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Items: 1 to 50 of 97

1.

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z.

Nucleic Acids Res. 2019 Nov 7. pii: gkz1054. doi: 10.1093/nar/gkz1054. [Epub ahead of print]

PMID:
31696234
2.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2.

Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F.

J Integr Bioinform. 2019 Jun 20;16(2). pii: /j/jib.2019.16.issue-2/jib-2019-0021/jib-2019-0021.xml. doi: 10.1515/jib-2019-0021.

3.

Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0.

Rougny A, Touré V, Moodie S, Balaur I, Czauderna T, Borlinghaus H, Dogrusoz U, Mazein A, Dräger A, Blinov ML, Villéger A, Haw R, Demir E, Mi H, Sorokin A, Schreiber F, Luna A.

J Integr Bioinform. 2019 Jun 13;16(2). pii: /j/jib.2019.16.issue-2/jib-2019-0022/jib-2019-0022.xml. doi: 10.1515/jib-2019-0022.

4.

Insights into Dynamic Network States Using Metabolomic Data.

Mostolizadeh R, Dräger A, Jamshidi N.

Methods Mol Biol. 2019;1978:243-258. doi: 10.1007/978-1-4939-9236-2_15.

PMID:
31119667
5.

The 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes.

Romano P, Céol A, Dräger A, Fiannaca A, Giugno R, La Rosa M, Milanesi L, Pfeffer U, Rizzo R, Shin SY, Xia J, Urso A.

BMC Bioinformatics. 2019 Apr 18;20(Suppl 4):125. doi: 10.1186/s12859-019-2681-0.

6.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Mısırlı G, Kalbasi R, Dräger A, Atalag K, Chelliah V, Cooling MT, Cook DL, Crook S, de Alba M, Friedman SH, Garny A, Gennari JH, Gleeson P, Golebiewski M, Hucka M, Juty N, Myers C, Olivier BG, Sauro HM, Scharm M, Snoep JL, Touré V, Wipat A, Wolkenhauer O, Waltemath D.

Brief Bioinform. 2019 Mar 22;20(2):540-550. doi: 10.1093/bib/bby087. Review.

7.

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO.

Nucleic Acids Res. 2018 Nov 16;46(20):10682-10696. doi: 10.1093/nar/gky752.

8.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2018 Mar 9;15(1). pii: /j/jib.2018.15.issue-1/jib-2017-0081/jib-2017-0081.xml. doi: 10.1515/jib-2017-0081.

9.

Recon3D enables a three-dimensional view of gene variation in human metabolism.

Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlić A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO.

Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19.

10.

A Padawan Programmer's Guide to Developing Software Libraries.

Yurkovich JT, Yurkovich BJ, Dräger A, Palsson BO, King ZA.

Cell Syst. 2017 Nov 22;5(5):431-437. doi: 10.1016/j.cels.2017.08.003. Epub 2017 Oct 4.

11.

Enemies and brothers in arms: Candida albicans and gram-positive bacteria.

Förster TM, Mogavero S, Dräger A, Graf K, Polke M, Jacobsen ID, Hube B.

Cell Microbiol. 2016 Dec;18(12):1709-1715. doi: 10.1111/cmi.12657. Epub 2016 Sep 14. Review.

PMID:
27552083
12.

Evaluation of rate law approximations in bottom-up kinetic models of metabolism.

Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO.

BMC Syst Biol. 2016 Jun 6;10(1):40. doi: 10.1186/s12918-016-0283-2.

13.

ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis.

Römer M, Eichner J, Dräger A, Wrzodek C, Wrzodek F, Zell A.

PLoS One. 2016 Feb 16;11(2):e0149263. doi: 10.1371/journal.pone.0149263. eCollection 2016.

14.

Coordinating Role of RXRα in Downregulating Hepatic Detoxification during Inflammation Revealed by Fuzzy-Logic Modeling.

Keller R, Klein M, Thomas M, Dräger A, Metzger U, Templin MF, Joos TO, Thasler WE, Zell A, Zanger UM.

PLoS Comput Biol. 2016 Jan 4;12(1):e1004431. doi: 10.1371/journal.pcbi.1004431. eCollection 2016 Jan.

15.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ.

J Integr Bioinform. 2015 Sep 4;12(2):271. doi: 10.2390/biecoll-jib-2015-271.

16.

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.

King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.

Nucleic Acids Res. 2016 Jan 4;44(D1):D515-22. doi: 10.1093/nar/gkv1049. Epub 2015 Oct 17.

17.

Do genome-scale models need exact solvers or clearer standards?

Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RM, Fong SS, Hatzimanikatis V, Herrgård MJ, Holder A, Hucka M, Hyduke D, Jamshidi N, Lee SY, Le Novère N, Lerman JA, Lewis NE, Ma D, Mahadevan R, Maranas C, Nagarajan H, Navid A, Nielsen J, Nielsen LK, Nogales J, Noronha A, Pal C, Palsson BO, Papin JA, Patil KR, Price ND, Reed JL, Saunders M, Senger RS, Sonnenschein N, Sun Y, Thiele I.

Mol Syst Biol. 2015 Oct 14;11(10):831. doi: 10.15252/msb.20156157. No abstract available.

18.

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.

Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.

BMC Syst Biol. 2015 Oct 9;9:68. doi: 10.1186/s12918-015-0212-9.

19.

Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.

King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.

PLoS Comput Biol. 2015 Aug 27;11(8):e1004321. doi: 10.1371/journal.pcbi.1004321. eCollection 2015 Aug.

20.

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.

Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT, Du B, Dräger A, Thomas A, Sun Y, Saunders MA, Palsson BO.

Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10810-5. doi: 10.1073/pnas.1501384112. Epub 2015 Aug 10.

21.

JSBML 1.0: providing a smorgasbord of options to encode systems biology models.

Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F, Netz E, Diamantikos A, Eichner J, Keller R, Wrzodek C, Fröhlich S, Lewis NE, Myers CJ, Le Novère N, Palsson BØ, Hucka M, Dräger A.

Bioinformatics. 2015 Oct 15;31(20):3383-6. doi: 10.1093/bioinformatics/btv341. Epub 2015 Jun 16.

22.

Improving collaboration by standardization efforts in systems biology.

Dräger A, Palsson BØ.

Front Bioeng Biotechnol. 2014 Dec 8;2:61. doi: 10.3389/fbioe.2014.00061. eCollection 2014. Review.

23.

TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.

Eichner J, Topf F, Dräger A, Wrzodek C, Wanke D, Zell A.

PLoS One. 2013 Dec 12;8(12):e82238. doi: 10.1371/journal.pone.0082238. eCollection 2013.

24.

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.

Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B, Wicks B, Gonçalves E, Dorier J, Page M, Monteiro PT, von Kamp A, Xenarios I, de Jong H, Hucka M, Klamt S, Thieffry D, Le Novère N, Saez-Rodriguez J, Helikar T.

BMC Syst Biol. 2013 Dec 10;7:135. doi: 10.1186/1752-0509-7-135.

25.

Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein.

Büchel F, Saliger S, Dräger A, Hoffmann S, Wrzodek C, Zell A, Kahle PJ.

BMC Neurosci. 2013 Nov 6;14:136. doi: 10.1186/1471-2202-14-136.

26.

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N.

BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116.

27.

High prognostic impact of flow cytometric minimal residual disease detection in acute myeloid leukemia: data from the HOVON/SAKK AML 42A study.

Terwijn M, van Putten WL, Kelder A, van der Velden VH, Brooimans RA, Pabst T, Maertens J, Boeckx N, de Greef GE, Valk PJ, Preijers FW, Huijgens PC, Dräger AM, Schanz U, Jongen-Lavrecic M, Biemond BJ, Passweg JR, van Gelder M, Wijermans P, Graux C, Bargetzi M, Legdeur MC, Kuball J, de Weerdt O, Chalandon Y, Hess U, Verdonck LF, Gratama JW, Oussoren YJ, Scholten WJ, Slomp J, Snel AN, Vekemans MC, Löwenberg B, Ossenkoppele GJ, Schuurhuis GJ.

J Clin Oncol. 2013 Nov 1;31(31):3889-97. doi: 10.1200/JCO.2012.45.9628. Epub 2013 Sep 23.

PMID:
24062400
28.

The systems biology simulation core algorithm.

Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A.

BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55.

29.

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

Vlaic S, Hoffmann B, Kupfer P, Weber M, Dräger A.

Bioinformatics. 2013 Sep 1;29(17):2216-7. doi: 10.1093/bioinformatics/btt370. Epub 2013 Jun 26.

PMID:
23803467
30.

Precise generation of systems biology models from KEGG pathways.

Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A.

BMC Syst Biol. 2013 Feb 21;7:15. doi: 10.1186/1752-0509-7-15.

31.

Qualitative translation of relations from BioPAX to SBML qual.

Büchel F, Wrzodek C, Mittag F, Dräger A, Eichner J, Rodriguez N, Le Novère N, Zell A.

Bioinformatics. 2012 Oct 15;28(20):2648-53. doi: 10.1093/bioinformatics/bts508. Epub 2012 Aug 24.

32.

Rationale for the clinical application of flow cytometry in patients with myelodysplastic syndromes: position paper of an International Consortium and the European LeukemiaNet Working Group.

van de Loosdrecht AA, Ireland R, Kern W, Della Porta MG, Alhan C, Balleisen JS, Bettelheim P, Bowen DT, Burbury K, Eidenschink L, Cazzola M, Chu SS, Cullen M, Cutler JA, Dräger AM, Feuillard J, Fenaux P, Font P, Germing U, Haase D, Hellström-Lindberg E, Johansson U, Kordasti S, Loken MR, Malcovati L, te Marvelde JG, Matarraz S, Milne T, Moshaver B, Mufti GJ, Nikolova V, Ogata K, Oelschlaegel U, Orfao A, Ossenkoppele GJ, Porwit A, Platzbecker U, Preijers F, Psarra K, Richards SJ, Subirá D, Seymour JF, Tindell V, Vallespi T, Valent P, van der Velden VH, Wells DA, de Witte TM, Zettl F, Béné MC, Westers TM.

Leuk Lymphoma. 2013 Mar;54(3):472-5. doi: 10.3109/10428194.2012.718341. Epub 2012 Sep 14. Review.

PMID:
22916713
33.

CySBML: a Cytoscape plugin for SBML.

König M, Dräger A, Holzhütter HG.

Bioinformatics. 2012 Sep 15;28(18):2402-3. doi: 10.1093/bioinformatics/bts432. Epub 2012 Jul 5.

PMID:
22772946
34.

Standardization of flow cytometry in myelodysplastic syndromes: a report from an international consortium and the European LeukemiaNet Working Group.

Westers TM, Ireland R, Kern W, Alhan C, Balleisen JS, Bettelheim P, Burbury K, Cullen M, Cutler JA, Della Porta MG, Dräger AM, Feuillard J, Font P, Germing U, Haase D, Johansson U, Kordasti S, Loken MR, Malcovati L, te Marvelde JG, Matarraz S, Milne T, Moshaver B, Mufti GJ, Ogata K, Orfao A, Porwit A, Psarra K, Richards SJ, Subirá D, Tindell V, Vallespi T, Valent P, van der Velden VH, de Witte TM, Wells DA, Zettl F, Béné MC, van de Loosdrecht AA.

Leukemia. 2012 Jul;26(7):1730-41. doi: 10.1038/leu.2012.30. Epub 2012 Feb 6.

PMID:
22307178
35.

Controlled vocabularies and semantics in systems biology.

Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N.

Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77.

36.

Implementation of flow cytometry in the diagnostic work-up of myelodysplastic syndromes in a multicenter approach: report from the Dutch Working Party on Flow Cytometry in MDS.

Westers TM, van der Velden VH, Alhan C, Bekkema R, Bijkerk A, Brooimans RA, Cali C, Dräger AM, de Haas V, Homburg C, de Jong A, Kuiper-Kramer PE, Leenders M, Lommerse I, te Marvelde JG, van der Molen-Sinke JK, Moshaver B, Mulder AB, Preijers FW, Schindhelm RK, van der Sluijs A, van Wering ER, Westra AH, van de Loosdrecht AA; Working Party on Flow Cytometry in MDS of Dutch Society of Cytometry (NVC).

Leuk Res. 2012 Apr;36(4):422-30. doi: 10.1016/j.leukres.2011.09.015. Epub 2011 Oct 6.

PMID:
21982641
37.

Inferring statin-induced gene regulatory relationships in primary human hepatocytes.

Schröder A, Wollnik J, Wrzodek C, Dräger A, Bonin M, Burk O, Thomas M, Thasler WE, Zanger UM, Zell A.

Bioinformatics. 2011 Sep 15;27(18):2473-7. doi: 10.1093/bioinformatics/btr416. Epub 2011 Jul 14.

PMID:
21757465
38.

KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats.

Wrzodek C, Dräger A, Zell A.

Bioinformatics. 2011 Aug 15;27(16):2314-5. doi: 10.1093/bioinformatics/btr377. Epub 2011 Jun 23.

39.

JSBML: a flexible Java library for working with SBML.

Dräger A, Rodriguez N, Dumousseau M, Dörr A, Wrzodek C, Le Novère N, Zell A, Hucka M.

Bioinformatics. 2011 Aug 1;27(15):2167-8. doi: 10.1093/bioinformatics/btr361. Epub 2011 Jun 22.

40.

Acute leukemias of ambiguous lineage: diagnostic consequences of the WHO2008 classification.

van den Ancker W, Terwijn M, Westers TM, Merle PA, van Beckhoven E, Dräger AM, Ossenkoppele GJ, van de Loosdrecht AA.

Leukemia. 2010 Jul;24(7):1392-6. doi: 10.1038/leu.2010.119. Epub 2010 May 20. No abstract available.

PMID:
20485373
41.

Restoration of the human stem cell niche after stem cell transplantation.

Zweegman S, Kessler FL, Celie JW, Janssen JJ, van den Born J, Schuurhuis GJ, Dräger AM.

Blood. 2009 Dec 17;114(26):5404-6; author reply 5406-7. doi: 10.1182/blood-2009-08-240176. No abstract available.

PMID:
20018929
42.

ModuleMaster: a new tool to decipher transcriptional regulatory networks.

Wrzodek C, Schröder A, Dräger A, Wanke D, Berendzen KW, Kronfeld M, Harter K, Zell A.

Biosystems. 2010 Jan;99(1):79-81. doi: 10.1016/j.biosystems.2009.09.005. Epub 2009 Oct 9.

PMID:
19819296
43.

BowTieBuilder: modeling signal transduction pathways.

Supper J, Spangenberg L, Planatscher H, Dräger A, Schröder A, Zell A.

BMC Syst Biol. 2009 Jun 30;3:67. doi: 10.1186/1752-0509-3-67.

44.

Standardization of flow cytometry in myelodysplastic syndromes: report from the first European LeukemiaNet working conference on flow cytometry in myelodysplastic syndromes.

van de Loosdrecht AA, Alhan C, Béné MC, Della Porta MG, Dräger AM, Feuillard J, Font P, Germing U, Haase D, Homburg CH, Ireland R, Jansen JH, Kern W, Malcovati L, Te Marvelde JG, Mufti GJ, Ogata K, Orfao A, Ossenkoppele GJ, Porwit A, Preijers FW, Richards SJ, Schuurhuis GJ, Subirá D, Valent P, van der Velden VH, Vyas P, Westra AH, de Witte TM, Wells DA, Loken MR, Westers TM.

Haematologica. 2009 Aug;94(8):1124-34. doi: 10.3324/haematol.2009.005801. Epub 2009 Jun 22.

45.

SBML2L(A)T(E)X: conversion of SBML files into human-readable reports.

Dräger A, Planatscher H, Motsou Wouamba D, Schröder A, Hucka M, Endler L, Golebiewski M, Müller W, Zell A.

Bioinformatics. 2009 Jun 1;25(11):1455-6. doi: 10.1093/bioinformatics/btp170. Epub 2009 Mar 23.

46.

Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies.

Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A.

BMC Syst Biol. 2009 Jan 14;3:5. doi: 10.1186/1752-0509-3-5.

47.

BioJava: an open-source framework for bioinformatics.

Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.

Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397. Epub 2008 Aug 8.

48.

SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks.

Dräger A, Hassis N, Supper J, Schröder A, Zell A.

BMC Syst Biol. 2008 Apr 30;2:39. doi: 10.1186/1752-0509-2-39.

49.

Identification of distinct prognostic subgroups in low- and intermediate-1-risk myelodysplastic syndromes by flow cytometry.

van de Loosdrecht AA, Westers TM, Westra AH, Dräger AM, van der Velden VH, Ossenkoppele GJ.

Blood. 2008 Feb 1;111(3):1067-77. Epub 2007 Oct 30.

PMID:
17971483
50.

Subendothelial heparan sulfate proteoglycans become major L-selectin and monocyte chemoattractant protein-1 ligands upon renal ischemia/reperfusion.

Celie JW, Rutjes NW, Keuning ED, Soininen R, Heljasvaara R, Pihlajaniemi T, Dräger AM, Zweegman S, Kessler FL, Beelen RH, Florquin S, Aten J, van den Born J.

Am J Pathol. 2007 Jun;170(6):1865-78.

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