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The bioinformatics of the yeast genome-A historical perspective.

Mewes HW.

Yeast. 2019 Apr;36(4):161-165. doi: 10.1002/yea.3378.


PhenoDis: a comprehensive database for phenotypic characterization of rare cardiac diseases.

Adler A, Kirchmeier P, Reinhard J, Brauner B, Dunger I, Fobo G, Frishman G, Montrone C, Mewes HW, Arnold M, Ruepp A.

Orphanet J Rare Dis. 2018 Jan 25;13(1):22. doi: 10.1186/s13023-018-0765-y.


KNIME4NGS: a comprehensive toolbox for next generation sequencing analysis.

Hastreiter M, Jeske T, Hoser J, Kluge M, Ahomaa K, Friedl MS, Kopetzky SJ, Quell JD, Mewes HW, Küffner R.

Bioinformatics. 2017 May 15;33(10):1565-1567. doi: 10.1093/bioinformatics/btx003.


Identification and Characterization of Carboxylesterases from Brachypodium distachyon Deacetylating Trichothecene Mycotoxins.

Schmeitzl C, Varga E, Warth B, Kugler KG, Malachová A, Michlmayr H, Wiesenberger G, Mayer KF, Mewes HW, Krska R, Schuhmacher R, Berthiller F, Adam G.

Toxins (Basel). 2015 Dec 25;8(1). pii: E6. doi: 10.3390/toxins8010006.


Stroma-Derived Connective Tissue Growth Factor Maintains Cell Cycle Progression and Repopulation Activity of Hematopoietic Stem Cells In Vitro.

Istvánffy R, Vilne B, Schreck C, Ruf F, Pagel C, Grziwok S, Henkel L, Prazeres da Costa O, Berndt J, Stümpflen V, Götze KS, Schiemann M, Peschel C, Mewes HW, Oostendorp RAJ.

Stem Cell Reports. 2015 Nov 10;5(5):702-715. doi: 10.1016/j.stemcr.2015.09.018. Epub 2015 Oct 29.


Implementing systems medicine within healthcare.

Kirschner M, Bauch A, Agusti A, Hilke S, Merk S, Pison C, Roldan J, Seidenath B, Wilken M, Wouters EF, Mewes HW, Heumann K, Maier D.

Genome Med. 2015 Sep 29;7:102. doi: 10.1186/s13073-015-0224-5.


The Fusarium graminearum genome reveals more secondary metabolite gene clusters and hints of horizontal gene transfer.

Sieber CM, Lee W, Wong P, Münsterkötter M, Mewes HW, Schmeitzl C, Varga E, Berthiller F, Adam G, Güldener U.

PLoS One. 2014 Oct 15;9(10):e110311. doi: 10.1371/journal.pone.0110311. eCollection 2014.


Large-scale modeling of condition-specific gene regulatory networks by information integration and inference.

Ellwanger DC, Leonhardt JF, Mewes HW.

Nucleic Acids Res. 2014 Dec 1;42(21). doi: 10.1093/nar/gku916. Epub 2014 Oct 7.


Rare variants in LRRK1 and Parkinson's disease.

Schulte EC, Ellwanger DC, Dihanich S, Manzoni C, Stangl K, Schormair B, Graf E, Eck S, Mollenhauer B, Haubenberger D, Pirker W, Zimprich A, Brücke T, Lichtner P, Peters A, Gieger C, Trenkwalder C, Mewes HW, Meitinger T, Lewis PA, Klünemann HH, Winkelmann J.

Neurogenetics. 2014 Mar;15(1):49-57. doi: 10.1007/s10048-013-0383-8. Epub 2013 Nov 16.


EXPANDS: expanding ploidy and allele frequency on nested subpopulations.

Andor N, Harness JV, Müller S, Mewes HW, Petritsch C.

Bioinformatics. 2014 Jan 1;30(1):50-60. doi: 10.1093/bioinformatics/btt622. Epub 2013 Oct 30.


SIMAP--the database of all-against-all protein sequence similarities and annotations with new interfaces and increased coverage.

Arnold R, Goldenberg F, Mewes HW, Rattei T.

Nucleic Acids Res. 2014 Jan;42(Database issue):D279-84. doi: 10.1093/nar/gkt970. Epub 2013 Oct 27.


Perspectives of a systems biology of the brain: the big data conundrum understanding psychiatric diseases.

Mewes HW.

Pharmacopsychiatry. 2013 May;46 Suppl 1:S2-9. doi: 10.1055/s-0033-1341481. Epub 2013 Apr 18. Review.


Systems biology of oscillatory processes in sleep and mental disorders.

Tretter F, Pogarell O, Rujescu D, Meisenzahl E, Mewes HW.

Pharmacopsychiatry. 2013 May;46 Suppl 1:S1. doi: 10.1055/s-0033-1341514. Epub 2013 Apr 18. No abstract available.


Functional characterization of two clusters of Brachypodium distachyon UDP-glycosyltransferases encoding putative deoxynivalenol detoxification genes.

Schweiger W, Pasquet JC, Nussbaumer T, Paris MP, Wiesenberger G, Macadré C, Ametz C, Berthiller F, Lemmens M, Saindrenan P, Mewes HW, Mayer KF, Dufresne M, Adam G.

Mol Plant Microbe Interact. 2013 Jul;26(7):781-92. doi: 10.1094/MPMI-08-12-0205-R.


Network-based SNP meta-analysis identifies joint and disjoint genetic features across common human diseases.

Arnold M, Hartsperger ML, Baurecht H, Rodríguez E, Wachinger B, Franke A, Kabesch M, Winkelmann J, Pfeufer A, Romanos M, Illig T, Mewes HW, Stümpflen V, Weidinger S.

BMC Genomics. 2012 Sep 18;13:490. doi: 10.1186/1471-2164-13-490.


Pharmacopsychiatry. Editorial.

Tretter F, Pogarell O, Rujescu D, Meisenzahl E, Mewes HW.

Pharmacopsychiatry. 2012 May;45 Suppl 1:S1. doi: 10.1055/s-0032-1311602. Epub 2012 May 7. No abstract available.


Human metabolic individuality in biomedical and pharmaceutical research.

Suhre K, Shin SY, Petersen AK, Mohney RP, Meredith D, Wägele B, Altmaier E; CARDIoGRAM, Deloukas P, Erdmann J, Grundberg E, Hammond CJ, de Angelis MH, Kastenmüller G, Köttgen A, Kronenberg F, Mangino M, Meisinger C, Meitinger T, Mewes HW, Milburn MV, Prehn C, Raffler J, Ried JS, Römisch-Margl W, Samani NJ, Small KS, Wichmann HE, Zhai G, Illig T, Spector TD, Adamski J, Soranzo N, Gieger C.

Nature. 2011 Aug 31;477(7362):54-60. doi: 10.1038/nature10354.


Affective disorders as complex dynamic diseases--a perspective from systems biology.

Tretter F, Gebicke-Haerter PJ, an der Heiden U, Rujescu D, Mewes HW, Turck CW.

Pharmacopsychiatry. 2011 May;44 Suppl 1:S2-8. doi: 10.1055/s-0031-1275278. Epub 2011 May 4.


Pharmacopsychiatry. Editorial.

Tretter F, Rujescu D, Turck CW, Mewes HW.

Pharmacopsychiatry. 2011 May;44 Suppl 1:S1. doi: 10.1055/s-0031-1275303. Epub 2011 May 4. No abstract available.


The sufficient minimal set of miRNA seed types.

Ellwanger DC, Büttner FA, Mewes HW, Stümpflen V.

Bioinformatics. 2011 May 15;27(10):1346-50. doi: 10.1093/bioinformatics/btr149. Epub 2011 Mar 26.


MIPS: curated databases and comprehensive secondary data resources in 2010.

Mewes HW, Ruepp A, Theis F, Rattei T, Walter M, Frishman D, Suhre K, Spannagl M, Mayer KF, Stümpflen V, Antonov A.

Nucleic Acids Res. 2011 Jan;39(Database issue):D220-4. doi: 10.1093/nar/gkq1157. Epub 2010 Nov 24.


Metabolic footprint of diabetes: a multiplatform metabolomics study in an epidemiological setting.

Suhre K, Meisinger C, Döring A, Altmaier E, Belcredi P, Gieger C, Chang D, Milburn MV, Gall WE, Weinberger KM, Mewes HW, Hrabé de Angelis M, Wichmann HE, Kronenberg F, Adamski J, Illig T.

PLoS One. 2010 Nov 11;5(11):e13953. doi: 10.1371/journal.pone.0013953.


Exome sequencing identifies ACAD9 mutations as a cause of complex I deficiency.

Haack TB, Danhauser K, Haberberger B, Hoser J, Strecker V, Boehm D, Uziel G, Lamantea E, Invernizzi F, Poulton J, Rolinski B, Iuso A, Biskup S, Schmidt T, Mewes HW, Wittig I, Meitinger T, Zeviani M, Prokisch H.

Nat Genet. 2010 Dec;42(12):1131-4. doi: 10.1038/ng.706. Epub 2010 Nov 7.


FGDB: revisiting the genome annotation of the plant pathogen Fusarium graminearum.

Wong P, Walter M, Lee W, Mannhaupt G, Münsterkötter M, Mewes HW, Adam G, Güldener U.

Nucleic Acids Res. 2011 Jan;39(Database issue):D637-9. doi: 10.1093/nar/gkq1016. Epub 2010 Nov 4.


Perspectives of a systems biology of the synapse: how to transform an indefinite data space into a model?

Mewes HW, Wachinger B, Stümpflen V.

Pharmacopsychiatry. 2010 May;43 Suppl 1:S2-8. doi: 10.1055/s-0030-1249666. Epub 2010 May 17.


A genome-wide perspective of genetic variation in human metabolism.

Illig T, Gieger C, Zhai G, Römisch-Margl W, Wang-Sattler R, Prehn C, Altmaier E, Kastenmüller G, Kato BS, Mewes HW, Meitinger T, de Angelis MH, Kronenberg F, Soranzo N, Wichmann HE, Spector TD, Adamski J, Suhre K.

Nat Genet. 2010 Feb;42(2):137-41. doi: 10.1038/ng.507. Epub 2009 Dec 27.


SIMAP--a comprehensive database of pre-calculated protein sequence similarities, domains, annotations and clusters.

Rattei T, Tischler P, Götz S, Jehl MA, Hoser J, Arnold R, Conesa A, Mewes HW.

Nucleic Acids Res. 2010 Jan;38(Database issue):D223-6. doi: 10.1093/nar/gkp949. Epub 2009 Nov 11.


CORUM: the comprehensive resource of mammalian protein complexes--2009.

Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW.

Nucleic Acids Res. 2010 Jan;38(Database issue):D497-501. doi: 10.1093/nar/gkp914. Epub 2009 Nov 1.


Approaching clinical proteomics: current state and future fields of application in cellular proteomics.

Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tárnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Wagener C, Wagner O, Schmitz G.

Cytometry A. 2009 Oct;75(10):816-32. doi: 10.1002/cyto.a.20779. Review.


A novel putative miRNA target enhancer signal.

Schmidt T, Mewes HW, Stümpflen V.

PLoS One. 2009 Jul 31;4(7):e6473. doi: 10.1371/journal.pone.0006473.


Large scale application of neural network based semantic role labeling for automated relation extraction from biomedical texts.

Barnickel T, Weston J, Collobert R, Mewes HW, Stümpflen V.

PLoS One. 2009 Jul 28;4(7):e6393. doi: 10.1371/journal.pone.0006393.


Approaching clinical proteomics: current state and future fields of application in fluid proteomics.

Apweiler R, Aslanidis C, Deufel T, Gerstner A, Hansen J, Hochstrasser D, Kellner R, Kubicek M, Lottspeich F, Maser E, Mewes HW, Meyer HE, Müllner S, Mutter W, Neumaier M, Nollau P, Nothwang HG, Ponten F, Radbruch A, Reinert K, Rothe G, Stockinger H, Tarnok A, Taussig MJ, Thiel A, Thiery J, Ueffing M, Valet G, Vandekerckhove J, Verhuven W, Wagener C, Wagner O, Schmitz G.

Clin Chem Lab Med. 2009;47(6):724-44. doi: 10.1515/CCLM.2009.167. Review.


GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists.

Antonov AV, Dietmann S, Wong P, Lutter D, Mewes HW.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W323-8. doi: 10.1093/nar/gkp313. Epub 2009 May 6.


PPI spider: a tool for the interpretation of proteomics data in the context of protein-protein interaction networks.

Antonov AV, Dietmann S, Rodchenkov I, Mewes HW.

Proteomics. 2009 May;9(10):2740-9. doi: 10.1002/pmic.200800612.


Sequence-based prediction of type III secreted proteins.

Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T.

PLoS Pathog. 2009 Apr;5(4):e1000376. doi: 10.1371/journal.ppat.1000376. Epub 2009 Apr 24. Erratum in: PLoS Pathog. 2009 Apr;5(4). doi: 10.1371/annotation/78659a32-7869-4b14-91a6-b301a588d937.


TICL--a web tool for network-based interpretation of compound lists inferred by high-throughput metabolomics.

Antonov AV, Dietmann S, Wong P, Mewes HW.

FEBS J. 2009 Apr;276(7):2084-94. doi: 10.1111/j.1742-4658.2009.06943.x.


Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes.

Kastenmüller G, Schenk ME, Gasteiger J, Mewes HW.

Genome Biol. 2009;10(3):R28. doi: 10.1186/gb-2009-10-3-r28. Epub 2009 Mar 10.


PLIPS, an automatically collected database of protein lists reported by proteomics studies.

Antonov AV, Dietmann S, Wong P, Igor R, Mewes HW.

J Proteome Res. 2009 Mar;8(3):1193-7. doi: 10.1021/pr800804d.


The DICS repository: module-assisted analysis of disease-related gene lists.

Dietmann S, Georgii E, Antonov A, Tsuda K, Mewes HW.

Bioinformatics. 2009 Mar 15;25(6):830-1. doi: 10.1093/bioinformatics/btp055. Epub 2009 Jan 28.


KEGG spider: interpretation of genomics data in the context of the global gene metabolic network.

Antonov AV, Dietmann S, Mewes HW.

Genome Biol. 2008;9(12):R179. doi: 10.1186/gb-2008-9-12-r179. Epub 2008 Dec 18.


Genetics meets metabolomics: a genome-wide association study of metabolite profiles in human serum.

Gieger C, Geistlinger L, Altmaier E, Hrabé de Angelis M, Kronenberg F, Meitinger T, Mewes HW, Wichmann HE, Weinberger KM, Adamski J, Illig T, Suhre K.

PLoS Genet. 2008 Nov;4(11):e1000282. doi: 10.1371/journal.pgen.1000282. Epub 2008 Nov 28.


CRONOS: the cross-reference navigation server.

Waegele B, Dunger-Kaltenbach I, Fobo G, Montrone C, Mewes HW, Ruepp A.

Bioinformatics. 2009 Jan 1;25(1):141-3. doi: 10.1093/bioinformatics/btn590. Epub 2008 Nov 13.


PEDANT covers all complete RefSeq genomes.

Walter MC, Rattei T, Arnold R, Güldener U, Münsterkötter M, Nenova K, Kastenmüller G, Tischler P, Wölling A, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D.

Nucleic Acids Res. 2009 Jan;37(Database issue):D408-11. doi: 10.1093/nar/gkn749. Epub 2008 Oct 21.


Complex phylogenetic profiling reveals fundamental genotype-phenotype associations.

Antonov AV, Mewes HW.

Comput Biol Chem. 2008 Dec;32(6):412-6. doi: 10.1016/j.compbiolchem.2008.07.003. Epub 2008 Jul 10.


Informatics and medicine--from molecules to populations.

Kuhn KA, Knoll A, Mewes HW, Schwaiger M, Bode A, Broy M, Daniel H, Feussner H, Gradinger R, Hauner H, Höfler H, Holzmann B, Horsch A, Kemper A, Krcmar H, Kochs EF, Lange R, Leidl R, Mansmann U, Mayr EW, Meitinger T, Molls M, Navab N, Nüsslin F, Peschel C, Reiser M, Ring J, Rummeny EJ, Schlichter J, Schmid R, Wichmann HE, Ziegler S.

Methods Inf Med. 2008;47(4):283-95.


An environmental perspective on large-scale genome clustering based on metabolic capabilities.

Kastenmüller G, Gasteiger J, Mewes HW.

Bioinformatics. 2008 Aug 15;24(16):i56-62. doi: 10.1093/bioinformatics/btn302.


FunCat functional inference with belief propagation and feature integration.

Surmeli D, Ratmann O, Mewes HW, Tetko IV.

Comput Biol Chem. 2008 Oct;32(5):375-7. doi: 10.1016/j.compbiolchem.2008.06.004. Epub 2008 Jul 3.


OREST: the online resource for EST analysis.

Waegele B, Schmidt T, Mewes HW, Ruepp A.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W140-4. doi: 10.1093/nar/gkn253. Epub 2008 May 7.


ProfCom: a web tool for profiling the complex functionality of gene groups identified from high-throughput data.

Antonov AV, Schmidt T, Wang Y, Mewes HW.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W347-51. doi: 10.1093/nar/gkn239. Epub 2008 May 6.


Bioinformatics analysis of targeted metabolomics--uncovering old and new tales of diabetic mice under medication.

Altmaier E, Ramsay SL, Graber A, Mewes HW, Weinberger KM, Suhre K.

Endocrinology. 2008 Jul;149(7):3478-89. doi: 10.1210/en.2007-1747. Epub 2008 Mar 27.


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