A citation-based method for searching scientific literature

Nicholas T Ingolia, Liana F Lareau, Jonathan S Weissman. Cell 2011
Times Cited: 1325







List of co-cited articles
1098 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity


Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.
Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
54

Global mapping of translation initiation sites in mammalian cells at single-nucleotide resolution.
Sooncheol Lee, Botao Liu, Soohyun Lee, Sheng-Xiong Huang, Ben Shen, Shu-Bing Qian. Proc Natl Acad Sci U S A 2012
370
25

Pervasive functional translation of noncanonical human open reading frames.
Jin Chen, Andreas-David Brunner, J Zachery Cogan, James K Nuñez, Alexander P Fields, Britt Adamson, Daniel N Itzhak, Jason Y Li, Matthias Mann, Manuel D Leonetti,[...]. Science 2020
171
20

The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.
Nicholas T Ingolia, Gloria A Brar, Silvia Rouskin, Anna M McGeachy, Jonathan S Weissman. Nat Protoc 2012
663
17

A micropeptide encoded by a putative long noncoding RNA regulates muscle performance.
Douglas M Anderson, Kelly M Anderson, Chi-Lun Chang, Catherine A Makarewich, Benjamin R Nelson, John R McAnally, Prasad Kasaragod, John M Shelton, Jen Liou, Rhonda Bassel-Duby,[...]. Cell 2015
648
16

Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation.
Ariel A Bazzini, Timothy G Johnstone, Romain Christiano, Sebastian D Mackowiak, Benedikt Obermayer, Elizabeth S Fleming, Charles E Vejnar, Miler T Lee, Nikolaus Rajewsky, Tobias C Walther,[...]. EMBO J 2014
386
15

A Peptide Encoded by a Putative lncRNA HOXB-AS3 Suppresses Colon Cancer Growth.
Jin-Zhou Huang, Min Chen, De Chen, Xing-Cheng Gao, Song Zhu, Hongyang Huang, Min Hu, Huifang Zhu, Guang-Rong Yan. Mol Cell 2017
290
14

The Translational Landscape of the Human Heart.
Sebastiaan van Heesch, Franziska Witte, Valentin Schneider-Lunitz, Jana F Schulz, Eleonora Adami, Allison B Faber, Marieluise Kirchner, Henrike Maatz, Susanne Blachut, Clara-Louisa Sandmann,[...]. Cell 2019
203
14

Transcriptome-wide measurement of translation by ribosome profiling.
Nicholas J McGlincy, Nicholas T Ingolia. Methods 2017
176
13

Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes.
Nicholas T Ingolia, Gloria A Brar, Noam Stern-Ginossar, Michael S Harris, Gaëlle J S Talhouarne, Sarah E Jackson, Mark R Wills, Jonathan S Weissman. Cell Rep 2014
377
13

Non-AUG translation: a new start for protein synthesis in eukaryotes.
Michael G Kearse, Jeremy E Wilusz. Genes Dev 2017
159
12

A human microprotein that interacts with the mRNA decapping complex.
Nadia G D'Lima, Jiao Ma, Lauren Winkler, Qian Chu, Ken H Loh, Elizabeth O Corpuz, Bogdan A Budnik, Jens Lykke-Andersen, Alan Saghatelian, Sarah A Slavoff. Nat Chem Biol 2017
129
12

Translational control by 5'-untranslated regions of eukaryotic mRNAs.
Alan G Hinnebusch, Ivaylo P Ivanov, Nahum Sonenberg. Science 2016
475
11

Peptidomic discovery of short open reading frame-encoded peptides in human cells.
Sarah A Slavoff, Andrew J Mitchell, Adam G Schwaid, Moran N Cabili, Jiao Ma, Joshua Z Levin, Amir D Karger, Bogdan A Budnik, John L Rinn, Alan Saghatelian. Nat Chem Biol 2013
361
11

Quantitative profiling of initiating ribosomes in vivo.
Xiangwei Gao, Ji Wan, Botao Liu, Ming Ma, Ben Shen, Shu-Bing Qian. Nat Methods 2015
138
11

A Regression-Based Analysis of Ribosome-Profiling Data Reveals a Conserved Complexity to Mammalian Translation.
Alexander P Fields, Edwin H Rodriguez, Marko Jovanovic, Noam Stern-Ginossar, Brian J Haas, Philipp Mertins, Raktima Raychowdhury, Nir Hacohen, Steven A Carr, Nicholas T Ingolia,[...]. Mol Cell 2015
123
11

STAR: ultrafast universal RNA-seq aligner.
Alexander Dobin, Carrie A Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, Thomas R Gingeras. Bioinformatics 2013
11

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans.
Sarah E Calvo, David J Pagliarini, Vamsi K Mootha. Proc Natl Acad Sci U S A 2009
513
11

Translation inhibitors cause abnormalities in ribosome profiling experiments.
Maxim V Gerashchenko, Vadim N Gladyshev. Nucleic Acids Res 2014
173
10

mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide.
Akinobu Matsumoto, Alessandra Pasut, Masaki Matsumoto, Riu Yamashita, Jacqueline Fung, Emanuele Monteleone, Alan Saghatelian, Keiichi I Nakayama, John G Clohessy, Pier Paolo Pandolfi. Nature 2017
310
10

A human short open reading frame (sORF)-encoded polypeptide that stimulates DNA end joining.
Sarah A Slavoff, Jinho Heo, Bogdan A Budnik, Leslyn A Hanakahi, Alan Saghatelian. J Biol Chem 2014
89
11

High-resolution view of the yeast meiotic program revealed by ribosome profiling.
Gloria A Brar, Moran Yassour, Nir Friedman, Aviv Regev, Nicholas T Ingolia, Jonathan S Weissman. Science 2012
348
10

A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle.
Benjamin R Nelson, Catherine A Makarewich, Douglas M Anderson, Benjamin R Winders, Constantine D Troupes, Fenfen Wu, Austin L Reese, John R McAnally, Xiongwen Chen, Ege T Kavalali,[...]. Science 2016
401
10


An update on sORFs.org: a repository of small ORFs identified by ribosome profiling.
Volodimir Olexiouk, Wim Van Criekinge, Gerben Menschaert. Nucleic Acids Res 2018
77
11

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq.
Julie L Aspden, Ying Chen Eyre-Walker, Rose J Phillips, Unum Amin, Muhammad Ali S Mumtaz, Michele Brocard, Juan-Pablo Couso. Elife 2014
182
9

Detecting actively translated open reading frames in ribosome profiling data.
Lorenzo Calviello, Neelanjan Mukherjee, Emanuel Wyler, Henrik Zauber, Antje Hirsekorn, Matthias Selbach, Markus Landthaler, Benedikt Obermayer, Uwe Ohler. Nat Methods 2016
203
9

Translation from unconventional 5' start sites drives tumour initiation.
Ataman Sendoel, Joshua G Dunn, Edwin H Rodriguez, Shruti Naik, Nicholas C Gomez, Brian Hurwitz, John Levorse, Brian D Dill, Daniel Schramek, Henrik Molina,[...]. Nature 2017
175
9

Emerging evidence for functional peptides encoded by short open reading frames.
Shea J Andrews, Joseph A Rothnagel. Nat Rev Genet 2014
318
9

Dynamics of ribosome scanning and recycling revealed by translation complex profiling.
Stuart K Archer, Nikolay E Shirokikh, Traude H Beilharz, Thomas Preiss. Nature 2016
115
8

Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments.
Liana F Lareau, Dustin H Hite, Gregory J Hogan, Patrick O Brown. Elife 2014
178
8

OpenProt: a more comprehensive guide to explore eukaryotic coding potential and proteomes.
Marie A Brunet, Mylène Brunelle, Jean-François Lucier, Vivian Delcourt, Maxime Levesque, Frédéric Grenier, Sondos Samandi, Sébastien Leblanc, Jean-David Aguilar, Pascal Dufour,[...]. Nucleic Acids Res 2019
47
17

Reinitiation involving upstream ORFs regulates ATF4 mRNA translation in mammalian cells.
Krishna M Vattem, Ronald C Wek. Proc Natl Acad Sci U S A 2004
8

Genome-wide identification and differential analysis of translational initiation.
Peng Zhang, Dandan He, Yi Xu, Jiakai Hou, Bih-Fang Pan, Yunfei Wang, Tao Liu, Christel M Davis, Erik A Ehli, Lin Tan,[...]. Nat Commun 2017
49
16

Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins.
Mitchell Guttman, Pamela Russell, Nicholas T Ingolia, Jonathan S Weissman, Eric S Lander. Cell 2013
482
8

Ribosome profiling reveals the what, when, where and how of protein synthesis.
Gloria A Brar, Jonathan S Weissman. Nat Rev Mol Cell Biol 2015
224
8

Improved Ribo-seq enables identification of cryptic translation events.
Florian Erhard, Anne Halenius, Cosima Zimmermann, Anne L'Hernault, Daniel J Kowalewski, Michael P Weekes, Stefan Stevanovic, Ralf Zimmer, Lars Dölken. Nat Methods 2018
73
10

Leucine-tRNA initiates at CUG start codons for protein synthesis and presentation by MHC class I.
Shelley R Starck, Vivian Jiang, Mariana Pavon-Eternod, Sharanya Prasad, Brian McCarthy, Tao Pan, Nilabh Shastri. Science 2012
143
8

Integrated proteogenomic deep sequencing and analytics accurately identify non-canonical peptides in tumor immunopeptidomes.
Chloe Chong, Markus Müller, HuiSong Pak, Dermot Harnett, Florian Huber, Delphine Grun, Marion Leleu, Aymeric Auger, Marion Arnaud, Brian J Stevenson,[...]. Nat Commun 2020
78
10


Translation from the 5' untranslated region shapes the integrated stress response.
Shelley R Starck, Jordan C Tsai, Keling Chen, Michael Shodiya, Lei Wang, Kinnosuke Yahiro, Manuela Martins-Green, Nilabh Shastri, Peter Walter. Science 2016
198
8


The mechanism of eukaryotic translation initiation and principles of its regulation.
Richard J Jackson, Christopher U T Hellen, Tatyana V Pestova. Nat Rev Mol Cell Biol 2010
7

A unifying model for mTORC1-mediated regulation of mRNA translation.
Carson C Thoreen, Lynne Chantranupong, Heather R Keys, Tim Wang, Nathanael S Gray, David M Sabatini. Nature 2012
907
7

Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate.
Colin Chih-Chien Wu, Amy Peterson, Boris Zinshteyn, Sergi Regot, Rachel Green. Cell 2020
73
9

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
7

SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci.
Yajing Hao, Lili Zhang, Yiwei Niu, Tanxi Cai, Jianjun Luo, Shunmin He, Bao Zhang, Dejiu Zhang, Yan Qin, Fuquan Yang,[...]. Brief Bioinform 2018
60
11

Landscape of transcription in human cells.
Sarah Djebali, Carrie A Davis, Angelika Merkel, Alex Dobin, Timo Lassmann, Ali Mortazavi, Andrea Tanzer, Julien Lagarde, Wei Lin, Felix Schlesinger,[...]. Nature 2012
7

A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation.
Liman Niu, Fangzhou Lou, Yang Sun, Libo Sun, Xiaojie Cai, Zhaoyuan Liu, Hong Zhou, Hong Wang, Zhikai Wang, Jing Bai,[...]. Sci Adv 2020
36
19

Global analysis of ribosome-associated noncoding RNAs unveils new modes of translational regulation.
Jérémie Bazin, Katja Baerenfaller, Sager J Gosai, Brian D Gregory, Martin Crespi, Julia Bailey-Serres. Proc Natl Acad Sci U S A 2017
99
7


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.