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	1. 518 Accesses	Research A simulation study comparing supertree and combined analysis methods using SMIDGen M Shel Swenson, François Barbançon, Tandy Warnow, C Randal Linder Algorithms for Molecular Biology 2010, 5:8 (4 January 2010) Abstract \| Full text \| PDF \| PubMed
	2. 430 Accesses	Research Efficient algorithms for training the parameters of hidden Markov models using stochastic expectation maximization (EM) training and Viterbi training Tin Y Lam, Irmtraud M Meyer Algorithms for Molecular Biology 2010, 5:38 (9 December 2010) Abstract \| Full text \| PDF \| PubMed
	3. 403 Accesses	Research Coexpression and coregulation analysis of time-series gene expression data in estrogen-induced breast cancer cell Anirban Bhar, Martin Haubrock, Anirban Mukhopadhyay, Ujjwal Maulik, Sanghamitra Bandyopadhyay, Edgar Wingender Algorithms for Molecular Biology 2013, 8:9 (23 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	4. 302 Accesses	Software article ViennaRNA Package 2.0 Ronny Lorenz, Stephan H Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F Stadler, Ivo L Hofacker Algorithms for Molecular Biology 2011, 6:26 (24 November 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	5. 255 Accesses	Research Estimation of alternative splicing isoform frequencies from RNA-Seq data Marius Nicolae, Serghei Mangul, Ion I Măndoiu, Alex Zelikovsky Algorithms for Molecular Biology 2011, 6:9 (19 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	6. 245 Accesses	Research Differential co-expression framework to quantify goodness of biclusters and compare biclustering algorithms Burton Chia, R Krishna Murthy Karuturi Algorithms for Molecular Biology 2010, 5:23 (28 May 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	7. 239 Accesses	Research Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules Valentina Boeva, Julien Clément, Mireille Régnier, Mikhail A Roytberg, Vsevolod J Makeev Algorithms for Molecular Biology 2007, 2:13 (10 October 2007) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	8. 237 Accesses	Research A normalization strategy for comparing tag count data Koji Kadota, Tomoaki Nishiyama, Kentaro Shimizu Algorithms for Molecular Biology 2012, 7:5 (5 April 2012) Abstract \| Full text \| PDF \| PubMed
	9. 198 Accesses	Research Gene Ontology consistent protein function prediction: the FALCON algorithm applied to six eukaryotic genomes Yiannis AI Kourmpetis, Aalt DJ van Dijk, Cajo JF ter Braak Algorithms for Molecular Biology 2013, 8:10 (27 March 2013) Abstract \| Provisional PDF \| PubMed
	10. 188 Accesses	Research Fast calculation of the quartet distance between trees of arbitrary degrees Chris Christiansen, Thomas Mailund, Christian NS Pedersen, Martin Randers, Martin Stissing Algorithms for Molecular Biology 2006, 1:16 (25 September 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	11. 185 Accesses	Research An enhancement of binary particle swarm optimization for gene selection in classifying cancer classes Mohd Saberi Mohamad, Sigeru Omatu, Safaai Deris, Michifumi Yoshioka, Afnizanfaizal Abdullah, Zuwairie Ibrahim Algorithms for Molecular Biology 2013, 8:15 (24 April 2013) Abstract \| Provisional PDF \| PubMed
	12. 180 Accesses	Research Wrapper-based selection of genetic features in genome-wide association studies through fast matrix operations Tapio Pahikkala, Sebastian Okser, Antti Airola, Tapio Salakoski, Tero Aittokallio Algorithms for Molecular Biology 2012, 7:11 (2 May 2012) Abstract \| Full text \| PDF \| ePUB \| PubMed
	13. 176 Accesses	Research Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem Sylvain Soliman Algorithms for Molecular Biology 2012, 7:15 (29 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	14. 174 Accesses	Research Characteristics of predictor sets found using differential prioritization Chia Ooi, Madhu Chetty, Shyh Teng Algorithms for Molecular Biology 2007, 2:7 (4 June 2007) Abstract \| Full text \| PDF \| PubMed
	15. 168 Accesses	Research Ultrametric networks: a new tool for phylogenetic analysis Alberto Apostolico, Matteo Comin, Andres Dress, Laxmi Parida Algorithms for Molecular Biology 2013, 8:7 (5 March 2013) Abstract \| Provisional PDF \| PubMed
	16. 164 Accesses	Research A tree-based method for the rapid screening of chemical fingerprints Thomas G Kristensen, Jesper Nielsen, Christian NS Pedersen Algorithms for Molecular Biology 2010, 5:9 (4 January 2010) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Using a kD grid and Multibit tree to screen molecular fingerprint databases for chemical compounds with high similarity scores, based on the Tanimoto coefficient, is three times quicker than earlier methods, allowing researchers to identify novel drug candidates more efficiently.
	17. 162 Accesses	Research DIALIGN-TX: greedy and progressive approaches for segment-based multiple sequence alignment Amarendran R Subramanian, Michael Kaufmann, Burkhard Morgenstern Algorithms for Molecular Biology 2008, 3:6 (27 May 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	18. 160 Accesses	Research Maximum Parsimony on Phylogenetic networks Lavanya Kannan, Ward C Wheeler Algorithms for Molecular Biology 2012, 7:9 (2 May 2012) Abstract \| Full text \| PDF \| PubMed
	19. 153 Accesses	Research Distributional fold change test – a statistical approach for detecting differential expression in microarray experiments Vadim Farztdinov, Fionnuala McDyer Algorithms for Molecular Biology 2012, 7:29 (2 November 2012) Abstract \| Full text \| PDF \| PubMed
	20. 152 Accesses	Research Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing maps Peter Meinicke, Thomas Lingner, Alexander Kaever, Kirstin Feussner, Cornelia Göbel, Ivo Feussner, Petr Karlovsky, Burkhard Morgenstern Algorithms for Molecular Biology 2008, 3:9 (26 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	21. 149 Accesses	Research Multiple sequence alignment with user-defined anchor points Burkhard Morgenstern, Sonja J Prohaska, Dirk Pöhler, Peter F Stadler Algorithms for Molecular Biology 2006, 1:6 (19 April 2006) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	22. 149 Accesses	Software article Jane: a new tool for the cophylogeny reconstruction problem Chris Conow, Daniel Fielder, Yaniv Ovadia, Ran Libeskind-Hadas Algorithms for Molecular Biology 2010, 5:16 (3 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	23. 149 Accesses	Research LocARNAscan: Incorporating thermodynamic stability in sequence and structure-based RNA homology search Sebastian Will, Michael F. Siebauer, Steffen Heyne, Jan Engelhardt, Peter F. Stadler, Kristin Reiche, Rolf Backofen Algorithms for Molecular Biology 2013, 8:14 (20 April 2013) Abstract \| Provisional PDF \| PubMed
	24. 146 Accesses	Research Reconciliation and local gene tree rearrangement can be of mutual profit Thi Hau Nguyen, Vincent Ranwez, Stéphanie Pointet, Anne-Muriel Arigon Chifolleau, Jean-Philippe Doyon, Vincent Berry Algorithms for Molecular Biology 2013, 8:12 (8 April 2013) Abstract \| Provisional PDF \| PubMed
	25. 144 Accesses	Meeting report Data Mining in Bioinformatics (BIOKDD) Mohammed J Zaki, George Karypis, Jiong Yang Algorithms for Molecular Biology 2007, 2:4 (11 April 2007) Abstract \| Full text \| PDF \| PubMed