Claude dePamphilis

Professor of Biology at the Pennsylvania State University

Lab Group

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.


Loren HonaasEric 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


Loren Honaas Loren Honaas - Postdoctoral Scholar, PhD Penn State University, 2014. Loren's 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."


“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.


Julia Naumann Postdoctoral Scholar on The Amborella Genome Project since 2015. Her major interest is plant molecular evolution. She has been working on different plant lineages, such as Piperales, Canellales, and Cornales. Currently, her research is focused on organellar genome evolution in parasitic plants (Hydnoraceae in particular) and Amborella.

Marcos Caraballo-Ortiz - PhD candidate, Biology. Marcos's interests include phylogeny, evolution of host selection, and taxonomy of parasitic plants (mistletoes), island biogeography, and taxonomy of Neotropical plants. His current research investigates the phylogenetic relationships of an endemic group of mistletoes from the Caribbean (Dendropemon, in Loranthaceae), including a taxonomic revision of the genus and examining possible factors influencing host selection and speciation in the genus. He is using transcriptomic datasets to build high resolution phylogenies at species level for Dendropemon and other related genera within the subtribe Psittacanthinae in Loranthaceae. Marcos has also conducted research in pollination biology, taxonomy, ecology, and floristics of Caribbean plants.


“ZhenzhenZhenzhen Yang - PhD candidate, Plant Biology. Zhenzhen's interests include plant sciences and evolutionary genomics. Zhenzhen has been working on the RNA-Seq data from the The Parasitic Plant Genome Project to reveal the genomic and evolutionary changes that contributed to the formation of the haustorium in parasitic plants. Her work has spanned from using the expression data, including RNA-Seq and microarray, to evolutionary studies, such as large-scale sequence phylogenies and molecular evolution analyses. She is currently following up on a previous PhD graduate's (Yeting Zhang) work on Horizontal Gene Transfer to unveil another mechanism of parasite evolution. In her spare time, Zhenzhen likes outdoor sports including running, biking, and hiking, as well as indoor activities, like playing the piano and cooking (desserts in particular).


Prakash Timilsena - PhD candidate, Biology.

Sam Jones - PhD candidate, Plant Biology.

“Huiting Huiting Zhang - PhD candidate, Plant Biology.


       

Past Students and Lab Associates:

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.

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.