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		Research A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S Nevalainen, Tero Aittokallio BioData Mining 2012, 5:2 (26 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New multilevel network layout algorithms allow researchers to create biologically relevant and visually pleasing network graphs for large datasets within a multi optimization framework.
		Software article Caipirini: using gene sets to rank literature Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Wanderley-Nogueira, Nina Soares-Cavalcanti, Reinhard Schneider BioData Mining 2012, 5:1 (1 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 'Caipirini', a new software program, allows ranking of biomedical literature based on biological relevance to gene sets, thereby enabling data from these high-throughput experiments to be more easily accessed.
		Research Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers J Nikolaj Dybowski, Mona Riemenschneider, Sascha Hauke, Martin Pyka, Jens Verheyen, Daniel Hoffmann, Dominik Heider BioData Mining 2011, 4:26 (14 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Machine-learning can be used to predict the resistance of HIV-1 to antiretroviral drugs like Bevirimat in order to identify which patients will benefit from these new drugs, thereby improving the provision of a personalized therapy.
		Editorial Mining the diseasome Davnah Urbach, Jason H Moore BioData Mining 2011, 4:25 (9 September 2011) Abstract \| Full text \| PDF \| PubMed
		Software article An R package implementation of multifactor dimensionality reduction Stacey J Winham, Alison A Motsinger-Reif BioData Mining 2011, 4:24 (16 August 2011) Abstract \| Full text \| PDF \| PubMed
		Research Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction Camelia Chira, Dragos Horvath, D Dumitrescu BioData Mining 2011, 4:23 (30 July 2011) Abstract \| Full text \| PDF \| PubMed
		Short report Detection of putative new mutacins by bioinformatic analysis using available web tools Guillaume G Nicolas BioData Mining 2011, 4:22 (14 July 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Evolving hard problems: Generating human genetics datasets with a complex etiology Daniel S Himmelstein, Casey S Greene, Jason H Moore BioData Mining 2011, 4:21 (7 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research Taxon ordering in phylogenetic trees by means of evolutionary algorithms Francesco Cerutti, Luigi Bertolotti, Tony L Goldberg, Mario Giacobini BioData Mining 2011, 4:20 (1 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization Sinan Erten, Gurkan Bebek, Rob M Ewing, Mehmet Koyutürk BioData Mining 2011, 4:19 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Discrete derivative: a data slicing algorithm for exploration of sharing biological networks between rheumatoid arthritis and coronary heart disease Guang Zheng, Miao Jiang, Xiaojuan He, Jing Zhao, Hongtao Guo, Gao Chen, Qinglin Zha, Aiping Lu BioData Mining 2011, 4:18 (23 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research Comprehensive analysis of human microRNA target networks Jun-ichi Satoh, Hiroko Tabunoki BioData Mining 2011, 4:17 (17 June 2011) Abstract \| Full text \| PDF \| PubMed
		Short report Interpol: An R package for preprocessing of protein sequences Dominik Heider, Daniel Hoffmann BioData Mining 2011, 4:16 (17 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation Pablo C Echeverría, Fedor Forafonov, Deo P Pandey, Guillaume Mühlebach, Didier Picard BioData Mining 2011, 4:15 (14 June 2011) Abstract \| Full text \| PDF \| PubMed
		Editorial Mining beyond the exome Davnah Urbach, Jason H Moore BioData Mining 2011, 4:14 (13 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Preprocessing differential methylation hybridization microarray data Shuying Sun, Yi-Wen Huang, Pearlly S Yan, Tim HM Huang, Shili Lin BioData Mining 2011, 4:13 (16 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research A comparison of machine learning techniques for survival prediction in breast cancer Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Mauro Antoniotti, Paolo Provero, Mario Giacobini BioData Mining 2011, 4:12 (11 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research The effects of linkage disequilibrium in large scale SNP datasets for MDR Benjamin J Grady, Eric S Torstenson, Marylyn D Ritchie BioData Mining 2011, 4:11 (5 May 2011) Abstract \| Full text \| PDF \| PubMed
		Review Using graph theory to analyze biological networks Georgios A Pavlopoulos, Maria Secrier, Charalampos N Moschopoulos, Theodoros G Soldatos, Sophia Kossida, Jan Aerts, Reinhard Schneider, Pantelis G Bagos BioData Mining 2011, 4:10 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research pGQL: A probabilistic graphical query language for gene expression time courses Ruben Schilling, Ivan G Costa, Alexander Schliep BioData Mining 2011, 4:9 (18 April 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR Britney L Grayson, Thomas M Aune BioData Mining 2011, 4:8 (13 April 2011) Abstract \| Full text \| PDF \| PubMed
		Editorial Data mining and the evolution of biological complexity Davnah Urbach, Jason H Moore BioData Mining 2011, 4:7 (10 April 2011) Abstract \| Full text \| PDF \| PubMed
		Editorial The spatial dimension in biological data mining Davnah Urbach, Jason H Moore BioData Mining 2011, 4:6 (10 April 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Sami K Kilpinen, Kalle A Ojala, Olli P Kallioniemi BioData Mining 2011, 4:5 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies Thorsten Lehr, Jing Yuan, Dirk Zeumer, Supriya Jayadev, Marylyn D Ritchie BioData Mining 2011, 4:4 (1 March 2011) Abstract \| Full text \| PDF \| PubMed

	All
		Research A multilevel layout algorithm for visualizing physical and genetic interaction networks, with emphasis on their modular organization Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S Nevalainen, Tero Aittokallio BioData Mining 2012, 5:2 (26 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary New multilevel network layout algorithms allow researchers to create biologically relevant and visually pleasing network graphs for large datasets within a multi optimization framework.
		Software article Caipirini: using gene sets to rank literature Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Wanderley-Nogueira, Nina Soares-Cavalcanti, Reinhard Schneider BioData Mining 2012, 5:1 (1 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary 'Caipirini', a new software program, allows ranking of biomedical literature based on biological relevance to gene sets, thereby enabling data from these high-throughput experiments to be more easily accessed.
		Research Improved Bevirimat resistance prediction by combination of structural and sequence-based classifiers J Nikolaj Dybowski, Mona Riemenschneider, Sascha Hauke, Martin Pyka, Jens Verheyen, Daniel Hoffmann, Dominik Heider BioData Mining 2011, 4:26 (14 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Machine-learning can be used to predict the resistance of HIV-1 to antiretroviral drugs like Bevirimat in order to identify which patients will benefit from these new drugs, thereby improving the provision of a personalized therapy.
		Editorial Mining the diseasome Davnah Urbach, Jason H Moore BioData Mining 2011, 4:25 (9 September 2011) Abstract \| Full text \| PDF \| PubMed
		Software article An R package implementation of multifactor dimensionality reduction Stacey J Winham, Alison A Motsinger-Reif BioData Mining 2011, 4:24 (16 August 2011) Abstract \| Full text \| PDF \| PubMed
		Research Hill-Climbing search and diversification within an evolutionary approach to protein structure prediction Camelia Chira, Dragos Horvath, D Dumitrescu BioData Mining 2011, 4:23 (30 July 2011) Abstract \| Full text \| PDF \| PubMed
		Short report Detection of putative new mutacins by bioinformatic analysis using available web tools Guillaume G Nicolas BioData Mining 2011, 4:22 (14 July 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Evolving hard problems: Generating human genetics datasets with a complex etiology Daniel S Himmelstein, Casey S Greene, Jason H Moore BioData Mining 2011, 4:21 (7 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research Taxon ordering in phylogenetic trees by means of evolutionary algorithms Francesco Cerutti, Luigi Bertolotti, Tony L Goldberg, Mario Giacobini BioData Mining 2011, 4:20 (1 July 2011) Abstract \| Full text \| PDF \| PubMed
		Research DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization Sinan Erten, Gurkan Bebek, Rob M Ewing, Mehmet Koyutürk BioData Mining 2011, 4:19 (24 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Discrete derivative: a data slicing algorithm for exploration of sharing biological networks between rheumatoid arthritis and coronary heart disease Guang Zheng, Miao Jiang, Xiaojuan He, Jing Zhao, Hongtao Guo, Gao Chen, Qinglin Zha, Aiping Lu BioData Mining 2011, 4:18 (23 June 2011) Abstract \| Full text \| PDF \| PubMed
		Research Comprehensive analysis of human microRNA target networks Jun-ichi Satoh, Hiroko Tabunoki BioData Mining 2011, 4:17 (17 June 2011) Abstract \| Full text \| PDF \| PubMed
		Short report Interpol: An R package for preprocessing of protein sequences Dominik Heider, Daniel Hoffmann BioData Mining 2011, 4:16 (17 June 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Detection of changes in gene regulatory patterns, elicited by perturbations of the Hsp90 molecular chaperone complex, by visualizing multiple experiments with an animation Pablo C Echeverría, Fedor Forafonov, Deo P Pandey, Guillaume Mühlebach, Didier Picard BioData Mining 2011, 4:15 (14 June 2011) Abstract \| Full text \| PDF \| PubMed
		Editorial Mining beyond the exome Davnah Urbach, Jason H Moore BioData Mining 2011, 4:14 (13 June 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Preprocessing differential methylation hybridization microarray data Shuying Sun, Yi-Wen Huang, Pearlly S Yan, Tim HM Huang, Shili Lin BioData Mining 2011, 4:13 (16 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research A comparison of machine learning techniques for survival prediction in breast cancer Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Mauro Antoniotti, Paolo Provero, Mario Giacobini BioData Mining 2011, 4:12 (11 May 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research The effects of linkage disequilibrium in large scale SNP datasets for MDR Benjamin J Grady, Eric S Torstenson, Marylyn D Ritchie BioData Mining 2011, 4:11 (5 May 2011) Abstract \| Full text \| PDF \| PubMed
		Review Using graph theory to analyze biological networks Georgios A Pavlopoulos, Maria Secrier, Charalampos N Moschopoulos, Theodoros G Soldatos, Sophia Kossida, Jan Aerts, Reinhard Schneider, Pantelis G Bagos BioData Mining 2011, 4:10 (28 April 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research pGQL: A probabilistic graphical query language for gene expression time courses Ruben Schilling, Ivan G Costa, Alexander Schliep BioData Mining 2011, 4:9 (18 April 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology A comparison of genomic copy number calls by Partek Genomics Suite, Genotyping Console and Birdsuite algorithms to quantitative PCR Britney L Grayson, Thomas M Aune BioData Mining 2011, 4:8 (13 April 2011) Abstract \| Full text \| PDF \| PubMed
		Editorial Data mining and the evolution of biological complexity Davnah Urbach, Jason H Moore BioData Mining 2011, 4:7 (10 April 2011) Abstract \| Full text \| PDF \| PubMed
		Editorial The spatial dimension in biological data mining Davnah Urbach, Jason H Moore BioData Mining 2011, 4:6 (10 April 2011) Abstract \| Full text \| PDF \| PubMed
		Methodology Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data Sami K Kilpinen, Kalle A Ojala, Olli P Kallioniemi BioData Mining 2011, 4:5 (31 March 2011) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
		Research Rule based classifier for the analysis of gene-gene and gene-environment interactions in genetic association studies Thorsten Lehr, Jing Yuan, Dirk Zeumer, Supriya Jayadev, Marylyn D Ritchie BioData Mining 2011, 4:4 (1 March 2011) Abstract \| Full text \| PDF \| PubMed