My research is centered on data integration and the development of high throughput data analysis methods to study regulation in cancer with a special focus on epigenetic regulation. I am a specialist in:
• ChIP-seq data analysis – transcription factors, histone modifications in normal and cancer cells,
• Analysis of whole genome / whole exome / target sequencing data – detection of copy number alterations and structural variants,
• Analysis of cancer RNA-seq - detection of abnormal transcripts expressed in cancer cells
I designed and implemented following data analysis methods that are publicly available:
1) Next generation sequencing
• FREEC – Prediction of copy number alterations and genotype in whole genome or exome-seq data.
• SVDetect – Detection of genomic structural variations from paired-end and mate-pair data (in collaboration with B. Zeitouni).
• SV-Bay – Detection of genomic structural variations from paired-end and mate-pair data using a Bayesian approach (in collaboration with D. Iakovishina).
• ONCOCNV – Detection of copy number changes in amplicon sequencing data (in collaboration with OncoDNA)
• MICSA – Transcription factor binding site detection using ChIP-seq data through de novo identification of binding motifs
• HMCan – Detection of histone modifications in ChIP-seq data (specifically in cancer genomes) (in collaboration with H. Ashoor).
• Nebula – Web-server for advanced ChIP-seq data analysis (transcription factors and histone modifications).
2) Sequence analysis
• ChIPmunk – Motif finding in ChIP-seq data (in collaboration with I. Kulakovskiy).
• AhoPro – Calculation of statistics for motif over-representation in DNA sequences.
• TandemSwan – Annotation of fuzzy tandem repeats in DNA sequences.
I collaborate with the laboratory of Biology of Cancer (Inserm U830, Paris) on several projects aiming to decipher epigenetic regulation in such pediatric cancers as neuroblastoma and Ewing sarcoma.