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1.

Research   Open Access Highly Accessed

Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life

Vincent S Smith, Simon D Rycroft, Kehan T Harman, Ben Scott, David Roberts BMC Bioinformatics 2009, 10(Suppl 14):S6 (10 November 2009)

Abstract | Full text | PDF | PubMed |  Editor’s summary

Scratchpads, a new social networking tool for natural history researchers and enthusiasts, links information from disparate sources, encourages data sharing, and promotes the ultimate goal of describing and synthesising all facets of the diversity of life.

2.

Methodology article   Open Access Highly Accessed

Multiple consensus trees: a method to separate divergent genes

Alain Guenoche BMC Bioinformatics 2013, 14:46 (9 February 2013)

Abstract | Provisional PDF | PubMed

3.

Methodology article   Open Access

A novel method for cross-species gene expression analysis

Erik Kristiansson, Tobias Österlund, Lina Gunnarsson, Gabriella Arne, D G Joakim Larsson, Olle Nerman BMC Bioinformatics 2013, 14:70 (27 February 2013)

Abstract | Provisional PDF

4.

Methodology article   Open Access

Statistical method on nonrandom clustering with application to somatic mutations in cancer

Jingjing Ye, Adam Pavlicek, Elizabeth A Lunney, Paul A Rejto, Chi-Hse Teng BMC Bioinformatics 2010, 11:11 (7 January 2010)

Abstract | Full text | PDF | PubMed

5.

Methodology article   Open Access Highly Accessed

Efficient alignment of pyrosequencing reads for re-sequencing applications

Francisco Fernandes, Paulo GS da Fonseca, Luis MS Russo, Arlindo L Oliveira, Ana T Freitas BMC Bioinformatics 2011, 12:163 (16 May 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

6.

Software   Open Access Highly Accessed

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

Bo Li, Colin N Dewey BMC Bioinformatics 2011, 12:323 (4 August 2011)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central |  Editor’s summary

RSEM is a new user-friendly software tool for quantifying transcript abundance from RNA-seq data that does not rely on a reference genome and is particularly useful for quantification with de novo transcriptome assemblies

7.

Software   Open Access Highly Accessed

TeraStitcher - A tool for fast automatic 3D-stitching of teravoxel-sized microscopy images

Alessandro Bria, Giulio Iannello BMC Bioinformatics 2012, 13:316 (27 November 2012)

Abstract | Full text | PDF | PubMed |  Editor’s summary

TeraStitcher, a freely available tool, permits retrieval and processing of images generated using approximate tile positions to stitch Teravoxel-sized tiled microscopy images from large amounts of data even on memory limited machines.

8.

Research article   Open Access Highly Accessed

A comparative evaluation of sequence classification programs

Adam L Bazinet, Michael P Cummings BMC Bioinformatics 2012, 13:92 (10 May 2012)

Abstract | Full text | PDF | PubMed

9.

Software   Open Access Highly Accessed

The taxonomic name resolution service: an online tool for automated standardization of plant names

Brad Boyle, Nicole Hopkins, Zhenyuan Lu, Juan Antonio Raygoza Garay, Dmitry Mozzherin, Tony Rees, Naim Matasci, Martha L Narro, William H Piel, Sheldon J Mckay, Sonya Lowry, Chris Freeland, Robert K Peet, Brian J Enquist BMC Bioinformatics 2013, 14:16 (16 January 2013)

Abstract | Full text | PDF | PubMed

10.

Methodology article   Open Access Highly Accessed

MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, Ca only models, Alternative alignments, and Non-sequential alignments

Shintaro Minami, Kengo Sawada, George Chikenji BMC Bioinformatics 2013, 14:24 (18 January 2013)

Abstract | Provisional PDF | PubMed

11.

Database   Open Access Highly Accessed

An integrated pharmacokinetics ontology and corpus for text mining

Heng-Yi Wu, Shreyas Karnik, Abhinita Subhadarshini, Zhiping Wang, Santosh Philips, Xu Han, Chienwei Chiang, Lei Liu, Malaz Boustani, Luis M Rocha, Sara K Quinney, David Flockhart, Lang Li BMC Bioinformatics 2013, 14:35 (1 February 2013)

Abstract | Full text | PDF | PubMed

12.

Research article   Open Access Highly Accessed

The evolutionary rate of antibacterial drug targets

Arkadiusz Gladki, Szymon Kaczanowski, Pawel Szczesny, Piotr Zielenkiewicz BMC Bioinformatics 2013, 14:36 (1 February 2013)

Abstract | Provisional PDF | PubMed

13.

Software   Open Access Highly Accessed

FANTOM: Functional and taxonomic analysis of metagenomes

Kemal Sanli, Fredrik H Karlsson, Intawat Nookaew, Jens Nielsen BMC Bioinformatics 2013, 14:38 (1 February 2013)

Abstract | Full text | PDF | PubMed

14.

Software   Open Access Highly Accessed

Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

Anthony G Doran, Christopher J Creevey BMC Bioinformatics 2013, 14:45 (8 February 2013)

Abstract | Full text | PDF | PubMed

15.

Methodology article   Open Access

Genome sequence-based species delimitation with confidence intervals and improved distance functions

Jan P Meier-Kolthoff, Alexander F Auch, Hans-Peter Klenk, Markus Göker BMC Bioinformatics 2013, 14:60 (21 February 2013)

Abstract | Provisional PDF | PubMed

16.

Research article   Open Access Highly Accessed

GeneRank: Using search engine technology for the analysis of microarray experiments

Julie L Morrison, Rainer Breitling, Desmond J Higham, David R Gilbert BMC Bioinformatics 2005, 6:233 (21 September 2005)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

17.

Methodology article   Open Access Highly Accessed

Statistical significance of quantitative PCR

Yann Karlen, Alan McNair, Sébastien Perseguers, Christian Mazza, Nicolas Mermod BMC Bioinformatics 2007, 8:131 (20 April 2007)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

18.

Research   Open Access

CMKb: a web-based prototype for integrating Australian Aboriginal customary medicinal plant knowledge

Jitendra Gaikwad, Varun Khanna, Subramanyam Vemulpad, Joanne Jamie, Jim Kohen, Shoba Ranganathan BMC Bioinformatics 2008, 9(Suppl 12):S25 (12 December 2008)

Abstract | Full text | PDF | PubMed | Cited on BioMed Central

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