Dr. Jennifer W. Weller
Office: Bioinformatics 353
9201 University City Blvd
Charlotte NC 28223
Office telephone: 704-687-7678
Lab: Bioinformatics 343, 345
Summer 2014 Office Hours: By appointment only
Summer Institute in Bioinformatics and Genomics
Summer Institute 2014 - For the first time, our department is offering a series of 4 courses this summer, that comprise our Certificate Program (for information about the certificate, our department's page about it is here ). The UNC Charlotte Summer School Web page is here .
The tuition and fees for our course are here (you can find the complete official set of fees on the UNCC Web site). I will be teaching the first session course, the Genomic Biotechnology Lab. In this course we will start with a sample and carry it through all the steps of library preparation and to sequencing
on the Ion Torrent PGM. We will discuss a variety of library-construction strategies, quality control tests, and first-pass data quality assessment. For real in-dpeth data analysis
subsequent sessions cover Statistics, then Genomics, and the final session will cover Pipeline Programming.
The program starts May 19th, 2014 with the Genomic Biotechnology Lab course.
For enrollment information please see the UNC Charlotte Graduate Admissions link: the Application deadline for summer sessions is April 1st. I recommend filling out the Contact form linked
here if you are interested.
A brochure has been produced if you would like to post it to encourage students SI Flyer.
This course is taught during the Fall semester each year, if you would like to see the teaching lab, some images are given here Flickr Lab Pics .
General Research Interests
I am interested in how structure affects function of nucleic acids, both biologically and in the performance of high-throughput assays.
High-throughput assays are produced in genomics experiments and used by bioinformaticians as the basis for most network inference studies.
In graduate school I investigated ribosome and chromatin structure/function correlations, so my current interests are a natural outcome of that perspective.
Currently I am interested in whether and when the presence of quadruplex and highly stable hairpins that form in the targets used in microarray and high-throughput short-read platforms affect outcomes. We have evidence that some structures give highly biased intensities/frequencies. With microarrays the signal is sometimes increased above the level of a perfect match, and we are trying to understand how to predict that outcome. In sequencing a structure can
produce the appearance of a short deletion, rather than a truncation, and we are attempting to predict that outcome with modeling as well. My group also investigates experimental methods that can normalize the effects described above. I have a long-standing interest in how omics data should be represented, and how to best store and use the data our experiments produce.
Side-projects: I like profiling organisms using molecular marker technologies, and building small databases of the information.
Research Supplement Pages
Links to Lab Software and Supplementary Material for Research Projects and Publications.
- A database we developed to speed up analysis rather than optimize curation: DataFATE - Carr and Weller
- We analyzed probes on the Affymetrix SNP6 chips to determine which are affected by the DNA processing steps. Until we can replicate an entire study we cannot publish the paper, but here are some lists of probes for those interested . SNP home
- A biophysics sensitive preprocessing pipeline for short-oligo microarray data (BMC bioinformatics 2010): BaFL - Thompson et al.
- A tool for selecting only the desired probes as members of a ProbeSet(BMC Bioinformatics 2011)- ArrayInitiative - Overall et al.
- An ovarian cancer Cancer Microarray meta-study using BaFL Home
- A biophysics sensitive preprocessing pipeline for long-oligo microarray data (BMC bioinformatics 2012) - Baciu et al
Fall 2013 BINF 6350/8350 Genomic Biotechnology Laboratory - please email me to request materials.
Spring 2014: BINF 6211/8211 Design and Implementation of Bioinformatics Databases - please email me to request materials
Summer Lab Experience for Olympic Highschool students : Biotechnology, Biodiversity and Bioinformatics (B3) Summer Camp
I organized the 2012 Workshop in Next-Generation Sequencing event, AKA WiNGS @ UNC Charlotte, May 17th-18th, 2012.
- In May 2013 the Workshop in Next-Generation Science was organized by Dr. Ann Loraine (Ann.Loraine@uncc.edu).
- The Functional Genomics Data Society (FGED) had a meeting in June 2013, in Seattle. I helped organize a workshop there. If you care about having access to properly annotated full data sets of either microarray or sequencing data, you should consider joining. Thanks to
the progenitor MGED society, microarray data is frequently submitted in a usable form, but high-throughput sequence data is sriously lagging behind. FGED meetings
- FGED small regional meeting in December 2013 will be in Charlotte - I will link to more information as it firms up.
Now supported by a Burroughs-Wellcome Educational Enhancement Grant (with Jeanne Smith)
Research experience for High School and Undergraduate students
- June 11-June 26, 2014. Here is a link to our upcoming summer camp. B3 2014 Home - some of this is under construction
- June 13-June 28, 2013. Here is a link to the last summer camp. B3 2013 Home
- June 11-29, 2012. The students ran their own Web site in 2012, but I had a general information site of scheduled activites that can be found here B3 2012 Home
- The pages from B3 in 2011 (I was the documenter, so this is pretty complete for protocols and pictures). B3 2011 Home
- The pages from the B3 prototype at UNCC . Science Camp 2010 Home
- Jayden Walsh, a junior at Olympic High School is participating in research in my lab, testing primers against DNA isolated from a number of chestnet species to identify markers useful for the B3 class to use, and looking at how the structure of
DNA affects our ability to accurately sequence it. Jayden has put together several pages describing his experience, which are linked here Walsh pages
- I have volunteered as a guest 'Scientist for a Day' as part of North Carolina's annual April activities aimed at exposing high school students to the work of research scientists.
- Research experience for Undergraduates: a number of undergraduate students have cycled through the lab, learning genomics techniques while assisting graduate students with their research projects. Please inquire if you are interested for Fall 2013.
Miscellaneous, Possibly Useful Information
Committees, Fall 2013
Recent Activity Reports
- I serve as the B&G department's lab safety/equipment/training committee chair - we try to make sure that everyone using labs knows prcedures for correct use and disposal of materials, and what types of declarations/records they are responsible for making.
- BiG department undergraduate curriculum and CCI college undergraduate curriculm committees
- BiG PhD students academic advisor, with Dr. Dennis Livesay.
- ADVANCE faculty mentor to new faculty in Biology.
- Past service: 5 years on the BioSafety and FALC committees.
Recent Resumes (includes Publications)
- Faculty Activity Report UNCC 2011 Activities from May 2010-May 2011.
- Short Form NIH format CV
- Long Version - for the detail-obsessed Resume
- Our facilities are pretty new - and we like to collaborate. This description is slanted towards my lab but does include shared resources: B&G Facilities 2012
UNCC Lab Members (2007-2014)