General Research Interests

My lab is 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 that is then used by bioinformaticians as the basis for variant detection, quantification of expression, and regulatory network inference studies. Early in my training I investigated both ribosome and chromatin structure/function correlations, interests that continue in current projects. Currently I am interested in modeling how target molecules fold under assay conditions, then predicting and testing the outcomese in high-throughput sequencing platforms. Specifically, so we get aberrant signals under those conditions? Do analysis pipelines take into account structure-dependent signal anomalies or are misinterpretations likely? We have evidence that some structures give highly biased intensities/frequencies on microarrays, where the signal arising from a probe bound to a mismatched target that folds in a thermodynamically favorable way can be greater than the binding between the probe and the perfectly matched target. Predicting the actual binding level has been difficult with current modeling tools. We have also shown, on both the Ion Torrent PGM and the Illumina MySeq that some template structures lead to sequence resullts that could be interpreted as a deletion, rather than a slow-down in the normal rate of polymerase progression. 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). Research Hobbies: I like profiling non-model 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): 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

Teaching

Class materials are now posted on the University Canvas pages - please email me for notes, handbooks, lab plans, etc. The course numbers are BINF 6350/8350 Genomic Biotechnology Laboratory and BINF 6211/8211 Design and Implementation of Bioinformatics Databases. The courses were taught by Drs. Ann Loraine and Cathy Moore and Jessica Schlueter ad Rebekah Rogers (Genomic Lab) and Dr. Andrew Carr and Dr. Jeremy Jay (Databases) while I was on sabbatical at the NSF (2015-2019).

Outreach

Summer Lab Experience for Olympic Highschool students : Biotechnology, Biodiversity and Bioinformatics (B3) Summer Camp

Supported by a Burroughs-Wellcome Educational Enhancement Grant (with Jeanne Smith)from 2013-2016.
• May 19 - May 21, 2016. Bioinformatics Boot Camp - materials available upon request
• June 12-June 26, 2015. A link to the pages for 2015 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 to 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 summer camp at UNCC in 2010. Science Camp 2010 Home

Research experience for High School and Undergraduate students

• 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 on sample collection and processing, followed by PCR and sequencing library preparation for one of our genomics projects.

Other Service

Committees, Fall 2014-2015 I took a leave of absence to serve as a program officer at the NSF from 2015 - 2019. In 2020 I will be serving on the following committees:

• Dept. Review Committee
Recent Activity Reports
• Faculty Activity Report UNCC 2019  Activities from Jan 2019-Dec 2019.
Biosketches, Awards, affiliations
• Short form - older, NSF format  2pg Bio and C&P
• Short form - Faculty activity report format, UNCC Weller_FAR_CV
• Long form 2020 complete  Long Resume
• Excellence in Graduate Teaching, CCI 2015 awardee
• Affililate Faculty George Mason University
Facilities Description
• 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 Weller Lab Members (2007-2015)