Project: Vertebrate head origin: an insight from genetics, single-cell transcriptomics, and machine learning
Supervisor
Iryna Kozmiková
Co-supervisor
Jan Pačes
Project description
The project will use bioinformatic analysis together with comparative approaches to individual cells, and machine learning to investigate how the vertebrate head evolved and what mechanisms control cell fate specification. The project will focus primarily on the analysis and comparison of single-cell RNA-seq datasets from different animal groups, including multi-omics and spatial transcriptomics, and will be closely linked to experimental validation in the wet lab environment. In addition, the student will have the opportunity to develop or apply machine learning approaches to link molecular changes to phenotype, including analysis of genetic mutants and exploratory behavioral phenotyping. Our group places great emphasis on biological interpretation: the student will therefore gain practical insight into developmental and evolutionary biology, supported by extensive experimental knowledge in the laboratory. This position offers an excellent environment for growth as an interdisciplinary scientist combining computational and experimental approaches.
Candidate profile
The evo-devo team of laboratory of Transcriptional regulation is searching for a highly motivated, enthusiastic and hard-working Ph.D. student. The candidate must have a basic knowledge of programming fundamentals in R and Python and should hold a master degree in genetics, molecular biology, cell biology, or in a related field. The candidate should be able to work independently as well as part of a research team and demonstrate critical thinking.
We offer a friendly and supporting environment in a state-of-the-art institution.
Suggested reading
Markos A, Kubovciak J, Mikula Mrstakova S, Zitova A, Paces J, Machacova S, Kozmik-Jr Z, Kozmik Z, Kozmikova I: Cell type and regulatory analysis in amphioxus illuminates evolutionary origin of the vertebrate head. Nat Commun 2024 15(1): 8859. [pubmed] [doi]
Kozmikova I, Kozmik Z: Wnt/β-catenin signaling is an evolutionarily conserved determinant of chordate dorsal organizer. Elife 20209:e56817. [pubmed] [doi]
Prummel KD, Hess C, Nieuwenhuize S, Parker HJ, Rogers KW, Kozmikova I, Racioppi C, Brombacher EC, Czarkwiani A, Knapp D, Burger S, Chiavacci E, Shah G, Burger A, Huisken J, Yun MH, Christiaen L, Kozmik Z, Müller P, Bronner M, Krumlauf R, Mosimann C: A conserved regulatory program initiates lateral plate mesoderm emergence across chordates. Nat Commun 201910(1): 3857. [pubmed] [doi]
Marlétaz F, Firbas PN, Maeso I, Tena JJ, Bogdanovic O, Perry M, Wyatt CDR, de la Calle-Mustienes E, Bertrand S, Burguera D, Acemel RD, van Heeringen SJ, Naranjo S, Herrera-Ubeda C, Skvortsova K, Jimenez-Gancedo S, Aldea D, Marquez Y, Buono L, Kozmikova I, Permanyer J, Louis A, Albuixech-Crespo B, Le Petillon Y, Leon A, Subirana L, Balwierz PJ, Duckett PE, Farahani E, Aury JM, Mangenot S, Wincker P, Albalat R, Benito-Gutiérrez È, Cañestro C, Castro F, D’Aniello S, Ferrier DEK, Huang S, Laudet V, Marais GAB, Pontarotti P, Schubert M, Seitz H, Somorjai I, Takahashi T, Mirabeau O, Xu A, Yu JK, Carninci P, Martinez-Morales JR, Crollius HR, Kozmik Z, Weirauch MT, Garcia-Fernàndez J, Lister R, Lenhard B, Holland PWH, Escriva H, Gómez-Skarmeta JL, Irimia M: Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature 2018564(7734): 64-70. [pubmed] [doi]
