Software & Datasets
Software
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- CSI-MAC (Cancer Selection Intensity using Model Averaged Clustering): A program that can be used to identify genes, gene regions, and sites that contribute to tumorigenesis when mutated, as well as to estimate the relative contribution of those genes, gene regions, and mutations to the somatic evolution of cancer.
- MASS-PRF (Model Averaged Site Selection with Poisson Random Field theory): A program that quantifies heterogeneity of selection intensity across sites within coding sequences by using polymorphism and divergence data.
- Download from GitHub: https://github.com/Townsend-Lab-Yale/MASSPRF
- Linux/Mac
- PhyDesign: a platform-independent web application that implements the Townsend (2007) phylogenetic informativeness analysis, providing a quantitative prediction of the utility of loci to solve specific phylogenetic questions.
- Download: PhyDesign package
- Platform: Web app
- Reference: doi.org (PhyDesign)
- LOX (Level Of eXpression): A program that employs Markov Chain Monte Carlo to estimate level of expression from census sequencing data sets with multiple treatments or samples.
- Download the archive (Version 1.8, February, 2012)
- MACML (Model Averaging Clustering by Maximum Likelihood): A program that clusters sequences into heterogeneous regions with specific site types, without requiring any prior knowledge.
- Download the archive (Version 1.1.2, December 2011) for
- View the MACML paper
- BAGEL (Bayesian Analysis of Gene Expression Levels): a program for the statistical analysis of spotted microarray data.
- Download Version 4.1, July 2009
- Download Version 4.0, March 2009
- View BAGEL Tutorial
- View some papers that have used the BAGEL software.
- KaKs_Calculator: A program that adopts model selection and model averaging to calculate nonsynonymous (Ka) and synonymous (Ks) substitution rates.
- Download the archive (Version 1.2) for
- View the KaKs_Calculator paper
- Contact information
- SeqPop: A program for computing population genetic statistics on sequence data, including Pn, Theta, Pi(i,j), Kst(*), Fst(*), and their Monte Carlo significance for population subdivision.
- Download the archive for
Datasets
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- Ortholog lists among fungal strains investigated for functional genomics in conidia germination, funded by USDA -- NIFA Plant-Associated Microbes and Plant-Microbe Interactions
- Wang, Z., K. Kin, F. López-Giráldez, H. Johannesson, and J. P. Townsend, 2012. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics and Biology 49: 533-543.
- Wang, Z., N. Lehr, F. Trail, and J. P. Townsend, 2012. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics and Biology 49(5): 405-413.
- Zhang, Z., and J.P. Townsend, 2009. Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Computational Biology 5(6): e1000421.
- Landry, C.R., J.P. Townsend, D.L. Hartl and D. Cavalieri, 2006. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 15: 575-591.
- Kasuga, T., J.P. Townsend, C. Tian, L.B. Gilbert, G. Mannhaupt, J.W. Taylor, and L.N. Glass, 2005. Long-oligomer microarray profiling in Neurospora crassa reveals the transcriptional program underlying biochemical and physiological events of conidial germination. Nucleic Acids Research 33(20): 6469-6485.
- Townsend, J.P., 2004. Resolution of large and small differences in gene expression using models for the Bayesian analysis of gene expression levels and spotted DNA microarrays. BMC Bioinformatics 5: 54. Simulated ratios:
- Townsend, J.P., D. Cavalieri, and D.L. Hartl. 2003. Population genetic variation in genome-wide gene expression in wine yeasts. Molecular Biology and Evolution 20 (6): 955-963.
- Townsend, J.P., and D.L. Hartl. 2002. Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biology 3 (12): research0071.1-0071.16.
- Manifold anomalies in gene expression in a vineyard isolate ofSaccharomyces cerevisiae revealed by DNA microarray analysisProceedings of the National Academy of Sciences
- Filigreed vs. filigreed data
- Filigreed vs. smooth data
- Wang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail f, Townsend J, Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa, Eukaryotic Cell, January 2014vol. 13 no. 1 154-169
- Nc lox EUKcell
- Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, et al. (2014) Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa. PLoS ONE 9(10): e110398. doi:10.1371/journal.pone.0110398
- Nd lox PLoSOne1
- Nt lox PLosOne2