A citation-based method for searching scientific literature

Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E Loveland, Jonathan M Mudge, Cristina Sisu, James C Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah Donaldson, Ian T Fiddes, Carlos García Girón, Jose Manuel Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L Howe, Toby Hunt, Osagie G Izuogu, Rory Johnson, Fergal J Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C P Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y Wolf, Jinuri Xu, Yucheng T Yang, Andrew Yates, Daniel Zerbino, Yan Zhang, Jyoti S Choudhary, Mark Gerstein, Roderic Guigó, Tim J P Hubbard, Manolis Kellis, Benedict Paten, Michael L Tress, Paul Flicek. Nucleic Acids Res 2021
Times Cited: 101







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



Times Cited
  Times     Co-cited
Similarity


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
23

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
19

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
18

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation.
Nuala A O'Leary, Mathew W Wright, J Rodney Brister, Stacy Ciufo, Diana Haddad, Rich McVeigh, Bhanu Rajput, Barbara Robbertse, Brian Smith-White, Danso Ako-Adjei,[...]. Nucleic Acids Res 2016
14

Ensembl 2021.
Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai,[...]. Nucleic Acids Res 2021
488
12

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

Global Cancer Statistics 2020: GLOBOCAN Estimates of Incidence and Mortality Worldwide for 36 Cancers in 185 Countries.
Hyuna Sung, Jacques Ferlay, Rebecca L Siegel, Mathieu Laversanne, Isabelle Soerjomataram, Ahmedin Jemal, Freddie Bray. CA Cancer J Clin 2021
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
9

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Aravind Subramanian, Pablo Tamayo, Vamsi K Mootha, Sayan Mukherjee, Benjamin L Ebert, Michael A Gillette, Amanda Paulovich, Scott L Pomeroy, Todd R Golub, Eric S Lander,[...]. Proc Natl Acad Sci U S A 2005
9

GENCODE reference annotation for the human and mouse genomes.
Adam Frankish, Mark Diekhans, Anne-Maud Ferreira, Rory Johnson, Irwin Jungreis, Jane Loveland, Jonathan M Mudge, Cristina Sisu, James Wright, Joel Armstrong,[...]. Nucleic Acids Res 2019
8


limma powers differential expression analyses for RNA-sequencing and microarray studies.
Matthew E Ritchie, Belinda Phipson, Di Wu, Yifang Hu, Charity W Law, Wei Shi, Gordon K Smyth. Nucleic Acids Res 2015
8

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
8


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

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.
Moran N Cabili, Cole Trapnell, Loyal Goff, Magdalena Koziol, Barbara Tazon-Vega, Aviv Regev, John L Rinn. Genes Dev 2011
7

Long Noncoding RNAs in Cancer Pathways.
Adam M Schmitt, Howard Y Chang. Cancer Cell 2016
7

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
7

Fast gapped-read alignment with Bowtie 2.
Ben Langmead, Steven L Salzberg. Nat Methods 2012
7

Salmon provides fast and bias-aware quantification of transcript expression.
Rob Patro, Geet Duggal, Michael I Love, Rafael A Irizarry, Carl Kingsford. Nat Methods 2017
7

The mutational constraint spectrum quantified from variation in 141,456 humans.
Konrad J Karczewski, Laurent C Francioli, Grace Tiao, Beryl B Cummings, Jessica Alföldi, Qingbo Wang, Ryan L Collins, Kristen M Laricchia, Andrea Ganna, Daniel P Birnbaum,[...]. Nature 2020
7

The Ensembl Variant Effect Predictor.
William McLaren, Laurent Gil, Sarah E Hunt, Harpreet Singh Riat, Graham R S Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham. Genome Biol 2016
7

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
7

Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs.
John L Rinn, Michael Kertesz, Jordon K Wang, Sharon L Squazzo, Xiao Xu, Samantha A Brugmann, L Henry Goodnough, Jill A Helms, Peggy J Farnham, Eran Segal,[...]. Cell 2007
6

Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities.
Sven Heinz, Christopher Benner, Nathanael Spann, Eric Bertolino, Yin C Lin, Peter Laslo, Jason X Cheng, Cornelis Murre, Harinder Singh, Christopher K Glass. Mol Cell 2010
6

The Encyclopedia of DNA elements (ENCODE): data portal update.
Carrie A Davis, Benjamin C Hitz, Cricket A Sloan, Esther T Chan, Jean M Davidson, Idan Gabdank, Jason A Hilton, Kriti Jain, Ulugbek K Baymuradov, Aditi K Narayanan,[...]. Nucleic Acids Res 2018
769
6

HTSeq--a Python framework to work with high-throughput sequencing data.
Simon Anders, Paul Theodor Pyl, Wolfgang Huber. Bioinformatics 2015
6


Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
6


StringTie enables improved reconstruction of a transcriptome from RNA-seq reads.
Mihaela Pertea, Geo M Pertea, Corina M Antonescu, Tsung-Cheng Chang, Joshua T Mendell, Steven L Salzberg. Nat Biotechnol 2015
6

Expanded encyclopaedias of DNA elements in the human and mouse genomes.
Jill E Moore, Michael J Purcaro, Henry E Pratt, Charles B Epstein, Noam Shoresh, Jessika Adrian, Trupti Kawli, Carrie A Davis, Alexander Dobin, Rajinder Kaul,[...]. Nature 2020
403
6

dbSNP: the NCBI database of genetic variation.
S T Sherry, M H Ward, M Kholodov, J Baker, L Phan, E M Smigielski, K Sirotkin. Nucleic Acids Res 2001
6


Initial sequencing and analysis of the human genome.
E S Lander, L M Linton, B Birren, C Nusbaum, M C Zody, J Baldwin, K Devon, K Dewar, M Doyle, W FitzHugh,[...]. Nature 2001
6

LNCipedia 5: towards a reference set of human long non-coding RNAs.
Pieter-Jan Volders, Jasper Anckaert, Kenneth Verheggen, Justine Nuytens, Lennart Martens, Pieter Mestdagh, Jo Vandesompele. Nucleic Acids Res 2019
217
5

GENCODE: the reference human genome annotation for The ENCODE Project.
Jennifer Harrow, Adam Frankish, Jose M Gonzalez, Electra Tapanari, Mark Diekhans, Felix Kokocinski, Bronwen L Aken, Daniel Barrell, Amonida Zadissa, Stephen Searle,[...]. Genome Res 2012
5


Molecular mechanisms of long noncoding RNAs.
Kevin C Wang, Howard Y Chang. Mol Cell 2011
5

The functions and unique features of long intergenic non-coding RNA.
Julia D Ransohoff, Yuning Wei, Paul A Khavari. Nat Rev Mol Cell Biol 2018
556
5

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology.
Laura Poliseno, Leonardo Salmena, Jiangwen Zhang, Brett Carver, William J Haveman, Pier Paolo Pandolfi. Nature 2010
5

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis.
Rajnish A Gupta, Nilay Shah, Kevin C Wang, Jeewon Kim, Hugo M Horlings, David J Wong, Miao-Chih Tsai, Tiffany Hung, Pedram Argani, John L Rinn,[...]. Nature 2010
5

Towards a complete map of the human long non-coding RNA transcriptome.
Barbara Uszczynska-Ratajczak, Julien Lagarde, Adam Frankish, Roderic Guigó, Rory Johnson. Nat Rev Genet 2018
259
5


edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
Mark D Robinson, Davis J McCarthy, Gordon K Smyth. Bioinformatics 2010
5


HISAT: a fast spliced aligner with low memory requirements.
Daehwan Kim, Ben Langmead, Steven L Salzberg. Nat Methods 2015
5

Full-length transcript characterization of SF3B1 mutation in chronic lymphocytic leukemia reveals downregulation of retained introns.
Alison D Tang, Cameron M Soulette, Marijke J van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J Wu, Angela N Brooks. Nat Commun 2020
105
5


PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions.
Michael F Lin, Irwin Jungreis, Manolis Kellis. Bioinformatics 2011
607
5


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.