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Irwin Jungreis
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An integrated encyclopedia of DNA elements in the human genome
ENCODE Project Consortium
Nature 489 (7414), 57, 2012
136082012
GENCODE reference annotation for the human and mouse genomes
A Frankish, M Diekhans, AM Ferreira, R Johnson, I Jungreis, J Loveland, ...
Nucleic acids research 47 (D1), D766-D773, 2019
24892019
A high-resolution map of human evolutionary constraint using 29 mammals
K Lindblad-Toh, M Garber, O Zuk, MF Lin, BJ Parker, S Washietl, ...
Nature 478 (7370), 476-482, 2011
12472011
Identification of functional elements and regulatory circuits by Drosophila modENCODE
S Roy, J Ernst, PV Kharchenko, P Kheradpour, N Negre, ML Eaton, ...
Science 330 (6012), 1787, 2010
10492010
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions
MF Lin, I Jungreis, M Kellis
Bioinformatics 27 (13), i275-i282, 2011
9592011
GENCODE 2021
A Frankish, M Diekhans, I Jungreis, J Lagarde, JE Loveland, JM Mudge, ...
Nucleic acids research 49 (D1), D916-D923, 2021
6452021
Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes
DE Neafsey, RM Waterhouse, MR Abai, SS Aganezov, MA Alekseyev, ...
Science 347 (6217), 1258522, 2015
5832015
Ebola virus epidemiology, transmission, and evolution during seven months in Sierra Leone
DJ Park, G Dudas, S Wohl, A Goba, SLM Whitmer, KG Andersen, ...
Cell 161 (7), 1516-1526, 2015
3372015
Genomic RNA elements drive phase separation of the SARS-CoV-2 nucleocapsid
C Iserman, CA Roden, MA Boerneke, RSG Sealfon, GA McLaughlin, ...
Molecular cell 80 (6), 1078-1091. e6, 2020
2482020
Evolution of enhanced innate immune evasion by SARS-CoV-2
LG Thorne, M Bouhaddou, AK Reuschl, L Zuliani-Alvarez, B Polacco, ...
Nature 602 (7897), 487-495, 2022
2472022
Evidence of abundant stop codon readthrough in Drosophila and other metazoa
I Jungreis, MF Lin, R Spokony, CS Chan, N Negre, A Victorsen, KP White, ...
Genome research 21 (12), 2096-2113, 2011
2342011
Evidence of efficient stop codon readthrough in four mammalian genes
G Loughran, MY Chou, IP Ivanov, I Jungreis, M Kellis, AM Kiran, ...
Nucleic acids research 42 (14), 8928-8938, 2014
2292014
Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue
J Ma, CC Ward, I Jungreis, SA Slavoff, AG Schwaid, J Neveu, BA Budnik, ...
Journal of proteome research 13 (3), 1757-1765, 2014
1752014
SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes
I Jungreis, R Sealfon, M Kellis
Nature communications 12 (1), 2642, 2021
1642021
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer
T Ouspenskaia, T Law, KR Clauser, S Klaeger, S Sarkizova, F Aguet, B Li, ...
Nature biotechnology 40 (2), 209-217, 2022
1282022
Improved identification and analysis of small open reading frame encoded polypeptides
J Ma, JK Diedrich, I Jungreis, C Donaldson, J Vaughan, M Kellis, ...
Analytical chemistry 88 (7), 3967-3975, 2016
1252016
Calcifediol treatment and hospital mortality due to COVID-19: a cohort study
JF Alcala-Diaz, L Limia-Perez, R Gomez-Huelgas, MD Martin-Escalante, ...
Nutrients 13 (6), 1760, 2021
892021
Standardized annotation of translated open reading frames
JM Mudge, J Ruiz-Orera, JR Prensner, MA Brunet, F Calvet, I Jungreis, ...
Nature biotechnology 40 (7), 994-999, 2022
872022
Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits
C Sun, J Huang, Y Wang, X Zhao, L Su, GWC Thomas, M Zhao, X Zhang, ...
Molecular biology and evolution 38 (2), 486-501, 2021
672021
Loose ends: almost one in five human genes still have unresolved coding status
F Abascal, D Juan, I Jungreis, L Martinez, M Rigau, JM Rodriguez, ...
Nucleic acids research 46 (14), 7070-7084, 2018
652018
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