Topic · Algorithms and Data Compression
Most cited papers in Algorithms and Data Compression
What are the most cited papers in Algorithms and Data Compression?
The most cited paper in Algorithms and Data Compression is "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs" (Stephen F. Altschul, 1997), with 75,032 citations. Next come "The Sequence Alignment/Map format and SAMtools" (69,061) and "Fast and accurate short read alignment with Burrows–Wheeler transform" (63,989).
Showing 50 of 99 papers. Every paper with more than 1,916 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | Gapped BLAST and PSI-BLAST: a new generation of protein database search programs Stephen F. Altschul · Nucleic Acids Research | Sep 1997 | 75,032 |
| 2 | The Sequence Alignment/Map format and SAMtools Heng Li, Bob Handsaker, Alec Wysoker et al. · Bioinformatics | 8 Jun 2009 | 69,061 |
| 3 | Fast and accurate short read alignment with Burrows–Wheeler transform Heng Li, Richard M. Durbin · Bioinformatics | 18 May 2009 | 63,989 |
| 4 | Fast gapped-read alignment with Bowtie 2 Ben Langmead, Steven L. Salzberg · Nature Methods | 4 Mar 2012 | 62,825 |
| 5 | XGBoost Tianqi Chen, Carlos Guestrin | 8 Aug 2016 | 53,418 |
| 6 | Fast Parallel Algorithms for Short-Range Molecular Dynamics Steven J. Plimpton · Journal of Computational Physics | Mar 1995 | 45,350 |
| 7 | The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools Julie Thompson · Nucleic Acids Research | 15 Dec 1997 | 39,325 |
| 8 | The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data Aaron McKenna, Matthew G. Hanna, Eric Banks et al. · Genome Research | 19 Jul 2010 | 30,696 |
| 9 | IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies Lam-Tung Nguyen, Heiko A. Schmidt, Arndt von Haeseler et al. · Molecular Biology and Evolution | 3 Nov 2014 | 28,418 |
| 10 | Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Ben Langmead, Cole Trapnell, Mihai Pop et al. · Genome biology | 4 Mar 2009 | 23,344 |
| 11 | Array programming with NumPy Cr Harris et al. · RePEc: Research Papers in Economics | 17 Sep 2020 | 18,804 |
| 12 | MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Kazutaka Katoh · Nucleic Acids Research | 15 Jul 2002 | 18,198 |
| 13 | Fast and accurate long-read alignment with Burrows–Wheeler transform Heng Li, Richard M. Durbin · Bioinformatics | 15 Jan 2010 | 13,151 |
| 14 | Conditional Random Fields: Probabilistic Models for Segmenting and Labeling Sequence Data John Lafferty, Andrew McCallum, Fernando C. N. Pereira · ScholarlyCommons (University of Pennsylvania) | 28 Jun 2001 | 12,952 |
| 15 | A Study of Cross-Validation and Bootstrap for Accuracy Estimation and Model Selection Ron Kohavi | 1995 | 10,735 |
| 16 | Tensor Decompositions and Applications Tamara G. Kolda, Brett W. Bader · SIAM Review | 5 Aug 2009 | 10,717 |
| 17 | Identification of common molecular subsequences Temple F. Smith, Michael S. Waterman · Journal of Molecular Biology | Mar 1981 | 10,175 |
| 18 | Foundations of statistical natural language processing Christopher D. Manning, Hinrich Schütze | 1999 | 9,960 |
| 19 | 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 |
| 20 | Canu: scalable and accurate long-read assembly via adaptive k -mer weighting and repeat separation Sergey Koren, Brian P. Walenz, Konstantin Berlin et al. · Genome Research | 15 Mar 2017 | 8,344 |
| 21 | An algorithm for suffix stripping Martin Porter · Data Technologies and Applications | Mar 1980 | 8,165 |
| 22 | Text categorization with Support Vector Machines: Learning with many relevant features Thorsten Joachims · Lecture notes in computer science | 1998 | 8,050 |
| 23 | Machine learning in automated text categorization Fabrizio Sebastiani · ACM Computing Surveys | Mar 2002 | 7,956 |
| 24 | Multidimensional binary search trees used for associative searching Jon Louis Bentley · Communications of the ACM | Sep 1975 | 7,627 |
| 25 | A Rapid Bootstrap Algorithm for the RAxML Web Servers Alexandros Stamatakis, Paul Hoover, Jacques Rougemont · Systematic Biology | Oct 2008 | 7,132 |
| 26 | Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Brent Ewing, LaDeana Hillier, Michael C. Wendl et al. · Genome Research | Mar 1998 | 7,077 |
| 27 | Factor graphs and the sum-product algorithm Frank R. Kschischang, Brendan J. Frey, Hans‐Andrea Loeliger · IEEE Transactions on Information Theory | 2001 | 6,555 |
| 28 | Survey of Clustering Algorithms Rui Xu, D. WunschII · IEEE Transactions on Neural Networks | May 2005 | 6,241 |
| 29 | Profile hidden Markov models. Sean R. Eddy · Bioinformatics | 1998 | 5,863 |
| 30 | A Greedy Algorithm for Aligning DNA Sequences Zheng Zhang, Scott Schwartz, Lukas Wagner et al. · Journal of Computational Biology | Feb 2000 | 5,704 |
| 31 | Combining labeled and unlabeled data with co-training Avrim L. Blum, Tom M. Mitchell | 24 Jul 1998 | 5,638 |
| 32 | A universal algorithm for sequential data compression J. Ziv, Abraham Lempel · IEEE Transactions on Information Theory | May 1977 | 5,517 |
| 33 | CAP3: A DNA Sequence Assembly Program Xiaoqiu Huang, Anup Madan · Genome Research | Sep 1999 | 5,381 |
| 34 | A fast, lock-free approach for efficient parallel counting of occurrences of k -mers Guillaume Marçais, Carl Kingsford · Bioinformatics | 7 Jan 2011 | 5,222 |
| 35 | Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Trisha L. Bailey, Charles Elkan · PubMed | 1994 | 5,115 |
| 36 | The Google file system Sanjay Ghemawat, Howard Gobioff, Shun-Tak A. Leung · ACM SIGOPS Operating Systems Review | 19 Oct 2003 | 5,006 |
| 37 | KAAS: an automatic genome annotation and pathway reconstruction server Yuki Moriya, Masumi Itoh, Shujiro Okuda et al. · Nucleic Acids Research | 8 May 2007 | 4,385 |
| 38 | Approximate nearest neighbors Piotr Indyk, Rajeev Motwani | 1998 | 4,253 |
| 39 | A Theory of the Learnable Leslie Gabriel Valiant · ACM eBooks | 1984 | 4,219 |
| 40 | MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies Dongwan Don Kang, Feng Li, Edward Kirton et al. · PeerJ | 26 Jul 2019 | 4,119 |
| 41 | SOAP2: an improved ultrafast tool for short read alignment Ruiqiang Li, Chang Yu, Yingrui Li et al. · Bioinformatics | 3 Jun 2009 | 3,935 |
| 42 | The JPEG still picture compression standard Gregory K. Wallace · Communications of the ACM | Apr 1991 | 3,800 |
| 43 | The global k-means clustering algorithm Aristidis C. Likas, Nikos Vlassis, Jakob J. Verbeek · Pattern Recognition | 28 Oct 2002 | 3,786 |
| 44 | Channel coding with multilevel/phase signals G. Ungerboeck · IEEE Transactions on Information Theory | 1982 | 3,779 |
| 45 | A hierarchical O(N log N) force-calculation algorithm Josh Barnes, Piet Hut · Nature | Dec 1986 | 3,735 |
| 46 | Fast and accurate de novo genome assembly from long uncorrected reads Robert Vaser, Ivan Sović, Niranjan Nagarajan et al. · Genome Research | 18 Jan 2017 | 3,569 |
| 47 | Algorithms on strings, trees, and sequences computer science and computational biology Dan Gusfield | 1997 | 3,534 |
| 48 | Sequence logos: a new way to display consensus sequences Thomas Dana Schneider, Robert M. Stephens · Nucleic Acids Research | 1990 | 3,515 |
| 49 | Compression of individual sequences via variable-rate coding J. Ziv, Abraham Lempel · IEEE Transactions on Information Theory | Sep 1978 | 3,474 |
| 50 | The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote Yang Liao, Gordon K. Smyth, Wei Shi · Nucleic Acids Research | 3 Apr 2013 | 3,448 |
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.