Macha Nikolski

CNRS Research Scientist, Bordeaux Bioinformatics Center & LaBRI


Head of the Bordeaux Bioinformatics Center (CBiB), Université Bordeaux

Leader of the Bioinformatics axis for the SIRIC BRIO

Macha Nikolski, credits: CNRS

Research overview

I am a computational biologist working mainly in genomics. Computational genomics requires the development of algorithms, statistical methodology and mathematical foundations, and a large part of my research is therefore on methods. Validating these methods, that is anwering biological questions by using computational approaches is central in my work. Therefore, method development goes always hand in hand with application, which in practical terms requires close collaboration with colleagues in the life sciences.

My career began in comparative genomics, and initially I was interested in genome annotation, determination of protein families using consensus clustering techniques and genome rearrangements. In this context I contributed to the yeast genomes' sequencing consortia. In parallel I have worked on building rigorous models of the dynamical behaviour of biological systems (eg. networks), on how is it possible to combine different models and on establishing properties about models' behaviors.

Currently, I'm particularly interested in applications of high-throughput sequencing data. My group develops methods for Next Generation Sequencing data analysis and de novo sequence assembly and its downstream analysis (genome assembly, variant detection, diversity analysis, biomarker identification, functional analysis). Methodological solutions are often a mix of algorithmics and machine learning.

genome rearrangements

Career overview

I have received my doctoral degree in Computer Science in 2000 from the University Bordeaux 1 under the direction of Antoine Rauzy, on the subject of binary decision diagrams and their application to the reliability analysis of complex industrial systems. I have subsequently worked for two years in the United States as a research engineer for Synopsys, before returning to France in 2002 to a position of Research Scientist (Chargee de Recherches) with the CNRS. For the academic year 2009-2010 I was at the Poncelet CNRS Laboratory in Moscow, Russia where I also held the responsibility of a group leader at the NII Genetika Institute. Since 2010 I lead the Bordeaux Bioinformatics Center, CBiB. I am also a member of the MABioVis team within the LaBRI.