Ribosome profiling

mRNA translation

Genetic Decoding

Protein Synthesis


Pasha received his Ph.D. at the Lomonosov Moscow State University in 1998. The topic of his thesis was studying the structure of the ribosome using photochemical cross-linking. After finishing his Ph.D. he briefly worked at the Max-Planck Institute for Molecular Genetics where he was involved in computer modeling of 23S rRNA topology within the 50S subunit of the bacterial ribosome. Then he spent several years at the Human Genetics Department at the University of Utah working in the area of translational recoding. He is now a Professor of Biomolecular Informatics and a Wellcome Trust Investigator at the University College Cork where he leads an active research group with interests in mRNA translation and diversity of the genetic decoding that uses a combination of computational and experimental approaches.


Know-How here


Yordanova MM, Loughran G, Zhdanov AM, Mariotti M, Kiniry SJ, O’Connor PBF, Andreev DE, Tzani I, Saffert P, Michel AM, Gladyshev VN, Papkovsky DB, Atkins JF, Baranov, PV. (2018) AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation. Nature 553:356-360.

Lobanov AV, Heaphy SM, Turanov AA, Gerashchenko MV, Pucciarelli S, Devaraj RR, Xie F, Petyuk VA, Smith RD, Klobutcher LA, Atkins JF, Miceli C, Hatfield DL, Baranov PV, Gladyshev VN. (2017) Position dependent termination and widespread obligatory frameshifting in Euplotes translation. Nat Struct Mol Biol 24:61-68. 

Heaphy SM, Mariotti M, Gladyshev VN, Atkins JF, Baranov PV. (2016) Novel ciliate genetic code variants including the reassignment of all three stop codons to sense codons in C. magnum. Mol Biol Evol 33:2885-2889.

Baranov PV, Atkins JF, Yordanova MM. (2015) Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning. Nature Reviews Genetics 16:517–529.

Andreev DE, O’Connor PBF, Zhdanov AV, RI, Shatsky IN, Papkovsky DB, Baranov PV. (2015) Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes. Genome Biology 16:90. 

Andreev DE, O’Connor PBF, Fahey C, Kenny EM, Terenin IM, Dmitriev SE, Cormican P, Morris DW, Shatsky IN, Baranov PV. (2015) Translation of 5′ leaders is pervasive in genes resistant to eIF2 repression. Elife 4:e03971.

Michel AM, Fox G, Kiran AM, De Bo C, O’Connor PBF, Heaphy SM, Mullan JPA, Donohue CA, Higgins DG, Baranov PV. (2014) GWIPS-viz: development of a ribo-seq genome browser. Nucleic Acids Res 42:D859-864. 

Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV. (2012) Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Research 22:2219-2229.

Ivanov IP, Firth AE, Michel AM, Atkins JF, Baranov PV. (2011) Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res 39:4220-4234.

Kiran A, Baranov PV. (2010) DARNED. A DAtabase of RNa EDiting in humans. Bioinformatics, 26:1772-1776.