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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. Trinh A, et al. Among authors: markowetz f. Genome Biol. 2014 Aug 26;15(8):442. doi: 10.1186/s13059-014-0442-y. Genome Biol. 2014. PMID: 25168174 Free PMC article.

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VULCAN integrates ChIP-seq with patient-derived co-expression networks to identify GRHL2 as a key co-regulator of ERa at enhancers in breast cancer.

Holding AN, Giorgi FM, Donnelly A, Cullen AE, Nagarajan S, Selth LA, Markowetz F. Holding AN, et al. Among authors: markowetz f. Genome Biol. 2019 May 13;20(1):91. doi: 10.1186/s13059-019-1698-z. Genome Biol. 2019. PMID: 31084623 Free PMC article.

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

Ross EM, Markowetz F. Ross EM, et al. Among authors: markowetz f. Genome Biol. 2016 Apr 15;17:69. doi: 10.1186/s13059-016-0929-9. Genome Biol. 2016. PMID: 27083415 Free PMC article.

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

Yuan K, Sakoparnig T, Markowetz F, Beerenwinkel N. Yuan K, et al. Among authors: markowetz f. Genome Biol. 2015 Feb 13;16(1):36. doi: 10.1186/s13059-015-0592-6. Genome Biol. 2015. PMID: 25786108 Free PMC article.

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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. Martins FC, et al. Among authors: markowetz f. Genome Biol. 2014 Dec 17;15(12):526. doi: 10.1186/s13059-014-0526-8. Genome Biol. 2014. PMID: 25608477 Free PMC article.

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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. Castro MA, et al. Among authors: markowetz f. Genome Biol. 2012 Apr 24;13(4):R29. doi: 10.1186/gb-2012-13-4-r29. Genome Biol. 2012. PMID: 22531049 Free PMC article.

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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. Yuan Y, et al. Among authors: markowetz f. Sci Transl Med. 2012 Oct 24;4(157):157ra143. doi: 10.1126/scitranslmed.3004330. Sci Transl Med. 2012. PMID: 23100629

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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. Ali HR, et al. Among authors: markowetz f. PLoS Med. 2016 Dec 13;13(12):e1002194. doi: 10.1371/journal.pmed.1002194. eCollection 2016 Dec. PLoS Med. 2016. PMID: 27959923 Free PMC article.

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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. Hilvo M, et al. Among authors: markowetz f. Cancer Res. 2016 Feb 15;76(4):796-804. doi: 10.1158/0008-5472.CAN-15-2298. Epub 2015 Dec 18. Cancer Res. 2016. PMID: 26685161 Free PMC article.

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Patient-specific data fusion defines prognostic cancer subtypes.

Yuan Y, Savage RS, Markowetz F. Yuan Y, et al. Among authors: markowetz f. PLoS Comput Biol. 2011 Oct;7(10):e1002227. doi: 10.1371/journal.pcbi.1002227. Epub 2011 Oct 20. PLoS Comput Biol. 2011. PMID: 22028636 Free PMC article.

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