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.