Please forward this error screen to 69. Our group develops mathematical, genomics and bioinformatics pdf, and computational methods to address scientific problems in molecular biology and genetics. The graduate students in our group are from the Department of Biostatistics at Yale School of Public Health or the Interdepartmental Doctoral Program in Computational Biology and Bioinformatics at Yale.
We collaborate with many research groups at Yale and other institutions on the biological basis and treatment of cancer, substance dependence, psychiatric disorders, aneurysm, hypertension, lung diseases, and others. We also collaborate with plant geneticists and evolutionary biologists using next generation sequencing and microarrays to identify genetic associations with various traits. It requires two matrices as input datasets. UCEs must be important by the very nature of their near-universal conservation across extremely divergent taxa. How do I identify UCEs? How do I collect UCE data?
UCE loci we are targeting. DNA libraries for the target UCEs, usually in multiplex. How do I analyze UCE data? The most complex part of using UCEs to understand evolutionary relationships, population structure, and population relationships is analyzing the DNA sequence data. We compiled a list of questions you may have that go beyond the details provided above. Peer-reviewed manuscripts describing our work. Target enrichment of ultraconserved elements from arthropods provides a genomic perspective on relationships among Hymenoptera.
Proc R Soc Lond B Biol Sci 281: 20140823. Comparative Studies at Shallow Evolutionary Time Scales. A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing. More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs. Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales.
Ultraconserved Elements Are Novel Phylogenomic Markers that Resolve Placental Mammal Phylogeny when Combined with Species Tree Analysis. Here’s a list of UCE-related talks at various conferences. Slides are available for each talk by clicking on the linked talk title. These talks should give a general idea of where we’re going with new research projects that use UCEs. Below are several commercial laboratories offering UCE enrichment as a service. Generally speaking, these commercial vendors will accept DNA extracts for enrichment, conduct the library preparation and enrichment steps, sequence the enriched libraries, and return the sequence data to you.
We are constantly evaluating the utility of given probe sets and probe designs, in addition to expanding the number of UCE loci we are targeting. We have several larger probes sets in the works, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. Please check back for updates. We designed probes from UCEs by including flanking sequence from chickens. Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across amniotes.
2,560 probes targeting 2,386 loci are a subset of this larger set of probes. Although this probe set is not, yet, referenced in a publication, we have been using it for some time across a variety of taxa with much success. We have several larger probes sets in the works for fishes, and we are also working on optimizing probe sets based on their capture success, phylogenetic utility, etc. We used these probes for our analysis of early diverging teleosts. We designed probes from UCEs by including flanking sequence from medaka. Because of the highly conserved nature of UCEs and their flanking sequence, we have found these probes work well across fishes.
Computer code for data analysis. Below are several software packages we have developed to help analyze data collected from UCE loci. We welcome all code contributions, from helping to improve the code, fix bugs, improve usability, and improve documentation, which is rather sparse, at the moment. All software packages are likely to contain bugs – use at your own risk.
Our main code repository for analyzing data collection from UCE loci. Contains command-line applications for assembling contigs from sequence data, finding which contigs align to UCEs, aligning UCE contigs, and preparing data for downstream analysis in mrbayes, raxml, and cloudforest. Capable of demultiplexing hundreds of sequence tagged libraries at once. A program for automated cleaning of fastq files from sequencing.