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Items: 50

1.

A quantitative mass spectrometry-based approach to monitor the dynamics of endogenous chromatin-associated protein complexes.

Papachristou EK, Kishore K, Holding AN, Harvey K, Roumeliotis TI, Chilamakuri CSR, Omarjee S, Chia KM, Swarbrick A, Lim E, Markowetz F, Eldridge M, Siersbaek R, D'Santos CS, Carroll JS.

Nat Commun. 2018 Jun 13;9(1):2311. doi: 10.1038/s41467-018-04619-5.

2.

Parallel factor ChIP provides essential internal control for quantitative differential ChIP-seq.

Guertin MJ, Cullen AE, Markowetz F, Holding AN.

Nucleic Acids Res. 2018 Jul 6;46(12):e75. doi: 10.1093/nar/gky252.

PMID:
29672735
3.

Analysis of heterogeneity in T2-weighted MR images can differentiate pseudoprogression from progression in glioblastoma.

Booth TC, Larkin TJ, Yuan Y, Kettunen MI, Dawson SN, Scoffings D, Canuto HC, Vowler SL, Kirschenlohr H, Hobson MP, Markowetz F, Jefferies S, Brindle KM.

PLoS One. 2017 May 17;12(5):e0176528. doi: 10.1371/journal.pone.0176528. eCollection 2017.

4.

Inferring modulators of genetic interactions with epistatic nested effects models.

Pirkl M, Diekmann M, van der Wees M, Beerenwinkel N, Fröhlich H, Markowetz F.

PLoS Comput Biol. 2017 Apr 13;13(4):e1005496. doi: 10.1371/journal.pcbi.1005496. eCollection 2017 Apr.

5.

All biology is computational biology.

Markowetz F.

PLoS Biol. 2017 Mar 9;15(3):e2002050. doi: 10.1371/journal.pbio.2002050. eCollection 2017 Mar.

6.

BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes.

de Santiago I, Liu W, Yuan K, O'Reilly M, Chilamakuri CS, Ponder BA, Meyer KB, Markowetz F.

Genome Biol. 2017 Feb 24;18(1):39. doi: 10.1186/s13059-017-1165-7.

7.

Master Regulators of Oncogenic KRAS Response in Pancreatic Cancer: An Integrative Network Biology Analysis.

Sivakumar S, de Santiago I, Chlon L, Markowetz F.

PLoS Med. 2017 Jan 31;14(1):e1002223. doi: 10.1371/journal.pmed.1002223. eCollection 2017 Jan.

8.

Patterns of Immune Infiltration in Breast Cancer and Their Clinical Implications: A Gene-Expression-Based Retrospective Study.

Ali HR, Chlon L, Pharoah PD, Markowetz F, Caldas C.

PLoS Med. 2016 Dec 13;13(12):e1002194. doi: 10.1371/journal.pmed.1002194. eCollection 2016 Dec.

9.

How Subclonal Modeling Is Changing the Metastatic Paradigm.

Macintyre G, Van Loo P, Corcoran NM, Wedge DC, Markowetz F, Hovens CM.

Clin Cancer Res. 2017 Feb 1;23(3):630-635. doi: 10.1158/1078-0432.CCR-16-0234. Epub 2016 Nov 18. Review.

10.

A saltationist theory of cancer evolution.

Markowetz F.

Nat Genet. 2016 Sep 28;48(10):1102-3. doi: 10.1038/ng.3687.

PMID:
27681287
11.

Practical and Robust Identification of Molecular Subtypes in Colorectal Cancer by Immunohistochemistry.

Trinh A, Trumpi K, De Sousa E Melo F, Wang X, de Jong JH, Fessler E, Kuppen PJ, Reimers MS, Swets M, Koopman M, Nagtegaal ID, Jansen M, Hooijer GK, Offerhaus GJ, Kranenburg O, Punt CJ, Medema JP, Markowetz F, Vermeulen L.

Clin Cancer Res. 2017 Jan 15;23(2):387-398. doi: 10.1158/1078-0432.CCR-16-0680. Epub 2016 Jul 26.

12.

OncoNEM: inferring tumor evolution from single-cell sequencing data.

Ross EM, Markowetz F.

Genome Biol. 2016 Apr 15;17:69. doi: 10.1186/s13059-016-0929-9.

13.

Accumulated Metabolites of Hydroxybutyric Acid Serve as Diagnostic and Prognostic Biomarkers of Ovarian High-Grade Serous Carcinomas.

Hilvo M, de Santiago I, Gopalacharyulu P, Schmitt WD, Budczies J, Kuhberg M, Dietel M, Aittokallio T, Markowetz F, Denkert C, Sehouli J, Frezza C, Darb-Esfahani S, Braicu EI.

Cancer Res. 2016 Feb 15;76(4):796-804. doi: 10.1158/0008-5472.CAN-15-2298. Epub 2015 Dec 18.

14.

Five selfish reasons to work reproducibly.

Markowetz F.

Genome Biol. 2015 Dec 8;16:274. doi: 10.1186/s13059-015-0850-7.

15.

Regulators of genetic risk of breast cancer identified by integrative network analysis.

Castro MA, de Santiago I, Campbell TM, Vaughn C, Hickey TE, Ross E, Tilley WD, Markowetz F, Ponder BA, Meyer KB.

Nat Genet. 2016 Jan;48(1):12-21. doi: 10.1038/ng.3458. Epub 2015 Nov 30.

16.

You Are Not Working for Me; I Am Working with You.

Markowetz F.

PLoS Comput Biol. 2015 Sep 24;11(9):e1004387. doi: 10.1371/journal.pcbi.1004387. eCollection 2015 Sep. No abstract available.

17.

BitPhylogeny: a probabilistic framework for reconstructing intra-tumor phylogenies.

Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N.

Genome Biol. 2015 Feb 13;16:36. doi: 10.1186/s13059-015-0592-6.

18.

Spatial and temporal heterogeneity in high-grade serous ovarian cancer: a phylogenetic analysis.

Schwarz RF, Ng CK, Cooke SL, Newman S, Temple J, Piskorz AM, Gale D, Sayal K, Murtaza M, Baldwin PJ, Rosenfeld N, Earl HM, Sala E, Jimenez-Linan M, Parkinson CA, Markowetz F, Brenton JD.

PLoS Med. 2015 Feb 24;12(2):e1001789. doi: 10.1371/journal.pmed.1001789. eCollection 2015 Feb.

19.

Combined image and genomic analysis of high-grade serous ovarian cancer reveals PTEN loss as a common driver event and prognostic classifier.

Martins FC, Santiago Id, Trinh A, Xian J, Guo A, Sayal K, Jimenez-Linan M, Deen S, Driver K, Mack M, Aslop J, Pharoah PD, Markowetz F, Brenton JD.

Genome Biol. 2014 Dec 17;15(12):526. doi: 10.1186/s13059-014-0526-8.

20.

Cancer evolution: mathematical models and computational inference.

Beerenwinkel N, Schwarz RF, Gerstung M, Markowetz F.

Syst Biol. 2015 Jan;64(1):e1-25. doi: 10.1093/sysbio/syu081. Epub 2014 Oct 7. Review.

21.

SANTA: quantifying the functional content of molecular networks.

Cornish AJ, Markowetz F.

PLoS Comput Biol. 2014 Sep 11;10(9):e1003808. doi: 10.1371/journal.pcbi.1003808. eCollection 2014 Sep.

22.

GoIFISH: a system for the quantification of single cell heterogeneity from IFISH images.

Trinh A, Rye IH, Almendro V, Helland A, Russnes HG, Markowetz F.

Genome Biol. 2014 Aug 26;15(8):442. doi: 10.1186/s13059-014-0442-y.

23.

Phylogenetic quantification of intra-tumour heterogeneity.

Schwarz RF, Trinh A, Sipos B, Brenton JD, Goldman N, Markowetz F.

PLoS Comput Biol. 2014 Apr 17;10(4):e1003535. doi: 10.1371/journal.pcbi.1003535. eCollection 2014 Apr.

24.

Master regulators of FGFR2 signalling and breast cancer risk.

Fletcher MN, Castro MA, Wang X, de Santiago I, O'Reilly M, Chin SF, Rueda OM, Caldas C, Ponder BA, Markowetz F, Meyer KB.

Nat Commun. 2013;4:2464. doi: 10.1038/ncomms3464.

25.

Dissecting cancer heterogeneity--an unsupervised classification approach.

Wang X, Markowetz F, De Sousa E Melo F, Medema JP, Vermeulen L.

Int J Biochem Cell Biol. 2013 Nov;45(11):2574-9. doi: 10.1016/j.biocel.2013.08.014. Epub 2013 Sep 1. Review.

PMID:
24004832
26.

Poor-prognosis colon cancer is defined by a molecularly distinct subtype and develops from serrated precursor lesions.

De Sousa E Melo F, Wang X, Jansen M, Fessler E, Trinh A, de Rooij LP, de Jong JH, de Boer OJ, van Leersum R, Bijlsma MF, Rodermond H, van der Heijden M, van Noesel CJ, Tuynman JB, Dekker E, Markowetz F, Medema JP, Vermeulen L.

Nat Med. 2013 May;19(5):614-8. doi: 10.1038/nm.3174. Epub 2013 Apr 14.

PMID:
23584090
27.

Quantitative image analysis of cellular heterogeneity in breast tumors complements genomic profiling.

Yuan Y, Failmezger H, Rueda OM, Ali HR, Gräf S, Chin SF, Schwarz RF, Curtis C, Dunning MJ, Bardwell H, Johnson N, Doyle S, Turashvili G, Provenzano E, Aparicio S, Caldas C, Markowetz F.

Sci Transl Med. 2012 Oct 24;4(157):157ra143. doi: 10.1126/scitranslmed.3004330. Erratum in: Sci Transl Med. 2012 Oct 24;4(157):161er6.

28.

Posterior association networks and functional modules inferred from rich phenotypes of gene perturbations.

Wang X, Castro MA, Mulder KW, Markowetz F.

PLoS Comput Biol. 2012;8(6):e1002566. doi: 10.1371/journal.pcbi.1002566. Epub 2012 Jun 28.

29.

Diverse epigenetic strategies interact to control epidermal differentiation.

Mulder KW, Wang X, Escriu C, Ito Y, Schwarz RF, Gillis J, Sirokmány G, Donati G, Uribe-Lewis S, Pavlidis P, Murrell A, Markowetz F, Watt FM.

Nat Cell Biol. 2012 Jun 24;14(7):753-63. doi: 10.1038/ncb2520.

30.

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.

Castro MA, Wang X, Fletcher MN, Meyer KB, Markowetz F.

Genome Biol. 2012 Apr 24;13(4):R29. doi: 10.1186/gb-2012-13-4-r29.

31.

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.

Curtis C, Shah SP, Chin SF, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y, Gräf S, Ha G, Haffari G, Bashashati A, Russell R, McKinney S; METABRIC Group, Langerød A, Green A, Provenzano E, Wishart G, Pinder S, Watson P, Markowetz F, Murphy L, Ellis I, Purushotham A, Børresen-Dale AL, Brenton JD, Tavaré S, Caldas C, Aparicio S.

Nature. 2012 Apr 18;486(7403):346-52. doi: 10.1038/nature10983.

32.

Patient-specific data fusion defines prognostic cancer subtypes.

Yuan Y, Savage RS, Markowetz F.

PLoS Comput Biol. 2011 Oct;7(10):e1002227. doi: 10.1371/journal.pcbi.1002227. Epub 2011 Oct 20.

33.

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer.

Yuan Y, Rueda OM, Curtis C, Markowetz F.

Bioinformatics. 2011 Oct 1;27(19):2679-85. doi: 10.1093/bioinformatics/btr450. Epub 2011 Jul 30.

PMID:
21804112
34.

A sparse regulatory network of copy-number driven gene expression reveals putative breast cancer oncogenes.

Yuan Y, Curtis C, Caldas C, Markowetz F.

IEEE/ACM Trans Comput Biol Bioinform. 2012 Jul-Aug;9(4):947-54. doi: 10.1109/TCBB.2011.105.

PMID:
21788678
35.

Differential C3NET reveals disease networks of direct physical interactions.

Altay G, Asim M, Markowetz F, Neal DE.

BMC Bioinformatics. 2011 Jul 21;12:296. doi: 10.1186/1471-2105-12-296.

36.

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data.

Szczurek E, Markowetz F, Gat-Viks I, Biecek P, Tiuryn J, Vingron M.

BMC Bioinformatics. 2011 Jun 21;12:249. doi: 10.1186/1471-2105-12-249.

37.

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

Wang X, Terfve C, Rose JC, Markowetz F.

Bioinformatics. 2011 Mar 15;27(6):879-80. doi: 10.1093/bioinformatics/btr028. Epub 2011 Jan 22.

38.

Evolutionary distances in the twilight zone--a rational kernel approach.

Schwarz RF, Fletcher W, Förster F, Merget B, Wolf M, Schultz J, Markowetz F.

PLoS One. 2010 Dec 31;5(12):e15788. doi: 10.1371/journal.pone.0015788.

39.

Mapping dynamic histone acetylation patterns to gene expression in nanog-depleted murine embryonic stem cells.

Markowetz F, Mulder KW, Airoldi EM, Lemischka IR, Troyanskaya OG.

PLoS Comput Biol. 2010 Dec 16;6(12):e1001034. doi: 10.1371/journal.pcbi.1001034.

40.

How to understand the cell by breaking it: network analysis of gene perturbation screens.

Markowetz F.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000655. doi: 10.1371/journal.pcbi.1000655. No abstract available.

41.

Systems-level dynamic analyses of fate change in murine embryonic stem cells.

Lu R, Markowetz F, Unwin RD, Leek JT, Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, Lemischka IR.

Nature. 2009 Nov 19;462(7271):358-62. doi: 10.1038/nature08575.

42.

Analyzing gene perturbation screens with nested effects models in R and bioconductor.

Fröhlich H, Beissbarth T, Tresch A, Kostka D, Jacob J, Spang R, Markowetz F.

Bioinformatics. 2008 Nov 1;24(21):2549-50. doi: 10.1093/bioinformatics/btn446. Epub 2008 Aug 21.

43.

Computational diagnostics with gene expression profiles.

Lottaz C, Kostka D, Markowetz F, Spang R.

Methods Mol Biol. 2008;453:281-96. doi: 10.1007/978-1-60327-429-6_15.

PMID:
18712310
44.

Structure learning in Nested Effects Models.

Tresch A, Markowetz F.

Stat Appl Genet Mol Biol. 2008;7(1):Article9. doi: 10.2202/1544-6115.1332. Epub 2008 Mar 1.

PMID:
18312214
45.

Inferring cellular networks--a review.

Markowetz F, Spang R.

BMC Bioinformatics. 2007 Sep 27;8 Suppl 6:S5. Review.

46.

Nested effects models for high-dimensional phenotyping screens.

Markowetz F, Kostka D, Troyanskaya OG, Spang R.

Bioinformatics. 2007 Jul 1;23(13):i305-12.

PMID:
17646311
47.

Computational identification of cellular networks and pathways.

Markowetz F, Troyanskaya OG.

Mol Biosyst. 2007 Jul;3(7):478-82. Epub 2007 May 14. Review.

PMID:
17579773
48.

Non-transcriptional pathway features reconstructed from secondary effects of RNA interference.

Markowetz F, Bloch J, Spang R.

Bioinformatics. 2005 Nov 1;21(21):4026-32. Epub 2005 Sep 13.

PMID:
16159925
49.

Molecular diagnosis. Classification, model selection and performance evaluation.

Markowetz F, Spang R.

Methods Inf Med. 2005;44(3):438-43.

PMID:
16113770
50.

Acetylcysteine for prevention of contrast nephropathy: meta-analysis.

Birck R, Krzossok S, Markowetz F, Schnülle P, van der Woude FJ, Braun C.

Lancet. 2003 Aug 23;362(9384):598-603.

PMID:
12944058

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