Claude dePamphilis - PhD, University of Georgia; Claude has active research projects probing the origins and rapid divergence of the earliest angiosperms (flowering plants), chloroplast genome evolution, and the evolution of parasitism in flowering plants. Claude's work is currently funded by The National Science Foundation through the Amborella Genome Project, the Parasitic Plant Genome Project, and the Monocot ATOL (Assembling The Tree of Life) Project. Claude teaches Honors Biology, Plant Taxonomy, and Bioinformatics at Penn State University.
Josh Der - Faculty Research Associate and Project Manager for The Amborella Genome Project. PhD Utah State University, 2010. Josh is broadly interested in the evolution of plants and their genomes, especially with respect to the genetic and genomic traits associated with major life history changes and diversification. His PhD research examined genome evolution in bracken fern (Pteridium). Josh sequenced and assembled the complete chloroplast genome of Pteridium and used variation in chloroplast DNA sequences to study global patterns of diversification and biogeography. Josh also characterized the first fern transcriptome using high-throughput cDNA sequencing and examined global patterns of RNA editing in the chloroplast transcriptome.
Eric Wafula - Bioinformatics Programmer (since 2009) and PhD candidate, Biology.
Loren Honaas - PhD candidate, IBIOS program. Loren's bachelors degree was in molecular and cell biology from Southeast Missouri State University. Before grad school he worked on plant-parasitic nematodes at the Donald Danforth Plant Science Center in Saint Louis Missouri. His scientific interests are broad, including imaging and nearly all aspects of cell biology, gene expression profiling and functional analysis of genes and their promoters. His current project in the dePamphilis lab focuses on comparing cell and tissue-specific transcriptomes of parasitic plants to identify genes involved in parasitism. When not in the lab, Loren's interests include biking, working on his house (really anything outdoors) and, from time to time, "being a little bit of a beer snob."
Yeting Zhang - PhD candidate since 2007, Genetics Program. Yeting joined Claude's lab in 2009. Yeting is interested in using bioinformatic tools analyzing transcriptomic/genomic data of parasitic plants. Her main interests focus on looking for evidence of horizontal gene transfer in parasitic plants, especially Orobanchaceae. Her work is funded by the Parasitic Plant Genome Project. She is also interested in looking for RNA movements between parasitic plants and host plants. She graduated from University of Science and Technology in China as a bachelor, majoring in Biological Sciences. She really enjoys cooking in her spare time. Yeting recently became a Mom with the arrival of baby William.
Marcos Caraballo - PhD candidate, Biology.
Zhenzhen Yang - PhD candidate, Plant Biology.
Prakash Timilsena - PhD candidate, Biology.
Paula Ralph - Lab Technician. Paula has been with the dePamphilis lab since 2005. When not booking travel, dealing with PSU paperwork or troubleshooting broken equipment, Paula trains undergrad lab assistants and works on building cDNA libraries for sequencing, along with other benchwork as needed. Paula enjoys hiking, camping, kayaking and contra dancing.
Past Students and Lab Associates:
Yuannian Jiao - PhD, Penn State University, 2011. Yuannian is interested in both molecular biology and bioinformatics. He has experience in plant molecular biology and microarray gene expression data mining. In the dePamphilis lab, he studied some interesting gene family function analyses and the role of ancient polyploidy in plant family diversification. His work led to the discovery that whole genome duplication events (WGDs) occurred around 320 mya, just prior to the diversification of extant seed plants, and around 190 mya, prior to the rapid diversification of extant angiosperms (flowering plants). Yuannian is currently a postdoctoral researcher at the University of Georgia in Andy Patterson's Lab.
Norman Wickett - Postdoctoral Research Associate, 2008-2011. PhD University of Connecticut, 2007. Norm worked on the Parasitic Plant Genome Project, with a focus on comparative evolutionary analyses and bioinformatics. His interest in parasitic plants stems from his dissertation work on a non-photosynthetic liverwort, Aneura mirabilis. In general he is interested in understanding the genomic changes associated with major life history transitions, from the conquest of land by plants to the switch from autotrophy to heterotrophy, and many questions in between.
Yan Zhang - PhD, Penn State University, 2012.
Aapjeet MS Biotech degree candidate and Lab Assistant, 2010-2011. Aapjeet managed to put in a significant number of hours in the dePamphilis lab, despite juggling the rigorous demands of the MS Biotech program at Penn State. Aapjeet assisted graduate student, Loren Honaas, with his study of the host/parasite interface interactions, co-culturing the parasite, Triphisaria versicolor, on Maize and performing RNA isolations. Aapjeet secured a summer internship at GlaxoSmithKline and plans to complete the MS Biotech coursework in the fall.
Yuchen Zhang - PhD, Penn State University, 2011.
Bastian Schaeferhoff - visiting doctoral candidate scholar from Germany, July 2009 - Oct. 2009.
Susann Wicke - visiting doctoral candidate scholar from Germany, July 2009 - Oct. 2009.
Man kyu Huh - visiting postdoctoral scholar from Korea, summer 2008 - summer 2009.
Roshan Ali - visiting doctoral candidate scholar from Pakistan, International Research Support Initiative Program, March 2008 - September 2008.
Kerr Wall - Research Programmer, 2001 - 2009; PhD Biology, 2004-2008; Kerr came from the IT industry as a web developer. Kerr built the databases, informatic pipelines, and web interfaces for the Floral Genome Project and the Ancestral Angiosperm Genome Project. Kerr is currently a Bioinformatics Scientist at BASF Plant Science in Raliegh-Durham, NC.
Stefan Wanke - visiting postdoctoral scholar, 2007, 2009.
Julia (Simon) Naumann - visiting postdoctoral scholar from the Wanke lab at TU Dresden in Germany - several visits since 2007.
Barbara Bliss - PhD, Penn State University, 2008. Barbara is now working for the USDA in Hawaii!
Jill Ricker Duarte - PhD, Penn State University, 2008; For her PhD work, Jill studied expression divergence during the evolution of single-copy and duplicate genes in flowering plants. Jill became a parent with the arrival of Gabriella on Sept. 2, 2008. (Congrats!!) Someday she hopes to get back to studying organellar gene transfer and spreading the word about how "plants" are just dry charophycean algae. When not in the lab, Jill enjoys cooking, photography, manga and philosophy of biology.
Melanie Roy - visiting doctoral candidate scholar from France, spring 2006, Fall 2007.
Abdelali (Ali) Barakat - Postdoctoral Research Associate, 2005 - 2007; Ali is continuing his work on microrRNAs (analyzing the distribution and the evolution and function of some microRNA families involved in flower development) in John Carlson's lab at Penn State Universtiy.
Kai Mueller - Adjunct Postdoctoral Scholar, summer 2006.
Jim Leebens-Mack - Research Associate; Jim's currently an Assistant Professor of Plant Biology at the University of Georgia.
Liying Cui - PhD 2006, Penn State University; M.A.S., Applied Statistics, 2005 (Penn State); B.S. Genetics, 2000 (Fudan University, Shanghai, China); While in the dePamphilis Lab, Liying worked on diverse topics related to genome evolutions and gene expression analysis. These included: 1)Gene Expression profile in floral organs based on ESTs and microarray data, 2)The genome duplication history of flowernig plants, 3)Chloroplast genome sequence analysis, 4)Co-development of software for organelle genome rearrangements. Liying is currently wroking as a statistician in the Washington, D.C. area.
Joel McNeal - PhD 2005, Penn State University; Joel's an outstanding botanist who worked on the evolution of dodder (Cuscuta), a parasitic vine, while in the dePamphilis lab. Joel has recently taken a Post Doctoral position in the Dept. of Organismic and Evolutionary Biology at Harvard University.
Alan Smith - PhD 2003, Vanderbilt Universty.
Andrea D. Wolfe - NSF Postdoctoral fellow 1994-1996; Andi is an Associate Professor of Plant Biology at Ohio State University. Andi studied the evolution of photosynthetic and ndh genes in parasitic Scrophulariaceae and Orobanchaeae. Her work led to the discovery that some Orobanche species retain an intact, apparently functional rbcL gene, while other species ahve only a remnant pseudogene. We continue to work together on trying to solve the mystery of what the function, if any, may be served by the intact rbcL genes. Andi's lab has active projects in the molecular systematics of Penstemon, as welll as several parasitic genrea of Scrophulariaceae.
Nelson D. (Ned) Young - Postdoctoral associate, 1994-1998; Ned's currently a Software Engineer in the Microbiology Department at U. Mass. Amherst. Ned's working in the Derek Lovley lab where he studies the comparative genomics, molecular evolution and system biology of the electricity-producing bacterium Geobacter. While in the dePamphilis lab, Ned's studies of plastic rps2 and matK gene sequences led to discoveries about the forces that influence rates of sequence evolution, plastid gene function, and the phylogenetic relationships of nonparasitic as well as parasitic scrophs.
Gordon Chenery - M.S. Vanderbilt Universty, 1995; Gordon's a high school teacher at Montgomery Bell Academy in Nashville, TN, who is working on a second master's degree in plant molecular systematics. Gordon developed mitochondrial atpa as a phylogenetic tool for angiosperms.
Todd Barkman - PhD University of Texas; postdoctoral associate in the laboratory; Currently an Assistant Professor of Biological Sciences at. While in the dePamphilis lab, Todd worked on mitochondrial gene and intron projects and plastid DNA molecular evolution in parasitic plants.
L. Michelle Bowe - PhD. 1997, Vanderbilt Unviersity; michelle is an Assistant Professor of Biology and Curator of the Herbarium at Southwest Missouri State University in Springfield, Missouri. Michelle was the first to develop the slowly evolving mitochondrial gene for molecular systematic studies in seed plants, and authored a seminal paper on the phylogenetic implications of RNA implications of RNA deidtion and gene processing.
Suneeti Jog - PhD botany, 2003 Cleveland State University; Suneeti is currently a post doctoral researcher with the Kansas Biological Survery, University of Kansas. While in dePamphilis lab, Suneeti was interested in plant molecular systematics and evolution.
Henrietta Croom - PhD, University of North Carolina, Chapel Hill; Henrietta is a Professor of Biology at the University of the South in Sewanee, TN and works with us on studies of the coxl gene and its associated group I intron in flowering plants. Henrietta was visiting the lab on sabbatical from Fall 1996 - Summer 1997.
Kim Steiner - PhD., UC Davis; Kim is Chairman and Associate Curator of the Biology Department at the California Academy of Sciences and a world expert on plants that produce oil-flowers. Kim has worked in our lab from time to time on Scrophulariaceae molecular systematics.
Gwenaele Coat - Gwenaele visited the lab from Roscoff, France in 1999-2000. She was fervently running the new CEQ 2000 on a 24-hour basis, pumping out those sequences.
Wayne Elisens - A Professor of Botany at the University of Oklahoma, Wayne spent a sabbatical year in our lab (1994) working on scroph molecular systematics and helped launch the plant mitochondrial gene project.