NGS sequencing approaches such as ChIP-seq, ATAC-seq and FAIRE-seq or RNA-seq can be used to understand the effects of chemotherapy drugs, on the chromatin structure and its potential impact on the regulation of gene expression. In this context we are developing analysis and statistical approaches for the characterization of genome wide chemotherapy drug binding regions. This include histone eviction effects, and functional annotations of key regions with previous available knowledge of histones and DNA modifiers.
During my master’s degree I studied cancer transcriptomics using system biology approaches to unravel the effects of environmental factors (Cd2+) with major breast cancer driver activity (Lubovac-Pilav et al. 2013). Afterwards during my PhD (Marie Skladovska-Curie - ESR) I explored analysis methods for sequencing technologies to characterize complex disease traits in renal diseases and cancer. Including RNA-seq, WGS, WES, microRNA-seq, SMRT-seq, and IonProton sequencing approaches to unravel disease-associated gene expression, disease driving genetic variants (SNPs, indels, loss of heterozygosity, copy-number variants, and gene fusions), differential splicing variants and disease-associated miRNAs. In my current postdoc position at the Neefjes lab I further developed my analysis skills for epigenomic sequencing approaches. This included ChIP-seq, ATAC-seq and FAIRE-seq to understand the effects of chemotherapy drugs (anthracyclines) on the chromatin structure and its potential impact on the regulation of gene expression. This included the development of statistical approaches (permutation-based) for the characterization of drug binding regions genome wide, histone eviction effects, and functional annotation of key regions with previous available knowledge of histones and DNA modifiers.
Detecting PKD1 variants in Polycystic Kidney Disease patients by single-molecule long-read sequencing
Daniel M. Borràs, Rolf H. A. M. Vossen, Michael Liem, Henk P. J. Buermans , Hans Dauwerse, Dave van Heusden, Ron T. Gansevoort, Johan T. den Dunnen, Bart Janssen, Dorien J. M. Peters, Monique Losekoot, Seyed Yahya Anvar.
Human Mutation (2017;38:870–879;
The use of transcriptomics in clinical applications
Daniel M. Borràs, Bart Janssen
Integration of Omics Approaches and Systems Biology for Clinical Applications
CE‐MS‐based proteomics in biomarker discovery and clinical application
Claudia Pontillo, Szymon Filip, Daniel M. Borràs, William Mullen, Antonia Vlahou, Harald Mischak;
Proteomics Clin. Appl. (2015, 9, 322–334; IF 2015: 3.03)