Université de Bordeaux
FHU SMART Small Artery Disease transdisciplinary project
Cluster of excellence

Dr. Macha Nikolski

Dr. Macha Nikolski, director for SMART data management and optimization, is research director at CNRS and head of the Bordeaux Bioinformatics Center (CBiB). Her main research axes are: (i) the analysis of omics data, especially algorithmic issues related to big data, (ii) the integration of biological data through network analysis approaches and, (iii) the development of predictive methods.

Summary CV

Macha Nikolski, PhD, born in 1972, is research director at CNRS and head of the Bordeaux Bioinformatics Center. Dr. Nikolski graduated from the Ecole Nationale Supérieure en Electronique et Informatique in Bordeaux, and from Berkeley University. She has a PhD in computer sciences and is accredited to direct research in bioinformatics. After working in a private research center in Boston, USA (Synopsis), she joined the CNRS to work on the application of methods used for industrial systems to biological systems. She played a central role in the development of comparative genomics methods, in particular applied to yeast. She then led a “young researcher team” at GosNIIGenetika in Moskow. Since she is back in France, her main research axes are: (i) the analysis of omics data and particularly the algorithmic issues related to big data, (ii) the integration of biological data through network analysis approaches and, (iii) the development of predictive methods (machine learning, data mining). She is also strongly involved in international efforts for standardization in bioinformatics research (HUPO PSI, MIASE, COSMOS). Macha Nikolski is a member of the Steering committee of the French Bioinformatics Institute.

Selected References

1. El-Kebir M, Soueidan H, Hume T, Beisser D, Dittrich M, Müller T, Blin G, Heringa J, Nikolski M, Wessels LF, Klau GW. xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model. Bioinformatics. 2015 May 27 / pii: btv316 / PMID:26023104

2. Waltemath D, Adams R, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru I, Nickerson D, Nielsen P, Nikolski M, Sahle S, Sauro  HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N. Minimum Information About a Simulation Experiment (MIASE). PLoS Comput Biol. 2011;7:e1001122

3. Jean G, Sherman DJ, Nikolski M. Mining the semantics of genome super-blocks to infer ancestral architectures. J Comput Biol. 2009 Sep;16(9):1267-84.

4. Alonso-Alemany D, Barré A, Beretta S, Bonizzoni P, Nikolski M, Valiente G. Further steps in TANGO: improved taxonomic assignment in metagenomics. Bioinformatics. 2014 Jan 1;30(1):17-23.

5. Soueidan H, Maurier F, Groppi A, Sirand-Pugnet P, Tardy F, Citti C, Dupuy V, Nikolski M. Finishing bacterial genome assemblies with Mix. BMC Bioinformatics. 2013;14 Suppl 15:S16.



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