A citation-based method for searching scientific literature

Eric W Sayers, Jeffrey Beck, Evan E Bolton, Devon Bourexis, James R Brister, Kathi Canese, Donald C Comeau, Kathryn Funk, Sunghwan Kim, William Klimke, Aron Marchler-Bauer, Melissa Landrum, Stacy Lathrop, Zhiyong Lu, Thomas L Madden, Nuala O'Leary, Lon Phan, Sanjida H Rangwala, Valerie A Schneider, Yuri Skripchenko, Jiyao Wang, Jian Ye, Barton W Trawick, Kim D Pruitt, Stephen T Sherry. Nucleic Acids Res 2021
Times Cited: 149







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



Times Cited
  Times     Co-cited
Similarity




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
441
9

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms.
Sudhir Kumar, Glen Stecher, Michael Li, Christina Knyaz, Koichiro Tamura. Mol Biol Evol 2018
9

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
734
8

DrugBank 5.0: a major update to the DrugBank database for 2018.
David S Wishart, Yannick D Feunang, An C Guo, Elvis J Lo, Ana Marcu, Jason R Grant, Tanvir Sajed, Daniel Johnson, Carin Li, Zinat Sayeeda,[...]. Nucleic Acids Res 2018
8

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


Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
S F Altschul, T L Madden, A A Schäffer, J Zhang, Z Zhang, W Miller, D J Lipman. Nucleic Acids Res 1997
6

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
6

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
6

BLAST+: architecture and applications.
Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer, Thomas L Madden. BMC Bioinformatics 2009
6

CDD/SPARCLE: the conserved domain database in 2020.
Shennan Lu, Jiyao Wang, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Gabriele H Marchler, James S Song,[...]. Nucleic Acids Res 2020
686
6

KEGG: integrating viruses and cellular organisms.
Minoru Kanehisa, Miho Furumichi, Yoko Sato, Mari Ishiguro-Watanabe, Mao Tanabe. Nucleic Acids Res 2021
886
5

miRBase: from microRNA sequences to function.
Ana Kozomara, Maria Birgaoanu, Sam Griffiths-Jones. Nucleic Acids Res 2019
5

PubChem in 2021: new data content and improved web interfaces.
Sunghwan Kim, Jie Chen, Tiejun Cheng, Asta Gindulyte, Jia He, Siqian He, Qingliang Li, Benjamin A Shoemaker, Paul A Thiessen, Bo Yu,[...]. Nucleic Acids Res 2021
551
5

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
119
5

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
5

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
5

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
5

Basic local alignment search tool.
S F Altschul, W Gish, W Miller, E W Myers, D J Lipman. J Mol Biol 1990
5

The InterPro protein families and domains database: 20 years on.
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj,[...]. Nucleic Acids Res 2021
375
5


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

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
148
4


KEGG: new perspectives on genomes, pathways, diseases and drugs.
Minoru Kanehisa, Miho Furumichi, Mao Tanabe, Yoko Sato, Kanae Morishima. Nucleic Acids Res 2017
4

The European Nucleotide Archive in 2020.
Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb,[...]. Nucleic Acids Res 2021
42
9

fastp: an ultra-fast all-in-one FASTQ preprocessor.
Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu. Bioinformatics 2018
4

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
4

A pneumonia outbreak associated with a new coronavirus of probable bat origin.
Peng Zhou, Xing-Lou Yang, Xian-Guang Wang, Ben Hu, Lei Zhang, Wei Zhang, Hao-Rui Si, Yan Zhu, Bei Li, Chao-Lin Huang,[...]. Nature 2020
4


GenBank.
Eric W Sayers, Mark Cavanaugh, Karen Clark, Kim D Pruitt, Conrad L Schoch, Stephen T Sherry, Ilene Karsch-Mizrachi. Nucleic Acids Res 2021
67
5

The international nucleotide sequence database collaboration.
Masanori Arita, Ilene Karsch-Mizrachi, Guy Cochrane. Nucleic Acids Res 2021
41
9


Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.
Sue Richards, Nazneen Aziz, Sherri Bale, David Bick, Soma Das, Julie Gastier-Foster, Wayne W Grody, Madhuri Hegde, Elaine Lyon, Elaine Spector,[...]. Genet Med 2015
4

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries.
Chirag Jain, Luis M Rodriguez-R, Adam M Phillippy, Konstantinos T Konstantinidis, Srinivas Aluru. Nat Commun 2018
4

Prodigal: prokaryotic gene recognition and translation initiation site identification.
Doug Hyatt, Gwo-Liang Chen, Philip F Locascio, Miriam L Land, Frank W Larimer, Loren J Hauser. BMC Bioinformatics 2010
4

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Salvador Capella-Gutiérrez, José M Silla-Martínez, Toni Gabaldón. Bioinformatics 2009
4

Shifting the genomic gold standard for the prokaryotic species definition.
Michael Richter, Ramon Rosselló-Móra. Proc Natl Acad Sci U S A 2009
4

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools.
Christian Quast, Elmar Pruesse, Pelin Yilmaz, Jan Gerken, Timmy Schweer, Pablo Yarza, Jörg Peplies, Frank Oliver Glöckner. Nucleic Acids Res 2013
4

NCBI Taxonomy: a comprehensive update on curation, resources and tools.
Conrad L Schoch, Stacy Ciufo, Mikhail Domrachev, Carol L Hotton, Sivakumar Kannan, Rogneda Khovanskaya, Detlef Leipe, Richard Mcveigh, Kathleen O'Neill, Barbara Robbertse,[...]. Database (Oxford) 2020
213
4

The European Bioinformatics Institute: empowering cooperation in response to a global health crisis.
Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen McDonagh, Paul Flicek, Johanna McEntyre, Ewan Birney, Rolf Apweiler. Nucleic Acids Res 2021
14
21

SMART: recent updates, new developments and status in 2020.
Ivica Letunic, Supriya Khedkar, Peer Bork. Nucleic Acids Res 2021
226
3

Rfam 14: expanded coverage of metagenomic, viral and microRNA families.
Ioanna Kalvari, Eric P Nawrocki, Nancy Ontiveros-Palacios, Joanna Argasinska, Kevin Lamkiewicz, Manja Marz, Sam Griffiths-Jones, Claire Toffano-Nioche, Daniel Gautheret, Zasha Weinberg,[...]. Nucleic Acids Res 2021
124
3

The IMG/M data management and analysis system v.6.0: new tools and advanced capabilities.
I-Min A Chen, Ken Chu, Krishnaveni Palaniappan, Anna Ratner, Jinghua Huang, Marcel Huntemann, Patrick Hajek, Stephan Ritter, Neha Varghese, Rekha Seshadri,[...]. Nucleic Acids Res 2021
125
3

RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences.
Stephen K Burley, Charmi Bhikadiya, Chunxiao Bi, Sebastian Bittrich, Li Chen, Gregg V Crichlow, Cole H Christie, Kenneth Dalenberg, Luigi Di Costanzo, Jose M Duarte,[...]. Nucleic Acids Res 2021
292
3

The UCSC Genome Browser database: 2019 update.
Maximilian Haeussler, Ann S Zweig, Cath Tyner, Matthew L Speir, Kate R Rosenbloom, Brian J Raney, Christopher M Lee, Brian T Lee, Angie S Hinrichs, Jairo Navarro Gonzalez,[...]. Nucleic Acids Res 2019
407
3

The Sequence Read Archive: explosive growth of sequencing data.
Yuichi Kodama, Martin Shumway, Rasko Leinonen. Nucleic Acids Res 2012
505
3

Identification of common molecular subsequences.
T F Smith, M S Waterman. J Mol Biol 1981
3


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.