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Volume 13;  2012

Correspondence

Methods for visual mining of genomic and proteomic data atlases
John Boyle, Richard Kreisberg, Ryan Bressler, Sarah Killcoyne
BMC Bioinformatics. 2012; 13: 58. Published online 2012 April 23. doi: 10.1186/1471-2105-13-58
PMCID:
PMC3352268
Abstract Full Text PDF–6.4M

Database

MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
Akhil Kumar, Patrick F Suthers, Costas D Maranas
BMC Bioinformatics. 2012; 13: 6. Published online 2012 January 10. doi: 10.1186/1471-2105-13-6
PMCID:
PMC3277463
Abstract Full Text PDF–1.1M
PupDB: a database of pupylated proteins
Chun-Wei Tung
BMC Bioinformatics. 2012; 13: 40. Published online 2012 March 16. doi: 10.1186/1471-2105-13-40
PMCID:
PMC3314583
Abstract Full Text PDF–836K

Software

GuiTope: an application for mapping random-sequence peptides to protein sequences
Rebecca F Halperin, Phillip Stafford, Jack S Emery, Krupa Arun Navalkar, Stephen Albert Johnston
BMC Bioinformatics. 2012; 13: 1. Published online 2012 January 3. doi: 10.1186/1471-2105-13-1
PMCID:
PMC3280184
Abstract Full Text PDF–5.9M
ABrowse - a customizable next-generation genome browser framework
Lei Kong, Jun Wang, Shuqi Zhao, Xiaocheng Gu, Jingchu Luo, Ge Gao
BMC Bioinformatics. 2012; 13: 2. Published online 2012 January 5. doi: 10.1186/1471-2105-13-2
PMCID:
PMC3265404
Abstract Full Text PDF–634K Supplementary Material
proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
David Rosenkranz, Hans Zischler
BMC Bioinformatics. 2012; 13: 5. Published online 2012 January 10. doi: 10.1186/1471-2105-13-5
PMCID:
PMC3293768
Abstract Full Text PDF–819K Supplementary Material
An integrative variant analysis suite for whole exome next-generation sequencing data
Danny Challis, Jin Yu, Uday S Evani, Andrew R Jackson, Sameer Paithankar, Cristian Coarfa, Aleksandar Milosavljevic, Richard A Gibbs, Fuli Yu
BMC Bioinformatics. 2012; 13: 8. Published online 2012 January 12. doi: 10.1186/1471-2105-13-8
PMCID:
PMC3292476
Abstract Full Text PDF–705K Supplementary Material
PyElph - a software tool for gel images analysis and phylogenetics
Ana Brânduşa Pavel, Cristian Ioan Vasile
BMC Bioinformatics. 2012; 13: 9. Published online 2012 January 13. doi: 10.1186/1471-2105-13-9
PMCID:
PMC3299638
Abstract Full Text PDF–639K Supplementary Material
Developing a powerful In Silico tool for the discovery of novel caspase-3 substrates: a preliminary screening of the human proteome
Muneef Ayyash, Hashem Tamimi, Yaqoub Ashhab
BMC Bioinformatics. 2012; 13: 14. Published online 2012 January 23. doi: 10.1186/1471-2105-13-14
PMCID:
PMC3324375
Abstract Full Text PDF–495K Supplementary Material
The EnzymeTracker: an open-source laboratory information management system for sample tracking
Thomas Triplet, Gregory Butler
BMC Bioinformatics. 2012; 13: 15. Published online 2012 January 26. doi: 10.1186/1471-2105-13-15
PMCID:
PMC3353834
Abstract Full Text PDF–2.5M Supplementary Material
graphite - a Bioconductor package to convert pathway topology to gene network
Gabriele Sales, Enrica Calura, Duccio Cavalieri, Chiara Romualdi
BMC Bioinformatics. 2012; 13: 20. Published online 2012 January 31. doi: 10.1186/1471-2105-13-20
PMCID:
PMC3296647
Abstract Full Text PDF–3.9M Supplementary Material
miRTrail - a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases
Cedric Laczny, Petra Leidinger, Jan Haas, Nicole Ludwig, Christina Backes, Andreas Gerasch, Michael Kaufmann, Britta Vogel, Hugo A Katus, Benjamin Meder, Cord Stähler, Eckart Meese, Hans-Peter Lenhof, Andreas Keller
BMC Bioinformatics. 2012; 13: 36. Published online 2012 February 22. doi: 10.1186/1471-2105-13-36
PMCID:
PMC3352041
Abstract Full Text PDF–1.5M
PhiSiGns: an online tool to identify signature genes in phages and design PCR primers for examining phage diversity
Bhakti Dwivedi, Robert Schmieder, Dawn B Goldsmith, Robert A Edwards, Mya Breitbart
BMC Bioinformatics. 2012; 13: 37. Published online 2012 March 4. doi: 10.1186/1471-2105-13-37
PMCID:
PMC3314551
Abstract Full Text PDF–1.7M
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II
John Archer, Greg Baillie, Simon J Watson, Paul Kellam, Andrew Rambaut, David L Robertson
BMC Bioinformatics. 2012; 13: 47. Published online 2012 March 23. doi: 10.1186/1471-2105-13-47
PMCID:
PMC3359224
Abstract Full Text PDF–2.2M

Research Articles

Self-organizing ontology of biochemically relevant small molecules
Leonid L Chepelev, Janna Hastings, Marcus Ennis, Christoph Steinbeck, Michel Dumontier
BMC Bioinformatics. 2012; 13: 3. Published online 2012 January 6. doi: 10.1186/1471-2105-13-3
PMCID:
PMC3267649
Abstract Full Text PDF–1.3M Supplementary Material
A comparison study on feature selection of DNA structural properties for promoter prediction
Yanglan Gan, Jihong Guan, Shuigeng Zhou
BMC Bioinformatics. 2012; 13: 4. Published online 2012 January 7. doi: 10.1186/1471-2105-13-4
PMCID:
PMC3280155
Abstract Full Text PDF–1.6M Supplementary Material
Protein docking prediction using predicted protein-protein interface
Bin Li, Daisuke Kihara
BMC Bioinformatics. 2012; 13: 7. Published online 2012 January 10. doi: 10.1186/1471-2105-13-7
PMCID:
PMC3287255
Abstract Full Text PDF–3.7M Supplementary Material
Core module biomarker identification with network exploration for breast cancer metastasis
Ruoting Yang, Bernie J Daigle, Jr, Linda R Petzold, Francis J Doyle, III
BMC Bioinformatics. 2012; 13: 12. Published online 2012 January 18. doi: 10.1186/1471-2105-13-12
PMCID:
PMC3349569
Abstract Full Text PDF–3.2M Supplementary Material
Training text chunkers on a silver standard corpus: can silver replace gold?
Ning Kang, Erik M van Mulligen, Jan A Kors
BMC Bioinformatics. 2012; 13: 17. Published online 2012 January 30. doi: 10.1186/1471-2105-13-17
PMCID:
PMC3280170
Abstract Full Text PDF–164K
Independent Principal Component Analysis for biologically meaningful dimension reduction of large biological data sets
Fangzhou Yao, Jeff Coquery, Kim-Anh Lê Cao
BMC Bioinformatics. 2012; 13: 24. Published online 2012 February 3. doi: 10.1186/1471-2105-13-24
PMCID:
PMC3298499
Abstract Full Text PDF–582K Supplementary Material
Model-based peak alignment of metabolomic profiling from comprehensive two-dimensional gas chromatography mass spectrometry
Jaesik Jeong, Xue Shi, Xiang Zhang, Seongho Kim, Changyu Shen
BMC Bioinformatics. 2012; 13: 27. Published online 2012 February 8. doi: 10.1186/1471-2105-13-27
PMCID:
PMC3323827
Abstract Full Text PDF–529K Supplementary Material
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences
Yang Ding, William A Lorenz, Jeffrey H Chuang
BMC Bioinformatics. 2012; 13: 32. Published online 2012 February 14. doi: 10.1186/1471-2105-13-32
PMCID:
PMC3298695
Abstract Full Text PDF–778K
The Bone Dysplasia Ontology: integrating genotype and phenotype information in the skeletal dysplasia domain
Tudor Groza, Jane Hunter, Andreas Zankl
BMC Bioinformatics. 2012; 13: 50. Published online 2012 March 26. doi: 10.1186/1471-2105-13-50
PMCID:
PMC3338382
Abstract Full Text PDF–868K
Detecting disease-associated genes with confounding variable adjustment and the impact on genomic meta-analysis: With application to major depressive disorder
Xingbin Wang, Yan Lin, Chi Song, Etienne Sibille, George C Tseng
BMC Bioinformatics. 2012; 13: 52. Published online 2012 March 29. doi: 10.1186/1471-2105-13-52
PMCID:
PMC3342232
Abstract Full Text PDF–745K Supplementary Material

Methodology Articles

MIPHENO: data normalization for high throughput metabolite analysis
Shannon M Bell, Lyle D Burgoon, Robert L Last
BMC Bioinformatics. 2012; 13: 10. Published online 2012 January 13. doi: 10.1186/1471-2105-13-10
PMCID:
PMC3278354
Abstract Full Text PDF–562K Supplementary Material
TDT-HET: A new transmission disequilibrium test that incorporates locus heterogeneity into the analysis of family-based association data
Douglas Londono, Steven Buyske, Stephen J Finch, Swarkar Sharma, Carol A Wise, Derek Gordon
BMC Bioinformatics. 2012; 13: 13. Published online 2012 January 20. doi: 10.1186/1471-2105-13-13
PMCID:
PMC3292499
Abstract Full Text PDF–483K Supplementary Material
Automatic categorization of diverse experimental information in the bioscience literature
Ruihua Fang, Gary Schindelman, Kimberly Van Auken, Jolene Fernandes, Wen Chen, Xiaodong Wang, Paul Davis, Mary Ann Tuli, Steven J Marygold, Gillian Millburn, Beverley Matthews, Haiyan Zhang, Nick Brown, William M Gelbart, Paul W Sternberg
BMC Bioinformatics. 2012; 13: 16. Published online 2012 January 26. doi: 10.1186/1471-2105-13-16
PMCID:
PMC3305665
Abstract Full Text PDF–279K Supplementary Material
Propagating semantic information in biochemical network models
Marvin Schulz, Edda Klipp, Wolfram Liebermeister
BMC Bioinformatics. 2012; 13: 18. Published online 2012 January 30. doi: 10.1186/1471-2105-13-18
PMCID:
PMC3340317
Abstract Full Text PDF–2.0M Supplementary Material
Analysis of energy-based algorithms for RNA secondary structure prediction
Monir Hajiaghayi, Anne Condon, Holger H Hoos
BMC Bioinformatics. 2012; 13: 22. Published online 2012 February 1. doi: 10.1186/1471-2105-13-22
PMCID:
PMC3347993
Abstract Full Text PDF–540K Supplementary Material
Markov Chain Ontology Analysis (MCOA)
H Robert Frost, Alexa T McCray
BMC Bioinformatics. 2012; 13: 23. Published online 2012 February 3. doi: 10.1186/1471-2105-13-23
PMCID:
PMC3329418
Abstract Full Text PDF–1019K Supplementary Material
Identification of polymorphic inversions from genotypes
Alejandro Cáceres, Suzanne S Sindi, Benjamin J Raphael, Mario Cáceres, Juan R González
BMC Bioinformatics. 2012; 13: 28. Published online 2012 February 9. doi: 10.1186/1471-2105-13-28
PMCID:
PMC3296650
Abstract Full Text PDF–830K Supplementary Material
Method: automatic segmentation of mitochondria utilizing patch classification, contour pair classification, and automatically seeded level sets
Richard J Giuly, Maryann E Martone, Mark H Ellisman
BMC Bioinformatics. 2012; 13: 29. Published online 2012 February 9. doi: 10.1186/1471-2105-13-29
PMCID:
PMC3293777
Abstract Full Text PDF–7.2M
Assessing statistical significance in causal graphs
Leonid Chindelevitch, Po-Ru Loh, Ahmed Enayetallah, Bonnie Berger, Daniel Ziemek
BMC Bioinformatics. 2012; 13: 35. Published online 2012 February 20. doi: 10.1186/1471-2105-13-35
PMCID:
PMC3307026
Abstract Full Text PDF–813K Supplementary Material
Mouse obesity network reconstruction with a variational Bayes algorithm to employ aggressive false positive control
Benjamin A Logsdon, Gabriel E Hoffman, Jason G Mezey
BMC Bioinformatics. 2012; 13: 53. Published online 2012 April 2. doi: 10.1186/1471-2105-13-53
PMCID:
PMC3338387
Abstract Full Text PDF–1.7M Supplementary Material
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