Derek Pavelec, PhD
Position title: Director of Bioinformatics, UW Biotechnology Center, University of Wisconsin–Madison
Phone: Advisor: Dr. Kennedy Scott
Molecular biologist and computer scientist with experience using genetic, molecular, and bioinformatic techniques to identify and characterize important factors for endogenous gene regulation and small RNA biogenesis.
I have experience generating and analyzing high-throughput sequencing data, and developing an analysis pipeline for targeted resequencing of human genes in a CAP/CLIA approved laboratory.
I am interested in the genetics and molecular biology of gene regulation and developing software to support scientific workflows and analysis.
- Oversee the company’s informatics staff, and aid the development of new software to support large scale sequencing of disease related genes.
- Molecular biologist with experience using genetic and molecular techniques to identify and characterize several novel RNAi factors important for endogenous gene regulation. Emphasis on RNA regulation and small RNA biogenesis.
- Molecular biology: DNA/RNA isolation, high-throughput sequencing, qRT-PCR, in vitro transcription and translation• Genetics: Human, C. elegans (strain construction, mutagenesis, screens, mapping, epistasis); basic fly• Computer: Bioinformatics, C#, Java programming, SQL, Unix/Linix/Windows, computer maintenance• Other: cell culture, in situ, imunoflourecence, protein purification
- Guang S, Bochner AF, Burkhart KB, Burton N, Pavelec DM, Kennedy S. (2010)Small regulatory RNAs inhibit RNA polymerase II during the elongation phase of transcription. Nature. 465:1097-1101. PMCID: PMC2892551
- Welker NC, Pavelec DM, Nix DA, Duchaine TF, Kennedy S, and Bass BL (2010). Dicer’s helicase domain is required for accumulation of some, but not all, C. elegans endogenous siRNAs. RNA. 16:893-903. Epub 2010 Mar 30. PMCID: PMC2856884
- Gent JI, Lamm AT, Pavelec DM, Maniar JM, Parameswaran P, Tao L, Kennedy S, Fire AZ (2010). Distinct phases of siRNA synthesis in an endogenous RNAi pathway in C. elegans soma. Mol Cell. 37:679-689. PMCID: PMC2838994
- Pavelec DM, Lachowiec J, Duchaine TF, Smith HE, and Kennedy S (2009).Requirement for ERI/DICER Complex in Endogenous RNAi and Sperm Development in Caenorhabditis elegans. Genetics. 183:1283-1295. PMCID: PMC2787421
- Guang S, Bochner AF, Pavelec DM, Burkhart KB, Harding S, Lachowiec J, and Kennedy S (2008). An Argonaute transports siRNAs from the cytoplasm to the nucleus. Science. 321:537-541. PMCID: 2771369