A citation-based method for searching scientific literature

Nicholas T Ingolia, Sina Ghaemmaghami, John R S Newman, Jonathan S Weissman. Science 2009
Times Cited: 2113







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



Times Cited
  Times     Co-cited
Similarity



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
630
20

Transcriptome-wide measurement of translation by ribosome profiling.
Nicholas J McGlincy, Nicholas T Ingolia. Methods 2017
152
15

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome.
Ben Langmead, Cole Trapnell, Mihai Pop, Steven L Salzberg. Genome Biol 2009
13

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
13

Translation inhibitors cause abnormalities in ribosome profiling experiments.
Maxim V Gerashchenko, Vadim N Gladyshev. Nucleic Acids Res 2014
163
12

Improved Ribosome-Footprint and mRNA Measurements Provide Insights into Dynamics and Regulation of Yeast Translation.
David E Weinberg, Premal Shah, Stephen W Eichhorn, Jeffrey A Hussmann, Joshua B Plotkin, David P Bartel. Cell Rep 2016
196
12

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
12

Translation of 5' leaders is pervasive in genes resistant to eIF2 repression.
Dmitry E Andreev, Patrick B F O'Connor, Ciara Fahey, Elaine M Kenny, Ilya M Terenin, Sergey E Dmitriev, Paul Cormican, Derek W Morris, Ivan N Shatsky, Pavel V Baranov. Elife 2015
177
12


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
133
11


Global quantification of mammalian gene expression control.
Björn Schwanhäusser, Dorothea Busse, Na Li, Gunnar Dittmar, Johannes Schuchhardt, Jana Wolf, Wei Chen, Matthias Selbach. Nature 2011
10

Ribosome profiling reveals the what, when, where and how of protein synthesis.
Gloria A Brar, Jonathan S Weissman. Nat Rev Mol Cell Biol 2015
213
10

Understanding Biases in Ribosome Profiling Experiments Reveals Signatures of Translation Dynamics in Yeast.
Jeffrey A Hussmann, Stephanie Patchett, Arlen Johnson, Sara Sawyer, William H Press. PLoS Genet 2015
133
10

riboWaltz: Optimization of ribosome P-site positioning in ribosome profiling data.
Fabio Lauria, Toma Tebaldi, Paola Bernabò, Ewout J N Groen, Thomas H Gillingwater, Gabriella Viero. PLoS Comput Biol 2018
51
19


Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources.
Gene-Wei Li, David Burkhardt, Carol Gross, Jonathan S Weissman. Cell 2014
672
10

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
10

Cotranslational assembly of protein complexes in eukaryotes revealed by ribosome profiling.
Ayala Shiber, Kristina Döring, Ulrike Friedrich, Kevin Klann, Dorina Merker, Mostafa Zedan, Frank Tippmann, Günter Kramer, Bernd Bukau. Nature 2018
118
9

Quantitative profiling of initiating ribosomes in vivo.
Xiangwei Gao, Ji Wan, Botao Liu, Ming Ma, Ben Shen, Shu-Bing Qian. Nat Methods 2015
130
9


The Sequence Alignment/Map format and SAMtools.
Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin. Bioinformatics 2009
8

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
192
8

ViennaRNA Package 2.0.
Ronny Lorenz, Stephan H Bernhart, Christian Höner Zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker. Algorithms Mol Biol 2011
8


Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress.
Maxim V Gerashchenko, Alexei V Lobanov, Vadim N Gladyshev. Proc Natl Acad Sci U S A 2012
179
7

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
7

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
7

Translational control by 5'-untranslated regions of eukaryotic mRNAs.
Alan G Hinnebusch, Ivaylo P Ivanov, Nahum Sonenberg. Science 2016
440
7

Codon optimality, bias and usage in translation and mRNA decay.
Gavin Hanson, Jeff Coller. Nat Rev Mol Cell Biol 2018
217
7

Dom34 rescues ribosomes in 3' untranslated regions.
Nicholas R Guydosh, Rachel Green. Cell 2014
219
7

Dynamics of ribosome scanning and recycling revealed by translation complex profiling.
Stuart K Archer, Nikolay E Shirokikh, Traude H Beilharz, Thomas Preiss. Nature 2016
106
7

Ribonuclease selection for ribosome profiling.
Maxim V Gerashchenko, Vadim N Gladyshev. Nucleic Acids Res 2017
66
10


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
331
7

High-precision analysis of translational pausing by ribosome profiling in bacteria lacking EFP.
Christopher J Woolstenhulme, Nicholas R Guydosh, Rachel Green, Allen R Buskirk. Cell Rep 2015
132
6

Genome-wide Survey of Ribosome Collision.
Peixun Han, Yuichi Shichino, Tilman Schneider-Poetsch, Mari Mito, Satoshi Hashimoto, Tsuyoshi Udagawa, Kenji Kohno, Minoru Yoshida, Yuichiro Mishima, Toshifumi Inada,[...]. Cell Rep 2020
31
19

Positively charged residues are the major determinants of ribosomal velocity.
Catherine A Charneski, Laurence D Hurst. PLoS Biol 2013
173
6

The effect of tRNA levels on decoding times of mRNA codons.
Alexandra Dana, Tamir Tuller. Nucleic Acids Res 2014
132
6


Causal signals between codon bias, mRNA structure, and the efficiency of translation and elongation.
Cristina Pop, Silvi Rouskin, Nicholas T Ingolia, Lu Han, Eric M Phizicky, Jonathan S Weissman, Daphne Koller. Mol Syst Biol 2014
148
6

Balanced codon usage optimizes eukaryotic translational efficiency.
Wenfeng Qian, Jian-Rong Yang, Nathaniel M Pearson, Calum Maclean, Jianzhi Zhang. PLoS Genet 2012
185
6

Selective ribosome profiling reveals the cotranslational chaperone action of trigger factor in vivo.
Eugene Oh, Annemarie H Becker, Arzu Sandikci, Damon Huber, Rachna Chaba, Felix Gloge, Robert J Nichols, Athanasios Typas, Carol A Gross, Günter Kramer,[...]. Cell 2011
283
6



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
350
6

Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster.
Joshua G Dunn, Catherine K Foo, Nicolette G Belletier, Elizabeth R Gavis, Jonathan S Weissman. Elife 2013
224
6

Conservation of uORF repressiveness and sequence features in mouse, human and zebrafish.
Guo-Liang Chew, Andrea Pauli, Alexander F Schier. Nat Commun 2016
81
7

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
487
6


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.