. PMID: 35884925 Free PMC article.

A modular systems biological modelling framework studies cyclic nucleotide signaling in platelets.
Breitenbach T, Englert N, Osmanoglu Ö, Rukoyatkina N, Wangorsch G, Heinze K, Friebe A, Butt E, Feil R, Dittrich M, Gambaryan S, Dandekar T. J Theor Biol. 2022 Oct 7;550:111222. doi: 10.1016/j.jtbi.2022.111222. Epub 2022 Jul 16. PMID: 35843440 Free article.

Optimization of synthetic molecular reporters for a mesenchymal glioblastoma transcriptional program by integer programing.
Breitenbach T, Schmitt MJ, Dandekar T. Bioinformatics. 2022 Sep 2;38(17):4162-4171. doi: 10.1093/bioinformatics/btac488. PMID: 35809064

Deciphering Pro-angiogenic Transcription Factor Profiles in Hypoxic Human Endothelial Cells by Combined Bioinformatics and in vitro Modeling.
Schmidt A, Fuchs M, Stojanović SD, Liang C, Schmidt K, Jung M, Xiao K, Weusthoff J, Just A, Pfanne A, Distler JHW, Dandekar T, Fiedler J, Thum T, Kunz M. Front Cardiovasc Med. 2022 Jun 17;9:877450. doi: 10.3389/fcvm.2022.877450. eCollection 2022. PMID: 35783871 Free PMC article.

Cisplatin-Induced Reproductive Toxicity and Oxidative Stress: Ameliorative Effect of Kinetin.
Abdel-Latif R, Fathy M, Anwar HA, Naseem M, Dandekar T, Othman EM. Antioxidants (Basel). 2022 Apr 28;11(5):863. doi: 10.3390/antiox11050863. PMID: 35624727 Free PMC article.

EMT, Stemness, and Drug Resistance in Biological Context: A 3D Tumor Tissue/In Silico Platform for Analysis of Combinatorial Treatment in NSCLC with Aggressive KRAS-Biomarker Signatures.
Peindl M, Göttlich C, Crouch S, Hoff N, Lüttgens T, Schmitt F, Pereira JGN, May C, Schliermann A, Kronenthaler C, Cheufou D, Reu-Hofer S, Rosenwald A, Weigl E, Walles T, Schüler J, Dandekar T, Nietzer S, Dandekar G. Cancers (Basel). 2022 Apr 27;14(9):2176. doi: 10.3390/cancers14092176. PMID: 35565305 Free PMC article.

Cytokinins: Wide-Spread Signaling Hormones from Plants to Humans with High Medical Potential.
Fathy M, Saad Eldin SM, Naseem M, Dandekar T, Othman EM. Nutrients. 2022 Apr 2;14(7):1495. doi: 10.3390/nu14071495. PMID: 35406107 Free PMC article. Review.

ACKR3 regulates platelet activation and ischemia-reperfusion tissue injury.
Rohlfing AK, Kolb K, Sigle M, Ziegler M, Bild A, Münzer P, Sudmann J, Dicenta V, Harm T, Manke MC, Geue S, Kremser M, Chatterjee M, Liang C, von Eysmondt H, Dandekar T, Heinzmann D, Günter M, von Ungern-Sternberg S, Büttcher M, Castor T, Mencl S, Langhauser F, Sies K, Ashour D, Beker MC, Lämmerhofer M, Autenrieth SE, Schäffer TE, Laufer S, Szklanna P, Maguire P, Heikenwalder M, Müller KAL, Hermann DM, Kilic E, Stumm R, Ramos G, Kleinschnitz C, Borst O, Langer HF, Rath D, Gawaz M. Nat Commun. 2022 Apr 5;13(1):1823. doi: 10.1038/s41467-022-29341-1. PMID: 35383158 Free PMC article.

Toward Zero Variance in Proteomics Sample Preparation: Positive-Pressure FASP in 96-Well Format (PF96) Enables Highly Reproducible, Time- and Cost-Efficient Analysis of Sample Cohorts.
Loroch S, Kopczynski D, Schneider AC, Schumbrutzki C, Feldmann I, Panagiotidis E, Reinders Y, Sakson R, Solari FA, Vening A, Swieringa F, Heemskerk JWM, Grandoch M, Dandekar T, Sickmann A. J Proteome Res. 2022 Apr 1;21(4):1181-1188. doi: 10.1021/acs.jproteome.1c00706. Epub 2022 Mar 22. PMID: 35316605 Free PMC article.

Editorial: Innovative Strategies From Synthetic Biology and Bacterial Pathways to Master Biochemical Environmental Challenges.
Eisenhaber F, Thakar J, Ponte-Sucre A, Dandekar T. Front Bioeng Biotechnol. 2022 Jan 11;9:828632. doi: 10.3389/fbioe.2021.828632. eCollection 2021. PMID: 35087812 Free PMC article. No abstract available.

Influence of breast cancer risk factors on proliferation and DNA damage in human breast glandular tissues: role of intracellular estrogen levels, oxidative stress and estrogen biotransformation.
Wunder J, Pemp D, Cecil A, Mahdiani M, Hauptstein R, Schmalbach K, Geppert LN, Ickstadt K, Esch HL, Dandekar T, Lehmann L. Arch Toxicol. 2022 Feb;96(2):673-687. doi: 10.1007/s00204-021-03198-7. Epub 2021 Dec 18. PMID: 34921608 Free PMC article.

Antibody ligation of CEACAM1, CEACAM3, and CEACAM6, differentially enhance the cytokine release of human neutrophils in responses to Candida albicans.
Klaile E, Prada Salcedo JP, Klassert TE, Besemer M, Bothe AK, Durotin A, Müller MM, Schmitt V, Luther CH, Dittrich M, Singer BB, Dandekar T, Slevogt H. Cell Immunol. 2022 Jan;371:104459. doi: 10.1016/j.cellimm.2021.104459. Epub 2021 Nov 24. PMID: 34847408 Free article.

A translational study: Involvement of miR-21-5p in development and maintenance of neuropathic pain via immune-related targets CCL5 and YWHAE.
Karl-Schöller F, Kunz M, Kreß L, Held M, Egenolf N, Wiesner A, Dandekar T, Sommer C, Üçeyler N. Exp Neurol. 2022 Jan;347:113915. doi: 10.1016/j.expneurol.2021.113915. Epub 2021 Nov 7. PMID: 34758342

An In Vitro and In Silico Study of the Enhanced Antiproliferative and Pro-Oxidant Potential of Olea europaea L. cv. Arbosana Leaf Extract via Elastic Nanovesicles (Spanlastics).
Alnusaire TS, Sayed AM, Elmaidomy AH, Al-Sanea MM, Albogami S, Albqmi M, Alowaiesh BF, Mostafa EM, Musa A, Youssif KA, Refaat H, Othman EM, Dandekar T, Alaaeldin E, Ghoneim MM, Abdelmohsen UR. Antioxidants (Basel). 2021 Nov 23;10(12):1860. doi: 10.3390/antiox10121860. PMID: 34942963 Free PMC article.

CoxBase: an Online Platform for Epidemiological Surveillance, Visualization, Analysis, and Typing of Coxiella burnetii Genomic Sequences.
Fasemore AM, Helbich A, Walter MC, Dandekar T, Vergnaud G, Förstner KU, Frangoulidis D. mSystems. 2021 Dec 21;6(6):e0040321. doi: 10.1128/mSystems.00403-21. Epub 2021 Dec 21. PMID: 34931882 Free PMC article.

Topological Analysis of the Carbon-Concentrating CETCH Cycle and a Photorespiratory Bypass Reveals Boosted CO₂-Sequestration by Plants.
Osmanoglu Ö, Khaled AlSeiari M, AlKhoori HA, Shams S, Bencurova E, Dandekar T, Naseem M. Front Bioeng Biotechnol. 2021 Nov 1;9:708417. doi: 10.3389/fbioe.2021.708417. eCollection 2021. PMID: 34790651 Free PMC article.

Scaffold Searching of FDA and EMA-Approved Drugs Identifies Lead Candidates for Drug Repurposing in Alzheimer's Disease.
Shityakov S, Skorb EV, Förster CY, Dandekar T. Front Chem. 2021 Oct 22;9:736509. doi: 10.3389/fchem.2021.736509. eCollection 2021. PMID: 34751244 Free PMC article.

An Ebola, Neisseria and Trypanosoma human protein interaction census reveals a conserved human protein cluster targeted by various human pathogens.
Gupta SK, Ponte-Sucre A, Bencurova E, Dandekar T. Comput Struct Biotechnol J. 2021 Sep 16;19:5292-5308. doi: 10.1016/j.csbj.2021.09.017. eCollection 2021. PMID: 34745452 Free PMC article.

Staphylococcusaureus Transcriptome Data and Metabolic Modelling Investigate the Interplay of Ser/Thr Kinase PknB, Its Phosphatase Stp, the glmR/yvcK Regulon and the cdaA Operon for Metabolic Adaptation.
Liang C, Rios-Miguel AB, Jarick M, Neurgaonkar P, Girard M, François P, Schrenzel J, Ibrahim ES, Ohlsen K, Dandekar T. Microorganisms. 2021 Oct 14;9(10):2148. doi: 10.3390/microorganisms9102148. PMID: 34683468 Free PMC article.

Aspergillus fumigatus versus Genus Aspergillus: Conservation, Adaptive Evolution and Specific Virulence Genes.
Gupta SK, Srivastava M, Osmanoglu Ö, Xu Z, Brakhage AA, Dandekar T. Microorganisms. 2021 Sep 23;9(10):2014. doi: 10.3390/microorganisms9102014. PMID: 34683335 Free PMC article.

Alveolar Regeneration in COVID-19 Patients: A Network Perspective.
Gupta SK, Srivastava M, Minocha R, Akash A, Dangwal S, Dandekar T. Int J Mol Sci. 2021 Oct 19;22(20):11279. doi: 10.3390/ijms222011279. PMID: 34681944 Free PMC article. Review.

An effective model of endogenous clocks and external stimuli determining circadian rhythms.
Breitenbach T, Helfrich-Förster C, Dandekar T. Sci Rep. 2021 Aug 9;11(1):16165. doi: 10.1038/s41598-021-95391-y. PMID: 34373483 Free PMC article.

Modeling Immune Dynamics in Plants Using JIMENA-Package.
Osmanoglu Ö, Shams S, Dandekar T, Naseem M. Methods Mol Biol. 2021;2328:183-189. doi: 10.1007/978-1-0716-1534-8_11. PMID: 34251626

Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals.
Scherer M, Fleishman SJ, Jones PR, Dandekar T, Bencurova E. Front Bioeng Biotechnol. 2021 Jun 15;9:673005. doi: 10.3389/fbioe.2021.673005. eCollection 2021. PMID: 34211966 Free PMC article. Review.

Rapid proliferation due to better metabolic adaptation results in full virulence of a filament-deficient Candida albicans strain.
Dunker C, Polke M, Schulze-Richter B, Schubert K, Rudolphi S, Gressler AE, Pawlik T, Prada Salcedo JP, Niemiec MJ, Slesiona-Künzel S, Swidergall M, Martin R, Dandekar T, Jacobsen ID. Nat Commun. 2021 Jun 23;12(1):3899. doi: 10.1038/s41467-021-24095-8. PMID: 34162849 Free PMC article.

Design, Synthesis, and Anticancer Screening for Repurposed Pyrazolo[3,4-d]pyrimidine Derivatives on Four Mammalian Cancer Cell Lines.
Othman EM, Bekhit AA, Anany MA, Dandekar T, Ragab HM, Wahid A. Molecules. 2021 May 16;26(10):2961. doi: 10.3390/molecules26102961. PMID: 34065773 Free PMC article.

RhoA/Cdc42 signaling drives cytoplasmic maturation but not endomitosis in megakaryocytes.
Heib T, Hermanns HM, Manukjan G, Englert M, Kusch C, Becker IC, Gerber A, Wackerbarth LM, Burkard P, Dandekar T, Balkenhol J, Jahn D, Beck S, Meub M, Dütting S, Stigloher C, Sauer M, Cherpokova D, Schulze H, Brakebusch C, Nieswandt B, Nagy Z, Pleines I. Cell Rep. 2021 May 11;35(6):109102. doi: 10.1016/j.celrep.2021.109102. PMID: 33979620 Free article.

Modeling of stringent-response reflects nutrient stress induced growth impairment and essential amino acids in different Staphylococcus aureus mutants.
Audretsch C, Gratani F, Wolz C, Dandekar T. Sci Rep. 2021 May 6;11(1):9651. doi: 10.1038/s41598-021-88646-1. PMID: 33958641 Free PMC article.

Population-Predicted MHC Class II Epitope Presentation of SARS-CoV-2 Structural Proteins Correlates to the Case Fatality Rates of COVID-19 in Different Countries.
Liang C, Bencurova E, Psota E, Neurgaonkar P, Prelog M, Scheller C, Dandekar T. Int J Mol Sci. 2021 Mar 5;22(5):2630. doi: 10.3390/ijms22052630. PMID: 33807854 Free PMC article.

In vitro skin culture media influence the viability and inflammatory response of primary macrophages.
Griffoni C, Neidhart B, Yang K, Groeber-Becker F, Maniura-Weber K, Dandekar T, Walles H, Rottmar M. Sci Rep. 2021 Mar 29;11(1):7070. doi: 10.1038/s41598-021-86486-7. PMID: 33782484 Free PMC article.

Modulatory and Toxicological Perspectives on the Effects of the Small Molecule Kinetin.
Othman EM, Fathy M, Bekhit AA, Abdel-Razik AH, Jamal A, Nazzal Y, Shams S, Dandekar T, Naseem M. Molecules. 2021 Jan 28;26(3):670. doi: 10.3390/molecules26030670. PMID: 33525350 Free PMC article.

An optimized genetically encoded dual reporter for simultaneous ratio imaging of Ca²⁺ and H⁺ reveals new insights into ion signaling in plants.
Li K, Prada J, Damineli DSC, Liese A, Romeis T, Dandekar T, Feijó JA, Hedrich R, Konrad KR. New Phytol. 2021 Jun;230(6):2292-2310. doi: 10.1111/nph.17202. Epub 2021 Feb 18. PMID: 33455006 Free PMC article.

A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2.
Prada JP, Wangorsch G, Kucka K, Lang I, Dandekar T, Wajant H. Bioinformatics. 2021 May 5;37(5):669-676. doi: 10.1093/bioinformatics/btaa844. PMID: 32991680

Approach for Characterizing Propofol Binding Affinities to Serum Albumins from Different Species.
Shityakov S, Fischer A, Su KP, Hussein AA, Dandekar T, Broscheit J. Novel. ACS Omega. 2020 Sep 30;5(40):25543-25551. doi: 10.1021/acsomega.0c01295. PMID: 33073080; PMCID: PMC7557242.

A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2.
Prada JP, Wangorsch G, Kucka K, Lang I, Dandekar T, Wajant H. Bioinformatics. 2020 Sep 29:btaa844. doi: 10.1093/bioinformatics/btaa844. Epub ahead of print. PMID: 32991680.

Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem.
Naseem M, Osmanoğlu Ö, Kaltdorf M, Alblooshi AAMA, Iqbal J, Howari FM, Srivastava M, Dandekar T. Int J Mol Sci. 2020 Aug 11;21(16):5745. doi: 10.3390/ijms21165745. PMID: 32796535; PMCID: PMC7460820.

Integrated structural and functional analysis of the protective effects of kinetin against oxidative stress in mammalian cellular systems.
Naseem M, Othman EM, Fathy M, Iqbal J, Howari FM, AlRemeithi FA, Kodandaraman G, Stopper H, Bencurova E, Vlachakis D, Dandekar T.Sci Rep. 2020 Aug 7;10(1):13330. doi: 10.1038/s41598-020-70253-1. PMID: 32770053; PMCID: PMC7414151.

Chagas Disease: Detection of Trypanosoma cruzi by a New, High-Specific Real Time PCR.
Kann S, Kunz M, Hansen J, Sievertsen J, Crespo JJ, Loperena A, Arriens S, Dandekar T. J Clin Med. 2020 May 18;9(5):1517. doi: 10.3390/jcm9051517. PMID: 32443464; PMCID: PMC7291166.

Integrative functional genomics decodes herpes simplex virus 1.
Whisnant AW, Jürges CS, Hennig T, Wyler E, Prusty B, Rutkowski AJ, L'hernault A, Djakovic L, Göbel M, Döring K, Menegatti J, Antrobus R, Matheson NJ, Künzig
FWH, Mastrobuoni G, Bielow C, Kempa S, Liang C, Dandekar T, Zimmer R, Landthaler M, Grässer F, Lehner PJ, Friedel CC, Erhard F, Dölken L. Nat Commun. 2020 Apr 27;11(1):2038. doi: 10.1038/s41467-020-15992-5. PMID: 32341360; PMCID: PMC7184758.

Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches.
Shityakov S, Bencurova E, Förster C, Dandekar T. BMC Bioinformatics. 2020 Apr 3;21(1):132. doi: 10.1186/s12859-020-3461-6. PMID: 32245400; PMCID: PMC7126183.

Rational Drug Design of Axl Tyrosine Kinase Type I Inhibitors as Promising Candidates Against Cancer.
Sarukhanyan E, Shityakov S, Dandekar T. Front Chem. 2020 Feb 4;7:920. doi: 10.3389/fchem.2019.00920. PMID: 32117858; PMCID: PMC7010640.

Delaying memory decline: different options and emerging solutions.
Schneider F, Horowitz A, Lesch KP, Dandekar T. Transl Psychiatry. 2020 Jan 21;10(1):13. doi: 10.1038/s41398-020-0697-x. PMID: 32066684; PMCID: PMC7026464.

Genome-wide inference of the Camponotus floridanus protein-protein interaction network using homologous mapping and interacting domain profile pairs.
Gupta SK, Srivastava M, Osmanoglu Ö, Dandekar T. Sci Rep. 2020 Feb 11;10(1):2334. doi: 10.1038/s41598-020-59344-1. PMID: 32047225; PMCID: PMC7012867.

Platelet glycoprotein VI promotes metastasis through interaction with cancer cell-derived galectin-3.
Mammadova-Bach E, Gil-Pulido J, Sarukhanyan E, Burkard P, Shityakov S, Schonhart C, Stegner D, Remer K, Nurden P, Nurden AT, Dandekar T, Nehez L, Dank M, Braun A, Mezzano D, Abrams SI, Nieswandt B. Blood. 2020
Apr 2;135(14):1146-1160. doi: 10.1182/blood.2019002649. PMID: 32040544.

Synthetic Rewiring of Plant CO<sub>2</sub> Sequestration Galvanizes Plant Biomass Production.
Naseem M, Osmanoglu Ö, Dandekar T. Trends Biotechnol. 2020 Apr;38(4):354-359. doi: 10.1016/j.tibtech.2019.12.019. Epub 2020 Jan 17. PMID: 31959363.

Connecting Cancer Pathways to Tumor Engines: A Stratification Tool for Colorectal Cancer Combining Human In Vitro Tissue Models with Boolean In Silico Models.
Baur F, Nietzer SL, Kunz M, Saal F, Jeromin J, Matschos S, Linnebacher M, Walles H, Dandekar T, Dandekar G. Cancers (Basel). 2019 Dec 20;12(1):28. doi: 10.3390/cancers12010028. PMID: 31861874; PMCID: PMC7017315.

Mapping a Transcriptome-Guided Arabidopsis SAM Interactome.
Naseem M, Osmanoglu O, Iqbal J, Howari FM, AlRemeithi FA, Kaltdorf M, Dandekar T. Methods Mol Biol. 2020;2094:113-118. doi: 10.1007/978-1-0716-0183-9_12. PubMed PMID: 31797296.

Molecular Modeling of the Interaction Between Stem Cell Peptide and Immune Receptor in Plants.
Naseem M, Srivastava M, Osmanoglu O, Iqbal J, Howari FM, AlRemeithi FA, Dandekar T. Methods Mol Biol. 2020;2094:67-77. doi:10.1007/978-1-0716-0183-9_8. PubMed PMID: 31797292.

Bacterial Shoot Apical Meristem Inoculation Assay.
Naseem M, Gun G, Osmanoglu O, AlRemeithi FA, Iqbal J, Dandekar T. Methods Mol Biol. 2020;2094:17-22. doi:10.1007/978-1-0716-0183-9_2. PubMed PMID: 31797286.

BCdatabaser: on-the-fly reference database creation for (meta-)barcoding.
Keller A, Hohlfeld S, Kolter A, Schultz J, Gemeinholzer B, Ankenbrand MJ. Bioinformatics. 2020 Jan 6. pii: btz960. doi: 10.1093/bioinformatics/btz960.
[Epub ahead of print] PubMed PMID: 31904820.

Acquiring Control: The Evolution of Stomatal Signalling Pathways.
Sussmilch FC, Schultz J, Hedrich R, Roelfsema MRG. Trends Plant Sci. (2019). 24(4) 342--351.

Floral Species Richness Correlates with Changes in the Nutritional Quality of Larval Diets in a Stingless Bee.
Trinkl M, Kaluza BF, Wallace H, Heard TA. textbfKeller A, Leonhardt SD. Insects (2020). 11(2)

Susceptibility of red mason bee larvae to bacterial threats due to microbiome exchange with imported pollen provisions.
Voulgari-Kokota A, Steffan-Dewenter I, Keller A. Insects (2020) 11(6)

Venus flytrap microbiotas withstand harsh conditions during prey digestion.
Sickel W, Van de Weyer AL, Bemm F, Schultz J, Keller A. FEMS Microbiol. Ecol. (2019). 95(3)

Connecting Cancer Pathways to Tumor Engines: A Stratification Tool for Colorectal Cancer Combining Human In Vitro Tissue Models with Boolean In Silico Models.
Baur F, Nietzer SL, Kunz M, Saal F, Jeromin J, Matschos S, Linnebacher M, Walles H, Dandekar T, Dandekar G. Cancers (Basel). 2019 Dec 20;12(1). pii: E28. doi:10.3390/cancers12010028. PubMed PMID: 31861874.

The New Genetic Landscape of Cushing's Disease: Deubiquitinases in the Spotlight.
Sbiera S, Kunz M, Weigand I, Deutschbein T, Dandekar T, Fassnacht M. Cancers (Basel). 2019 Nov 8;11(11). pii: E1761. doi: 10.3390/cancers11111761. PubMed PMID: 31717455; PubMed Central PMCID: PMC6895825.

C(60) Fullerene as an Effective Nanoplatform of Alkaloid Berberine Delivery into Leukemic Cells.
Grebinyk A, Prylutska S, Buchelnikov A, Tverdokhleb N, Grebinyk S, Evstigneev M, Matyshevska O, Cherepanov V, Prylutskyy Y, Yashchuk V, Naumovets A, Ritter U, Dandekar T, Frohme M. Pharmaceutics. 2019 Nov 8;11(11). pii: E586. doi: 10.3390/pharmaceutics11110586. PubMed PMID: 31717305; PubMed Central PMCID: PMC6920783.

Eugenol Exerts Apoptotic Effect and Modulates the Sensitivity of HeLa Cells to Cisplatin and Radiation.
Fathy M, Fawzy MA, Hintzsche H, Nikaido T, Dandekar T, Othman EM. Molecules. 2019 Nov 3;24(21). pii: E3979. doi:10.3390/molecules24213979. PubMed PMID: 31684176.

Comprehensive Flux Modeling of Chlamydia trachomatis Proteome and qRT-PCR Data Indicate Biphasic Metabolic Differences Between Elementary Bodies and Reticulate Bodies During Infection.
Yang M, Rajeeve K, Rudel T, Dandekar T. Front Microbiol. 2019 Oct 15;10:2350. doi: 10.3389/fmicb.2019.02350. eCollection 2019. PubMed PMID: 31681215; PubMed Central PMCID: PMC6803457.

C. elegans protein interaction network analysis probes RNAi validated pro-longevity effect of nhr-6, a human homolog of tumor suppressor Nr4a1.
Akhoon BA, Gupta SK, Tiwari S, Rathor L, Pant A, Singh N, Gupta SK, Dandekar T, Pandey R. Sci Rep. 2019 Oct 31;9(1):15711. doi: 10.1038/s41598-019-51649-0. PubMed PMID: 31673088; PubMed Central PMCID: PMC6823380.

Synergy of Chemo- and Photodynamic Therapies with C(60) Fullerene-Doxorubicin Nanocomplex.
Grebinyk A, Prylutska S, Chepurna O, Grebinyk S, Prylutskyy Y, Ritter U, Ohulchanskyy TY, Matyshevska O, Dandekar T, Frohme M. Nanomaterials (Basel). 2019 Oct 30;9(11). pii: E1540. doi:10.3390/nano9111540. PubMed PMID: 31671590; PubMed Central PMCID: PMC6915635.

A comprehensive method protocol for annotation and integrated functional understanding of lncRNAs.
Kunz M, Wolf B, Fuchs M, Christoph J, Xiao K, Thum T, Atlan D, Prokosch HU, Dandekar T. Brief Bioinform. 2019 Oct 3. pii: bbz066. doi: 10.1093/bib/bbz066. [Epub ahead of print] PubMed PMID: 31578571.

Analyzing pharmacological intervention points: A method to calculate external stimuli to switch between steady states in regulatory networks.
Breitenbach T, Liang C, Beyersdorf N, Dandekar T. PLoS Comput Biol. 2019 Jul16;15(7):e1007075. doi: 10.1371/journal.pcbi.1007075. eCollection 2019 Jul. PubMed PMID: 31310618; PubMed Central PMCID: PMC6660093.

Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle.
Srivastava M, Bencurova E, Gupta SK, Weiss E, Löffler J, Dandekar T. Front Cell Infect Microbiol. 2019 May 22;9:168. doi: 10.3389/fcimb.2019.00168. eCollection 2019. PubMed PMID:31192161; PubMed Central PMCID: PMC6540932.

Vaccinia virus injected human tumors: oncolytic virus efficiency predicted by antigen profiling analysis fitted boolean models.
Cecil A, Gentschev I, Adelfinger M, Dandekar T, Szalay AA. Bioengineered. 2019 Dec;10(1):190-196. doi:10.1080/21655979.2019.1622220. PubMed PMID: 31142183; PubMed Central PMCID: PMC6550548.

Venus flytrap microbiotas withstand harsh conditions during prey digestion.
Sickel W, Van de Weyer AL, Bemm F, Schultz J, Keller A. FEMS Microbiol Ecol. 2019 Mar 1;95(3). doi: 10.1093/femsec/fiz010. PubMed PMID: 30649283.

Candida auris in Germany and Previous Exposure to Foreign Healthcare.
Hamprecht A, Barber AE, Mellinghoff SC, Thelen P, Walther G, Yu Y, Neurgaonkar P, Dandekar T, Cornely OA, Martin R, Kurzai O, and on behalf of the German Candida auris Study Group. Emerg Infect Dis. 2019 Sep; 25(9): 1763-1765. doi: 10.3201/eid2509.190262

Optimizing defence, counter-defence and counter-counter defence in parasitic and trophic interactions – A modelling study.
Schuster S, Ewald J, Dandekar T, Dühring S. arXiv:1907.04820 [q-bio.SC]

How to Steer and Control ERK and the ERK Signaling Cascade Exemplified by Looking at Cardiac Insufficiency.
Breitenbach T, Lorenz K, Dandekar T. Int J Mol Sci. 2019, xx, 5; doi: 10.3390/ijmsxx010005

In silico signaling modeling to understand cancer pathways and treatment responses.
Kunz M, Jeromin J, Fuchs M, Christoph J, Veronesi G, Flentje M, Nietzer S, Dandekar G, Dandekar T. Briefings in Bioinf, 00(00), 2019, 1-3. doi: 10.1093/bib/bbz033

Plasma steroid metabolome profiling for the diagnosis of adrenocortical carcinoma.
Schweitzer S, Kunz M, Kurlbaum M, Vey J, Kendl S, Deutschbein T, Hahner S, Fassnacht M, Dandekar T, Kroiss M. Eur J Endocrinol. 2019 Feb 1; 180(2):117-125. doi: 10.1530/EJE-18-0782

Complexation with C60 Fullerene Increases Doxorubicin Efficiency against Leukemic Cells In Vitro.
Grebinyk A, Prylutska S, Grebinyk S, Prylutskyy Y, Ritter U, Matyshevska O, Dandekar T, Frohme M. Nanoscale Res Lett. 2019 Feb 20;14(1):61. doi: 10.1186/s11671-019-2894-1

IntelliEppi: Intelligent Reaction Monitoring and Holistic Data Management System for the Molecular Biology Lab.
Neuberger A, Zeeshan A, Dandekar T. In book: Advances in Information and Communication. Lecture Notes in Networks and Systems, Edition: 69, Publisher: Springer, pp.392-407. doi: 10.1007/978-3-030-12388-8_28

Fecal SCFAs and SCFA-producing bacteria in gut microbiome of human NAFLD as a putative link to systemic T-cell activation and advanced disease.
Rau M, Rehman A, Dittrich M, Groen AK, Hermanns HM, Seyfried F, Beyersdorf N, Dandekar T, Rosenstiel P, Geier A. United European Gastroenterol J. 2018 Dec;6(10):1496-1507. doi: 10.1177/2050640618804444. Epub 2018 Sep 30. PMID: 30574320

Systems Biology Analysis to Understand Regulatory miRNA Networks in Lung Cancer.
Kunz M, Pittroff A, Dandekar T. Methods Mol Biol. 2018;1819:235-247. doi: 10.1007/978-1-4939-8618-7_11. PMID: 30421407.

Automated classification of synaptic vesicles in electron tomograms of C. elegans using machine learning.
Kaltdorf KV, Theiss M, Markert SM, Zhen M, Dandekar T, Stigloher C, Kollmannsberger P. PLoS One. 2018 Oct 8;13(10):e0205348. doi: 10.1371/journal.pone.0205348. eCollection 2018. PMID: 30296290.

Functional genomics identifies AMPD2 as a new prognostic marker for undifferentiated pleomorphic sarcoma.
Orth MF, Gerke JS, Knösel T, Altendorf-Hofmann A, Musa J, Alba-Rubio R, Stein S, Hölting TLB, Cidre-Aranaz F, Romero-Pérez L, Dallmayer M, Baldauf MC, Marchetto A, Sannino G, Knott MML, Wehweck F, Ohmura S, Li J, Hakozaki M, Kirchner T, Dandekar T, Butt E, Grünewald TGP. Int J Cancer. 2018 Sep 28. doi: 10.1002/ijc.31903. [Epub ahead of print] PMID: 30267407.

HPLC-ESI-MS method for C₆₀ fullerene mitochondrial content quantification.
Grebinyk A, Grebinyk S, Prylutska S, Ritter U, Matyshevska O, Dandekar T, Frohme M. Data Brief. 2018 Jul 10;19:2047-2052. doi: 10.1016/j.dib.2018.06.089. eCollection 2018 Aug. PMID: 30229080.

Evaluation of Aspergillus and Mucorales specific T-cells and peripheral blood mononuclear cell cytokine signatures as biomarkers of environmental mold exposure.
Page L, Weis P, Müller T, Dittrich M, Lazariotou M, Dragan M, Waaga-Gasser AM, Helm J, Dandekar T, Einsele H, Löffler J, Ullmann AJ, Wurster S. Int J Med Microbiol. 2018 Dec;308(8):1018-1026. doi: 10.1016/j.ijmm.2018.09.002. Epub 2018 Sep 3. PMID: 30201279.

Omics and bioinformatics applied to vaccine development against Borrelia.
Bencurova E, Gupta SK, Oskoueian E, Bhide M, Dandekar T. Mol Omics. 2018 Oct 8;14(5):330-340. doi: 10.1039/c8mo00130h. PMID: 30113617.

Analysis of Nickel-Binding Proteins from Various Animal Sera.
Šimková, J., M. Milkovičová, M. Valko-Rokytovská, Z. Kostecká, E. Bencúrová, L. Pulzová, Ľ. Čomor, and M. R. Bhide. Folia Veterinaria 62, no. 2 (2018): 59-66.

Nanocellulose: A New Multifunctional Tool for RNA Systems Biology Research.
Bencurova E, Kunz M, Dandekar T. (2018) Systems Biology (pp. 373-401). Springer, Cham.

In Silico Designed Axl Receptor Blocking Drug Candidates Against Zika Virus Infection.
Sarukhanyan E, Shityakov S, Dandekar T. ACS Omega. 2018 May 31;3(5):5281-5290. doi: 10.1021/acsomega.8b00223. Epub 2018 May 16. PMID: 30023915.

Identification of Antifungal Targets Based on Computer Modeling.
Bencurova E, Gupta S, Sarukhanyan E, Dandekar T. J Fungi (Basel). 2018 Jul 4;4(3). pii: E81. doi: 10.3390/jof4030081. Review. PMID: 29973534.

C₆₀ fullerene accumulation in human leukemic cells and perspectives of LED-mediated photodynamic therapy.
Grebinyk A, Grebinyk S, Prylutska S, Ritter U, Matyshevska O, Dandekar T, Frohme M. Free Radic Biol Med. 2018 Aug 20;124:319-327. doi: 10.1016/j.freeradbiomed.2018.06.022. Epub 2018 Jun 27. PMID: 29940354.

A combined tissue-engineered/in silico signature tool patient stratification in lung cancer.
Göttlich C, Kunz M, Zapp C, Nietzer SL, Walles H, Dandekar T, Dandekar G. Mol Oncol. 2018 Aug;12(8):1264-1285. doi: 10.1002/1878-0261.12323. Epub 2018 Jun 22. PMID: 29797762.

An open source tool for automatic spatiotemporal assessment of calcium transients and local 'signal-close-to-noise' activity in calcium imaging data.
Prada J, Sasi M, Martin C, Jablonka S, Dandekar T, Blum R. PLoS Comput Biol. 2018 Mar 30;14(3):e1006054. doi: 10.1371/journal.pcbi.1006054. eCollection 2018 Mar. PMID: 29601577.

A new triple system DNA-Nanosilver-Berberine for cancer therapy.
Grebinyk, A., Yashchuk, V., Bashmakova, N. et al. Appl Nanosci (2018). https://doi.org/10.1007/s13204-018-0688-x.

The Cytokinin-Activating LOG-Family Proteins Are Not Lysine Decarboxylases.
Naseem M, Bencurova E, Dandekar T. Trends Biochem Sci. 2018 Mar 7. pii: S0968-0004(18)30002-1. doi: 10.1016/j.tibs.2018.01.002. [Epub ahead of print]

Proteomics of Aspergillus fumigatus conidia-containing phagolysosomes identifies processes governing immune evasion.
Schmidt H, Vlaic S, Krüger T, Schmidt F, Balkenhohl J, Dandekar T, Guthke R, Kniemeyer O, Heinekamp T, Brakhage AA. Mol Cell Proteomics. 2018 Mar 5. pii: mcp.RA117.000069. doi: 10.1074/mcp.RA117.000069. [Epub ahead of print]

TRPM7 Kinase Controls Calcium Responses in Arterial Thrombosis and Stroke in Mice.
Gotru SK, Chen W, Kraft P, Becker IC, Wolf K, Stritt S, Zierler S, Hermanns HM, Rao D, Perraud AL, Schmitz C, Zahedi RP, Noy PJ, Tomlinson MG, Dandekar T, Matsushita M, Chubanov V, Gudermann T, Stoll G, Nieswandt B, Braun A. Arterioscler Thromb Vasc Biol. 2018 Feb;38(2):344-352. doi: 10.1161/ATVBAHA.117.310391. Epub 2017 Nov 16.

Genetic profiling and surface proteome analysis of human atrial stromal cells and rat ventricular epicardium-derived cells reveals novel insights into their cardiogenic potential.
Temme S, Friebe D, Schmidt T, Poschmann G, Hesse J, Steckel B, Stühler K, Kunz M, Dandekar T, Ding Z, Akhyari P, Lichtenberg A, Schrader J. Stem Cell Res. 2017 Dec;25:183-190. doi: 10.1016/j.scr.2017.11.006. Epub 2017 Nov 7.

Mucorales spores induce a proinflammatory cytokine response in human mononuclear phagocytes and harbor no rodlet hydrophobins.
Wurster S, Thielen V, Weis P, Walther P, Elias J, Waaga-Gasser AM, Dragan M, Dandekar T, Einsele H, Löffler J, Ullmann AJ. Virulence. 2017 Nov 17;8(8):1708-1718. doi: 10.1080/21505594.2017.1342920. Epub 2017 Aug 8.

Plant-Pathogen Maneuvering over Apoplastic Sugars.
Naseem M, Kunz M, Dandekar T. Trends Plant Sci. 2017 Sep;22(9):740-743. doi: 10.1016/j.tplants.2017.07.001. Epub 2017 Aug 2. Review.

MicroRNA-21 versus microRNA-34: Lung cancer promoting and inhibitory microRNAs analysed in silico and in vitro and their clinical impact.
Kunz M, Göttlich C, Walles T, Nietzer S, Dandekar G, Dandekar T. Tumour Biol. 2017 Jul;39(7):1010428317706430. doi: 10.1177/1010428317706430. Review.

Modelling the host-pathogen interactions of macrophages and Candida albicans using Game Theory and dynamic optimization.
Dühring S, Ewald J, Germerodt S, Kaleta C, Dandekar T, Schuster S. J R Soc Interface. 2017 Jul;14(132). pii: 20170095. doi: 10.1098/rsif.2017.0095.

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.

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

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

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.

'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]

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.

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.

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.

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.

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

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.

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.

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.

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

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

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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