Publications and pre-prints by LAPTI members.

With citations

If you didn't write it down, it didn't happen.

Larry Zana


Palu CC, Ribeiro-Alves M, Wu Y, Lawlor B, Baranov PV, Kelly B, Walsh P. (2019) Simplicity DiffExpress: a bespoke cloud-based interface for RNA-seq differential expression modeling and analysis. Frontiers in Genetics 10:356. (PDF).

Meydan S, Marks J, Klepacki D, Sharma V, Baranov PV, Firth AE, Margus T, Kefi A, Vazquez-Laslop N, Mankin AS. (2019) Retapamulin-Assisted Ribosome Profiling Reveals the Alternative Bacterial Proteome. Mol Cell pii: S1097-2765(19)30107-8. (PDF).

Gerresheim GK, Bathke J, Michel AM, Andreev DE, Shalamova LA, Rossbach O, Hu P, Glebe D, Fricke M, Marz M, Goesmann A, Kiniry SJ, Baranov PV, Shatsky IN, Niepmann M. (2019) Cellular Gene Expression during Hepatitis C Virus Replication as Revealed by Ribosome Profiling. Int J Mol Sci. 20:1321 (PDF).

Hardy S, Kostantin E, Wang SJ, Hristova T, Galicia-Vazquez G, Baranov PV, Pelletier J, Tremblay ML. (2019) Magnesium-sensitive upstream ORF controls PRL phosphatase expression to mediate energy metabolism. Proc Natl Acad Sci U S A. 116:2925-2934 (PDF).

Kiniry SJ, O'Connor PBF, Michel AM, Baranov PV. (2019) Trips-Viz: a transcriptome browser for exploring Ribo-Seq data. Nucleic Acids Res 47:D847-D852 (PDF).


Kumari R, Michel AM, Baranov PV. (2018) PausePred and Rfeet: Webtools for inferring ribosome pauses and visualizing footprint density from ribosome profiling data. RNA 24:1297-1304. (PDF).

Rogozin IB, Gertz EM, Baranov P, Poliakov E, Schaffer AA. (2018) Genome-wide changes in protein translation efficiency are associated with autism. Genome Biol Evol 10: 1902-1919. (PDF).

Andreev DE* Arnold M*, Kiniry SJ, Loughran G, Michel AM, Rachinskiy D, Baranov PV. (2018) TASEP modelling provides a parsimonious explanation for the ability of a single uORF to derepress translation during the Integrated Stress Response. eLife 7:e32563. (PDF).

bioRxiv 2017 (PrePrint)

Kiniry SJ, Michel AM, Baranov PV. (2018) The GWIPS-viz Browser. Current Protocols in Bioinformatics e50. (PDF).

Jantsch M, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schafer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R. (2018) Positioning Europe for the EPITRANSCRIPTOMICS challenge. RNA Biol 19:1-8. (PDF).

Andreev DE, Dmitriev SE, Loughran G, Terenin IM, Baranov PV, Shatsky IN. (2018) Translation control of mRNAs encoding mammalian translation initiation factors. Gene 651:174-182. (PDF).

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 (PDF) Also see News and Views summarizing the finiding and a computer simulation illustrating the mechanism.

Michel AM, Kiniry SJ, O'Connor PBF, Mullan JP, Baranov, PV. (2018) GWIPS-viz: 2018 update. Nucleic Acids Res 46:D823-D830 (PDF)


Davies SJ, Ryan J, O'Connor PBF, Kenny E, Morris D, Baranov PV, O'Connor R, McCarthy TV. (2017) Itm2a silencing rescues lamin A mediated inhibition of 3T3-L1 adipocyte differentiation. Adipocyte 6:259-276. (PDF).

Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF. (2017) Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis. Nucleic Acids Res 45:10156-10167.(PDF).

Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF. (2017) Stimulation of reverse transcriptase generated cDNAs with specific indels by template RNA structure: retrotransposon, dNTP balance, RT-reagent usage. Nucleic Acids Res 45:10143-10155. (PDF).

Karim MR, Michel A, Zappa A, Baranov P, Sahay R, Rebholz-Schuhmann D. (2017) Improving data workflow systems with cloud services and use of open data for bioinformatics research. Brief Bioinform 19:1035-1050 (PDF).

Zhdanov AV, Andreev DE, Baranov PV, Papkovsky DB. (2017) Low energy costs of F1Fo ATP synthase reversal in colon carcinoma cells deficient in mitochondrial complex IV. Free Radic Biol Med 106:184-195 (PDF).

Andreev DE#, O'Connor PBF, Loughran G, Dmitriev SE Baranov PV#, Shatsky IN#. (2017) Insights into the mechanisms of eukaryotic translation gained with Ribosome Profiling. Nucleic Acids Res 45:513-526 (PDF).

Atkins JF, Loughran G, Baranov PV. (2017) A [Cu]rious Ribosomal Profiling Pattern Leads to the Discovery of Ribosomal Frameshifting in the Synthesis of a Copper Chaperone. Mol Cell 65:203-204 (PDF).

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 (PDF) Also see a perspective in Science.


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 Condylostoma magnum. Mol Biol Evol. 33:2885-2889 (PDF) Also see a perspective in Science.

O'Connor PB, Andreev DE, Baranov PV. (2016) Comparative survey of the relative impact of mRNA features on local ribosome profiling read density. Nat Commun. 7:12915 (PDF) On-line supplementary material: RUST software and RUST diagrams of Ribo-seq datasets.

BioRxiv 2015 (PrePrint)

Atkins JF, Loughran G, Bhatt PR, Firth AE, Baranov PV. (2016) Ribosomal frameshifting and transcriptional slippage: From genetic steganography and cryptography to adventitious use. Nucleic Acids Res. 44:7007-7078 (PDF)

Baranov PV, Loughran G. (2016) Catch me if you can: trapping scanning ribosomes in their footsteps. Nat Struct Mol Biol. 23:703-704 (PDF)

Tzani I, Ivanov IP, Andreev DA, Dean KA, Baranov PV, Atkins JF, Loughran G. (2016) Systematic analysis of the PTEN 5’ leader identifies a major AUU initiated proteoform. Open Biol 6:150203 (PDF)

Michel AM, Mullan JPA, Velayudhan V, O'Connor PBF, Donohue C, Baranov PV. (2016) RiboGalaxy: a browser based platform for the alignment, analysis and visualization of ribosome profiling data. RNA Biology 3:316-319 (PDF)

Baranov PV, Michel AM.(2016) Illuminating translation with ribosome profiling spectra. Nat Methods 13:123-124 (PDF)

Yerlikaya S, Meusburger M, Kumari R, Huber A, Anrather D, Costanzo M, Boone C, Ammerer G, Baranov PV, Loewith R. (2016) TORC1 and TORC2 collude to regulate Ribosomal Protein S6 phosphorylation in Saccharomyces cerevisiae. Mol Biol Cell E27:397-409 (PDF)


Dieudonne FX, O'Connor PB, Gubler-Jaquier P, Yasrebi H, Conne B, Nikolaev S, Antonarakis S, Baranov PV, Curran J. (2015) The effect of heterogeneous Transcription Start Sites (TSS) on the translatome: implications for the mammalian cellular phenotype. BMC Genomics 16:986 (PDF)

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 (PDF)

Andreev DE*, O'Connor PBF*, Zhdanov AV, Dmitriev 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 (PDF)On-line supplementary material: Ribosome profiles of individual transcripts with novel features

Penno C, Sharma V, Coakley A, O'Connell Motherway M, van Sinderen D, Lubkowska L, Kireeva ML, Kashlev M, Baranov PV, Atkins JF. (2015) Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators. Proc Natl Acad Sci U S A. 112:E1984-1993 (PDF)

Michel AM, Ahern AM, Donohue CA, Baranov PV. (2015) GWIPS-viz as a tool for exploring ribosome profiling evidence supporting the synthesis of alternative proteoforms. Proteomics 15:2410-2416 (PDF)

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 (PDF).


Michel AM, Andreev DE, Baranov PV (2014) Computational approach for calculating the probability of eukaryotic translation initiation from ribo-seq data that takes into account leaky scanning. BMC Bioinformatics, 15:380. (PDF).

Loughran G, Chou MY, Ivanov IP, Jungries I, Kellis M, Kiran AM, Baranov PV, Atkins JF. (2014) Evidence of efficient stop codon readthrough in four mammalian genes. Nucleic Acids Res, 42:8928-8938. (PDF).

Sharma V, Prere MF, Canal I, Firth AE, Atkins JF, Baranov PV, Fayet O. (2014) Analysis of tetra- and hepta-nucleotides motifs promoting -1 ribosomal frameshifting in Escherichia coli. Nucleic Acids Res, 42:7210-7225. (PDF). On-line Supplementary material: Clusters of genes containing heptameric patterns.

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. (PDF).


Atkins JF, Baranov PV. (2013) Molecular biology: Antibiotic re-frames decoding. Nature, 503:478-479. (PDF).

Michel AM, Baranov PV. (2013) Ribosome profiling: A Hi-Def monitor for protein synthesis at the genome-wide scale. WIREs RNA, 4:473-490. (PDF).

Antonov I, Coakley A, Atkins JF, Baranov PV, Borodovsky M. (2013) Identification of the nature of reading frame transitions observed in prokaryotic genomes. Nucleic Acids Res, 41:6514-6530 (PDF).

O'Connor PBF, Li GW, Weissman JS, Atkins JF, Baranov PV. (2013) rRNA:mRNA pairing alters the length and the symmetry of mRNA protected fragments in ribosome profiling experiments. Bioinformatics, 29:1488-1491 (PDF).

Antonov I, Baranov P, Borodovsky M. (2013) GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences. Nucleic Acids Res, 41:152-160 (PDF).

Kiran A, O'Mahony J, Sanjeev K, Baranov PV (2013) Darned in 2013: Inclusion of model organisms and linking with Wikipedia. Nucleic Acids Res, 41:258-261 (PDF).


Michel AM, Roy Choudhury K, Firth AE, Ingolia NT, Atkins, JF, Baranov PV. (2012) Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res, 22:2219-2229 (PDF). On-line supplementary material

Sharma V, Murphy DP, Provan G, Baranov PV. (2012) CodonLogo: A sequence logo based viewer for codon patterns. Bioinformatics, 15:1935-1936 (PDF).


Kiran A, Loughran G, O'Mahony JJ, Baranov PV. (2011) Identification of A-to-I RNA editing: Dotting the i's in the human transcriptome. Biochemistry (Mosc), 76:915-923 (PDF).

Sharma V, Firth AE, Antonov I, Fayet O, Atkins JF, Borodovsky M, Baranov PV. (2011) A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment. Mol Biol Evol, 28:3195-3211 (PDF). On-line Supplementary material: Clusters of recoded bacterial genes.

Baranov PV, Wills NM, Barriscale KA, Firth AE, Jud MC, Letsou A, Manning G, Atkins JF. (2011) Programmed ribosomal frameshifting in the expression of the regulator of intestinal stem cell proliferation, adenomatous polyposis coli (APC). RNA Biol, 8:637-647 (PDF).

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. (PDF). On-line Supplementary material: Multiple sequence alignment and MLOGD analysis of newly discovered and previously identified non-AUG initiated genes.

Gurvich OL, Näall SJ, Baranov PV, Björk GR, Atkins JF. (2011) Two groups of phenylalanine biosynthetic operon leader peptides genes: a high level of apparently incidental frameshifting in decoding Escherichia coli pheL. Nucleic Acids Res, 39:3019-3092 (PDF)


Atkins JF, Baranov PV. (2010) The distinction between recoding and codon reassignment. Genetics, 185:1535-1536. (PDF)

Kiran A, Baranov PV. (2010) DARNED. A DAtabase of RNa EDiting in humans. Bioinformatics, 26:772-776. (PDF)

Baranov PV, Gurvich OL. (2010) Sequences promoting recoding are singular genomic elements. In Atkins, John F.; Gesteland, Raymond F. (Eds.) Recoding: Expansion of Decoding Rules Enriches Gene Expression. Springer. pp. 301-320. ((PDF))

Firth AE, Bekaert M, Baranov PV. (2010) Computational resources for studying recoding. In Atkins, John F.; Gesteland, Raymond F. (Eds.) Recoding: Expansion of Decoding Rules Enriches Gene Expression. Springer. pp. 435-462.((PDF))

Bekaert M, Firth AE, Zhang Y, Gladyshev VN, Atkins JF, Baranov PV (2010) RECODE-2: New location, novel concept, more genes. Nucleic Acids Res, 38:D69-74.(PDF)


Baranov PV, Venin M, Provan G. (2009) Codon Size Reduction as the Origin of the Triplet Genetic Code. PLoS One, 4:e5708.(PDF).


Bekaert M, Ivanov IP, Atkins JF, Baranov PV. (2008) Ornithine decarboxylase antizyme finder (OAF): Fast and reliable detection of antizymes with frameshifts in mRNAs. BMC Bioinformatics, 9:178.(PDF).


Atkins JF, Baranov PV. (2007) Duality in the genetic code. Nature, 448: 1004-1005.(PDF).

* - equal contribution; # - joint corresponding authors