Most cited papers in Scientific Computing and Data Management
What are the most cited papers in Scientific Computing and Data Management?
The most cited paper in Scientific Computing and Data Management is "UCSF Chimera—A visualization system for exploratory research and analysis" (Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al., 2004), with 48,801 citations. Next come "SciPy 1.0: fundamental algorithms for scientific computing in Python" (40,161) and "Clustal W and Clustal X version 2.0" (29,302).
Showing 50 of 100 papers. Every paper with more than 1,167 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | UCSF Chimera—A visualization system for exploratory research and analysis Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Journal of Computational Chemistry | Jul 2004 | 48,801 |
| 2 | SciPy 1.0: fundamental algorithms for scientific computing in Python Pauli Virtanen et al. · Nature Methods | 3 Feb 2020 | 40,161 |
| 3 | Clustal W and Clustal X version 2.0 Mark Larkin, Gordon Blackshields, Nigel P. Brown et al. · Bioinformatics | 10 Sep 2007 | 29,302 |
| 4 | The REDCap consortium: Building an international community of software platform partners Paul A. Harris, Robert J. Taylor, Brenda L. Minor et al. · Journal of Biomedical Informatics | 9 May 2019 | 25,189 |
| 5 | Array programming with NumPy Charles R. Harris et al. · Nature | 16 Sep 2020 | 23,885 |
| 6 | Welcome to the Tidyverse Hadley Wickham et al. · The Journal of Open Source Software | 21 Nov 2019 | 22,949 |
| 7 | Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data Matthew D. Kearse, Richard Moir, Amy Swango Wilson et al. · Bioinformatics | 27 Apr 2012 | 21,229 |
| 8 | bibliometrix : An R-tool for comprehensive science mapping analysis Massimo Aria, Corrado Cuccurullo · Journal of Informetrics | 12 Sep 2017 | 15,825 |
| 9 | Bioconductor: open software development for computational biology and bioinformatics Robert C. Gentleman et al. · Genome biology | 15 Sep 2004 | 12,632 |
| 10 | First-principles simulation: ideas, illustrations and the CASTEP code Matthew Segall, Philip J. D. Lindan, Matt I. J. Probert et al. · Journal of Physics Condensed Matter | 8 Mar 2002 | 11,917 |
| 11 | VSEARCH: a versatile open source tool for metagenomics Torbjørn Rognes, Tomáš Flouri, Ben Nichols et al. · PeerJ | 18 Oct 2016 | 11,418 |
| 12 | Avogadro: an advanced semantic chemical editor, visualization, and analysis platform Marcus D. Hanwell, Donald Ephraim Curtis, David C. Lonie et al. · Journal of Cheminformatics | 13 Aug 2012 | 10,759 |
| 13 | UCSF ChimeraX : Structure visualization for researchers, educators, and developers Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Protein Science | 3 Sep 2020 | 10,674 |
| 14 | A Design Framework for Instrumenting Analytic Provenance for Problem-Solving Tasks Lingxue Yang, Pierre Morizet‐Mahoudeaux, Anne Guénand et al. · Advances in intelligent systems and computing | 2018 | 6,603 |
| 15 | The Anatomy of the Grid: Enabling Scalable Virtual Organizations Ian Foster, Carl Kesselman, Steven Tuecke · The International Journal of High Performance Computing Applications | Aug 2001 | 6,580 |
| 16 | ImageJ2: ImageJ for the next generation of scientific image data Curtis Rueden, Johannes Schindelin, Mark Hiner et al. · BMC Bioinformatics | 29 Nov 2017 | 6,379 |
| 17 | UCSF ChimeraX: Meeting modern challenges in visualization and analysis Thomas D. Goddard, Conrad C. Huang, Elaine C. Meng et al. · Protein Science | 14 Jul 2017 | 6,046 |
| 18 | The Pfam protein families database in 2019 Sara El-Gebali, Jaina Mistry, Alex Bateman et al. · Nucleic Acids Research | 9 Oct 2018 | 5,256 |
| 19 | How good are my data and what is the resolution? Philip Rainsford Evans, Garib N. Murshudov · Acta Crystallographica Section D Biological Crystallography | 12 Jun 2013 | 5,147 |
| 20 | Comparison of PubMed, Scopus, Web of Science, and Google Scholar: strengths and weaknesses Matthew E. Falagas, Eleni I. Pitsouni, George A. Malietzis et al. · The FASEB Journal | 20 Sep 2007 | 5,038 |
| 21 | circlize implements and enhances circular visualization in R Zuguang Gu, Lei Gu, Roland Eils et al. · Bioinformatics | 14 Jun 2014 | 4,735 |
| 22 | The Cancer Imaging Archive (TCIA): Maintaining and Operating a Public Information Repository Kenneth Clark, Bruce A. Vendt, Kirk Smith et al. · Journal of Imaging Informatics in Medicine | 24 Jul 2013 | 4,730 |
| 23 | Nextflow enables reproducible computational workflows Paolo Di Tommaso, Maria Chatzou, Evan W. Floden et al. · Nature Biotechnology | Apr 2017 | 4,440 |
| 24 | The nf-core framework for community-curated bioinformatics pipelines Philip Ewels, Alexander Peltzer, Sven Fillinger et al. · Nature Biotechnology | 13 Feb 2020 | 4,389 |
| 25 | deepTools: a flexible platform for exploring deep-sequencing data Fidel Ramírez, Friederike Dündar, Sarah K. Diehl et al. · Nucleic Acids Research | 5 May 2014 | 4,306 |
| 26 | Generic Mapping Tools: Improved Version Released Paul Wessel, Walter H. F. Smith, Remko Scharroo et al. · Eos | 5 Nov 2013 | 4,121 |
| 27 | The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Enis Afgan, Dannon Baker, Bérénice Batut et al. · Nucleic Acids Research | 3 May 2018 | 4,017 |
| 28 | AliView: a fast and lightweight alignment viewer and editor for large datasets Anders O. Larsson · Bioinformatics | 5 Aug 2014 | 3,951 |
| 29 | [26] Raster3D: Photorealistic molecular graphics Ethan A. Merritt, David Bacon · Methods in enzymology on CD-ROM/Methods in enzymology | 1997 | 3,759 |
| 30 | A manifesto for reproducible science Marcus Robert Munafo, Brian A. Nosek, Dorothy Bishop et al. · Nature Human Behaviour | 10 Jan 2017 | 3,631 |
| 31 | Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences Jeremy Goecks, ANTON Y NEKRUTENKO, James Taylor et al. · Genome biology | 25 Aug 2010 | 3,572 |
| 32 | Wikidata Denny Vrandečić, Markus Krötzsch · Communications of the ACM | 23 Sep 2014 | 3,414 |
| 33 | Unipro UGENE: a unified bioinformatics toolkit Konstantin Okonechnikov, Olga Golosova, Mikhail Fursov et al. · Bioinformatics | 24 Feb 2012 | 3,350 |
| 34 | XSEDE: Accelerating Scientific Discovery John W. Towns, Timothy M. Cockerill, Maytal Dahan et al. · Computing in Science & Engineering | 25 Jul 2014 | 3,332 |
| 35 | Snakemake—a scalable bioinformatics workflow engine Johannes Köster, Sven Rahmann · Bioinformatics | 20 Aug 2012 | 3,230 |
| 36 | Science mapping software tools: Review, analysis, and cooperative study among tools Manuel J. Cobo, Antonio Gabriel López-Herrera, Enrique Herrera‐Viedma et al. · Journal of the American Society for Information Science and Technology | 2 May 2011 | 3,215 |
| 37 | Basis Set Exchange: A Community Database for Computational Sciences Karen L. Schuchardt, Brett Didier, Todd Elsethagen et al. · Journal of Chemical Information and Modeling | 12 Apr 2007 | 3,189 |
| 38 | Verification, Validation, and Confirmation of Numerical Models in the Earth Sciences Наоми Орескес, Kristin Shrader‐Frechette, Kenneth Belitz · Science | 4 Feb 1994 | 3,049 |
| 39 | Cloud Computing and Grid Computing 360-Degree Compared Ian Foster, Yong Zhao, Ioan Raicu et al. | Nov 2008 | 2,917 |
| 40 | Laboratory life: The social construction of scientific facts James Bliss Austin · Social Science & Medicine | 1982 | 2,910 |
| 41 | Singularity: Scientific containers for mobility of compute Gregory M. Kurtzer, Vanessa Sochat, Michael W. Bauer · PLoS ONE | 11 May 2017 | 2,867 |
| 42 | Redefine statistical significance Daniel Jacob Benjamin et al. · Nature Human Behaviour | 31 Aug 2017 | 2,853 |
| 43 | InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams Henry Heberle, Gabriela Vaz Meirelles, Felipe Rodrigues da Silva et al. · BMC Bioinformatics | 20 May 2015 | 2,772 |
| 44 | Jupyter Notebooks – a publishing format for reproducible computational workflows Thomas A. Kluyver, Benjamin Ragan-Kelley, Pérez Fernando et al. · IOS Press eBooks | 2016 | 2,619 |
| 45 | MadGraph 5: going beyond Johan Alwall, Michel Herquet, Fabio Maltoni et al. · Journal of High Energy Physics | Jun 2011 | 2,609 |
| 46 | Search and sequence analysis tools services from EMBL-EBI in 2022 Fábio Madeira, Matt Pearce, Adrian R. Tivey et al. · Nucleic Acids Research | 28 Mar 2022 | 2,558 |
| 47 | Raster3D Version 2.0. A program for photorealistic molecular graphics Ethan A. Merritt, Michael E. P. Murphy · Acta Crystallographica Section D Biological Crystallography | Nov 1994 | 2,531 |
| 48 | Apache Spark Matei Zaharia, Reynold Xin, Patrick Wendell et al. · Communications of the ACM | 28 Oct 2016 | 2,450 |
| 49 | The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update Enis Afgan, Dannon Baker, Marius van den Beek et al. · Nucleic Acids Research | 2 May 2016 | 2,369 |
| 50 | AdapterRemoval v2: rapid adapter trimming, identification, and read merging Mikkel Schubert, Stinus Lindgreen, Ludovic Orlando · BMC Research Notes | 11 Feb 2016 | 2,333 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.