A citation-based method for searching scientific literature

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, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G Izuogu, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj P Sakthivel, Ahamed I Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth R IIsley, Nick Langridge, Jane E Loveland, Fergal J Martin, Jonathan M Mudge, Joanella Morales, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Fiona Cunningham, Andrew D Yates, Daniel R Zerbino, Paul Flicek. Nucleic Acids Res 2021
Times Cited: 403







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



Times Cited
  Times     Co-cited
Similarity


Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Michael I Love, Wolfgang Huber, Simon Anders. Genome Biol 2014
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
14


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
12


Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
M Ashburner, C A Ball, J A Blake, D Botstein, H Butler, J M Cherry, A P Davis, K Dolinski, S S Dwight, J T Eppig,[...]. Nat Genet 2000
9

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
8


The human genome browser at UCSC.
W James Kent, Charles W Sugnet, Terrence S Furey, Krishna M Roskin, Tom H Pringle, Alan M Zahler, David Haussler. Genome Res 2002
8

KEGG: kyoto encyclopedia of genes and genomes.
M Kanehisa, S Goto. Nucleic Acids Res 2000
7

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
7

The UCSC Genome Browser database: 2021 update.
Jairo Navarro Gonzalez, Ann S Zweig, Matthew L Speir, Daniel Schmelter, Kate R Rosenbloom, Brian J Raney, Conner C Powell, Luis R Nassar, Nathan D Maulding, Christopher M Lee,[...]. Nucleic Acids Res 2021
114
7

GENCODE 2021.
Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E Loveland, Jonathan M Mudge, Cristina Sisu, James C Wright, Joel Armstrong, If Barnes,[...]. Nucleic Acids Res 2021
77
9

NCBI GEO: archive for functional genomics data sets--update.
Tanya Barrett, Stephen E Wilhite, Pierre Ledoux, Carlos Evangelista, Irene F Kim, Maxim Tomashevsky, Kimberly A Marshall, Katherine H Phillippy, Patti M Sherman, Michelle Holko,[...]. Nucleic Acids Res 2013
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 reactome pathway knowledgebase.
Bijay Jassal, Lisa Matthews, Guilherme Viteri, Chuqiao Gong, Pascual Lorente, Antonio Fabregat, Konstantinos Sidiropoulos, Justin Cook, Marc Gillespie, Robin Haw,[...]. Nucleic Acids Res 2020
991
6


Comprehensive Integration of Single-Cell Data.
Tim Stuart, Andrew Butler, Paul Hoffman, Christoph Hafemeister, Efthymia Papalexi, William M Mauck, Yuhan Hao, Marlon Stoeckius, Peter Smibert, Rahul Satija. Cell 2019
5

Expression Atlas update: from tissues to single cells.
Irene Papatheodorou, Pablo Moreno, Jonathan Manning, Alfonso Muñoz-Pomer Fuentes, Nancy George, Silvie Fexova, Nuno A Fonseca, Anja Füllgrabe, Matthew Green, Ni Huang,[...]. Nucleic Acids Res 2020
174
5

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
5

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
5

Genenames.org: the HGNC and VGNC resources in 2021.
Susan Tweedie, Bryony Braschi, Kristian Gray, Tamsin E M Jones, Ruth L Seal, Bethan Yates, Elspeth A Bruford. Nucleic Acids Res 2021
73
6

The DisGeNET knowledge platform for disease genomics: 2019 update.
Janet Piñero, Juan Manuel Ramírez-Anguita, Josep Saüch-Pitarch, Francesco Ronzano, Emilio Centeno, Ferran Sanz, Laura I Furlong. Nucleic Acids Res 2020
516
5


ClinVar: improving access to variant interpretations and supporting evidence.
Melissa J Landrum, Jennifer M Lee, Mark Benson, Garth R Brown, Chen Chao, Shanmuga Chitipiralla, Baoshan Gu, Jennifer Hart, Douglas Hoffman, Wonhee Jang,[...]. Nucleic Acids Res 2018
5

Trimmomatic: a flexible trimmer for Illumina sequence data.
Anthony M Bolger, Marc Lohse, Bjoern Usadel. Bioinformatics 2014
5

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
5

KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
811
5

OMIM.org: Online Mendelian Inheritance in Man (OMIM®), an online catalog of human genes and genetic disorders.
Joanna S Amberger, Carol A Bocchini, François Schiettecatte, Alan F Scott, Ada Hamosh. Nucleic Acids Res 2015
893
4

Database resources of the National Center for Biotechnology Information.
Eric W Sayers, Jeffrey Beck, Evan E Bolton, Devon Bourexis, James R Brister, Kathi Canese, Donald C Comeau, Kathryn Funk, Sunghwan Kim, William Klimke,[...]. Nucleic Acids Res 2021
139
4

RNA-Seq: a revolutionary tool for transcriptomics.
Zhong Wang, Mark Gerstein, Michael Snyder. Nat Rev Genet 2009
4

The EMBL-EBI search and sequence analysis tools APIs in 2019.
Fábio Madeira, Young Mi Park, Joon Lee, Nicola Buso, Tamer Gur, Nandana Madhusoodanan, Prasad Basutkar, Adrian R N Tivey, Simon C Potter, Robert D Finn,[...]. Nucleic Acids Res 2019
4

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
4


miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
4

FlyBase: updates to the Drosophila melanogaster knowledge base.
Aoife Larkin, Steven J Marygold, Giulia Antonazzo, Helen Attrill, Gilberto Dos Santos, Phani V Garapati, Joshua L Goodman, L Sian Gramates, Gillian Millburn, Victor B Strelets,[...]. Nucleic Acids Res 2021
140
4

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Pablo Cingolani, Adrian Platts, Le Lily Wang, Melissa Coon, Tung Nguyen, Luan Wang, Susan J Land, Xiangyi Lu, Douglas M Ruden. Fly (Austin) 2012
4


The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.
Aaron McKenna, Matthew Hanna, Eric Banks, Andrey Sivachenko, Kristian Cibulskis, Andrew Kernytsky, Kiran Garimella, David Altshuler, Stacey Gabriel, Mark Daly,[...]. Genome Res 2010
4

Pfam: The protein families database in 2021.
Jaina Mistry, Sara Chuguransky, Lowri Williams, Matloob Qureshi, Gustavo A Salazar, Erik L L Sonnhammer, Silvio C E Tosatto, Lisanna Paladin, Shriya Raj, Lorna J Richardson,[...]. Nucleic Acids Res 2021
661
4


An improved pig reference genome sequence to enable pig genetics and genomics research.
Amanda Warr, Nabeel Affara, Bronwen Aken, Hamid Beiki, Derek M Bickhart, Konstantinos Billis, William Chow, Lel Eory, Heather A Finlayson, Paul Flicek,[...]. Gigascience 2020
74
5

Mouse Genome Database (MGD) 2019.
Carol J Bult, Judith A Blake, Cynthia L Smith, James A Kadin, Joel E Richardson. Nucleic Acids Res 2019
309
4

Integrative analysis of 111 reference human epigenomes.
Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller,[...]. Nature 2015
4

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
357
4

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
723
4

APPRIS 2017: principal isoforms for multiple gene sets.
Jose Manuel Rodriguez, Juan Rodriguez-Rivas, Tomás Di Domenico, Jesús Vázquez, Alfonso Valencia, Michael L Tress. Nucleic Acids Res 2018
58
6

Initial sequencing and comparative analysis of the mouse genome.
Robert H Waterston, Kerstin Lindblad-Toh, Ewan Birney, Jane Rogers, Josep F Abril, Pankaj Agarwal, Richa Agarwala, Rachel Ainscough, Marina Alexandersson, Peter An,[...]. Nature 2002
4


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.