2015

Chill

It's mid-November. Madison is getting cold again and everyone is preparing for another long winter. The best part of seasons in Madison is that each one has a distinctive character. Most years, I feel like these long days of winter are among the most productive, while in the summer it is more relaxed as people spend time outside.

2015 has been very busy. Many senior staff have had the opportunity to make exciting career transitions. Matt Reynolds, a Scientist in the lab, received his own NIH R01 grant to explore alloimmunization as an HIV vaccine. Adam Bailey successfully defended his PhD thesis and returned to med school to complete his MD. Justin Greene accepted a scientist position at the Oregon Health and Sciences University working with longtime friend of the lab Jonah Sacha. Finally, after our lab visited Promega Corporation this summer to discuss possible collaborations Michael Lauck was sufficiently impressed with their work that he joined their team. While these transitions are difficult for our lab, I'm delighted to see members of the lab advance and succeed in their careers.

Though we've had personnel turnover, it has been a productive year. We recently published a review paper on simian arteriviruses. Earlier in the year, we described the first animal model for human pegivirus infection and recently received a new NIH R01 grant to further develop this model. Understanding cellular immunity to HIV/SIV remains a priority and we continue to study cellular adoptive transfers and define CD8+ and CD4+ T cell epitopes. We are also doing a lot of work with immunogenetics and genomics. With help from the Center for High Throughput Computing, we used thousands of CPUs to analyze whole genome and whole exome sequences from hundreds of macaques. Technologically, the biggest change in the year has been our adaptation of Pacific Biosciences deep sequencing to characterize full-length MHC, KIR, and FCGR transcripts. For the first time, we are able to catalog hundreds of novel allelic variants at these loci, which will hopefully improve out understanding about how variation in these genes influences infectious disease resistance.

If you are reading this in anticipation of applying to do PhD research at UW-Madison in 2016, I am most likely to take students with three or more years of independent funding because this allows students the greatest flexibility in developing a research project that matches their interests. I have had open PVLs for technicians and scientists throughout 2015, so if you are interested in joining our team with a BS or PhD, I encourage you to apply or contact me for additional information. I seek motivated, talented, creative, team-oriented individuals who are interested in conducting world-class infectious disease research.

Refresh

It's been a while since I've updated the main page, but it isn't from lack of activity in the lab. The last year has been really eventful. Some highlights include:

- Several lab staff moving on to new opportunities in graduate and medical school
- Developing the first animal model for studying GB virus C…and showing that GBV-C may protect from Ebola mortality
- Discovering simian arteriviruses in captive baboons and new populations of wild primates
- Publishing a new method for studying HIV drug resistance efficiently
- Using whole genome sequencing to look for new genes associated with spontaneous HIV/SIV control
- Working towards characterizing all the genetic variation in Mauritian macaques
- Characterizing full-length major histocompatibility complex transcript and gene sequences using a variety of deep sequencing platforms.

I'm writing this on the heels of a busy fall of travel, which included trips to Cape Town, Washington D.C., Rio de Janeiro, Portland, and Sao Paulo. It is great fun to have such wonderful collaborators and colleagues to visit around the world.

Finally, I know this is the time of year when many people who visit my website are applying to UW-Madison for graduate school. Here is a short FAQ for you:

Are you taking new graduate students in fall, 2015? I will consider taking students who have three years or more independent funding. Most incoming students do not realize that it costs a lab like mine about $50,000 a year to support a graduate student. During the first two years, when students are taking classes and have other programatic requirements, time in the lab is limited - making the effective cost of a PhD student even higher. Moreover, students who have their own funding can have more flexibility by developing projects that are not funded by existing grants.

I am interested in your lab. Can I be directly admitted? No. I believe rotations in multiple labs are essential. Consequently, I do not accept students from programs that require one-on-one matching between students and investigators as a criteria for acceptance to UW-Madison.

What skills should a prospective student bring to the lab? See my graduate student philosophy, which still holds up pretty well even though I initially wrote it nearly ten years ago. It is now also essential that prospective students have a strong quantitative background because of the large datasets we are generating and analyzing. This doesn't mean you need to be an expert computer programmer when you join the lab, but it means you must be comfortable learning how to work with large datasets, command line tools, and basic programming (e.g., Python)