Publications by authors named "Irwin Jungreis"

29Publications

Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid.

Authors:
Christiane Iserman Christine A Roden Mark A Boerneke Rachel S G Sealfon Grace A McLaughlin Irwin Jungreis Ethan J Fritch Yixuan J Hou Joanne Ekena Chase A Weidmann Chandra L Theesfeld Manolis Kellis Olga G Troyanskaya Ralph S Baric Timothy P Sheahan Kevin M Weeks Amy S Gladfelter

Mol Cell 2020 12 27;80(6):1078-1091.e6. Epub 2020 Nov 27.

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. Electronic address:

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December 2020

GENCODE 2021.

Authors:
Adam Frankish Mark Diekhans Irwin Jungreis Julien Lagarde Jane E Loveland Jonathan M Mudge Cristina Sisu James C Wright Joel Armstrong If Barnes Andrew Berry Alexandra Bignell Carles Boix Silvia Carbonell Sala Fiona Cunningham Tomás Di Domenico Sarah Donaldson Ian T Fiddes Carlos García Girón Jose Manuel Gonzalez Tiago Grego Matthew Hardy Thibaut Hourlier Kevin L Howe Toby Hunt Osagie G Izuogu Rory Johnson Fergal J Martin Laura Martínez Shamika Mohanan Paul Muir Fabio C P Navarro Anne Parker Baikang Pei Fernando Pozo Ferriol Calvet Riera Magali Ruffier Bianca M Schmitt Eloise Stapleton Marie-Marthe Suner Irina Sycheva Barbara Uszczynska-Ratajczak Maxim Y Wolf Jinuri Xu Yucheng T Yang Andrew Yates Daniel Zerbino Yan Zhang Jyoti S Choudhary Mark Gerstein Roderic Guigó Tim J P Hubbard Manolis Kellis Benedict Paten Michael L Tress Paul Flicek

Nucleic Acids Res 2021 01;49(D1):D916-D923

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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January 2021

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy.

Authors:
Maria Kousi Onuralp Söylemez Aysegül Ozanturk Niki Mourtzi Sebastian Akle Irwin Jungreis Jean Muller Christopher A Cassa Harrison Brand Jill Anne Mokry Maxim Y Wolf Azita Sadeghpour Kelsey McFadden Richard A Lewis Michael E Talkowski Hélène Dollfus Manolis Kellis Erica E Davis Shamil R Sunyaev Nicholas Katsanis

Nat Genet 2020 11 12;52(11):1145-1150. Epub 2020 Oct 12.

Center for Human Disease Modeling, Duke University Medical Center, Durham, NC, USA.

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November 2020

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.

Authors:
Irwin Jungreis Rachel Sealfon Manolis Kellis

Res Sq 2020 Oct 1. Epub 2020 Oct 1.

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October 2020

Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits.

Authors:
Cheng Sun Jiaxing Huang Yun Wang Xiaomeng Zhao Long Su Gregg W C Thomas Mengya Zhao Xingtan Zhang Irwin Jungreis Manolis Kellis Saverio Vicario Igor V Sharakhov Semen M Bondarenko Martin Hasselmann Chang N Kim Benedict Paten Luca Penso-Dolfin Li Wang Yuxiao Chang Qiang Gao Ling Ma Lina Ma Zhang Zhang Hongbo Zhang Huahao Zhang Livio Ruzzante Hugh M Robertson Yihui Zhu Yanjie Liu Huipeng Yang Lele Ding Quangui Wang Dongna Ma Weilin Xu Cheng Liang Michael W Itgen Lauren Mee Gang Cao Ze Zhang Ben M Sadd Matthew W Hahn Sarah Schaack Seth M Barribeau Paul H Williams Robert M Waterhouse Rachel Lockridge Mueller

Mol Biol Evol 2021 Jan;38(2):486-501

Department of Biology, Colorado State University, Fort Collins, CO.

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January 2021

Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast.

Authors:
Amy R Eisenberg Andrea L Higdon Ina Hollerer Alexander P Fields Irwin Jungreis Paige D Diamond Manolis Kellis Marko Jovanovic Gloria A Brar

Cell Syst 2020 Aug 24;11(2):145-160.e5. Epub 2020 Jul 24.

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address:

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August 2020

Specific viral RNA drives the SARS CoV-2 nucleocapsid to phase separate.

Authors:
Christiane Iserman Christine Roden Mark Boerneke Rachel Sealfon Grace McLaughlin Irwin Jungreis Chris Park Avinash Boppana Ethan Fritch Yixuan J Hou Chandra Theesfeld Olga G Troyanskaya Ralph S Baric Timothy P Sheahan Kevin Weeks Amy S Gladfelter

bioRxiv 2020 Jun 12. Epub 2020 Jun 12.

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June 2020

Sarbecovirus comparative genomics elucidates gene content of SARS-CoV-2 and functional impact of COVID-19 pandemic mutations.

Authors:
Irwin Jungreis Rachel Sealfon Manolis Kellis

bioRxiv 2020 Jun 3. Epub 2020 Jun 3.

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA.

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June 2020

Evidence for a novel overlapping coding sequence in POLG initiated at a CUG start codon.

Authors:
Yousuf A Khan Irwin Jungreis James C Wright Jonathan M Mudge Jyoti S Choudhary Andrew E Firth Manolis Kellis

BMC Genet 2020 03 6;21(1):25. Epub 2020 Mar 6.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.

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March 2020

Few SINEs of life: Alu elements have little evidence for biological relevance despite elevated translation.

Authors:
Laura Martinez-Gomez Federico Abascal Irwin Jungreis Fernando Pozo Manolis Kellis Jonathan M Mudge Michael L Tress

NAR Genom Bioinform 2020 Mar 19;2(1):lqz023. Epub 2019 Dec 19.

Bioinformatics Unit, Spanish National Cancer Research Centre, 28029 Madrid, Spain.

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March 2020

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.

Authors:
Jonathan M Mudge Irwin Jungreis Toby Hunt Jose Manuel Gonzalez James C Wright Mike Kay Claire Davidson Stephen Fitzgerald Ruth Seal Susan Tweedie Liang He Robert M Waterhouse Yue Li Elspeth Bruford Jyoti S Choudhary Adam Frankish Manolis Kellis

Genome Res 2019 12 19;29(12):2073-2087. Epub 2019 Sep 19.

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, Massachusetts 02139, USA.

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December 2019

Elucidation of Codon Usage Signatures across the Domains of Life.

Authors:
Eva Maria Novoa Irwin Jungreis Olivier Jaillon Manolis Kellis

Mol Biol Evol 2019 10;36(10):2328-2339

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.

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October 2019

A gene expression atlas of embryonic neurogenesis in reveals complex spatiotemporal regulation of lncRNAs.

Authors:
Alexandra L McCorkindale Philipp Wahle Sascha Werner Irwin Jungreis Peter Menzel Chinmay J Shukla Rúben Lopes Pereira Abreu Rafael A Irizarry Irmtraud M Meyer Manolis Kellis Robert P Zinzen

Development 2019 03 28;146(6). Epub 2019 Mar 28.

Laboratory for Systems Biology of Neural Tissue Differentiation, Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrueck Centre for Molecular Medicine (MDC) in the Helmholtz Association, Robert-Roessle-Strasse 12, 13125 Berlin, Germany

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March 2019

Corrigendum: Loose ends: almost one in five human genes still have unresolved coding status.

Authors:
Federico Abascal David Juan Irwin Jungreis Manolis Kellis Laura Martinez Maria Rigau Jose Manuel Rodriguez Jesus Vazquez Michael L Tress

Nucleic Acids Res 2018 12;46(22):12194

Bioinformatics Unit, Spanish National Cancer Research Centre, Madrid, Spain.

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December 2018

GENCODE reference annotation for the human and mouse genomes.

Authors:
Adam Frankish Mark Diekhans Anne-Maud Ferreira Rory Johnson Irwin Jungreis Jane Loveland Jonathan M Mudge Cristina Sisu James Wright Joel Armstrong If Barnes Andrew Berry Alexandra Bignell Silvia Carbonell Sala Jacqueline Chrast Fiona Cunningham Tomás Di Domenico Sarah Donaldson Ian T Fiddes Carlos García Girón Jose Manuel Gonzalez Tiago Grego Matthew Hardy Thibaut Hourlier Toby Hunt Osagie G Izuogu Julien Lagarde Fergal J Martin Laura Martínez Shamika Mohanan Paul Muir Fabio C P Navarro Anne Parker Baikang Pei Fernando Pozo Magali Ruffier Bianca M Schmitt Eloise Stapleton Marie-Marthe Suner Irina Sycheva Barbara Uszczynska-Ratajczak Jinuri Xu Andrew Yates Daniel Zerbino Yan Zhang Bronwen Aken Jyoti S Choudhary Mark Gerstein Roderic Guigó Tim J P Hubbard Manolis Kellis Benedict Paten Alexandre Reymond Michael L Tress Paul Flicek

Nucleic Acids Res 2019 01;47(D1):D766-D773

European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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January 2019

Loose ends: almost one in five human genes still have unresolved coding status.

Authors:
Federico Abascal David Juan Irwin Jungreis Manolis Kellis Laura Martinez Maria Rigau Jose Manuel Rodriguez Jesus Vazquez Michael L Tress

Nucleic Acids Res 2018 08;46(14):7070-7084

Bioinformatics Unit, Spanish National Cancer Research Centre, Madrid, Spain.

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August 2018

Stop codon readthrough generates a C-terminally extended variant of the human vitamin D receptor with reduced calcitriol response.

Authors:
Gary Loughran Irwin Jungreis Ioanna Tzani Michael Power Ruslan I Dmitriev Ivaylo P Ivanov Manolis Kellis John F Atkins

J Biol Chem 2018 03 31;293(12):4434-4444. Epub 2018 Jan 31.

From the School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland,

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March 2018

Evolutionary Dynamics of Abundant Stop Codon Readthrough.

Authors:
Irwin Jungreis Clara S Chan Robert M Waterhouse Gabriel Fields Michael F Lin Manolis Kellis

Mol Biol Evol 2016 12 7;33(12):3108-3132. Epub 2016 Sep 7.

MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA

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December 2016

Improved Identification and Analysis of Small Open Reading Frame Encoded Polypeptides.

Authors:
Jiao Ma Jolene K Diedrich Irwin Jungreis Cynthia Donaldson Joan Vaughan Manolis Kellis John R Yates Alan Saghatelian

Anal Chem 2016 Apr 24;88(7):3967-75. Epub 2016 Mar 24.

Salk Institute for Biological Studies, Clayton Foundation Laboratories for Peptide Biology , 10010 North Torrey Pines Road, La Jolla, California 92037, United States.

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April 2016

Ebola Virus Epidemiology, Transmission, and Evolution during Seven Months in Sierra Leone.

Authors:
Daniel J Park Gytis Dudas Shirlee Wohl Augustine Goba Shannon L M Whitmer Kristian G Andersen Rachel S Sealfon Jason T Ladner Jeffrey R Kugelman Christian B Matranga Sarah M Winnicki James Qu Stephen K Gire Adrianne Gladden-Young Simbirie Jalloh Dolo Nosamiefan Nathan L Yozwiak Lina M Moses Pan-Pan Jiang Aaron E Lin Stephen F Schaffner Brian Bird Jonathan Towner Mambu Mamoh Michael Gbakie Lansana Kanneh David Kargbo James L B Massally Fatima K Kamara Edwin Konuwa Josephine Sellu Abdul A Jalloh Ibrahim Mustapha Momoh Foday Mohamed Yillah Bobbie R Erickson Tara Sealy Dianna Blau Christopher Paddock Aaron Brault Brian Amman Jane Basile Scott Bearden Jessica Belser Eric Bergeron Shelley Campbell Ayan Chakrabarti Kimberly Dodd Mike Flint Aridth Gibbons Christin Goodman John Klena Laura McMullan Laura Morgan Brandy Russell Johanna Salzer Angela Sanchez David Wang Irwin Jungreis Christopher Tomkins-Tinch Andrey Kislyuk Michael F Lin Sinead Chapman Bronwyn MacInnis Ashley Matthews James Bochicchio Lisa E Hensley Jens H Kuhn Chad Nusbaum John S Schieffelin Bruce W Birren Marc Forget Stuart T Nichol Gustavo F Palacios Daouda Ndiaye Christian Happi Sahr M Gevao Mohamed A Vandi Brima Kargbo Edward C Holmes Trevor Bedford Andreas Gnirke Ute Ströher Andrew Rambaut Robert F Garry Pardis C Sabeti

Cell 2015 Jun;161(7):1516-26

Broad Institute of Harvard and MIT, 75 Ames Street, Cambridge, MA 02142, USA; Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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June 2015