Dr. Jennifer Walsh Weller, Ph.D.How do I recognize her?

This GMU page is maintained as a courtesy, I am an Associate Professor, Bioinformatics program, at UNC-Charlotte starting in June 2007

Note my new affiliation:
204 Cameron room 220
UNC-Charlotte
9201 University City Blvd
Charlotte NC 28223
main office telephone: 704-687-8541
e-mail: jweller2@uncc.edu


General Research interests

My formal training is in chemistry, biochemistry and biophysics; subsequently I have done research in molecular genetics of plant-pathogen interactions and the development and application of molecular markers and gene expression methodologies. I pursued these interests while working at Perkin-Elmer/Applied Biosystems from 1994-1999. After developing AFLP marker systems for a variety of genomes,we began to develop cDNA-AFLPs as a gene expression evaluation system. As with any highly parallel genomics technology, data overload quickly became the primary bottleneck to understanding our results. This led to a segue into bioinformatics, through a position at the National Center for Genome Resources in Santa Fe, NM. As group leader of the Sequence and of the Gene Expression groups, my teams developed pipelines for EST analysis (a frequent precursor to microarray design) and to a gene expression data management system. My current research interests involve a systematic investigation and evaluation of the behavior of the complex mixture of probes and targets on microarrays, and the integration of data from a variety of microarray platforms (SNP, aCGH, ge, ChIP, exon) into a coherent and interpretable whole.

Current Courses:

Spring 2008

UNCC BINF8211

Past Courses:

Fall 2007 Presentations
BINF 6100 Cloning, Sequencing and PCR Link to Lecture link

Spring 2007 Courses
BINF 650 Introduction to Bioinformatic Database Design - please contact me if you are interested in the content of the course
BINF 739-002 Network Based Models in Bioinformatics and Biocomputing - please contact me if you are interested in the content of the course.

Fall 2006 Courses were Biotechnology (BINF 633) and Microarray Design and Analysis (BINF 636). Two lectures on Bioinformatics data types and the relevant databases were given in CSI 710. - please contact me if you are interested in the content of these lectures

Summer 2006 courses at Korea University were Forensic Sciences and Moelcular Biotechnology, with Dr.s Seto and Kinser. Syllabi and notes are available upon request.

Spring 2006 Courses
BINF 637 DNA Forensics (primary instructor Dr. Mark Wilson).- please contact me if you are interested in the content of these lectures
BINF 733 Microarray Analysis Methods (primary instructor Dr. Jeff Solka).- please contact me if you are interested in the content of these lectures
BINF 704 Graduate Seminar Series

Research Grants

NSF-Funded GeneX Brief Description

The 2003-2006 Annual Reports and associated publications, code and scripts are available upon request.

The 2007 Annual Report is available here Final Report link

The 2007 Final Report is available here 2007 Annual Report link

The final code base is available as a zip'd file here Code link

Installation directions and other documentation are available as a zip'd file here Install Documentation link

Link to Source Forge GeneX project repository link

Link to pdf of NSF OpenGeneX grant proposal link

NIGMS (funding began in Fall 2005; Gibas-Weller collaboration): "Optimization of oligonucleotide array design" Abstract

Cynthia Gibas' Web site is at UNC-Charlotte, please check there for our progress reports


Aug 2007 Formal Resume - Very Complete  CV

Publications - see CV for complete list

Selected publications

  1. Inman, J.T., Flores, H.R., May, G.D., Weller, J.W., and Bell, C.J. (2001) "A High-Throughput Distributed DNA Sequence Analysis and Database System" IBM Systems Journal, 40(2) 464-486. link to pdf
  2. Mangalam, H., Stewart, J., Zhou, J., Schlauch, K., Waugh, M., Chen, G., Farmer, A., Colello, G., Weller, J. "GeneX: An Open Source gene expression database and integrated tool set" IBM Systems Journal, 40(2) 552-569. link
  3. Hraber, P.T. and Weller, J.W. "On the species of origin: diagnosing the source of symbiotic transcripts" Genome Biology 2001: 2(9) 37.1-37.13. link to pdf
  4. Mao, C., Cushman, J.C., May, G.D., Weller, J.W. "ESTAP : an automated system for the analysis of EST data" Bioinformatics (2003) 19: 1720-1722. link to pdf
  5. Lee, J.K., Laudeman, T., Kanter, J., James, T., Siadaty, M.S., Knaus, W.A., Prorok, A., Bao, Y., Freeman, B., Puiu, D., Wen, L., Buck, G.A., Schlauch, K., Weller, J., Mangalam, H.J., Fox, J.W. "GeneX Va: VBC Open Source Microarray Database and Analysis Software for Multiple Users in Biomedical Research" Benchmarks, Biotechniques. 2004 Apr;36(4):634-8, 640, 642. link to pdf
  6. Ratushna, V., Weller, J., Gibas, C. "Secondary structure as a confounding factor in synthetic oligomer microarray design" BMC Genomics 6:31 (2005). link to pdf
  7. Higgs, B.W., Weller, J.W. and Solka, J.L. (2006) “Spectral Embedding Finds Meaningful (Relevant) Structure in Image and Microarray Data” BMC Bioinformatics 7:74.
  8. Kumari, S., Verma, L., and Weller, J. (2007) “AffyMAPSDetector: A Tool To Detect SNPs In Affymetrix GeneChipTM Expression Arrays” BMC Bioinformatics 8:276.
  9. Overall, CC, Solka, JL, Weller, JW, Priebe, CE (2006) “Anomaly Detection in Genetic Networks.” Joint Statistical Meeting (JSM),Seattle, WA. 37.

Supplementary Materials link for the paper “AffyMAPSDetector: A Tool To Detect SNPs In Affymetrix GeneChipTM Expression Arrays” BMC Bioinformatics 8:276. is given here: this site includes downloadable code, data sets, and some additional results of analyses reported in the paper; these are in addition to the material provided as Supplementary files by the journal.