A citation-based method for searching scientific literature

Mark D Wilkinson, Michel Dumontier, I Jsbrand Jan Aalbersberg, Gabrielle Appleton, Myles Axton, Arie Baak, Niklas Blomberg, Jan-Willem Boiten, Luiz Bonino da Silva Santos, Philip E Bourne, Jildau Bouwman, Anthony J Brookes, Tim Clark, Mercè Crosas, Ingrid Dillo, Olivier Dumon, Scott Edmunds, Chris T Evelo, Richard Finkers, Alejandra Gonzalez-Beltran, Alasdair J G Gray, Paul Groth, Carole Goble, Jeffrey S Grethe, Jaap Heringa, Peter A C 't Hoen, Rob Hooft, Tobias Kuhn, Ruben Kok, Joost Kok, Scott J Lusher, Maryann E Martone, Albert Mons, Abel L Packer, Bengt Persson, Philippe Rocca-Serra, Marco Roos, Rene van Schaik, Susanna-Assunta Sansone, Erik Schultes, Thierry Sengstag, Ted Slater, George Strawn, Morris A Swertz, Mark Thompson, Johan van der Lei, Erik van Mulligen, Jan Velterop, Andra Waagmeester, Peter Wittenburg, Katherine Wolstencroft, Jun Zhao, Barend Mons. Sci Data 2016
Times Cited: 1903







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



Times Cited
  Times     Co-cited
Similarity


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
96
6

The European Genome-phenome Archive of human data consented for biomedical research.
Ilkka Lappalainen, Jeff Almeida-King, Vasudev Kumanduri, Alexander Senf, John Dylan Spalding, Saif Ur-Rehman, Gary Saunders, Jag Kandasamy, Mario Caccamo, Rasko Leinonen,[...]. Nat Genet 2015
182
4

The PRIDE database and related tools and resources in 2019: improving support for quantification data.
Yasset Perez-Riverol, Attila Csordas, Jingwen Bai, Manuel Bernal-Llinares, Suresh Hewapathirana, Deepti J Kundu, Avinash Inuganti, Johannes Griss, Gerhard Mayer, Martin Eisenacher,[...]. Nucleic Acids Res 2019
4

BioContainers: an open-source and community-driven framework for software standardization.
Felipe da Veiga Leprevost, Björn A Grüning, Saulo Alves Aflitos, Hannes L Röst, Julian Uszkoreit, Harald Barsnes, Marc Vaudel, Pablo Moreno, Laurent Gatto, Jonas Weber,[...]. Bioinformatics 2017
82
4

The NCBI Taxonomy database.
Scott Federhen. Nucleic Acids Res 2012
570
4

ChEBI in 2016: Improved services and an expanding collection of metabolites.
Janna Hastings, Gareth Owen, Adriano Dekker, Marcus Ennis, Namrata Kale, Venkatesh Muthukrishnan, Steve Turner, Neil Swainston, Pedro Mendes, Christoph Steinbeck. Nucleic Acids Res 2016
281
4

Announcing the worldwide Protein Data Bank.
Helen Berman, Kim Henrick, Haruki Nakamura. Nat Struct Biol 2003
4

BioMagResBank.
Eldon L Ulrich, Hideo Akutsu, Jurgen F Doreleijers, Yoko Harano, Yannis E Ioannidis, Jundong Lin, Miron Livny, Steve Mading, Dimitri Maziuk, Zachary Miller,[...]. Nucleic Acids Res 2008
4

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
118
4

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
3

The NCBI dbGaP database of genotypes and phenotypes.
Matthew D Mailman, Michael Feolo, Yumi Jin, Masato Kimura, Kimberly Tryka, Rinat Bagoutdinov, Luning Hao, Anne Kiang, Justin Paschall, Lon Phan,[...]. Nat Genet 2007
672
3

The European Nucleotide Archive in 2019.
Clara Amid, Blaise T F Alako, Vishnukumar Balavenkataraman Kadhirvelu, Tony Burdett, Josephine Burgin, Jun Fan, Peter W Harrison, Sam Holt, Abdulrahman Hussein, Eugene Ivanov,[...]. Nucleic Acids Res 2020
47
6

The international nucleotide sequence database collaboration.
Ilene Karsch-Mizrachi, Toshihisa Takagi, Guy Cochrane. Nucleic Acids Res 2018
81
3

The Sequence Read Archive: explosive growth of sequencing data.
Yuichi Kodama, Martin Shumway, Rasko Leinonen. Nucleic Acids Res 2012
464
3

Public Data Archiving in Ecology and Evolution: How Well Are We Doing?
Dominique G Roche, Loeske E B Kruuk, Robert Lanfear, Sandra A Binning. PLoS Biol 2015
75
4



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
3

The Cancer Genome Atlas Pan-Cancer analysis project.
John N Weinstein, Eric A Collisson, Gordon B Mills, Kenna R Mills Shaw, Brad A Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M Stuart. Nat Genet 2013
3

PDBe: improved findability of macromolecular structure data in the PDB.
David R Armstrong, John M Berrisford, Matthew J Conroy, Aleksandras Gutmanas, Stephen Anyango, Preeti Choudhary, Alice R Clark, Jose M Dana, Mandar Deshpande, Roisin Dunlop,[...]. Nucleic Acids Res 2020
41
7

ChEMBL: towards direct deposition of bioassay data.
David Mendez, Anna Gaulton, A Patrícia Bento, Jon Chambers, Marleen De Veij, Eloy Félix, María Paula Magariños, Juan F Mosquera, Prudence Mutowo, Michal Nowotka,[...]. Nucleic Acids Res 2019
293
3

Nextflow enables reproducible computational workflows.
Paolo Di Tommaso, Maria Chatzou, Evan W Floden, Pablo Prieto Barja, Emilio Palumbo, Cedric Notredame. Nat Biotechnol 2017
337
3

A Harmonized Data Quality Assessment Terminology and Framework for the Secondary Use of Electronic Health Record Data.
Michael G Kahn, Tiffany J Callahan, Juliana Barnard, Alan E Bauck, Jeff Brown, Bruce N Davidson, Hossein Estiri, Carsten Goerg, Erin Holve, Steven G Johnson,[...]. EGEMS (Wash DC) 2016
130
3

COVID-19 pandemic reveals the peril of ignoring metadata standards.
Lynn M Schriml, Maria Chuvochina, Neil Davies, Emiley A Eloe-Fadrosh, Robert D Finn, Philip Hugenholtz, Christopher I Hunter, Bonnie L Hurwitz, Nikos C Kyrpides, Folker Meyer,[...]. Sci Data 2020
14
21

Human Disease Ontology 2018 update: classification, content and workflow expansion.
Lynn M Schriml, Elvira Mitraka, James Munro, Becky Tauber, Mike Schor, Lance Nickle, Victor Felix, Linda Jeng, Cynthia Bearer, Richard Lichenstein,[...]. Nucleic Acids Res 2019
103
3

Bioconda: sustainable and comprehensive software distribution for the life sciences.
Björn Grüning, Ryan Dale, Andreas Sjödin, Brad A Chapman, Jillian Rowe, Christopher H Tomkins-Tinch, Renan Valieris, Johannes Köster. Nat Methods 2018
276
3

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
3

A global reference for human genetic variation.
Adam Auton, Lisa D Brooks, Richard M Durbin, Erik P Garrison, Hyun Min Kang, Jan O Korbel, Jonathan L Marchini, Shane McCarthy, Gil A McVean, Gonçalo R Abecasis. Nature 2015
3

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
3

Applications of machine learning in drug discovery and development.
Jessica Vamathevan, Dominic Clark, Paul Czodrowski, Ian Dunham, Edgardo Ferran, George Lee, Bin Li, Anant Madabhushi, Parantu Shah, Michaela Spitzer,[...]. Nat Rev Drug Discov 2019
300
3

SCIENTIFIC STANDARDS. Promoting an open research culture.
B A Nosek, G Alter, G C Banks, D Borsboom, S D Bowman, S J Breckler, S Buck, C D Chambers, G Chin, G Christensen,[...]. Science 2015
558
3

The Protein Data Bank.
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov, P E Bourne. Nucleic Acids Res 2000
3

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
111
3

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
400
3

BioSamples database: an updated sample metadata hub.
Mélanie Courtot, Luca Cherubin, Adam Faulconbridge, Daniel Vaughan, Matthew Green, David Richardson, Peter Harrison, Patricia L Whetzel, Helen Parkinson, Tony Burdett. Nucleic Acids Res 2019
23
13

The international nucleotide sequence database collaboration.
Masanori Arita, Ilene Karsch-Mizrachi, Guy Cochrane. Nucleic Acids Res 2021
20
15


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
2

BBMRI-ERIC Directory: 515 Biobanks with Over 60 Million Biological Samples.
Petr Holub, Morris Swertz, Robert Reihs, David van Enckevort, Heimo Müller, Jan-Eric Litton. Biopreserv Biobank 2016
37
5


NCBI's Database of Genotypes and Phenotypes: dbGaP.
Kimberly A Tryka, Luning Hao, Anne Sturcke, Yumi Jin, Zhen Y Wang, Lora Ziyabari, Moira Lee, Natalia Popova, Nataliya Sharopova, Masato Kimura,[...]. Nucleic Acids Res 2014
245
2

The "All of Us" Research Program.
Joshua C Denny, Joni L Rutter, David B Goldstein, Anthony Philippakis, Jordan W Smoller, Gwynne Jenkins, Eric Dishman. N Engl J Med 2019
209
2

Genetic epidemiology of COPD (COPDGene) study design.
Elizabeth A Regan, John E Hokanson, James R Murphy, Barry Make, David A Lynch, Terri H Beaty, Douglas Curran-Everett, Edwin K Silverman, James D Crapo. COPD 2010
680
2

A new initiative on precision medicine.
Francis S Collins, Harold Varmus. N Engl J Med 2015
2

The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.
Katarzyna Tomczak, Patrycja Czerwińska, Maciej Wiznerowicz. Contemp Oncol (Pozn) 2015
2

The Gene Expression Omnibus Database.
Emily Clough, Tanya Barrett. Methods Mol Biol 2016
513
2

DDBJ Database updates and computational infrastructure enhancement.
Osamu Ogasawara, Yuichi Kodama, Jun Mashima, Takehide Kosuge, Takatomo Fujisawa. Nucleic Acids Res 2020
13
15

ArrayExpress update - from bulk to single-cell expression data.
Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A Fonseca, Robert Petryszak, Irene Papatheodorou,[...]. Nucleic Acids Res 2019
174
2

The availability of research data declines rapidly with article age.
Timothy H Vines, Arianne Y K Albert, Rose L Andrew, Florence Débarre, Dan G Bock, Michelle T Franklin, Kimberly J Gilbert, Jean-Sébastien Moore, Sébastien Renaut, Diana J Rennison. Curr Biol 2014
116
2

A manifesto for reproducible science.
Marcus R Munafò, Brian A Nosek, Dorothy V M Bishop, Katherine S Button, Christopher D Chambers, Nathalie Percie du Sert, Uri Simonsohn, Eric-Jan Wagenmakers, Jennifer J Ware, John P A Ioannidis. Nat Hum Behav 2017
165
2


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.