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Items: 1 to 50 of 173

1.

Tools for Understanding miRNA-mRNA Interactions for Reproducible RNA Analysis.

Bagnacani A, Wolfien M, Wolkenhauer O.

Methods Mol Biol. 2019;1912:199-214. doi: 10.1007/978-1-4939-8982-9_8.

PMID:
30635895
2.

Workflow Development for the Functional Characterization of ncRNAs.

Wolfien M, Brauer DL, Bagnacani A, Wolkenhauer O.

Methods Mol Biol. 2019;1912:111-132. doi: 10.1007/978-1-4939-8982-9_5.

PMID:
30635892
3.

Harmonizing semantic annotations for computational models in biology.

Neal ML, König M, Nickerson D, Misirli 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. 2018 Nov 21. doi: 10.1093/bib/bby087. [Epub ahead of print]

PMID:
30462164
4.

Integrative workflows for network analysis.

Khan FM, Gupta SK, Wolkenhauer O.

Essays Biochem. 2018 Oct 26;62(4):549-561. doi: 10.1042/EBC20180005. Print 2018 Oct 26. Review.

PMID:
30366988
5.

A systematic survey of centrality measures for protein-protein interaction networks.

Ashtiani M, Salehzadeh-Yazdi A, Razaghi-Moghadam Z, Hennig H, Wolkenhauer O, Mirzaie M, Jafari M.

BMC Syst Biol. 2018 Jul 31;12(1):80. doi: 10.1186/s12918-018-0598-2.

6.

Identifying frequent patterns in biochemical reaction networks: a workflow.

Lambusch F, Waltemath D, Wolkenhauer O, Sandkuhl K, Rosenke C, Henkel R.

Database (Oxford). 2018 Jan 1;2018. doi: 10.1093/database/bay051.

7.

Evolution of computational models in BioModels Database and the Physiome Model Repository.

Scharm M, Gebhardt T, Touré V, Bagnacani A, Salehzadeh-Yazdi A, Wolkenhauer O, Waltemath D.

BMC Syst Biol. 2018 Apr 12;12(1):53. doi: 10.1186/s12918-018-0553-2.

8.

Whither systems medicine?

Apweiler R, Beissbarth T, Berthold MR, Blüthgen N, Burmeister Y, Dammann O, Deutsch A, Feuerhake F, Franke A, Hasenauer J, Hoffmann S, Höfer T, Jansen PL, Kaderali L, Klingmüller U, Koch I, Kohlbacher O, Kuepfer L, Lammert F, Maier D, Pfeifer N, Radde N, Rehm M, Roeder I, Saez-Rodriguez J, Sax U, Schmeck B, Schuppert A, Seilheimer B, Theis FJ, Vera J, Wolkenhauer O.

Exp Mol Med. 2018 Mar 2;50(3):e453. doi: 10.1038/emm.2017.290. Review.

9.

Unveiling network-based functional features through integration of gene expression into protein networks.

Jalili M, Gebhardt T, Wolkenhauer O, Salehzadeh-Yazdi A.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2349-2359. doi: 10.1016/j.bbadis.2018.02.010. Epub 2018 Feb 18. Review.

PMID:
29466699
10.

MiR-205-5p and miR-342-3p cooperate in the repression of the E2F1 transcription factor in the context of anticancer chemotherapy resistance.

Lai X, Gupta SK, Schmitz U, Marquardt S, Knoll S, Spitschak A, Wolkenhauer O, Pützer BM, Vera J.

Theranostics. 2018 Jan 1;8(4):1106-1120. doi: 10.7150/thno.19904. eCollection 2018.

11.

Quick tips for creating effective and impactful biological pathways using the Systems Biology Graphical Notation.

Touré V, Le Novère N, Waltemath D, Wolkenhauer O.

PLoS Comput Biol. 2018 Feb 15;14(2):e1005740. doi: 10.1371/journal.pcbi.1005740. eCollection 2018 Feb. No abstract available.

12.

A web platform for the network analysis of high-throughput data in melanoma and its use to investigate mechanisms of resistance to anti-PD1 immunotherapy.

Dreyer FS, Cantone M, Eberhardt M, Jaitly T, Walter L, Wittmann J, Gupta SK, Khan FM, Wolkenhauer O, Pützer BM, Jäck HM, Heinzerling L, Vera J.

Biochim Biophys Acta Mol Basis Dis. 2018 Jun;1864(6 Pt B):2315-2328. doi: 10.1016/j.bbadis.2018.01.020. Epub 2018 Feb 23.

PMID:
29410200
13.

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide.

Singh KP, Baweja L, Wolkenhauer O, Rahman Q, Gupta SK.

J Comput Aided Mol Des. 2018 Mar;32(3):487-496. doi: 10.1007/s10822-018-0103-4. Epub 2018 Feb 3.

PMID:
29397519
14.

Diagnostic Potential of Imaging Flow Cytometry.

Doan M, Vorobjev I, Rees P, Filby A, Wolkenhauer O, Goldfeld AE, Lieberman J, Barteneva N, Carpenter AE, Hennig H.

Trends Biotechnol. 2018 Jul;36(7):649-652. doi: 10.1016/j.tibtech.2017.12.008. Epub 2018 Jan 31.

15.

Model-Based Phenotypic Signatures Governing the Dynamics of the Stem and Semi-differentiated Cell Populations in Dysplastic Colonic Crypts.

Nikolov S, Santos G, Wolkenhauer O, Vera J.

Bull Math Biol. 2018 Feb;80(2):360-384. doi: 10.1007/s11538-017-0378-y. Epub 2017 Dec 7.

PMID:
29218591
16.

Comprehensive functional enrichment analysis of male infertility.

Razavi SM, Sabbaghian M, Jalili M, Divsalar A, Wolkenhauer O, Salehzadeh-Yazdi A.

Sci Rep. 2017 Nov 17;7(1):15778. doi: 10.1038/s41598-017-16005-0.

17.

A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression.

Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O.

Methods Mol Biol. 2018;1702:247-276. doi: 10.1007/978-1-4939-7456-6_12.

PMID:
29119509
18.

Mammalian γ2 AMPK regulates intrinsic heart rate.

Yavari A, Bellahcene M, Bucchi A, Sirenko S, Pinter K, Herring N, Jung JJ, Tarasov KV, Sharpe EJ, Wolfien M, Czibik G, Steeples V, Ghaffari S, Nguyen C, Stockenhuber A, Clair JRS, Rimmbach C, Okamoto Y, Yang D, Wang M, Ziman BD, Moen JM, Riordon DR, Ramirez C, Paina M, Lee J, Zhang J, Ahmet I, Matt MG, Tarasova YS, Baban D, Sahgal N, Lockstone H, Puliyadi R, de Bono J, Siggs OM, Gomes J, Muskett H, Maguire ML, Beglov Y, Kelly M, Dos Santos PPN, Bright NJ, Woods A, Gehmlich K, Isackson H, Douglas G, Ferguson DJP, Schneider JE, Tinker A, Wolkenhauer O, Channon KM, Cornall RJ, Sternick EB, Paterson DJ, Redwood CS, Carling D, Proenza C, David R, Baruscotti M, DiFrancesco D, Lakatta EG, Watkins H, Ashrafian H.

Nat Commun. 2017 Nov 2;8(1):1258. doi: 10.1038/s41467-017-01342-5.

19.

Cardiac Function Improvement and Bone Marrow Response -: Outcome Analysis of the Randomized PERFECT Phase III Clinical Trial of Intramyocardial CD133+ Application After Myocardial Infarction.

Steinhoff G, Nesteruk J, Wolfien M, Kundt G; PERFECT Trial Investigators Group, Börgermann J, David R, Garbade J, Große J, Haverich A, Hennig H, Kaminski A, Lotz J, Mohr FW, Müller P, Oostendorp R, Ruch U, Sarikouch S, Skorska A, Stamm C, Tiedemann G, Wagner FM, Wolkenhauer O.

EBioMedicine. 2017 Aug;22:208-224. doi: 10.1016/j.ebiom.2017.07.022. Epub 2017 Jul 29.

20.

Unraveling a tumor type-specific regulatory core underlying E2F1-mediated epithelial-mesenchymal transition to predict receptor protein signatures.

Khan FM, Marquardt S, Gupta SK, Knoll S, Schmitz U, Spitschak A, Engelmann D, Vera J, Wolkenhauer O, Pützer BM.

Nat Commun. 2017 Aug 4;8(1):198. doi: 10.1038/s41467-017-00268-2.

21.

Identification of Antineoplastic Targets with Systems Approaches, Using Resveratrol as an In-Depth Case Study.

Singh N, Freiesleben S, Wolkenhauer O, Shukla Y, Gupta SK.

Curr Pharm Des. 2017;23(32):4773-4793. doi: 10.2174/1381612823666170710152918.

PMID:
28699531
22.

Customized workflow development and data modularization concepts for RNA-Sequencing and metatranscriptome experiments.

Lott SC, Wolfien M, Riege K, Bagnacani A, Wolkenhauer O, Hoffmann S, Hess WR.

J Biotechnol. 2017 Nov 10;261:85-96. doi: 10.1016/j.jbiotec.2017.06.1203. Epub 2017 Jul 1. Review.

23.

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy.

Grüning BA, Fallmann J, Yusuf D, Will S, Erxleben A, Eggenhofer F, Houwaart T, Batut B, Videm P, Bagnacani A, Wolfien M, Lott SC, Hoogstrate Y, Hess WR, Wolkenhauer O, Hoffmann S, Akalin A, Ohler U, Stadler PF, Backofen R.

Nucleic Acids Res. 2017 Jul 3;45(W1):W560-W566. doi: 10.1093/nar/gkx409.

24.

Cardiac Cell Therapies for the Treatment of Acute Myocardial Infarction: A Meta-Analysis from Mouse Studies.

Lang CI, Wolfien M, Langenbach A, Müller P, Wolkenhauer O, Yavari A, Ince H, Steinhoff G, Krause BJ, David R, Glass Ä.

Cell Physiol Biochem. 2017;42(1):254-268. doi: 10.1159/000477324. Epub 2017 May 25.

25.

Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer's disease.

Winter F, Bludszuweit-Philipp C, Wolkenhauer O.

J Cereb Blood Flow Metab. 2018 Feb;38(2):304-316. doi: 10.1177/0271678X17693024. Epub 2017 Mar 8.

26.

(Epi)genetic Inheritance in Schistosoma mansoni: A Systems Approach.

Cosseau C, Wolkenhauer O, Padalino G, Geyer KK, Hoffmann KF, Grunau C.

Trends Parasitol. 2017 Apr;33(4):285-294. doi: 10.1016/j.pt.2016.12.002. Epub 2016 Dec 28. Review.

27.

MicroRNA and Transcription Factor Gene Regulatory Network Analysis Reveals Key Regulatory Elements Associated with Prostate Cancer Progression.

Sadeghi M, Ranjbar B, Ganjalikhany MR, M Khan F, Schmitz U, Wolkenhauer O, Gupta SK.

PLoS One. 2016 Dec 22;11(12):e0168760. doi: 10.1371/journal.pone.0168760. eCollection 2016.

28.

Evolution of Centrality Measurements for the Detection of Essential Proteins in Biological Networks.

Jalili M, Salehzadeh-Yazdi A, Gupta S, Wolkenhauer O, Yaghmaie M, Resendis-Antonio O, Alimoghaddam K.

Front Physiol. 2016 Aug 26;7:375. doi: 10.3389/fphys.2016.00375. eCollection 2016. No abstract available.

29.

Deciphering hallmark processes of aging from interaction networks.

Smita S, Lange F, Wolkenhauer O, Köhling R.

Biochim Biophys Acta. 2016 Nov;1860(11 Pt B):2706-15. doi: 10.1016/j.bbagen.2016.07.017. Epub 2016 Jul 25. Review.

PMID:
27456767
30.

COMODI: an ontology to characterise differences in versions of computational models in biology.

Scharm M, Waltemath D, Mendes P, Wolkenhauer O.

J Biomed Semantics. 2016 Jul 11;7(1):46. doi: 10.1186/s13326-016-0080-2.

31.

Understanding microRNA-mediated gene regulatory networks through mathematical modelling.

Lai X, Wolkenhauer O, Vera J.

Nucleic Acids Res. 2016 Jul 27;44(13):6019-35. doi: 10.1093/nar/gkw550. Epub 2016 Jun 17.

32.

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine.

Waltemath D, Wolkenhauer O.

IEEE Trans Biomed Eng. 2016 Oct;63(10):1999-2006. doi: 10.1109/TBME.2016.2555481. Epub 2016 Jun 2.

PMID:
27295645
33.

Autocrine TGF-β/ZEB/microRNA-200 signal transduction drives epithelial-mesenchymal transition: Kinetic models predict minimal drug dose to inhibit metastasis.

Rateitschak K, Kaderali L, Wolkenhauer O, Jaster R.

Cell Signal. 2016 Aug;28(8):861-70. doi: 10.1016/j.cellsig.2016.03.002. Epub 2016 Mar 19.

PMID:
27000495
34.

TRAPLINE: a standardized and automated pipeline for RNA sequencing data analysis, evaluation and annotation.

Wolfien M, Rimmbach C, Schmitz U, Jung JJ, Krebs S, Steinhoff G, David R, Wolkenhauer O.

BMC Bioinformatics. 2016 Jan 6;17:21. doi: 10.1186/s12859-015-0873-9.

35.

Network-Assisted Disease Classification and Biomarker Discovery.

Strunz S, Wolkenhauer O, de la Fuente A.

Methods Mol Biol. 2016;1386:353-74. doi: 10.1007/978-1-4939-3283-2_16. Review.

PMID:
26677191
36.

RNA Systems Biology for Cancer: From Diagnosis to Therapy.

Amirkhah R, Farazmand A, Wolkenhauer O, Schmitz U.

Methods Mol Biol. 2016;1386:305-30. doi: 10.1007/978-1-4939-3283-2_14. Review.

PMID:
26677189
37.

Dissecting Long-Term Glucose Metabolism Identifies New Susceptibility Period for Metabolic Dysfunction in Aged Mice.

Chauhan A, Weiss H, Koch F, Ibrahim SM, Vera J, Wolkenhauer O, Tiedge M.

PLoS One. 2015 Nov 5;10(11):e0140858. doi: 10.1371/journal.pone.0140858. eCollection 2015.

38.

The role of microRNAs in the resistance to colorectal cancer treatments.

Amirkhah R, Farazmand A, Irfan-Maqsood M, Wolkenhauer O, Schmitz U.

Cell Mol Biol (Noisy-le-grand). 2015 Oct 30;61(6):17-23. Review.

PMID:
26518892
39.

An algorithm to detect and communicate the differences in computational models describing biological systems.

Scharm M, Wolkenhauer O, Waltemath D.

Bioinformatics. 2016 Feb 15;32(4):563-70. doi: 10.1093/bioinformatics/btv484. Epub 2015 Oct 21.

40.

Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures.

Wang Y, Alla V, Goody D, Gupta SK, Spitschak A, Wolkenhauer O, Pützer BM, Engelmann D.

Nucleic Acids Res. 2016 Jan 8;44(1):117-33. doi: 10.1093/nar/gkv885. Epub 2015 Sep 8.

41.

The RNA world in the 21st century-a systems approach to finding non-coding keys to clinical questions.

Schmitz U, Naderi-Meshkin H, Gupta SK, Wolkenhauer O, Vera J.

Brief Bioinform. 2016 May;17(3):380-92. doi: 10.1093/bib/bbv061. Epub 2015 Sep 1. Review.

PMID:
26330575
42.

Personalized cancer immunotherapy using Systems Medicine approaches.

Gupta SK, Jaitly T, Schmitz U, Schuler G, Wolkenhauer O, Vera J.

Brief Bioinform. 2016 May;17(3):453-67. doi: 10.1093/bib/bbv046. Epub 2015 Jul 14. Review.

PMID:
26174229
43.

Naïve Bayes classifier predicts functional microRNA target interactions in colorectal cancer.

Amirkhah R, Farazmand A, Gupta SK, Ahmadi H, Wolkenhauer O, Schmitz U.

Mol Biosyst. 2015 Aug;11(8):2126-34. doi: 10.1039/c5mb00245a.

PMID:
26086375
44.

Systems approach to the study of brain damage in the very preterm newborn.

Leviton A, Gressens P, Wolkenhauer O, Dammann O.

Front Syst Neurosci. 2015 Apr 14;9:58. doi: 10.3389/fnsys.2015.00058. eCollection 2015.

45.

Annotation-based feature extraction from sets of SBML models.

Alm R, Waltemath D, Wolfien M, Wolkenhauer O, Henkel R.

J Biomed Semantics. 2015 Apr 15;6:20. doi: 10.1186/s13326-015-0014-4. eCollection 2015.

46.

Reduced adolescent-age spatial learning ability associated with elevated juvenile-age superoxide levels in complex I mouse mutants.

Mayer J, Reichart G, Tokay T, Lange F, Baltrusch S, Junghanss C, Wolkenhauer O, Jaster R, Kunz M, Tiedge M, Ibrahim S, Fuellen G, Köhling R.

PLoS One. 2015 Apr 8;10(4):e0123863. doi: 10.1371/journal.pone.0123863. eCollection 2015.

47.

Combining computational models, semantic annotations and simulation experiments in a graph database.

Henkel R, Wolkenhauer O, Waltemath D.

Database (Oxford). 2015 Mar 8;2015. pii: bau130. doi: 10.1093/database/bau130. Print 2015.

48.

Chk1 and Wee1 control genotoxic-stress induced G2-M arrest in melanoma cells.

Vera J, Raatz Y, Wolkenhauer O, Kottek T, Bhattacharya A, Simon JC, Kunz M.

Cell Signal. 2015 May;27(5):951-60. doi: 10.1016/j.cellsig.2015.01.020. Epub 2015 Feb 12.

PMID:
25683911
49.

miR-638 promotes melanoma metastasis and protects melanoma cells from apoptosis and autophagy.

Bhattacharya A, Schmitz U, Raatz Y, Schönherr M, Kottek T, Schauer M, Franz S, Saalbach A, Anderegg U, Wolkenhauer O, Schadendorf D, Simon JC, Magin T, Vera J, Kunz M.

Oncotarget. 2015 Feb 20;6(5):2966-80.

50.

MicroRNA-mRNA interactions in colorectal cancer and their role in tumor progression.

Amirkhah R, Schmitz U, Linnebacher M, Wolkenhauer O, Farazmand A.

Genes Chromosomes Cancer. 2015 Mar;54(3):129-41. doi: 10.1002/gcc.22231. Review.

PMID:
25620079

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