Claude dePamphilis

Professor of Biology at the Pennsylvania State University

Lab Group 2018
dePamphilis Lab, June 2018
Kenya trip June 2018
Straddling the equator in Kenya, June 2018

Current members:

Claude dePamphilis 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 and the Parasitic Plant Genome Project. Claude teaches Honors Biology, Plant Taxonomy, and Bioinformatics at Penn State University.


Paula RalphPaula Ralph - Senior Research 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 preparing samples for sequencing, along with other benchwork as needed. Paula enjoys hiking, gardening and contra dancing.


Eric WafulaEric Wafula - Bioinformatics Programmer (since 2009) and Ph.D candidate, Biology. Eric works as full-time computer scientist in the lab, as well as pursuing a PhD in Biology. Eric plays a lead role as bioinformatics programmer on NSF grants to develop new databases, pipeline analyses, and methods to gain novel insights into the evolutionary history of genomes, gene families, and the tree of life. He also helps junior scientists in the dePamphilis and other labs to learn bioinformatics programming and its application to a wide range of biological problems


       

Prakash Timilsena - PhD candidate, Biology. Prakash is using bioinformatic analysis of transcriptome and genome-scale datasets to investigate the phylogenetic relationships between plant families in the Monocots, including mycoheterotrophic Monocots.

“Huiting Huiting Zhang - PhD candidate, Plant Biology. Huiting is using a plant transformation system to characterize the "parasitism genes" identified by collaborators in the Parasitic Plant Genome Project in Tryphysaria versicolor. Huiting enjoys exploring in the woods, photography and anything to do with flowers. Oh - and Pokemon Go!


Elizabeth Kelly - PhD candidate, Plant Biology. Elizabeth is studying haustorial initiation and host-parasite signaling in the parasitic Orobanchaceae. When not in the lab, she can be found in the Buckhout Greenhouse, where she is an assitant greenhouse manager, or at the rink with her roller derby team!


       

Wen-Bin Yu - Visiting Research Associate since September 2015. Wen-Bin received his Ph.D. in Botany at Kunming Institute of Botany, Chinese Academy Sciences (CAS) in 2011. Currently, he is an Associate Professor of Botany (since August 2014) at the Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, CAS. Wen-Bin is focusing on systematics and evolution of parasitic plants using DNA sequences and genomic data, with an emphasis on Orobanchaceae. He is also interested in plant taxonomy and botanical nomenclature.


       

Uma Venkatesh - Post-Doctoral Fellow, PhD in Botany from Karnatak University, Dharwad, India. Uma is working on a long-term DNA and RNA Barcoding project of all the accessioned cultivar, native and naturalized plant species in the Arboretum at Penn State. Recently she received a small grant from The Garden Club of America to study 3 native and rare parasitic plants of Pennsylvania. She is also involved in the ongoing Mid Atlantic megalopolis digitization project at the PAC herbarium which involves imaging of 65,000 herbarium specimens from Mid-Atlantic states. Uma writes popular science articles in Kannada, a south Indian language. She enjoys traveling, hiking, reading & photography.


Airong Li - is a visiting Professor from the Kunming Institute of Botany, Chinese Academy of Sciences. Her research interests focus on multi-species interactions among Pedicularis (root hemiparasites), host plants and soil microorganisms. With a particular interest in rhizosphere processes, Airong uses ecological, physiological and molecular approaches to understand the basis of the multi-species interactions. Her ultimate goal is to unravel mechanisms driving dynamics in plant communities in which Pedicularis occurs so as to contribute toward effective ecosystem management.


“ChunceChunce Guo - Postdoctoral Scholar, PhD Institute of Botany, Chinese Academy of Sciences, 2012. Chunce's interests include phylogenetic and evolutionary analysis of gene families, molecular and evolutionary mechanisms of duplicate genes, and comparative evolutionary genomics. His current project focuses on the study of the evolution of floral genes and the origin of flowering plants.


       

Juan Cerda - PhD candidate, Bioinformatics and Genomics.


“NateNate Person - Bioinformatics Analyst and PhD candidate in the Bioinformatics and Genomics Program. Nate works as a full time Bioinformatics Analyst at Geisinger, as well as pursuing a PhD in the dePamphills lab.


       
Lab Group 2015
dePamphilis Lab, July 2015

Past Students and Lab Associates:

Marcos Caraballo-Ortiz - Ph.D. Biology, Penn State University, 2017. Marcos began a postdoctoral position at the Smithsonian Institution in January 2018, studying plants of the Caribbean and South and Central America. Marcos is a world-renowned expert on Caribbean mistletoes.

Zhenzhen Yang - Ph.D. Plant Biology, Penn State University, 2016. Zhenzhen is currently a Postdoctoral associate with Professor Haifan Lin, Shanghai and Yale University.

Loren Honaas - Ph.D. Plant Biology, Penn State University, 2013. After a completing a Postdoc at Penn State, Loren is now a Research Scientist at the USDA-ARS Tree Fruit Laboratory in Wenatchee, WA.

Josh Der - Former 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. Josh has recently joined the faculty at UC Fullerton.

Julia Naumann - visiting Postdoctoral scholar from Germany, Summer 2015 - fall 2017.

Yeting Zhang - PhD Genetics, Penn State University, 2014. Yeting is currently a Postdoctoral student at Rutgers University. Yeting uses bioinformatic tools to analyze transcriptomic/genomic data. The main focus of her research while in Claude's Lab was on horizontal gene transfer in parasitic plants, especially in Orobanchaceae.

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 an internship at GlaxoSmithKline.

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 from Germany, 2007, 2009.

Barbara Bliss - PhD, Penn State University, 2008.

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’s work focused on microrRNAs (analyzing the distribution and the evolution and function of some microRNA families involved in flower development).

Kai Mueller - Adjunct Postdoctoral Scholar from Germany, summer 2006.

Jim Leebens-Mack - Research Associate; Jim is currently an Associate 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 (Andi) 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 have only a remnant pseudogene. Andi's lab has active projects in the molecular systematics of Penstemon, as well as several parasitic genera of Scrophulariaceae.

Nelson D. (Ned) Young - Postdoctoral Associate, 1994-1998; While in the dePamphilis lab, Ned's studies of plastid 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 University, 1995; Gordon was a high school teacher at Montgomery Bell Academy in Nashville, TN, while working on a second master's degree in plant molecular systematics at Penn State. Gordon developed mitochondrial atpa as a phylogenetic tool for angiosperms.

Todd Barkman - PhD University of Texas; Postdoctoral Associate in dePamphilis Lab; 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 University; 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 editing and gene processing.

Suneeti Jog - PhD botany, 2003 Cleveland State University; 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.