A wide variety of biological processes and signals are mediated by patterns detectable at the sequence level in proteins, DNA and RNA. For example, one facet of transcriptional regulation of genes involves proteins (transcription factors) recognizing and binding to specific DNA sequence patterns. Other examples of important biological sequence patterns include protein structural domains, microRNAs and the protein target sequences of kinases. The MEME suite of bioinformatics software tools provide biologists with powerful methods for discovering, analyzing and interpreting biological sequence patterns of many types, including those mentioned above. The suite includes one tool - MEME -- that biologists use to discover novel sequence patterns (motifs), and three tools -- Meta-MEME, MCAST and MAST -- that biologists use to search sequence databases for matches to motif-based sequence models. This grant will enable us to dramatically improve the scientific value of the suite to the thousands of biologists who already use it. These improvements will be visible to the biologist using the suite as increased availability, better support, better user-interface and documentation, more powerful algorithms, better interoperability, and faster release cycles. We will achieve these goals via a combination of three specific aims: (1) improved software engineering, (2) ongoing support and (3) continued software development of the suite.
| Larney, Christian; Bailey, Timothy L; Koopman, Peter (2015) Conservation analysis of sequences flanking the testis-determining gene Sry in 17 mammalian species. BMC Dev Biol 15:34 |
| O'Connor, Timothy R; Bailey, Timothy L (2014) Creating and validating cis-regulatory maps of tissue-specific gene expression regulation. Nucleic Acids Res 42:11000-10 |
| O'Brien, Aidan; Bailey, Timothy L (2014) GT-Scan: identifying unique genomic targets. Bioinformatics 30:2673-5 |
| Ma, Wenxiu; Noble, William S; Bailey, Timothy L (2014) Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat Protoc 9:1428-50 |
| Lajoie, Mathieu; Hsu, Yu-Chih; Gronostajski, Richard M et al. (2014) An overlapping set of genes is regulated by both NFIB and the glucocorticoid receptor during lung maturation. BMC Genomics 15:231 |
| Thandapani, Palaniraja; O'Connor, Timothy R; Bailey, Timothy L et al. (2013) Defining the RGG/RG motif. Mol Cell 50:613-23 |
| Buske, Fabian A; Bauer, Denis C; Mattick, John S et al. (2013) Triplex-Inspector: an analysis tool for triplex-mediated targeting of genomic loci. Bioinformatics 29:1895-7 |
| Bailey, Timothy; Krajewski, Pawel; Ladunga, Istvan et al. (2013) Practical guidelines for the comprehensive analysis of ChIP-seq data. PLoS Comput Biol 9:e1003326 |
| Bailey, Timothy L; Machanick, Philip (2012) Inferring direct DNA binding from ChIP-seq. Nucleic Acids Res 40:e128 |
| Peterson, Kevin A; Nishi, Yuichi; Ma, Wenxiu et al. (2012) Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev 26:2802-16 |
Showing the most recent 10 out of 30 publications
