Most cited papers in Machine Learning in Bioinformatics
What are the most cited papers in Machine Learning in Bioinformatics?
The most cited paper in Machine Learning in Bioinformatics is "CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice" (Julie Thompson, Desmond G. Higgins, Toby J. Gibson, 1994), with 65,356 citations. Next come "Highly accurate protein structure prediction with AlphaFold" (47,486) and "clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters" (39,704).
Showing 50 of 100 papers. Every paper with more than 2,633 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Julie Thompson, Desmond G. Higgins, Toby J. Gibson · Nucleic Acids Research | 1994 | 65,356 |
| 2 | Highly accurate protein structure prediction with AlphaFold John Jumper et al. · Nature | 15 Jul 2021 | 47,486 |
| 3 | clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters Guangchuang Yu, Li-Gen Wang, Yanyan Han et al. · OMICS A Journal of Integrative Biology | 28 Mar 2012 | 39,704 |
| 4 | Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Da Wei Huang, Brad T. Sherman, Richard A. Lempicki · Nature Protocols | 18 Dec 2008 | 37,929 |
| 5 | Search and clustering orders of magnitude faster than BLAST R. C. Edgar · Bioinformatics | 12 Aug 2010 | 22,013 |
| 6 | Fast and sensitive protein alignment using DIAMOND Benjamin Buchfink, Chao Xie, Daniel H. Huson · Nature Methods | 17 Nov 2014 | 15,753 |
| 7 | Prodigal: prokaryotic gene recognition and translation initiation site identification Doug Hyatt, Gwo-Liang Chen, Philip F. LoCascio et al. · BMC Bioinformatics | 8 Mar 2010 | 13,697 |
| 8 | Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences Weizhong Li, Adam Godzik · Bioinformatics | 26 May 2006 | 12,422 |
| 9 | A general method applicable to the search for similarities in the amino acid sequence of two proteins Saul B. Needleman, Christian D. Wunsch · Journal of Molecular Biology | Mar 1970 | 11,585 |
| 10 | VSEARCH: a versatile open source tool for metagenomics Torbjørn Rognes, Tomáš Flouri, Ben Nichols et al. · PeerJ | 18 Oct 2016 | 11,418 |
| 11 | Improved tools for biological sequence comparison. William R. Pearson, David J. Lipman · Proceedings of the National Academy of Sciences | Apr 1988 | 11,369 |
| 12 | InterProScan 5: genome-scale protein function classification PHILIP M. JONES, David Binns, Hsin-Yu Chang et al. · Bioinformatics | 22 Jan 2014 | 10,355 |
| 13 | ColabFold: making protein folding accessible to all Milot Mirdita, Konstantin Schütze, Yoshitaka Moriwaki et al. · Nature Methods | 30 May 2022 | 10,120 |
| 14 | MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization Kazutaka Katoh, John Rozewicki, Kazunori D. Yamada · Briefings in Bioinformatics | 7 Aug 2017 | 9,431 |
| 15 | SignalP 4.0: discriminating signal peptides from transmembrane regions Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne et al. · Nature Methods | 29 Sep 2011 | 9,256 |
| 16 | AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models Mihály Váradi et al. · Nucleic Acids Research | 19 Oct 2021 | 8,593 |
| 17 | BLAT —The BLAST -Like Alignment Tool W. James Kent · Genome Research | 20 Mar 2002 | 8,442 |
| 18 | Pfam: The protein families database in 2021 Jaina Mistry, Sara Chuguransky, Lowri Williams et al. · Nucleic Acids Research | 6 Oct 2020 | 8,165 |
| 19 | KEGG as a reference resource for gene and protein annotation Minoru I. Kanehisa, Yoko Sato, Masayuki Kawashima et al. · Nucleic Acids Research | 17 Oct 2015 | 8,051 |
| 20 | Molecular signatures database (MSigDB) 3.0 Arthur Liberzon, Aravind N. Subramanian, Reid M. Pinchback et al. · Bioinformatics | 5 May 2011 | 7,971 |
| 21 | Accelerated Profile HMM Searches Sean R. Eddy · PLoS Computational Biology | 20 Oct 2011 | 7,781 |
| 22 | cytoHubba: identifying hub objects and sub-networks from complex interactome Chia-Hao Chin, Shu-Hwa Chen, Hsin-Hung Wu et al. · BMC Systems Biology | Dec 2014 | 7,025 |
| 23 | Genome sequence-based species delimitation with confidence intervals and improved distance functions Jan P. Meier‐Kolthoff, Alexander F. Auch, Hans-Peter Klenk et al. · BMC Bioinformatics | 21 Feb 2013 | 6,885 |
| 24 | Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm P. Naresh Kumar, Steven Henikoff, Pauline C. Ng · Nature Protocols | 25 Jun 2009 | 6,821 |
| 25 | On the Properties of Neural Machine Translation: Encoder–Decoder Approaches Kyunghyun Cho, Bart van Merriënboer, Dzmitry Bahdanau et al. | 2014 | 6,731 |
| 26 | Toward understanding the origin and evolution of cellular organisms Minoru I. Kanehisa · Protein Science | 23 Aug 2019 | 6,691 |
| 27 | Pfam: the protein families database ROBERT FINN, Alex Bateman, Jody Clements et al. · Nucleic Acids Research | 27 Nov 2013 | 6,604 |
| 28 | HMMER web server: interactive sequence similarity searching ROBERT FINN, Jody Clements, Sean R. Eddy · Nucleic Acids Research | 18 May 2011 | 6,555 |
| 29 | Improved Prediction of Signal Peptides: SignalP 3.0 Jannick Dyrløv Bendtsen, Henrik Nielsen, Gunnar von Heijne et al. · Journal of Molecular Biology | 11 Jun 2004 | 6,413 |
| 30 | SCOP: A structural classification of proteins database for the investigation of sequences and structures Alexey G. Murzin, Steven E. Brenner, Tim Hubbard et al. · Journal of Molecular Biology | Apr 1995 | 6,359 |
| 31 | Protein Identification and Analysis Tools in the ExPASy Server Marc Ronald Wilkins, Elisabeth Gasteiger, Amos Bairoch et al. · Humana Press eBooks | 14 Nov 2003 | 6,262 |
| 32 | OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Li Li, Christian J. Stoeckert, David S. Roos · Genome Research | Sep 2003 | 6,221 |
| 33 | Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment Jürgen Cox, Nadin Neuhauser, Annette Michalski et al. · Journal of Proteome Research | 21 Jan 2011 | 5,975 |
| 34 | ExPASy: the proteomics server for in-depth protein knowledge and analysis Elisabeth Gasteiger · Nucleic Acids Research | 24 Jun 2003 | 5,809 |
| 35 | GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database Pierre-Alain Chaumeil, Aaron James Mussig, Philip Hugenholtz et al. · Bioinformatics | 14 Nov 2019 | 5,727 |
| 36 | Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ Jürgen Cox, Marco Y. Hein, Christian A. Luber et al. · Molecular & Cellular Proteomics | 18 Jun 2014 | 5,646 |
| 37 | MITOS: Improved de novo metazoan mitochondrial genome annotation Matthias Bernt, Alexander Donath, Frank Jühling et al. · Molecular Phylogenetics and Evolution | 6 Sep 2012 | 5,583 |
| 38 | Evolutionary-scale prediction of atomic-level protein structure with a language model Zeming Lin, Halil Akin, Roshan Rao et al. · Science | 16 Mar 2023 | 5,573 |
| 39 | Sensitive protein alignments at tree-of-life scale using DIAMOND Benjamin Buchfink, Klaus Reuter, Hajk‐Georg Drost · Nature Methods | Apr 2021 | 5,436 |
| 40 | Targeted Branching for the Maximum Independent Set Problem Using Graph Neural Networks Silva, Gabriel, Rodrigues, Mário, Teixeira, António et al. · DROPS (Schloss Dagstuhl – Leibniz Center for Informatics) | 2024 | 5,418 |
| 41 | Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites Henrik Nielsen, Jacob Engelbrecht, Søren Brunak et al. · Protein Engineering Design and Selection | 1997 | 5,394 |
| 42 | A review of feature selection techniques in bioinformatics Yvan Saeys, Iñaki Inza, Pedro Larrañaga · Bioinformatics | 24 Aug 2007 | 5,372 |
| 43 | The KEGG resource for deciphering the genome Minoru Kanehisa · Nucleic Acids Research | 17 Dec 2003 | 5,322 |
| 44 | I-TASSER server for protein 3D structure prediction Yang Zhang · BMC Bioinformatics | 23 Jan 2008 | 5,282 |
| 45 | Mosaic organization of DNA nucleotides Chung‐Kang Peng, Sergey V. Buldyrev, Shlomo Havlin et al. · Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics | Feb 1994 | 5,081 |
| 46 | MAFFT version 5: improvement in accuracy of multiple sequence alignment Kazutaka Katoh · Nucleic Acids Research | 19 Jan 2005 | 5,033 |
| 47 | SignalP 5.0 improves signal peptide predictions using deep neural networks José Juan Almagro Armenteros, Konstantinos D. Tsirigos, Casper Kaae Sønderby et al. · Nature Biotechnology | 18 Feb 2019 | 4,807 |
| 48 | The COG database: a tool for genome-scale analysis of protein functions and evolution Roman L. Tatusov · Nucleic Acids Research | 2000 | 4,760 |
| 49 | NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins Kim D. Pruitt, Tatiana A. Tatusova, D. R. Maglott · Nucleic Acids Research | 27 Nov 2006 | 4,718 |
| 50 | Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins Jean-Pierre Garnier, David J. Osguthorpe, Barry Robson · Journal of Molecular Biology | Mar 1978 | 4,566 |
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.