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	1. 903 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
	2. 849 Accesses	Research Fractal MapReduce decomposition of sequence alignment Jonas S Almeida, Alexander Gruneberg, Wolfgang Maass, Susana Vinga Algorithms for Molecular Biology 2012, 7:12 (2 May 2012) Abstract \| Provisional PDF \| PubMed
	3. 423 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 \| Provisional PDF \| PubMed
	4. 370 Accesses	Research Reconciling taxonomy and phylogenetic inference: formalism and algorithms for describing discord and inferring taxonomic roots Frederick A Matsen, Aaron Gallagher Algorithms for Molecular Biology 2012, 7:8 (2 May 2012) Abstract \| Provisional PDF \| PubMed
	5. 362 Accesses	Research Maximum Parsimony on Phylogenetic Networks Lavanya Kannan, Ward C Wheeler Algorithms for Molecular Biology 2012, 7:9 (2 May 2012) Abstract \| Provisional PDF \| PubMed
	6. 347 Accesses	Research Pattern matching through Chaos Game Representation: bridging numerical and discrete data structures for biological sequence analysis Susana Vinga, Alexandra M Carvalho, Alexandre P Francisco, Luis MS Russo, Jonas S Almeida Algorithms for Molecular Biology 2012, 7:10 (2 May 2012) Abstract \| Provisional PDF \| PubMed
	7. 327 Accesses	Research Computing evolutionary distinctiveness indices in large scale analysis Iain Martyn, Tyler S Kuhn, Arne O Mooers, Vincent Moulton, Andreas Spillner Algorithms for Molecular Biology 2012, 7:6 (13 April 2012) Abstract \| Full text \| PDF \| PubMed
	8. 323 Accesses	Research Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity Koji Kadota, Yuji Nakai, Kentaro Shimizu Algorithms for Molecular Biology 2009, 4:7 (22 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	9. 259 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
	10. 250 Accesses	Research A polynomial time algorithm for calculating the probability of a ranked gene tree given a species tree Tanja Stadler, James H. Degnan Algorithms for Molecular Biology 2012, 7:7 (30 April 2012) Abstract \| Provisional PDF \| PubMed
	11. 249 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
	12. 207 Accesses	Research A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements Stefan Enroth, Claes R Andersson, Robin Andersson, Claes Wadelius, Mats G Gustafsson, Jan Komorowski Algorithms for Molecular Biology 2012, 7:2 (16 January 2012) Abstract \| Full text \| PDF \| PubMed
	13. 202 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
	14. 201 Accesses	Research A weighted average difference method for detecting differentially expressed genes from microarray data Koji Kadota, Yuji Nakai, Kentaro Shimizu Algorithms for Molecular Biology 2008, 3:8 (26 June 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	15. 189 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
	16. 182 Accesses	Research A linear programming approach for estimating the structure of a sparse linear genetic network from transcript profiling data Sahely Bhadra, Chiranjib Bhattacharyya, Nagasuma R Chandra, I Saira Mian Algorithms for Molecular Biology 2009, 4:5 (24 February 2009) Abstract \| Full text \| PDF \| PubMed
	17. 181 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
	18. 175 Accesses	Software article CHSMiner: a GUI tool to identify chromosomal homologous segments Zhen Wang, Guohui Ding, Zhonghao Yu, Lei Liu, Yixue Li Algorithms for Molecular Biology 2009, 4:2 (15 January 2009) Abstract \| Full text \| PDF \| PubMed \| 1 comment
	19. 175 Accesses	Research Back-translation for discovering distant protein homologies in the presence of frameshift mutations Marta Gîrdea, Laurent Noé, Gregory Kucherov Algorithms for Molecular Biology 2010, 5:6 (4 January 2010) Abstract \| Full text \| PDF \| PubMed
	20. 174 Accesses	Research Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation Rodrigo Gouveia-Oliveira, Anders G Pedersen Algorithms for Molecular Biology 2007, 2:12 (3 October 2007) Abstract \| Full text \| PDF \| PubMed \| 1 comment
	21. 173 Accesses	Software article AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences Darío Guerrero, Rocío Bautista, David P Villalobos, Francisco R Cantón, M Gonzalo Claros Algorithms for Molecular Biology 2010, 5:24 (2 June 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	22. 171 Accesses	Research QTL/microarray approach using pathway information Hirokazu Matsuda, Yukio Taniguchi, Hiroaki Iwaisaki Algorithms for Molecular Biology 2012, 7:1 (15 January 2012) Abstract \| Full text \| PDF \| PubMed
	23. 162 Accesses	Research Robinson-Foulds Supertrees Mukul S Bansal, J Gordon Burleigh, Oliver Eulenstein, David Fernández-Baca Algorithms for Molecular Biology 2010, 5:18 (24 February 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	24. 159 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
	25. 159 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.