Nicholas T. Ingolia

发表

An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries

Anna M. McGeachy, Zuriah A. Meacham, Nicholas T. Ingolia, 2018, bioRxiv.

Mammalian microRNAs predominantly act to decrease target mRNA levels

Nicholas T. Ingolia, D. Bartel, J. Weissman, 2010, Nature.

Systems biology: Reverse engineering the cell

Nicholas T. Ingolia, J. Weissman, 2008, Nature.

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments

Anna M. McGeachy, Nicholas T. Ingolia, J. Weissman, 2012, Nature Protocols.

Ribosome Profiling of Mouse Embryonic Stem Cells Reveals the Complexity and Dynamics of Mammalian Proteomes

Nicholas T. Ingolia, J. Weissman, L. F. Lareau, 2011, Cell.

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

Nicholas T. Ingolia, S. Ghaemmaghami, J. Weissman, 2009, Science.

Positive-Feedback Loops as a Flexible Biological Module

Nicholas T. Ingolia, A. Murray, A. Murray, 2007, Current Biology.

Ribosome profiling: new views of translation, from single codons to genome scale

Nicholas T. Ingolia, 2014, Nature Reviews Genetics.

Ribosome Footprint Profiling of Translation throughout the Genome

Nicholas T. Ingolia, 2016, Cell.

Observation of dually decoded regions of the human genome using ribosome profiling data

Audrey M. Michel, Nicholas T. Ingolia, J. F. Atkins, 2012, Genome research.

High-Resolution View of the Yeast Meiotic Program Revealed by Ribosome Profiling

Nicholas T. Ingolia, N. Friedman, M. Yassour, 2011, Science.

The translational landscape of mTOR signalling steers cancer initiation and metastasis

Nicholas T. Ingolia, J. Weissman, K. Shokat, 2012, Nature.

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

Nicholas T. Ingolia, E. Lander, J. Weissman, 2013, Cell.

Genome-wide annotation and quantitation of translation by ribosome profiling.

Nicholas T Ingolia, Anna M. McGeachy, Nicholas T. Ingolia, 2013, Current protocols in molecular biology.

The Growing Toolbox for Protein Synthesis Studies.

Nicholas T. Ingolia, Shintaro Iwasaki, 2017, Trends in biochemical sciences.

Transcriptome-wide measurement of translation by ribosome profiling.

Nicholas T Ingolia, Nicholas J. McGlincy, Nicholas T. Ingolia, 2017, Methods.

Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.

Nicholas T Ingolia, Nicholas T. Ingolia, Michael S Harris, 2014, Cell reports.

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation.

Aviv Regev, Nir Hacohen, Marko Jovanovic, 2015, Molecular cell.

Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation

Daphne Koller, Nicholas T Ingolia, Nicholas T. Ingolia, 2014, Molecular systems biology.

Identification of Long-Lived Proteins Reveals Exceptional Stability of Essential Cellular Structures

John R. Yates, Jeffrey N. Savas, Nicholas T. Ingolia, 2013, Cell.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Peer Bork, Martin Beck, Murat Iskar, 2015, Cell systems.

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

Kotb Abdelmohsen, Myriam Gorospe, Supriyo De, 2014, Nature Communications.

History Matters

Andrew W. Murray, Nicholas T. Ingolia, A. Murray, 2002, Science.

The Ups and Downs of Modeling the Cell Cycle

Andrew W. Murray, Nicholas T. Ingolia, A. Murray, 2004, Current Biology.

A burst in T cell receptor translation mediated by eIF3 interactions with T cell receptor mRNAs

Nicholas T. Ingolia, J. Cate, A. Marson, 2019, bioRxiv.

Double stranded DNA breaks and genome editing trigger loss of ribosomal protein RPS27A

Zuriah A. Meacham, Nicholas T. Ingolia, J. Corn, 2021, The FEBS journal.

squirrels and relation with mitochondrial proton leak Regulation of UCP1 and UCP3 in arctic ground

Nicholas T. Ingolia, L. Halsey, Y. Handrich, 2006 .

Molecular recording of calcium signaling via calcium-dependent protein proximity labeling

Nicholas T. Ingolia, Y. Jan, T. Dawson, 2022, bioRxiv.

The N-terminal and central domains of CoV-2 nsp1 play key functional roles in suppression of cellular gene expression and preservation of viral gene expression

Nicholas T. Ingolia, J. Cate, E. Hartenian, 2021, bioRxiv.

Standardized annotation of translated open reading frames

Jonathan M. Mudge, Nicholas T. Ingolia, A. Frankish, 2022, Nature Biotechnology.

A parasitic fungus employs mutated eIF4A to survive on rocaglate-synthesizing Aglaia plants

Nicholas T. Ingolia, K. Shirasu, P. Gan, 2022, bioRxiv.

Topology robustness in the segment polarity network.

Nicholas T. Ingolia, 2004 .

Ribosomal protein S7 ubiquitination during ER stress in yeast is associated with selective mRNA translation and stress outcome

Nicholas T. Ingolia, T. Inada, Y. Saeki, 2020, Scientific Reports.

Decoding Human Cytomegalovirus

Marco Y. Hein, Nicholas T. Ingolia, B. Shen, 2012, Science.

Signal transduction. History matters.

Nicholas T. Ingolia, A. Murray, 2002, Science.

Ribosome Profiling as a Tool to Decipher Viral Complexity.

Nicholas T. Ingolia, Noam Stern-Ginossar, 2015, Annual review of virology.

Ganglion-specific splicing of TRPV1 underlies infrared sensation in vampire bats

Nicholas T. Ingolia, J. Weissman, D. Julius, 2011, Nature.

Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice

Nicholas T. Ingolia, J. Yates, Pavol Genzor, 2014, The EMBO journal.

Ribosomal protein RPL26 is the principal target of UFMylation

Joshua E. Elias, Nicholas T. Ingolia, J. Elias, 2019, Proceedings of the National Academy of Sciences.

Ubiquitination of stalled ribosome triggers ribosome-associated quality control

Nicholas T. Ingolia, T. Inada, Y. Saeki, 2017, Nature Communications.

Dynamic Regulation of a Ribosome Rescue Pathway in Erythroid Cells and Platelets.

Nicholas T. Ingolia, R. Green, J. Wangen, 2016, Cell reports.

The Translation Inhibitor Rocaglamide Targets a Bimolecular Cavity between eIF4A and Polypurine RNA.

Shintaro Iwasaki, Kaori Fukuzawa, Nicholas T Ingolia, 2019, Molecular cell.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

Jonathan M. Mudge, Nicholas T. Ingolia, M. Gerstein, 2021, bioRxiv.

eIF4B stimulates translation of long mRNAs with structured 5′ UTRs and low closed-loop potential but weak dependence on eIF4G

Nicholas T. Ingolia, A. Hinnebusch, Fujun Zhou, 2016, Proceedings of the National Academy of Sciences.

Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A

Nicholas T. Ingolia, A. Hinnebusch, Fujun Zhou, 2015, Genome research.

Topology and Robustness in the Drosophila Segment Polarity Network

Nicholas T Ingolia, Nicholas T. Ingolia, 2004, PLoS biology.

PTEN Is a Potent Suppressor of Small Cell Lung Cancer

Nicholas T. Ingolia, D. MacPherson, A. Nikitin, 2014, Molecular Cancer Research.

Extensive stage-regulation of translation revealed by ribosome profiling of Trypanosoma brucei

Nicholas T. Ingolia, P. Myler, M. Parsons, 2014, BMC Genomics.

Defects in mRNA Translation in LRRK2-Mutant hiPSC-Derived Dopaminergic Neurons Lead to Dysregulated Calcium Homeostasis.

Nicholas T. Ingolia, D. Surmeier, I. Martin, 2020, Cell stem cell.

Starting too soon: upstream reading frames repress downstream translation

Anna M. McGeachy, Nicholas T. Ingolia, 2016, EMBO Journal.

The small molecule ISRIB reverses the effects of eIF2α phosphorylation on translation and stress granule assembly

Anna M. McGeachy, Nicholas T. Ingolia, P. Walter, 2015, eLife.

Surveying the global landscape of post-transcriptional regulators

Anna M. McGeachy, Zuriah A. Meacham, Nicholas T. Ingolia, 2021, bioRxiv.

MYC-Driven Small-Cell Lung Cancer is Metabolically Distinct and Vulnerable to Arginine Depletion

Nicholas T. Ingolia, Kristofer C. Berrett, R. Deberardinis, 2019, Clinical Cancer Research.

Rapid Creation and Quantitative Monitoring of High Coverage shRNA Libraries

Michael T. McManus, Nicholas T. Ingolia, J. Weissman, 2009, Nature Methods.

Ribosome rescue factor PELOTA modulates translation start site choice and protein isoform levels of transcription factor C/EBPα

Nicholas T. Ingolia, Lucas Ferguson, Samantha G. Fernandez, 2023, bioRxiv.

Repression of ferritin light chain translation by human eIF3

Nicholas T. Ingolia, J. Cate, A. S. Lee, 2019, eLife.

Orthogonal regulation of ferritin translation by human eIF3 and the iron response proteins

Nicholas T. Ingolia, J. Cate, D. McSwiggen, 2018, bioRxiv.

Ribosome Profiling: Global Views of Translation.

Jeffrey A. Hussmann, Nicholas T. Ingolia, J. Weissman, 2018, Cold Spring Harbor perspectives in biology.

Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability in cancer

Nicholas T. Ingolia, J. Olzmann, S. Dixon, 2022, bioRxiv.

Slowed decay of mRNAs enhances platelet specific translation.

Nicholas T. Ingolia, R. Green, Eric W. Mills, 2017, Blood.

Low-bias ncRNA libraries using ordered two-template relay: Serial template jumping by a modified retroelement reverse transcriptase

Nicholas T. Ingolia, R. Schekman, K. Collins, 2021, Proceedings of the National Academy of Sciences.

Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9

Nicholas T. Ingolia, Janet M. Young, G. Barton, 2016, Proceedings of the National Academy of Sciences.

Cell fate determination by ubiquitin-dependent regulation of translation

Nicholas T. Ingolia, M. Rapé, Shintaro Iwasaki, 2015, Nature.

A genome-scale CRISPR interference guide library enables comprehensive phenotypic profiling in yeast

Nicholas J. McGlincy, Zuriah A. Meacham, Nicholas T. Ingolia, 2020, bioRxiv.

Current Protocols in Molecular Biology BASIC PROTOCOL RIBOSOME PROFILING IN CULTURED MAMMALIAN CELLS

Anna M. McGeachy, Nicholas T. Ingolia, J. Weissman, 2013 .

Double Stranded DNA Breaks and Genome Editing Trigger Ribosome Remodeling and Translational Shutdown

Zuriah A. Meacham, Nicholas T. Ingolia, S. Wyman, 2018 .

Proximity RNA labeling by APEX-Seq Reveals the Organization of Translation Initiation Complexes and Repressive RNA Granules

Nicholas T. Ingolia, Shintaro Iwasaki, Alejandro Padrón, 2018, bioRxiv.

Dysregulated mRNA Translation in the G2019S LRRK2 and LRRK2 Knock-Out Mouse Brains

Nicholas T. Ingolia, I. Martin, T. Dawson, 2021, eNeuro.

Ribosome Profiling Analysis of In Vivo Translation

Nicholas T. Ingolia, 2014 .

Ubiquitination of stalled ribosome triggers ribosome-associated quality control

Nicholas T. Ingolia, T. Inada, Y. Saeki, 2017, Nature Communications.

Post-Translational Dosage Compensation Buffers Genetic Perturbations to Stoichiometry of Protein Complexes

Nicholas T. Ingolia, H. Moriya, Shintaro Iwasaki, 2017, PLoS genetics.

Genome-wide translational profiling by ribosome footprinting.

Nicholas T Ingolia, Nicholas T. Ingolia, 2010, Methods in enzymology.

Experience-dependent translational state defined by cell type-specific ribosome profiling

Nicholas T. Ingolia, P. Greengard, T. Dawson, 2017, bioRxiv.

Aneuploid yeast strains exhibit defects in cell growth and passage through START

Nicholas T. Ingolia, U. Sauer, J. Weissman, 2013, Molecular biology of the cell.

Neuronal UCP1 expression suggests a mechanism for local thermogenesis during hibernation

Nicholas T. Ingolia, G. Shulman, Elena O. Gracheva, 2015, Proceedings of the National Academy of Sciences.

Streamlined and sensitive mono- and diribosome profiling in yeast and human cells

Nicholas T. Ingolia, K. Collins, A. Mok, 2023, bioRxiv.

A methodology for discovering novel brain-relevant peptides: Combination of ribosome profiling and peptidomics

Nicholas T. Ingolia, R. Cole, C. Ubaida-Mohien, 2020, Neuroscience Research.

A Bicistronic MAVS Transcript Highlights a Class of Truncated Variants in Antiviral Immunity

Nicholas T. Ingolia, Sky W. Brubaker, Jonathan C. Kagan, 2014, Cell.

Dual targeting of DDX3 and eIF4A by the translation inhibitor rocaglamide A.

Nicholas T. Ingolia, M. Sodeoka, S. Floor, 2020, Cell chemical biology.

Tracking the Missing Footprints of Idle Ribosomes.

Nicholas T. Ingolia, 2017, Cell systems.

Rocaglates convert DEAD-box protein eIF4A into a sequence-selective translational repressor

Nicholas T. Ingolia, S. Floor, Shintaro Iwasaki, 2016, Nature.

Phosphorylation of mRNA-Binding Proteins Puf1 and Puf2 by TORC2-Activated Protein Kinase Ypk1 Alleviates Their Repressive Effects

Nicholas T. Ingolia, J. Thorner, F. Roelants, 2021, Membranes.

CiBER-seq dissects genetic networks by quantitative CRISPRi profiling of expression phenotypes

Zuriah A. Meacham, Nicholas T. Ingolia, Lucas Ferguson, 2020, Science.

The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression

Nicholas T. Ingolia, J. Cate, E. Hartenian, 2021, Cell Reports.

PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity

Sang Yoon Lee, Nicholas T. Ingolia, P. De Camilli, 2012, The Journal of cell biology.

PtdIns4P synthesis by PI4KIIIα at the plasma membrane and its impact on plasma membrane identity

Sang Yoon Lee, Nicholas T. Ingolia, P. De Camilli, 2012, Journal of Cell Biology.

Robust T cell activation requires an eIF3-driven burst in T cell receptor translation

Jamie H. D. Cate, Nicholas T. Ingolia, A. Marson, 2021, bioRxiv.

Dynamic post-transcriptional regulation by Mrn1 links cell wall homeostasis to mitochondrial structure and function

Nicholas T. Ingolia, M. Brothers, Michael Ly, 2021, PLoS genetics.

Analyzing the Composition and Organization of Ribonucleoprotein Complexes by APEX-Seq.

Nicholas T. Ingolia, Alejandro Padrón, 2022, Methods in molecular biology.

Identification of compounds that decrease the fidelity of start codon recognition by the eukaryotic translational machinery.

Nicholas T. Ingolia, A. Hinnebusch, J. Pelletier, 2011, RNA.

An Accessible Continuous-Culture Turbidostat for Pooled Analysis of Complex Libraries.

Nicholas T Ingolia, Anna M. McGeachy, Zuriah A. Meacham, 2019, ACS synthetic biology.

Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen

Nicholas T. Ingolia, R. Vance, Kevin C. Barry, 2017, eLife.

Seeing translation

Nicholas T. Ingolia, Shintaro Iwasaki, 2016, Science.

Molecular recording of calcium concentration via calcium-dependent protein proximity labeling

Nicholas T. Ingolia, Y. Jan, Helen S. Bateup, 2023, bioRxiv.

Dysregulation of amino acid metabolism upon rapid depletion of cap-binding protein eIF4E

Nicholas J. McGlincy, Nicholas T. Ingolia, Paige D. Diamond, 2023, bioRxiv.

A specific eIF4A paralog facilitates LARP1-mediated translation repression during mTORC1 inhibition

Nicholas T. Ingolia, Shintaro Iwasaki, Takuhiro Ito, 2021, bioRxiv.

Cell Cycle: Bistability Is Needed for Robust Cycling

Nicholas T. Ingolia, 2005, Current Biology.

Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.

Sarah E. Jackson, Nicholas T. Ingolia, J. Weissman, 2014, Cell reports.

Ribosome stalling during selenoprotein translation exposes a ferroptosis vulnerability

Nicholas T. Ingolia, S. Dixon, M. Bassik, 2022, Nature Chemical Biology.

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

Nicholas T. Ingolia, P. Bork, M. Hetzer, 2015, Cell systems.

PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity

Nicholas T. Ingolia, S. Srikantan, G. M. Wilson, 2014, Nature Communications.

Differences in codon bias and GC content contribute to the balanced expression of TLR7 and TLR9

Nicholas T. Ingolia, Janet M. Young, G. Barton, 2016, Proceedings of the National Academy of Sciences.

Dbp1 is a low performance paralog of RNA helicase Ded1 that drives impaired translation and heat stress response

Nicholas T. Ingolia, G. Brar, E. N. Powers, 2024, bioRxiv.

Formaldehyde regulates S-adenosylmethionine biosynthesis and one-carbon metabolism

Nicholas T. Ingolia, M. Esteller, Carl C. Ward, 2023, Science.

Cancer-associated mRNAs regulated by the Helix-Loop-Helix motif of human EIF3A By Marina Volegova A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division

Nicholas T. Ingolia, A. Lapinaite, N. Lintner, 2018 .