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Nicholas T. Ingolia, Ph.D. - Publications

Affiliations: 
Molecular and Cell Biology University of California, Berkeley, Berkeley, CA, United States 
 2006 Harvard University, Cambridge, MA, United States 
Area:
Molecular basis and physiological roles of the Translational control of gene expression through global and genome-wide analyses
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74 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Powers EN, Kuwayama N, Sousa C, Reynaud K, Jovanovic M, Ingolia NT, Brar GA. Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response. Biorxiv : the Preprint Server For Biology. PMID 38260653 DOI: 10.1101/2024.01.12.575095  0.371
2023 Lyons EF, Devanneaux LC, Muller RY, Freitas AV, Meacham ZA, McSharry MV, Trinh VN, Rogers AJ, Ingolia NT, Lareau LF. Codon optimality modulates protein output by tuning translation initiation. Biorxiv : the Preprint Server For Biology. PMID 38076849 DOI: 10.1101/2023.11.27.568910  0.363
2023 Mestre-Fos S, Ferguson L, Trinidad M, Ingolia NT, Cate JHD. eIF3 engages with 3'-UTR termini of highly translated mRNAs in neural progenitor cells. Biorxiv : the Preprint Server For Biology. PMID 37986910 DOI: 10.1101/2023.11.11.566681  0.34
2023 Ferguson L, Upton HE, Pimentel SC, Mok A, Lareau LF, Collins K, Ingolia NT. Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells. Nature Methods. 20: 1704-1715. PMID 37783882 DOI: 10.1038/s41592-023-02028-1  0.401
2023 Reynaud K, McGeachy AM, Noble D, Meacham ZA, Ingolia NT. Surveying the global landscape of post-transcriptional regulators. Nature Structural & Molecular Biology. PMID 37231154 DOI: 10.1038/s41594-023-00999-5  0.394
2023 Diamond PD, McGlincy NJ, Ingolia NT. Dysregulation of amino acid metabolism upon rapid depletion of cap-binding protein eIF4E. Biorxiv : the Preprint Server For Biology. PMID 37214807 DOI: 10.1101/2023.05.11.540079  0.363
2023 Chen M, Kumakura N, Saito H, Muller R, Nishimoto M, Mito M, Gan P, Ingolia NT, Shirasu K, Ito T, Shichino Y, Iwasaki S. A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing plants. Elife. 12. PMID 36852480 DOI: 10.7554/eLife.81302  0.586
2023 Fernandez SG, Ferguson L, Ingolia NT. Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα. Biorxiv : the Preprint Server For Biology. PMID 36711859 DOI: 10.1101/2023.01.16.524343  0.333
2022 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, ... ... Ingolia NT, et al. Standardized annotation of translated open reading frames. Nature Biotechnology. PMID 35831657 DOI: 10.1038/s41587-022-01369-0  0.481
2022 Muller RY, Meacham ZA, Ingolia NT. Plasmid and Sequencing Library Preparation for CRISPRi Barcoded Expression Reporter Sequencing (CiBER-seq) in . Bio-Protocol. 12: e4376. PMID 35530514 DOI: 10.21769/BioProtoc.4376  0.327
2022 Padrón A, Ingolia N. Analyzing the Composition and Organization of Ribonucleoprotein Complexes by APEX-Seq. Methods in Molecular Biology (Clifton, N.J.). 2428: 277-289. PMID 35171486 DOI: 10.1007/978-1-0716-1975-9_17  0.358
2021 Mendez AS, Ly M, González-Sánchez AM, Hartenian E, Ingolia NT, Cate JH, Glaunsinger BA. The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression. Cell Reports. 109841. PMID 34624207 DOI: 10.1016/j.celrep.2021.109841  0.316
2021 Galez HA, Roelants FM, Palm SM, Reynaud KK, Ingolia NT, Thorner J. Phosphorylation of mRNA-Binding Proteins Puf1 and Puf2 by TORC2-Activated Protein Kinase Ypk1 Alleviates Their Repressive Effects. Membranes. 11. PMID 34209236 DOI: 10.3390/membranes11070500  0.337
2020 Chen M, Asanuma M, Takahashi M, Shichino Y, Mito M, Fujiwara K, Saito H, Floor SN, Ingolia NT, Sodeoka M, Dodo K, Ito T, Iwasaki S. Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A. Cell Chemical Biology. PMID 33296667 DOI: 10.1016/j.chembiol.2020.11.008  0.683
2020 Matsuki Y, Matsuo Y, Nakano Y, Iwasaki S, Yoko H, Udagawa T, Li S, Saeki Y, Yoshihisa T, Tanaka K, Ingolia NT, Inada T. Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome. Scientific Reports. 10: 19669. PMID 33184379 DOI: 10.1038/s41598-020-76239-3  0.676
2020 Kim JW, Yin X, Jhaldiyal A, Khan MR, Martin I, Xie Z, Perez-Rosello T, Kumar M, Abalde-Atristain L, Xu J, Chen L, Eacker SM, Surmeier DJ, Ingolia NT, Dawson TM, et al. Defects in mRNA Translation in LRRK2-Mutant hiPSC-Derived Dopaminergic Neurons Lead to Dysregulated Calcium Homeostasis. Cell Stem Cell. PMID 32846140 DOI: 10.1016/J.Stem.2020.08.002  0.328
2019 Padrón A, Iwasaki S, Ingolia NT. Proximity RNA Labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules. Molecular Cell. 75: 875-887.e5. PMID 31442426 DOI: 10.1016/J.Molcel.2019.07.030  0.695
2019 Pulos-Holmes MC, Srole DN, Juarez MG, Lee AS, McSwiggen DT, Ingolia NT, Cate JH. Repression of ferritin light chain translation by human eIF3. Elife. 8. PMID 31414986 DOI: 10.7554/Elife.48193  0.411
2019 McGeachy AM, Meacham ZA, Ingolia NT. An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries. Acs Synthetic Biology. 8: 844-856. PMID 30908907 DOI: 10.1021/Acssynbio.8B00529  0.37
2019 Walczak CP, Leto DE, Zhang L, Riepe C, Muller RY, DaRosa PA, Ingolia NT, Elias JE, Kopito RR. Ribosomal protein RPL26 is the principal target of UFMylation. Proceedings of the National Academy of Sciences of the United States of America. PMID 30626644 DOI: 10.1073/Pnas.1816202116  0.41
2018 Iwasaki S, Iwasaki W, Takahashi M, Sakamoto A, Watanabe C, Shichino Y, Floor SN, Fujiwara K, Mito M, Dodo K, Sodeoka M, Imataka H, Honma T, Fukuzawa K, Ito T, ... Ingolia NT, et al. The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA. Molecular Cell. PMID 30595437 DOI: 10.1016/J.Molcel.2018.11.026  0.702
2018 Ingolia NT, Hussmann JA, Weissman JS. Ribosome Profiling: Global Views of Translation. Cold Spring Harbor Perspectives in Biology. PMID 30037969 DOI: 10.1101/Cshperspect.A032698  0.663
2017 Matsuo Y, Ikeuchi K, Saeki Y, Iwasaki S, Schmidt C, Udagawa T, Sato F, Tsuchiya H, Becker T, Tanaka K, Ingolia NT, Beckmann R, Inada T. Ubiquitination of stalled ribosome triggers ribosome-associated quality control. Nature Communications. 8: 159. PMID 28757607 DOI: 10.1038/S41467-017-00188-1  0.711
2017 Ingolia NT. Tracking the Missing Footprints of Idle Ribosomes. Cell Systems. 4: 583-584. PMID 28662383 DOI: 10.1016/J.Cels.2017.06.008  0.403
2017 McGlincy NJ, Ingolia NT. Transcriptome-wide measurement of translation by ribosome profiling. Methods (San Diego, Calif.). PMID 28579404 DOI: 10.1016/J.Ymeth.2017.05.028  0.481
2017 Iwasaki S, Ingolia NT. The Growing Toolbox for Protein Synthesis Studies. Trends in Biochemical Sciences. PMID 28566214 DOI: 10.1016/J.Tibs.2017.05.004  0.707
2017 Barry KC, Ingolia NT, Vance RE. Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen. Elife. 6. PMID 28383283 DOI: 10.7554/Elife.22707  0.334
2017 Mills EW, Green R, Ingolia NT. Slowed decay of mRNAs enhances platelet specific translation. Blood. PMID 28213379 DOI: 10.1182/Blood-2016-08-736108  0.393
2017 Ishikawa K, Makanae K, Iwasaki S, Ingolia NT, Moriya H. Post-Translational Dosage Compensation Buffers Genetic Perturbations to Stoichiometry of Protein Complexes. Plos Genetics. 13: e1006554. PMID 28121980 DOI: 10.1371/Journal.Pgen.1006554  0.693
2017 Barry KC, Ingolia NT, Vance RE. Author response: Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen Elife. DOI: 10.7554/Elife.22707.022  0.31
2016 Mills EW, Wangen J, Green R, Ingolia NT. Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets. Cell Reports. 17: 1-10. PMID 27681415 DOI: 10.1016/J.Celrep.2016.08.088  0.432
2016 Sen ND, Zhou F, Harris MS, Ingolia NT, Hinnebusch AG. eIF4B stimulates translation of long mRNAs with structured 5' UTRs and low closed-loop potential but weak dependence on eIF4G. Proceedings of the National Academy of Sciences of the United States of America. PMID 27601676 DOI: 10.1073/Pnas.1612398113  0.461
2016 Iwasaki S, Ingolia NT. PROTEIN TRANSLATION. Seeing translation. Science (New York, N.Y.). 352: 1391-2. PMID 27313023 DOI: 10.1126/Science.Aag1039  0.712
2016 Iwasaki S, Floor SN, Ingolia NT. Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature. PMID 27309803 DOI: 10.1038/Nature17978  0.723
2016 Ingolia NT. Ribosome Footprint Profiling of Translation throughout the Genome. Cell. 165: 22-33. PMID 27015305 DOI: 10.1016/J.Cell.2016.02.066  0.524
2016 McGeachy AM, Ingolia NT. Starting too soon: upstream reading frames repress downstream translation. The Embo Journal. PMID 26896443 DOI: 10.15252/Embj.201693946  0.423
2015 Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. Cell Systems. 1: 224-237. PMID 27135913 DOI: 10.1016/J.Cels.2015.08.012  0.781
2015 Stern-Ginossar N, Ingolia NT. Ribosome Profiling as a Tool to Decipher Viral Complexity. Annual Review of Virology. 2: 335-49. PMID 26958919 DOI: 10.1146/Annurev-Virology-100114-054854  0.471
2015 Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS. A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation. Molecular Cell. 60: 816-27. PMID 26638175 DOI: 10.1016/J.Molcel.2015.11.013  0.796
2015 Werner A, Iwasaki S, McGourty CA, Medina-Ruiz S, Teerikorpi N, Fedrigo I, Ingolia NT, Rape M. Cell-fate determination by ubiquitin-dependent regulation of translation. Nature. 525: 523-7. PMID 26399832 DOI: 10.1038/Nature14978  0.666
2015 Sen ND, Zhou F, Ingolia NT, Hinnebusch AG. Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A. Genome Research. 25: 1196-205. PMID 26122911 DOI: 10.1101/Gr.191601.115  0.323
2015 Sidrauski C, McGeachy AM, Ingolia NT, Walter P. The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly. Elife. 4. PMID 25719440 DOI: 10.7554/Elife.05033  0.388
2015 Sen ND, Zhou F, Ingolia NT, Hinnebusch AG. Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A Genome Research. 25: 1196-1205. DOI: 10.1101/gr.191601.115  0.303
2015 Ori A, Toyama BH, Harris MS, Bock T, Iskar M, Bork P, Ingolia NT, Hetzer MW, Beck M. Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats Cell Systems. 1: 224-237. DOI: 10.1016/j.cels.2015.08.012  0.739
2014 Pop C, Rouskin S, Ingolia NT, Han L, Phizicky EM, Weissman JS, Koller D. Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation. Molecular Systems Biology. 10: 770. PMID 25538139 DOI: 10.15252/Msb.20145524  0.784
2014 Yoon JH, De S, Srikantan S, Abdelmohsen K, Grammatikakis I, Kim J, Kim KM, Noh JH, White EJ, Martindale JL, Yang X, Kang MJ, Wood WH, Noren Hooten N, Evans MK, ... ... Ingolia NT, et al. PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nature Communications. 5: 5248. PMID 25366541 DOI: 10.1038/Ncomms6248  0.467
2014 Jensen BC, Ramasamy G, Vasconcelos EJ, Ingolia NT, Myler PJ, Parsons M. Extensive stage-regulation of translation revealed by ribosome profiling of Trypanosoma brucei. Bmc Genomics. 15: 911. PMID 25331479 DOI: 10.1186/1471-2164-15-911  0.474
2014 Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Reports. 8: 1365-79. PMID 25159147 DOI: 10.1016/J.Celrep.2014.07.045  0.623
2014 Castañeda J, Genzor P, van der Heijden GW, Sarkeshik A, Yates JR, Ingolia NT, Bortvin A. Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. The Embo Journal. 33: 1999-2019. PMID 25063675 DOI: 10.15252/Embj.201386855  0.456
2014 Brubaker SW, Gauthier AE, Mills EW, Ingolia NT, Kagan JC. A bicistronic MAVS transcript highlights a class of truncated variants in antiviral immunity. Cell. 156: 800-11. PMID 24529381 DOI: 10.1016/J.Cell.2014.01.021  0.456
2014 Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nature Reviews. Genetics. 15: 205-13. PMID 24468696 DOI: 10.1038/Nrg3645  0.482
2013 Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR, Hetzer MW. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell. 154: 971-82. PMID 23993091 DOI: 10.1016/J.Cell.2013.07.037  0.765
2013 Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Genome-wide annotation and quantitation of translation by ribosome profiling. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. Unit 4.18. PMID 23821443 DOI: 10.1002/0471142727.Mb0418S103  0.8
2013 Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell. 154: 240-51. PMID 23810193 DOI: 10.1016/J.Cell.2013.06.009  0.628
2013 Thorburn RR, Gonzalez C, Brar GA, Christen S, Carlile TM, Ingolia NT, Sauer U, Weissman JS, Amon A. Aneuploid yeast strains exhibit defects in cell growth and passage through START. Molecular Biology of the Cell. 24: 1274-89. PMID 23468524 DOI: 10.1091/Mbc.E12-07-0520  0.463
2013 Yang WR, Mills EW, Rodic N, Ingolia NT, Boeke JD, Levitsky HI, Burns KH. What transposable elements are differentially translated in lung cancer? Journal For Immunotherapy of Cancer. 1. DOI: 10.1186/2051-1426-1-S1-P139  0.359
2012 Stern-Ginossar N, Weisburd B, Michalski A, Le VT, Hein MY, Huang SX, Ma M, Shen B, Qian SB, Hengel H, Mann M, Ingolia NT, Weissman JS. Decoding human cytomegalovirus. Science (New York, N.Y.). 338: 1088-93. PMID 23180859 DOI: 10.1126/Science.1227919  0.607
2012 Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments. Nature Protocols. 7: 1534-50. PMID 22836135 DOI: 10.1038/Nprot.2012.086  0.801
2012 Michel AM, Choudhury KR, Firth AE, Ingolia NT, Atkins JF, Baranov PV. Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Research. 22: 2219-29. PMID 22593554 DOI: 10.1101/Gr.133249.111  0.401
2012 Hsieh AC, Liu Y, Edlind MP, Ingolia NT, Janes MR, Sher A, Shi EY, Stumpf CR, Christensen C, Bonham MJ, Wang S, Ren P, Martin M, Jessen K, Feldman ME, et al. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature. 485: 55-61. PMID 22367541 DOI: 10.1038/Nature10912  0.518
2012 Brar GA, Yassour M, Friedman N, Regev A, Ingolia NT, Weissman JS. High-resolution view of the yeast meiotic program revealed by ribosome profiling. Science (New York, N.Y.). 335: 552-7. PMID 22194413 DOI: 10.1126/Science.1215110  0.647
2011 Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 147: 789-802. PMID 22056041 DOI: 10.1016/J.Cell.2011.10.002  0.659
2011 Gracheva EO, Cordero-Morales JF, González-Carcacía JA, Ingolia NT, Manno C, Aranguren CI, Weissman JS, Julius D. Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats. Nature. 476: 88-91. PMID 21814281 DOI: 10.1038/Nature10245  0.468
2011 Ingolia N. Many paths to the same end: histone transcripts recruit canonical initiation factors through unconventional interactions. Molecular Cell. 41: 133-5. PMID 21255723 DOI: 10.1016/J.Molcel.2011.01.004  0.362
2011 Takacs JE, Neary TB, Ingolia NT, Saini AK, Martin-Marcos P, Pelletier J, Hinnebusch AG, Lorsch JR. Identification of compounds that decrease the fidelity of start codon recognition by the eukaryotic translational machinery. Rna (New York, N.Y.). 17: 439-52. PMID 21220547 DOI: 10.1261/Rna.2475211  0.366
2010 Ingolia NT. Genome-wide translational profiling by ribosome footprinting. Methods in Enzymology. 470: 119-42. PMID 20946809 DOI: 10.1016/S0076-6879(10)70006-9  0.524
2010 Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature. 466: 835-40. PMID 20703300 DOI: 10.1038/Nature09267  0.586
2010 Gracheva EO, Ingolia NT, Kelly YM, Cordero-Morales JF, Hollopeter G, Chesler AT, Sánchez EE, Perez JC, Weissman JS, Julius D. Molecular basis of infrared detection by snakes. Nature. 464: 1006-11. PMID 20228791 DOI: 10.1038/Nature08943  0.456
2009 Bassik MC, Lebbink RJ, Churchman LS, Ingolia NT, Patena W, LeProust EM, Schuldiner M, Weissman JS, McManus MT. Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nature Methods. 6: 443-5. PMID 19448642 DOI: 10.1038/Nmeth.1330  0.766
2009 Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science (New York, N.Y.). 324: 218-23. PMID 19213877 DOI: 10.1126/Science.1168978  0.765
2008 Ingolia NT, Weissman JS. Systems biology: Reverse engineering the cell. Nature. 454: 1059-62. PMID 18756243 DOI: 10.1038/4541059A  0.465
2007 Ingolia NT, Murray AW. Positive-feedback loops as a flexible biological module. Current Biology : Cb. 17: 668-77. PMID 17398098 DOI: 10.1016/J.Cub.2007.03.016  0.47
2004 Ingolia NT, Murray AW. The ups and downs of modeling the cell cycle. Current Biology : Cb. 14: R771-7. PMID 15380091 DOI: 10.1016/J.Cub.2004.09.018  0.462
2002 Ingolia NT, Murray AW. Signal transduction. History matters. Science (New York, N.Y.). 297: 948-9. PMID 12169717 DOI: 10.1126/Science.1075222  0.41
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