Tristan M. Carland, PhD
Scripps Translational Science Institute
at The Scripps Research Institute
3344 North Torrey Pines Court, Suite 300
Welcome to our site
This website is dedicated to scientific interests and pursuits of myself and my virtual laboratory; a conglomeration of a small score of interns, volunteers, and a few colleagues from my research position - a few of their names can be found below and the full set here (link). My name is Tristan Carland and I am a postdoctoral researcher at the Scripps Translational Science Institute (STSI) of The Scripps Research Institute (TSRI). My background is in computer programming and marine biology and my interests are too many to summarize but generally orient around computational methods to analyze genetic (especially whole-genome) material. You can find my previous and current works in my CV (under about) and in my research links in the menu above. Included above also are some activities for the teaching of biology and bioinformatics, feel free to use them in your classes.
Current Projects List
The following projects are ones that I am actively pursuing, often with the overwhelming support of others. The language is phrased to be accessible to a wide audience and to expose possible projects for collaborators/interns/volunteers. It is worth mentioning that in none of these studies is any data relating to the identities of any patients available in any way to myself or the other persons involved, in keeping with standard practices for such studies.
In collaboration with Johnson and Johnson we have access to fifty genomes with a high depth of coverage (40x). The main goal is to search for genetic causes for the disease but the dataset is uniquely large (arrived as ~150gb per genome) and thus presents some noteworthy challenges. Our plans include a study of the tactics for these challenges as well as the study of the disease itself.
Kidney Transplant Rejection
This collaborative project with the laboratory of Daniel Salomon at TSRI is one of the projects for which we have the most analysis completed. The basic premise is an exome sequencing project of patients who have undergone a kidney transplantation and were either successful in keeping the transplant or suffered from a chronic necropathy. The prime search of this project is for any causative variants that could theoretically be screened for before someone is chosen to be the host to a donor kidney. The dataset is interesting and profound in that there has been exome sequencing of the 100 patients of mixed ethnicity (more on the way), and microarrays run (for general gene expression and specifically for miRNA expression levels). There are many possible side projects here ranging from the already begun hunt for miRNAs related to mutated seed regions, a gene set enrichment analysis, and I'm hoping to experiment with a new multi-loci analyses.
Alcoholism in Native Americans
One of our largest projects both in the size of the data and the collaboration. The partnering groups this time are Cindy Ehlers of TSRI, Ian Gizer of Missouri, and Kirk Wilhelmsen of UNC. The basic premise is that there is an unprecedented level of alcohol dependency found among native americans. The goal is to deduce if this is a genetic trait and how it works, the project has presently led to the full sequencing of nearly 600 individuals. These are low coverage whole genomes. We also have pedigree data available for a few particular families within the study. Some scalable projects could be to search out the degree of admixture (genetic mixing) found among them, search for mutations in genes known to be part of the alcohol metabolic pathway, or study the haplotypic relatedness of a family to search out the levels of presence of some characterized genetic diseases. Beyond this we have a large set of other phenotypes to study.
Continually ongoing study, now in it's fourth iteration. In this case we have two female cousins (maternally) with the same eating disorder despite different conditions. The basic premise is that whatever they share from their Mothers (Sisters) may be the culprit. This dataset includes two trios, meaning Mom/Dad/Child trifectas, that were fully sequenced and phased. This is a collaboration with the Price foundation and papers on the matter can be found by looking for anything authored by Nicholas Schork and Cinnamon Bloss. Some tools that we would love to get running on these data include VAAST and Germline.
This interesting project seeks to find any genetic tricks that certain long-lived organisms may have evolved. Fine examples of organisms to study include the bowhead whale (reaches 200 yo), the naked mole rat, and a genus of tropical bats. The genomes of several of these organisms are available and so far I've seen that we have data for their cellur responses and can derive correlation matrices from phylogenetic modeling.
Through a collaboration with TGen and the Van Andel institute we have been given the full genome sequences for the Lundehund and Golden Retriever dog breeds. This is a project with many great possibilities ranging from new methods to tackle de novo sequencing with short reads using assisted assembly techniques to answering questions about polymorphisms between the breeds.
Lots of other projects are ongoing around the lab and I have a pack of small ones up my sleeve. One particular one is to utilize a new batch of Nvidia Tesla boards that TSRI just had installed, the possibilties are incredible and could be applied to most any project. Another is to get a program called Hugeseq running for the lab - it is a wonderful variant calling pipeline, in a similar vein we've been toying with Cortex_con and Cortex_var.
Experimental bioinformatics space
In bioinformatics (or computational biology), computer systems are your laboratory. As such, this site may become unavailable at times. This particular machine was added as a low-powered computational workspace for certain tasks that may time some time. During these moments, it may be greatly slowed or even break down. We will be more proud than ashamed of these moments for testing the limits of the machinery is a valiant persuit.
Virtual laboratory - Affiliates
The following is a list of interns and volunteers involved in the research here, in my virtual laboratory space, all adding to the science and technical support of this space. For a full listing including my other colleagues at STSI, please go here (link)
Mr. Canter is an experienced programmer remotely voluteering here in this experimentation in the development of faster genetic sequence alignment routines.
Ms. Choi was a 2012 Summer Undergraduate Research Intern at STSI via TSRI. She researched genetic markers concerning the link between diabetes and kidney disease in kidney transplant patients.
Ms. Gunner was also a 2012 Summer Undergraduate Research Intern at STSI via Scripps Health. She made valiant strides in an association analysis of exome-chip data from a Native American tribe, the phenotype was alcoholism.
Mr. Osborne is an experienced GNU/Linux administrator, remotely volunteering here, who has been a key player in getting our systems running efficiently and in managing our larger data stores.
Mr. Shipman is a research programmer at STSI working with us on graphical processing (or GPU) acceleration to multi-loci statistical association analyses.