BMC Bioinformatics

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Mistaken Identifiers: Gene name errors can be introduced inadvertently when using Excel in bioinformatics

Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett and John N Weinstein*

BMC Bioinformatics 2004, 5:80 doi:10.1186/1471-2105-5-80

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Research   Open Access

Annotating the human genome with Disease Ontology

John D Osborne, Jared Flatow, Michelle Holko, Simon M Lin, Warren A Kibbe, Lihua Zhu, Maria I Danila, Gang Feng, Rex L Chisholm BMC Genomics 2009, 10(Suppl 1):S6 (7 July 2009)

Database   Open Access

CellMiner: a relational database and query tool for the NCI-60 cancer cell lines

Uma T Shankavaram, Sudhir Varma, David Kane, Margot Sunshine, Krishna K Chary, William C Reinhold, Yves Pommier, John N Weinstein BMC Genomics 2009, 10:277 (23 June 2009)

Research   Open Access

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

Pan Du, Warren A Kibbe, Simon M Lin Biology Direct 2007, 2:16 (31 May 2007)

Commentary   Open Access Highly Accessed

A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB

Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert, Joseph White, Patricia L Whetzel, Farrell Wymore, Helen Parkinson, Ugis Sarkans, Catherine A Ball, Alvis Brazma BMC Bioinformatics 2006, 7:489 (6 November 2006)

A new spreadsheet-based format for microarray data, MAGE-TAB, is simple to use and fully compliant with MIAME and MAGE-ML standards making it very suitable for labs without bioinformatics expertise.

Software   Open Access

Goulphar: rapid access and expertise for standard two-color microarray normalization methods

Sophie Lemoine, Florence Combes, Nicolas Servant, Stéphane Le Crom BMC Bioinformatics 2006, 7:467 (23 October 2006)

Review   Free Highly Accessed

Text-mining and information-retrieval services for molecular biology

Martin Krallinger, Alfonso Valencia Genome Biology 2005, 6:224 (28 June 2005)

A range of text-mining applications have been developed recently that will improve access to knowledge for biologists and database annotators.

Software   Open Access Highly Accessed

CoPub Mapper: mining MEDLINE based on search term co-publication

Blaise TF Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman, Guido Jenster BMC Bioinformatics 2005, 6:51 (11 March 2005)

Software   Open Access

GenomeViz: visualizing microbial genomes

Rohit Ghai, Torsten Hain, Trinad Chakraborty BMC Bioinformatics 2004, 5:198 (15 December 2004)