Probabilistic Soft Interventions in Conditional Gaussian Networks. - Florian Markowetz; Steffen Grossmann; Rainer Spang (AISTATS, 2005)

Non-transcriptional pathway features reconstructed from secondary effects of RNA interference. - Florian Markowetz; Jacques Bloch; Rainer Spang (Bioinform., 2005)

Probabilistic Models for Gene Silencing Data (Probabilistische Modelle für RNA-Interferenz-Daten) - Florian Markowetz (2006)

Nested effects models for high-dimensional phenotyping screens. - Florian Markowetz; Dennis Kostka; Olga G. Troyanskaya; Rainer Spang (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Inferring cellular networks - a review. - Florian Markowetz; Rainer Spang (BMC Bioinform., 2007)

Analyzing gene perturbation screens with nested effects models in R and bioconductor. - Holger Fröhlich; Tim Beißbarth; Achim Tresch; Dennis Kostka; Juby Jacob; Rainer Spang; Florian Markowetz (Bioinform., 2008)

A sparse regulatory network of copy-number driven expression reveals putative breast cancer oncogenes. - Yinyin Yuan; Christina Curtis; Carlos Caldas; Florian Markowetz (BIBM, 2010)

How to Understand the Cell by Breaking It: Network Analysis of Gene Perturbation Screens. - Florian Markowetz (PLoS Comput. Biol., 2010)

Mapping Dynamic Histone Acetylation Patterns to Gene Expression in Nanog-Depleted Murine Embryonic Stem Cells. - Florian Markowetz; Klaas W. Mulder; Edoardo M. Airoldi; Ihor Lemischka; Olga G. Troyanskaya (PLoS Comput. Biol., 2010)

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens. - Xin Wang 008; Camille Terfve; John C. Rose; Florian Markowetz (Bioinform., 2011)

Penalized regression elucidates aberration hotspots mediating subtype-specific transcriptional responses in breast cancer. - Yinyin Yuan; Oscar M. Rueda; Christina Curtis; Florian Markowetz (Bioinform., 2011)

Differential C3NET reveals disease networks of direct physical interactions. - Gokmen Altay; Mohammad Asim; Florian Markowetz; David E. Neal (BMC Bioinform., 2011)

Deregulation upon DNA damage revealed by joint analysis of context-specific perturbation data. - Ewa Szczurek; Florian Markowetz; Irit Gat-Viks; Przemyslaw Biecek; Jerzy Tiuryn; Martin Vingron (BMC Bioinform., 2011)

Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes. - Yinyin Yuan; Richard S. Savage; Florian Markowetz (PLoS Comput. Biol., 2011)

Posterior Association Networks and Functional Modules Inferred from Rich Phenotypes of Gene Perturbations. - Xin Wang 008; Mauro A. A. Castro; Klaas W. Mulder; Florian Markowetz (PLoS Comput. Biol., 2012)

A Sparse Regulatory Network of Copy-Number Driven Gene Expression Reveals Putative Breast Cancer Oncogenes. - Yinyin Yuan; Christina Curtis; Carlos Caldas; Florian Markowetz (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

SANTA: Quantifying the Functional Content of Molecular Networks. - Alex J. Cornish; Florian Markowetz (PLoS Comput. Biol., 2014)

Phylogenetic Quantification of Intra-tumour Heterogeneity. - Roland F. Schwarz; Anne Trinh; Botond Sipos; James D. Brenton; Nick Goldman; Florian Markowetz (PLoS Comput. Biol., 2014)

You Are Not Working for Me; I Am Working with You. - Florian Markowetz (PLoS Comput. Biol., 2015)

Inferring modulators of genetic interactions with epistatic nested effects models. - Martin Pirkl; Madeline Diekmann; Marlies van der Wees; Niko Beerenwinkel; Holger Fröhlich; Florian Markowetz (PLoS Comput. Biol., 2017)

Estimating the predictability of cancer evolution. - Sayed-Rzgar Hosseini; Ramón Díaz-Uriarte; Florian Markowetz; Niko Beerenwinkel (Bioinform., 2019)

Tissue-specific and interpretable sub-segmentation of whole tumour burden on CT images by unsupervised fuzzy clustering. - Leonardo Rundo; Lucian Beer; Stephan Ursprung; Paula Martin-Gonzalez; Florian Markowetz; James D. Brenton; Mireia Crispin-Ortuzar; Evis Sala; Ramona Woitek (Comput. Biol. Medicine, 2020)

The evolutionary history of 2,658 cancers. - Moritz Gerstung; Clemency Jolly; Ignaty Leshchiner; Stefan C. Dentro; Santiago Gonzalez; Thomas J. Mitchell; Yulia Rubanova; Pavana Anur; Kaixian Yu; Maxime Tarabichi; Amit G. Deshwar; Jeff Wintersinger; et al. (Nat., 2020)

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes. - Esther Rheinbay; Morten Muhlig Nielsen; Federico Abascal; Jeremiah Wala; Ofer Shapira; Grace Tiao; Henrik Hornshøj; Julian M. Hess; Randi Istrup Juul; Ziao Lin; Lars Feuerbach; Radhakrishnan Sabarinathan; et al. (Nat., 2020)

Predictive Modelling of Highly Multiplexed Tumour Tissue Images by Graph Neural Networks. - Paula Martin-Gonzalez; Mireia Crispin-Ortuzar; Florian Markowetz (iMIMIC/TDA4MedicalData@MICCAI, 2021)

Allele-specific multi-sample copy number segmentation in ASCAT. - Edith M. Ross; Kerstin Haase; Peter Van Loo; Florian Markowetz (Bioinform., 2021)

A Dirichlet-multinomial mixed model for determining differential abundance of mutational signatures. - Lena Morrill Gavarró; Dominique-Laurent Couturier; Florian Markowetz (BMC Bioinform., 2025)