A citation-based method for searching scientific literature

Michael F Lin, Irwin Jungreis, Manolis Kellis. Bioinformatics 2011
Times Cited: 607







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



Times Cited
  Times     Co-cited
Similarity


CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine.
Lei Kong, Yong Zhang, Zhi-Qiang Ye, Xiao-Qiao Liu, Shu-Qi Zhao, Liping Wei, Ge Gao. Nucleic Acids Res 2007
30

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.
Liguo Wang, Hyun Jung Park, Surendra Dasari, Shengqin Wang, Jean-Pierre Kocher, Wei Li. Nucleic Acids Res 2013
944
23

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts.
Liang Sun, Haitao Luo, Dechao Bu, Guoguang Zhao, Kuntao Yu, Changhai Zhang, Yuanning Liu, Runsheng Chen, Yi Zhao. Nucleic Acids Res 2013
884
22

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
221
19

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features.
Yu-Jian Kang, De-Chang Yang, Lei Kong, Mei Hou, Yu-Qi Meng, Liping Wei, Ge Gao. Nucleic Acids Res 2017
456
19

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
675
18

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
Cole Trapnell, Brian A Williams, Geo Pertea, Ali Mortazavi, Gordon Kwan, Marijke J van Baren, Steven L Salzberg, Barbara J Wold, Lior Pachter. Nat Biotechnol 2010
17

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
214
15

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
15

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
198
15


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
393
14

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
14

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
335
13

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
496
13

Genome regulation by long noncoding RNAs.
John L Rinn, Howard Y Chang. Annu Rev Biochem 2012
13


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
140
12

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
Adam Siepel, Gill Bejerano, Jakob S Pedersen, Angie S Hinrichs, Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth, Ladeana W Hillier, Stephen Richards,[...]. Genome Res 2005
12

Accurate annotation of human protein-coding small open reading frames.
Thomas F Martinez, Qian Chu, Cynthia Donaldson, Dan Tan, Maxim N Shokhirev, Alan Saghatelian. Nat Chem Biol 2020
62
19

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
12

The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.
Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, Hagen Tilgner, Gregory Guernec, David Martin, Angelika Merkel, David G Knowles,[...]. Genome Res 2012
11

sORF finder: a program package to identify small open reading frames with high coding potential.
Kousuke Hanada, Kenji Akiyama, Tetsuya Sakurai, Tetsuro Toyoda, Kazuo Shinozaki, Shin-Han Shiu. Bioinformatics 2010
70
15

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
128
11

An atlas of human long non-coding RNAs with accurate 5' ends.
Chung-Chau Hon, Jordan A Ramilowski, Jayson Harshbarger, Nicolas Bertin, Owen J L Rackham, Julian Gough, Elena Denisenko, Sebastian Schmeier, Thomas M Poulsen, Jessica Severin,[...]. Nature 2017
543
11

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
11

The Pfam protein families database.
Marco Punta, Penny C Coggill, Ruth Y Eberhardt, Jaina Mistry, John Tate, Chris Boursnell, Ningze Pang, Kristoffer Forslund, Goran Ceric, Jody Clements,[...]. Nucleic Acids Res 2012
11

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
382
11

Unique features of long non-coding RNA biogenesis and function.
Jeffrey J Quinn, Howard Y Chang. Nat Rev Genet 2016
10

Long non-coding RNAs as a source of new peptides.
Jorge Ruiz-Orera, Xavier Messeguer, Juan Antonio Subirana, M Mar Alba. Elife 2014
290
10

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
391
10

A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma.
Maolei Zhang, Kun Zhao, Xiaoping Xu, Yibing Yang, Sheng Yan, Ping Wei, Hui Liu, Jianbo Xu, Feizhe Xiao, Huangkai Zhou,[...]. Nat Commun 2018
344
10

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
10

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
10

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
187
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
84
11

Classification and function of small open reading frames.
Juan-Pablo Couso, Pedro Patraquim. Nat Rev Mol Cell Biol 2017
125
10

Gene regulation by long non-coding RNAs and its biological functions.
Luisa Statello, Chun-Jie Guo, Ling-Ling Chen, Maite Huarte. Nat Rev Mol Cell Biol 2021
828
10


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
311
9

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.
Stefan Washietl, Sven Findeiss, Stephan A Müller, Stefan Kalkhof, Martin von Bergen, Ivo L Hofacker, Peter F Stadler, Nick Goldman. RNA 2011
125
9

A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?
Leonardo Salmena, Laura Poliseno, Yvonne Tay, Lev Kats, Pier Paolo Pandolfi. Cell 2011
9

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
369
9

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
424
9

Extensive identification and analysis of conserved small ORFs in animals.
Sebastian D Mackowiak, Henrik Zauber, Chris Bielow, Denise Thiel, Kamila Kutz, Lorenzo Calviello, Guido Mastrobuoni, Nikolaus Rajewsky, Stefan Kempa, Matthias Selbach,[...]. Genome Biol 2015
107
9

Toddler: an embryonic signal that promotes cell movement via Apelin receptors.
Andrea Pauli, Megan L Norris, Eivind Valen, Guo-Liang Chew, James A Gagnon, Steven Zimmerman, Andrew Mitchell, Jiao Ma, Julien Dubrulle, Deepak Reyon,[...]. Science 2014
370
9

The landscape of long noncoding RNAs in the human transcriptome.
Matthew K Iyer, Yashar S Niknafs, Rohit Malik, Udit Singhal, Anirban Sahu, Yasuyuki Hosono, Terrence R Barrette, John R Prensner, Joseph R Evans, Shuang Zhao,[...]. Nat Genet 2015
9

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
9

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.
Jonathan M Mudge, Irwin Jungreis, Toby Hunt, Jose Manuel Gonzalez, James C Wright, Mike Kay, Claire Davidson, Stephen Fitzgerald, Ruth Seal, Susan Tweedie,[...]. Genome Res 2019
26
34

Mining for Micropeptides.
Catherine A Makarewich, Eric N Olson. Trends Cell Biol 2017
114
9


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.