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1.
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Molecular ecological network analyses
Ye Deng, Yi-Huei Jiang, Yunfeng Yang, Zhili He, Feng Luo, Jizhong Zhou BMC Bioinformatics 2012, 13:113 (30 May 2012)
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Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom
Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L Reichel, Nathan R Stewart, Ryan D Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W Sykes, Jason N Burris, Joseph J Bozell, (Max) Zong-Ming Cheng, Douglas G Hayes, Nicole Labbe, Mark Davis, C Neal Stewart, Joshua S Yuan BMC Bioinformatics 2009, 10(Suppl 11):S3 (8 October 2009)
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| PubMed | Cited on BioMed Central
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Artificial and natural duplicates in pyrosequencing reads of metagenomic data
Beifang Niu, Limin Fu, Shulei Sun, Weizhong Li BMC Bioinformatics 2010, 11:187 (13 April 2010)
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| PubMed | Cited on BioMed Central
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Scaffold filling, contig fusion and comparative gene order inference
Adriana Muñoz, Chunfang Zheng, Qian Zhu, Victor A Albert, Steve Rounsley, David Sankoff BMC Bioinformatics 2010, 11:304 (4 June 2010)
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| PubMed | Cited on BioMed Central
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CloVR: A virtual machine for automated and portable sequence analysis from the desktop using cloud computing
Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011)
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Editor’s summary
Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
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6.
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MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity
Dinesh K Barupal, Pradeep K Haldiya, Gert Wohlgemuth, Tobias Kind, Shanker L Kothari, Kent E Pinkerton, Oliver Fiehn BMC Bioinformatics 2012, 13:99 (16 May 2012)
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7.
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Self consistency grouping: a stringent clustering method
Bong-Hyun Kim, Bhadrachalam Chitturi, Nick V Grishin BMC Bioinformatics 2012, 13(Suppl 13):S3 (24 August 2012)
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Accuracy of RNA-Seq and its dependence on sequencing depth
Guoshuai Cai, Hua Li, Yue Lu, Xuelin Huang, Juhee Lee, Peter Müller, Yuan Ji, Shoudan Liang BMC Bioinformatics 2012, 13(Suppl 13):S5 (24 August 2012)
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svapls: an R package to correct for hidden factors of variability in gene expression studies
Sutirtha Chakraborty, Somnath Datta, Susmita Datta BMC Bioinformatics 2013, 14:236 (24 July 2013)
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A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments
Mikel Esnaola, Pedro Puig, David Gonzalez, Robert Castelo, Juan R Gonzalez BMC Bioinformatics 2013, 14:254 (21 August 2013)
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A multiple-alignment based primer design algorithm for genetically highly variable DNA targets
Johanna Brodin, Mohan Krishnamoorthy, Gayathri Athreya, Will Fischer, Peter Hraber, Cheryl Gleasner, Lance Green, Bette Korber, Thomas Leitner BMC Bioinformatics 2013, 14:255 (21 August 2013)
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A balanced iterative random forest for gene selection from microarray data
Ali Anaissi, Paul J Kennedy, Madhu Goyal, Daniel R Catchpoole BMC Bioinformatics 2013, 14:261 (27 August 2013)
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NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Yingtao Bi, Ramana V Davuluri BMC Bioinformatics 2013, 14:262 (27 August 2013)
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14.
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inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis
Patrícia Soares, Renato J Alves, Ana B Abecasis, Carlos Penha-Gonçalves, M Gabriela M Gomes, José B Pereira-Leal BMC Bioinformatics 2013, 14:264 (30 August 2013)
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15.
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Levenshtein error-correcting barcodes for multiplexed DNA sequencing
Tilo Buschmann, Leonid V Bystrykh BMC Bioinformatics 2013, 14:272 (11 September 2013)
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16.
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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)
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17.
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CoNVEX: copy number variation estimation in exome sequencing data using HMM
Kaushalya C Amarasinghe, Jason Li, Saman K Halgamuge BMC Bioinformatics 2013, 14(Suppl 2):S2 (21 January 2013)
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18.
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Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction
Kishore J Doshi, Jamie J Cannone, Christian W Cobaugh, Robin R Gutell BMC Bioinformatics 2004, 5:105 (5 August 2004)
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