Standardized annotation of translated open reading frames

Jonathan M. Mudge; Jorge Ruiz-Orera; John R. Prensner; Marie A. Brunet; Ferriol Calvet; Irwin Jungreis; Jose Manuel Gonzalez; Michele Magrane; Thomas F. Martinez; Jana Felicitas Schulz; Yucheng T. Yang; M. Mar Albà; Julie L. Aspden; Pavel V. Baranov; Ariel A. Bazzini; Elspeth Bruford; Maria Jesus Martin; Lorenzo Calviello; Anne Ruxandra Carvunis; Jin Chen; Juan Pablo Couso; Eric W. Deutsch; Paul Flicek; Adam Frankish; Mark Gerstein; Norbert Hubner; Nicholas T. Ingolia; Manolis Kellis; Gerben Menschaert; Robert L. Moritz; Uwe Ohler; Xavier Roucou; Alan Saghatelian; Jonathan S. Weissman; Sebastiaan van Heesch

doi:10.1038/s41587-022-01369-0

Standardized annotation of translated open reading frames

Jonathan M. Mudge, Jorge Ruiz-Orera, John R. Prensner, Marie A. Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, Michele Magrane, Thomas F. Martinez, Jana Felicitas Schulz, Yucheng T. Yang, M. Mar Albà, Julie L. Aspden, Pavel V. Baranov, Ariel A. Bazzini, Elspeth Bruford, Maria Jesus Martin, Lorenzo Calviello, Anne Ruxandra Carvunis, Jin ChenJuan Pablo Couso, Eric W. Deutsch, Paul Flicek, Adam Frankish, Mark Gerstein, Norbert Hubner, Nicholas T. Ingolia, Manolis Kellis, Gerben Menschaert, Robert L. Moritz, Uwe Ohler, Xavier Roucou, Alan Saghatelian, Jonathan S. Weissman, Sebastiaan van Heesch

Cecil H. and Ida Green Center For Reproductive Biology Sciences

Research output: Contribution to journal › Letter › peer-review

79 Scopus citations

Original language	English (US)
Pages (from-to)	994-999
Number of pages	6
Journal	Nature biotechnology
Volume	40
Issue number	7
DOIs	https://doi.org/10.1038/s41587-022-01369-0
State	Published - Jul 2022

ASJC Scopus subject areas

Biotechnology
Bioengineering
Applied Microbiology and Biotechnology
Molecular Medicine
Biomedical Engineering

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10.1038/s41587-022-01369-0

Cite this

Mudge, J. M., Ruiz-Orera, J., Prensner, J. R., Brunet, M. A., Calvet, F., Jungreis, I., Gonzalez, J. M., Magrane, M., Martinez, T. F., Schulz, J. F., Yang, Y. T., Albà, M. M., Aspden, J. L., Baranov, P. V., Bazzini, A. A., Bruford, E., Martin, M. J., Calviello, L., Carvunis, A. R., ... van Heesch, S. (2022). Standardized annotation of translated open reading frames. Nature biotechnology, 40(7), 994-999. https://doi.org/10.1038/s41587-022-01369-0

Mudge, JM, Ruiz-Orera, J, Prensner, JR, Brunet, MA, Calvet, F, Jungreis, I, Gonzalez, JM, Magrane, M, Martinez, TF, Schulz, JF, Yang, YT, Albà, MM, Aspden, JL, Baranov, PV, Bazzini, AA, Bruford, E, Martin, MJ, Calviello, L, Carvunis, AR, Chen, J, Couso, JP, Deutsch, EW, Flicek, P, Frankish, A, Gerstein, M, Hubner, N, Ingolia, NT, Kellis, M, Menschaert, G, Moritz, RL, Ohler, U, Roucou, X, Saghatelian, A, Weissman, JS & van Heesch, S 2022, 'Standardized annotation of translated open reading frames', Nature biotechnology, vol. 40, no. 7, pp. 994-999. https://doi.org/10.1038/s41587-022-01369-0

@article{1ef91d73c47146aaa4c3fa6860e3de16,

title = "Standardized annotation of translated open reading frames",

author = "Mudge, {Jonathan M.} and Jorge Ruiz-Orera and Prensner, {John R.} and Brunet, {Marie A.} and Ferriol Calvet and Irwin Jungreis and Gonzalez, {Jose Manuel} and Michele Magrane and Martinez, {Thomas F.} and Schulz, {Jana Felicitas} and Yang, {Yucheng T.} and Alb{\`a}, {M. Mar} and Aspden, {Julie L.} and Baranov, {Pavel V.} and Bazzini, {Ariel A.} and Elspeth Bruford and Martin, {Maria Jesus} and Lorenzo Calviello and Carvunis, {Anne Ruxandra} and Jin Chen and Couso, {Juan Pablo} and Deutsch, {Eric W.} and Paul Flicek and Adam Frankish and Mark Gerstein and Norbert Hubner and Ingolia, {Nicholas T.} and Manolis Kellis and Gerben Menschaert and Moritz, {Robert L.} and Uwe Ohler and Xavier Roucou and Alan Saghatelian and Weissman, {Jonathan S.} and {van Heesch}, Sebastiaan",

note = "Funding Information: A.F., J.M.M., F.C. and P.F. are supported by the Wellcome Trust (grant number 108749/Z/15/Z), the National Human Genome Research Institute (NHGRI) of the US National Institutes of Health (NIH) under award number 2U41HG007234 and the European Molecular Biology Laboratory (EMBL). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Ensembl is a registered trademark of EMBL. M.G. and Y.T.Y. are supported by NHGRI, NIH, under award number 2U41HG007234. I.J. and M.K. are supported by National Human Genome Research Institute of the NIH under award numbers 2U41HG007234 and R01 HG004037. UniProt is supported by the NHGRI, NIH, under award number (U24HG007822), EMBL core funds and the Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI). J.R.P. is supported by the Harvard K-12 in Central Nervous System tumors (5K12 CA 90354-18), the Alex{\textquoteright}s Lemonade Stand Foundation Young Investigator Award (no. 21-23983) and the Musella Foundation for Brain Tumor Research. T.F.M. is supported by the NIH under award number F32GM123685. M.M.A. acknowledges funding from the Spanish Government grant PGC2018-094091-B-I00 (MCI/AEI/FEDER, EU) and AGAUR grant 2017SGR01020. J.C. is supported by the NIH Pathway to Independence Award (R00 GM134154) and the Cancer Prevent and Research Institute of Texas (RR200095). J.S.W. is supported by the Howard Hughes Medical Institute. A.A.B. is supported by the Stowers Institute for Medical Research and the NIH (R01 GM136849). A.-R.C. is supported by funds provided by the Searle Scholars program, the Sloan Research Fellowship in Computational and Evolutionary Molecular Biology and the National Institute of General Medical Sciences, NIH, award number DP2GM137422. P.V.B. wishes to acknowledge the support from the Investigator in Science Award (grant number 210692/Z/18/Z) by SFI-HRB-Wellcome Trust Biomedical Research Partnership and from Russian Science Foundation (grant number 20-14-00121). N.H. is the recipient of a European Research Council advanced grant under the European Union{\textquoteright}s Horizon 2020 research and innovation programme (grant agreement no. AdG788970). N.H. is supported by a grant from the Leducq Foundation (11 CVD-01). The work of the HGNC is funded by the Wellcome Trust (208349/Z/17/Z) and the NHGRI, NIH (under award number U24HG003345). X.R. and M.A.B. are funded by the Canadian Institutes of Health Research, grant PJT-175322. X.R. is funded as a Canada Research Chair in functional proteomics and discovery of novel proteins. N.T.I. is supported by the NIH under award number R01 GM130996. R.L.M. and E.W.D. are supported by NIH grants R01GM087221, R24GM127667, U19AG023122, 1S10OD026936-01 and US National Science Foundation grant DBI-1933311. J.L.A. is supported by the Medical Research Council (MR/N000471/1). M.A.B. is supported by a Junior 1 fellowship from the Fonds de Recherche du Qu{\'e}bec–Sant{\'e}. ",

year = "2022",

month = jul,

doi = "10.1038/s41587-022-01369-0",

language = "English (US)",

volume = "40",

pages = "994--999",

journal = "Nature biotechnology",

issn = "1087-0156",

publisher = "Nature Publishing Group",

number = "7",

}

TY - JOUR

T1 - Standardized annotation of translated open reading frames

AU - Mudge, Jonathan M.

AU - Ruiz-Orera, Jorge

AU - Prensner, John R.

AU - Brunet, Marie A.

AU - Calvet, Ferriol

AU - Jungreis, Irwin

AU - Gonzalez, Jose Manuel

AU - Magrane, Michele

AU - Martinez, Thomas F.

AU - Schulz, Jana Felicitas

AU - Yang, Yucheng T.

AU - Albà, M. Mar

AU - Aspden, Julie L.

AU - Baranov, Pavel V.

AU - Bazzini, Ariel A.

AU - Bruford, Elspeth

AU - Martin, Maria Jesus

AU - Calviello, Lorenzo

AU - Carvunis, Anne Ruxandra

AU - Chen, Jin

AU - Couso, Juan Pablo

AU - Deutsch, Eric W.

AU - Flicek, Paul

AU - Frankish, Adam

AU - Gerstein, Mark

AU - Hubner, Norbert

AU - Ingolia, Nicholas T.

AU - Kellis, Manolis

AU - Menschaert, Gerben

AU - Moritz, Robert L.

AU - Ohler, Uwe

AU - Roucou, Xavier

AU - Saghatelian, Alan

AU - Weissman, Jonathan S.

AU - van Heesch, Sebastiaan

N1 - Funding Information: A.F., J.M.M., F.C. and P.F. are supported by the Wellcome Trust (grant number 108749/Z/15/Z), the National Human Genome Research Institute (NHGRI) of the US National Institutes of Health (NIH) under award number 2U41HG007234 and the European Molecular Biology Laboratory (EMBL). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. Ensembl is a registered trademark of EMBL. M.G. and Y.T.Y. are supported by NHGRI, NIH, under award number 2U41HG007234. I.J. and M.K. are supported by National Human Genome Research Institute of the NIH under award numbers 2U41HG007234 and R01 HG004037. UniProt is supported by the NHGRI, NIH, under award number (U24HG007822), EMBL core funds and the Swiss Federal Government through the State Secretariat for Education, Research and Innovation (SERI). J.R.P. is supported by the Harvard K-12 in Central Nervous System tumors (5K12 CA 90354-18), the Alex’s Lemonade Stand Foundation Young Investigator Award (no. 21-23983) and the Musella Foundation for Brain Tumor Research. T.F.M. is supported by the NIH under award number F32GM123685. M.M.A. acknowledges funding from the Spanish Government grant PGC2018-094091-B-I00 (MCI/AEI/FEDER, EU) and AGAUR grant 2017SGR01020. J.C. is supported by the NIH Pathway to Independence Award (R00 GM134154) and the Cancer Prevent and Research Institute of Texas (RR200095). J.S.W. is supported by the Howard Hughes Medical Institute. A.A.B. is supported by the Stowers Institute for Medical Research and the NIH (R01 GM136849). A.-R.C. is supported by funds provided by the Searle Scholars program, the Sloan Research Fellowship in Computational and Evolutionary Molecular Biology and the National Institute of General Medical Sciences, NIH, award number DP2GM137422. P.V.B. wishes to acknowledge the support from the Investigator in Science Award (grant number 210692/Z/18/Z) by SFI-HRB-Wellcome Trust Biomedical Research Partnership and from Russian Science Foundation (grant number 20-14-00121). N.H. is the recipient of a European Research Council advanced grant under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. AdG788970). N.H. is supported by a grant from the Leducq Foundation (11 CVD-01). The work of the HGNC is funded by the Wellcome Trust (208349/Z/17/Z) and the NHGRI, NIH (under award number U24HG003345). X.R. and M.A.B. are funded by the Canadian Institutes of Health Research, grant PJT-175322. X.R. is funded as a Canada Research Chair in functional proteomics and discovery of novel proteins. N.T.I. is supported by the NIH under award number R01 GM130996. R.L.M. and E.W.D. are supported by NIH grants R01GM087221, R24GM127667, U19AG023122, 1S10OD026936-01 and US National Science Foundation grant DBI-1933311. J.L.A. is supported by the Medical Research Council (MR/N000471/1). M.A.B. is supported by a Junior 1 fellowship from the Fonds de Recherche du Québec–Santé.

PY - 2022/7

Y1 - 2022/7

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JO - Nature biotechnology

JF - Nature biotechnology

IS - 7

ER -

Standardized annotation of translated open reading frames

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