Bioinformatics and Genomics

fyodor-kondrashov
Evolutionary Genomics

Group Structure

GROUP LEADER:
Fyodor Kondrashov (ICREA Research Professor)
POSTDOCTORAL FELLOWS:
Peter Vlasov, Romain Derelle, Maria Plyushcheva
STUDENTS:
Inna Povolotskaya, Margarita Meer, Onuralp Soylemez, Carla Bello, Alina Korbut
TECHNICIANS:
Victoria Pokusaeva, Oriol Pich, Julia Canet

Summary

Our group is interested in all aspects of genome evolution, structure and function. We typically use computational and theoretical methods to address various evolutionary issues. In the last year we have made steps to expand our experimental capabilities, in part thanks to a new collaboration with the group of Lucas Carey at the UPF.


Research Projects

  • Established that substitution patterns around nucleosome footprints are remarkably similar in eukaryotes and archaea and demonstrate that this is because of biased nucleosome repositioning.
  • Studied the DNA and RNA motifs of mTOR-regulated genes
  • Showed that non-essential genes are more likely to duplicate than essential genes leading to the observation that double knock-downs are comparatively unlikely to yield a phenotype.
  • Suggested that the mc1r locus is unlikely to lead to a Mendelian inheritance of pigmentation coloration in pigeons.
  • Participated in the study of the Capsaspora owxzarzaki genome, including its phylogenetic relationship in metazoan.

Selected Publications

  1. Warnecke T, Becker EA, Facciotti MT, Nislow C, Lehner B.
    “Conserved Substitution Patterns around Nucleosome Footprints in Eukaryotes and Archaea Derive from Frequent Nucleosome Repositioning through Evolution.”
    PLoS Computational Biology, 9(11):e1003373 (2013).
  2. Eliseeva IA, Vorontsov IE, Babeyev KE, Buyanova SM, Sysoeva MA, Kondrashov FA, Kulakovskiy IV.
    “In silico motif analysis suggests an interplay of transcriptional and translational control in mTOR response.”
    Translation, 1:e27469 (2013).
  3. Woods S, Coghlan A, Rivers D, Warnecke T, Jeffries SJ, Kwon T, et al.
    “Duplication and Retention Biases of Essential and Non-Essential Genes Revealed by Systematic Knockdown Analyses.”
    PLoS Genetics, 9(5):e1003330 (2013).
  4. Derelle R, Kondrashov FA, Arkhipov VY, Corbel H, Frantz A, Gasparini J, Jacquin L, Jacob G, Thibault S, Baudry E.
    “Color differences among feral pigeons (Columba livia) are not attributable to sequence variation in the coding region of the melanocortin-1 receptor gene (MC1R).”
    BMC Res Notes 6:310 (2013).
  5. Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A, Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I.
    “The Capsaspora genome reveals a complex unicellular prehistory of animals.”
    Nat Commun, 4:2325 (2013).