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Results: 1 to 20 of 30

1.

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.

PMID:
25210953
[PubMed - in process]
Free PMC Article
2.

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. [Epub ahead of print]

PMID:
25168174
[PubMed - as supplied by publisher]
3.

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.

PMID:
24743184
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
24043118
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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
[PubMed - indexed for MEDLINE]
6.

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
[PubMed - indexed for MEDLINE]
7.

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.

PMID:
23100629
[PubMed - indexed for MEDLINE]
Free Article
8.

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.

PMID:
22761558
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
22729083
[PubMed - indexed for MEDLINE]
10.

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.

PMID:
22531049
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22522925
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22028636
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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
[PubMed - indexed for MEDLINE]
Free Article
14.

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
[PubMed - indexed for MEDLINE]
15.

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.

PMID:
21777411
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
21693013
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
21258062
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
21209825
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
21187909
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20195495
[PubMed - indexed for MEDLINE]
Free PMC Article

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