Dr. Jennifer W. Weller
Office: Bioinformatics 353
9201 University City Blvd
Charlotte NC 28223
Office telephone: 704-687-7678 (but I will be out of the state)
Lab: Bioinformatics 343, 345
I will be serving as a Program Officer in the Division of Biological Infastructure at the National Science Foundation from Aug 1st, 2015 - July 31st, 2016. I will not be in Charlotte but I will maintain email contact through my uncc account.
General Research Interests
I am interested in how structure affects the function of nucleic acids, both biologically and in the performance of high-throughput assays.
High-throughput assays produce data in genomics experiments and are used by bioinformaticians as the basis for most network inference studies.
In graduate school I investigated both ribosome and chromatin structure/function correlations, so my current interests are a natural progression of my original studies.
Currently I am interested in modeling high-throughput sequencing or microarray assay conditions that promote target folding.
Do we get aberrant signals under those conditions?
Do analysis pipelines take into account this anomaly or are misinterpretations likely?
We have evidence that some structures give highly biased intensities/frequencies.
On microarrays the signal from folded templates is sometimes increased above the level predicted for a perfect match, and we are trying to understand how to predict that outcome.
We have also shown, on both the Ion Torrent PGM and the Illumina MySeq that some structures lead to what appears to be a deletion, rather than a truncation.
My group also investigates how to modify experimental conditions to allow unfolding of nucleic acid structures so that the assay produces data as expected.
I have a long-standing interest in how omics data should be represented and stored (ontologies and databases).
Hobbies: I like profiling non-model organisms using molecular marker technologies, and building small databases of the information.
UNCC Behavioral Genetics project, with Dr. Sara Levens of the Psychology department
- From Saliva supplied by volunteers we will analyze sequence variants in 26 gene regions associated with memory, cognition and habit-forming behaviors, using Illumina sequencing. We wiill also examine
the oral microbiome of the volunteers to see if changes are associated with success in the academic environment.
Health associations between diet and gut microbiome in several organisms
- We are collaborating with several labs interested in the combined effect of diet and the gut microbiome in health and available metabolite pools, carrying out sample purification and ILlumina sequencing.
American chestnut markers in related back-cross individuals.
- We are adapting the REST-Seq approach to the Illumina platform and examining DNA pools from two different sets of back-crossed individuals, with Steve Barilovits, Dr. Paul Sisco and Dr. Jared Westbrook of The American Chestnut Foundation
Adapting the Ion Torrent platform as an aptamer-protein sensor.
- Sushant Patil is developing experimental methods to extend the use of the IOn Torrent ISPs to the detection of ISP-bound aptamers and their bound proteins.
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): please inquire, original server taken off-line
- A tool for selecting only the desired probes as members of a ProbeSet(BMC Bioinformatics 2011)- please inquire, original server taken off-line
- An ovarian cancer Cancer Microarray meta-study using BaFL - please inquire, original server taken off-line
- A biophysics sensitive preprocessing pipeline for long-oligo microarray data (BMC bioinformatics 2012) -please inquire, original server taken off-line
Class materials are now posted on the University Moodle pages.
Fall 2014 BINF 6350/8350 Genomic Biotechnology Laboratory - please email me to request materials.
Spring 2015: 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
Now supported by a Burroughs-Wellcome Educational Enhancement Grant (with Jeanne Smith)
Research experience for High School and Undergraduate students
- June 12-June 26, 2015. Here is a link to our upcoming summer camp. B3 2015 Home
- June 11-June 26, 2014. A link to the pages for 2014 B3 2014 Home
- June 13-June 28, 2013. A link the the pages for 2013 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 primary 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 participated in research in my lab in 2013, 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
- Each April I volunteer as a guest 'Scientist for a Day' as part of North Carolina's annual Science Festival activities aimed at exposing middle and high school students to the work of research scientists.
- Research experience for Undergraduates: each year the lab accepts an undergraduate student to work in the lab, usually working DNA extraction and PCR for one of our genomics projects (see above). Josh Cepeda is our current volunteer (UNCC Behavioral Genetics project).
Committees, Fall 2014-2015
I will be taking a leave of absence for the coming year, my committee duties have been delegated to other faculty.
Recent Activity Reports
- Faculty Activity Report UNCC 2014 Activities from Jan 2014-Dec 2014.
- Our facilities are described here, note that we will train researchers who want to use the Ion Torrent PGM or Illumina MiSeq platforms, upon request.
This description is slanted towards resources found in my lab but does include shared department resources as I am made aware of them: B&G Facilities 2015
UNCC Lab Members (2007-2015)