Research Publications

Iwasaki S, Floor SN, Ingolia NT. Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor. Nature 534 (2016).
Newman ZR, Young JM, Ingolia NT, Barton GM. Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9. Proceedings of the National Academy of Sciences of the United States of America 113: E1362-71 (2016).
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 (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 (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 (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 (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 (2015).
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 (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 3rd, Noren Hooten N, Evans MK, Becker KG, Tripathi V, Prasanth KV, Wilson GM, Tuschl T, Ingolia NT, Hafner M, Gorospe M. PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nature communications 5: 5248 (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 (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 (2014).
Castañeda J, Genzor P, van der Heijden GW, Sarkeshik A, Yates JR 3rd, Ingolia NT, Bortvin A. Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. The EMBO journal 33: 1999 (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 (2014).
Toyama BH, Savas JN, Park SK, Harris MS, Ingolia NT, Yates JR 3rd, Hetzer MW. Identification of long-lived proteins reveals exceptional stability of essential cellular structures. Cell 154: 971 (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 (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. Mol Biol Cell 24: 1274 (2013).
Nakatsu F, Baskin JM, Chung J, Tanner LB, Shui G, Lee SY, Pirruccello M, Hao M, Ingolia NT, Wenk MR, De Camilli P. PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity. J Cell Biol 199: 1003 (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 338: 1088 (2012).
Michel AM, Roy Choudhury K, Firth AE, Ingolia NT, Atkins JF, Baranov PV. Observation of dually decoded regions of the human genome using ribosome profiling data. Genome Res 22: 2219 (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, Weissman JS, Shokat KM, Rommel C, Ruggero D. The translational landscape of mTOR signalling steers cancer initiation and metastasis. Nature 485: 55 (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 335: 552 (2012).
Ingolia NT, Lareau LF, Weissman JS. Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes. Cell 147: 789 (2011).
Gracheva EO, Cordero-Morales JF, Gonzalez-Carcacia 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 (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 17: 439 (2011).
Guo H, Ingolia NT, Weissman JS, Bartel DP. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 466: 835 (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 (2010).
Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218 (2009).
Ingolia NT, Murray AW. Positive-feedback loops as a flexible biological module. Curr Biol. 17: 668 (2007).
Ingolia NT. Topology and robustness in the Drosophila segment polarity network. PLoS Biol. 2: e123 (2004).

Methodology

Ingolia NT, Brar GA, Rouskin S, McGeachy AM, Weissman JS. Genome-wide annotation and quantitation of translation by ribosome profiling. Curr Protoc Mol Biol (2013).
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. Nat Protoc 7: 1534 (2012).
Ingolia NT. Genome-wide translational profiling by ribosome footprinting. Methods Enzymol 470: 119 (2010).

Reviews

Ingolia NT. Ribosome Footprint Profiling of Translation throughout the Genome. Cell 165: 22-33 (2016).
Stern-Ginossar N, Ingolia NT. Ribosome Profiling as a Tool to Decipher Viral Complexity. Annual review of virology 2: 335-49 (2015).
Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nature reviews. Genetics 15: 205 (2014).
Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet, advance online (2014).
Ingolia NT, Murray AW. The ups and downs of modeling the cell cycle. Curr Biol. 14: R771 (2004).

Commentary

Iwasaki S, Ingolia NT. Seeing translation. Nature 352: 1391-1392 (2016).
McGeachy AM, Ingolia NT. Starting too soon: upstream reading frames repress downstream translation. The EMBO journal 35: 699-700 (2016).
Ingolia NT. Many Paths to the Same End: Histone Transcripts Recruit Canonical Initiation Factors through Unconventional Interactions. Mol Cell 41: 133 (2011).
Fordyce P, Ingolia N. Integrating systems biology data to yield functional genomics insights. Genome Biology 12: 302 (2011).
Ingolia NT, Weissman JS. Systems biology: Reverse engineering the cell. Nature 454: 1059 (2008).
Ingolia NT, Murray AW. Signal transduction. History matters. Science 297: 948 (2002).