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List of works by Pavel Baranov

A [Cu]rious Ribosomal Profiling Pattern Leads to the Discovery of Ribosomal Frameshifting in the Synthesis of a Copper Chaperone.

scientific article published in January 2017

A new technique for the characterization of long-range tertiary contacts in large RNA molecules: insertion of a photolabel at a selected position in 16S rRNA within the Escherichia coli ribosome

scientific article published on June 1997

A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment

scientific article

AMD1 mRNA employs ribosome stalling as a mechanism for molecular memory formation.

scientific article published on 3 January 2018

ARFA: a program for annotating bacterial release factor genes, including prediction of programmed ribosomal frameshifting.

scientific article

Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli

scientific article

Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning

scientific article published on 11 August 2015

Catch me if you can: trapping scanning ribosomes in their footsteps

scientific article published in August 2016

Codon size reduction as the origin of the triplet genetic code

scientific article

CodonLogo: a sequence logo-based viewer for codon patterns.

scientific article published on 17 May 2012

Comparative survey of the relative impact of mRNA features on local ribosome profiling read density.

scientific article

Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning

scientific article

Computational methods for ribosome profiling data analysis

scientific article published on 24 November 2019

Darned in 2013: inclusion of model organisms and linking with Wikipedia

scientific article (publication date: 2013)

Diverse bacterial genomes encode an operon of two genes, one of which is an unusual class-I release factor that potentially recognizes atypical mRNA signals other than normal stop codons

scientific article

Evaluating data integrity in ribosome footprinting datasets through modelled polysome profiles

scientific article published in 2022

Evidence of efficient stop codon readthrough in four mammalian genes

scientific article

GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms

scientific article published on 23 April 2015

GWIPS-viz: 2018 update.

scientific article published on 5 September 2017

GWIPS-viz: development of a ribo-seq genome browser

scientific article published on 31 October 2013

GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences

scientific article

Genome-Wide Changes in Protein Translation Efficiency Are Associated with Autism.

scientific article

Identification of A-to-I RNA editing: dotting the i's in the human transcriptome.

scientific article published on August 2011

Identification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast

scientific article published in March 2022

Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences

scientific article

Illuminating translation with ribosome profiling spectra

scientific article published in January 2016

Insights into the mechanisms of eukaryotic translation gained with ribosome profiling

scientific article

Itm2a silencing rescues lamin A mediated inhibition of 3T3-L1 adipocyte differentiation.

scientific article published on 18 August 2017

Low energy costs of F1Fo ATP synthase reversal in colon carcinoma cells deficient in mitochondrial complex IV.

scientific article published on 9 February 2017

Molecular biology: Antibiotic re-frames decoding

scientific article published in November 2013

Nailing fingerprints in the stars

journal article; published in Nature on 2013-11-01

New features of 23S ribosomal RNA folding: the long helix 41-42 makes a "U-turn" inside the ribosome

scientific article published in June 1998

Novel Ciliate Genetic Code Variants Including the Reassignment of All Three Stop Codons to Sense Codons in Condylostoma magnum

scientific article

Observation of dually decoded regions of the human genome using ribosome profiling data

scientific article

Observation of the triplet metastable state of shallow donor pairs in AlN crystals with a negative-U behavior: a high-frequency EPR and ENDOR Study

scientific article published on 24 June 2008

Ornithine decarboxylase antizyme finder (OAF): fast and reliable detection of antizymes with frameshifts in mRNAs

scientific article

Overriding standard decoding: implications of recoding for ribosome function and enrichment of gene expression.

scientific article

Oxygen and glucose deprivation induces widespread alterations in mRNA translation within 20 minutes

scientific article published on 6 May 2015

P-site tRNA is a crucial initiator of ribosomal frameshifting.

scientific article published on February 2004

PausePred and Rfeet: webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data

scientific article published on 26 July 2018

Position-dependent termination and widespread obligatory frameshifting in Euplotes translation.

scientific article

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

scientific article published on 19 April 2018

Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators

scientific article published on 6 April 2015

Programmed ribosomal frameshifting in decoding the SARS-CoV genome

scientific article

Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC).

scientific article

RECODE 2003.

scientific article published on January 2003

Recode-2: new design, new search tools, and many more genes

scientific article

Recoding in bacteriophages and bacterial IS elements.

scientific article

Recoding: translational bifurcations in gene expression.

scientific article

Release factor 2 frameshifting sites in different bacteria.

scientific article published on 15 March 2002

Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use

scientific article (publication date: 6 September 2016)

Ribosome profiling: a Hi-Def monitor for protein synthesis at the genome-wide scale

scientific article

Sequences that direct significant levels of frameshifting are frequent in coding regions of Escherichia coli.

scientific article

Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis

scientific article

Systematic analysis of the PTEN 5' leader identifies a major AUU initiated proteoform

scientific article published on 25 May 2016

TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the integrated stress response.

scientific article

The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution

scientific article

The Database of Ribosomal Cross links (DRC).

scientific article published on January 1998

The Database of Ribosomal Cross-links: an update

scientific article published on January 1999

The GWIPS-viz Browser

scientific article published on 16 May 2018

The distinction between recoding and codon reassignment

scientific article published on August 2010

The potential use of complex derivatization procedures in comprehensive HPLC-MS/MS detection of anabolic steroids.

scientific article published on October 2010

Thousands of human non-AUG extended proteoforms lack evidence of evolutionary selection among mammals

scientific article published in 2022

Transcriptional slippage in bacteria: distribution in sequenced genomes and utilization in IS element gene expression

scientific article

Translation control of mRNAs encoding mammalian translation initiation factors.

scientific article published on 4 February 2018

Translation initiation downstream from annotated start codons in human mRNAs coevolves with the Kozak context

scientific article published on 15 July 2020

Translation of 5' leaders is pervasive in genes resistant to eIF2 repression

scientific journal article

Translation: Duality in the genetic code

scientific article published in Nature

Translational recoding signals between gag and pol in diverse LTR retrotransposons.

scientific article published on December 2003

Trips-Viz: a transcriptome browser for exploring Ribo-Seq data

scientific article published on 01 January 2019

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

scientific article published on 01 July 2021

Unusually efficient CUG initiation of an overlapping reading frame in POLG mRNA yields novel protein POLGARF

scientific article published on 21 September 2020

[Directed cleavage of the 16S rRNA molecule at a single internucleotide bond]

scientific article published on 01 February 1995

eIF2α controls memory consolidation via excitatory and somatostatin neurons

scientific article published on 07 October 2020

rRNA:mRNA pairing alters the length and the symmetry of mRNA-protected fragments in ribosome profiling experiments

scientific article published on 19 April 2013

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