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Claude dePamphilis

This is a preview profile on BiomedExperts - the first literature-based scientific social network. It brings the right researchers together and allows them to collaborate online. Collexis and Dell provide the BiomedExperts network of +1.5 Million pre-calculated profiles free of charge to researchers worldwide.

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Shan Hongyan; Zahn Laura; Guindon Stephane; Wall P Kerr; Kong Hongzhi; Ma Hong; DePamphilis Claude W; Leebens-Mack Jim
Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications.
Wall P Kerr; Leebens-Mack Jim; Chanderbali André S; Barakat Abdelali; Wolcott Erik; Liang Haiying; Landherr Lena; Tomsho Lynn P; Hu Yi; Carlson John E; Ma Hong; Schuster Stephan C; Soltis Douglas E; Soltis Pamela S; Altman Naomi; dePamphilis Claude W
Comparison of next generation sequencing technologies for transcriptome characterization.
McNeal Joel R; Kuehl Jennifer V; Boore Jeffrey L; Leebens-Mack Jim; dePamphilis Claude W
Parallel loss of plastid introns and their maturase in the genus Cuscuta.

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All Publications

2009: Shan Hongyan; Zahn Laura; Guindon Stephane; Wall P Kerr; Kong Hongzhi; Ma Hong; DePamphilis Claude W; Leebens-Mack Jim
Evolution of plant MADS box transcription factors: evidence for shifts in selection associated with early angiosperm diversification and concerted gene duplications.
Molecular biology and evolution 2009;26(10):2229-44.
2009: Wall P Kerr; Leebens-Mack Jim; Chanderbali André S; Barakat Abdelali; Wolcott Erik; Liang Haiying; Landherr Lena; Tomsho Lynn P; Hu Yi; Carlson John E; Ma Hong; Schuster Stephan C; Soltis Douglas E; Soltis Pamela S; Altman Naomi; dePamphilis Claude W
Comparison of next generation sequencing technologies for transcriptome characterization.
BMC genomics 2009;10():347.
2009: McNeal Joel R; Kuehl Jennifer V; Boore Jeffrey L; Leebens-Mack Jim; dePamphilis Claude W
Parallel loss of plastid introns and their maturase in the genus Cuscuta.
PloS one 2009;4(6):e5982.
2008: Hu Wei; dePamphilis Claude W; Ma Hong
Phylogenetic analysis of the plant-specific zinc finger-homeobox and mini zinc finger gene families.
Journal of integrative plant biology 2008;50(8):1031-45.
2008: Wickett Norman J; Zhang Yan; Hansen S Kellon; Roper Jessie M; Kuehl Jennifer V; Plock Sheila A; Wolf Paul G; DePamphilis Claude W; Boore Jeffrey L; Goffinet Bernard
Functional gene losses occur with minimal size reduction in the plastid genome of the parasitic liverwort Aneura mirabilis.
Molecular biology and evolution 2008;25(2):393-401.
2008: Wall P Kerr; Leebens-Mack Jim; Müller Kai F; Field Dawn; Altman Naomi S; dePamphilis Claude W
PlantTribes: a gene and gene family resource for comparative genomics in plants.
Nucleic acids research 2008;36(Database issue):D970-6.
2008: Yue Feng; Cui Liying; dePamphilis Claude W; Moret Bernard M E; Tang Jijun
Gene rearrangement analysis and ancestral order inference from chloroplast genomes with inverted repeat.
BMC genomics 2008;9 Suppl 1():S25.
2008: Soltis Douglas E; Albert Victor A; Leebens-Mack Jim; Palmer Jeffrey D; Wing Rod A; dePamphilis Claude W; Ma Hong; Carlson John E; Altman Naomi; Kim Sangtae; Wall P Kerr; Zuccolo Andrea; Soltis Pamela S
The Amborella genome: an evolutionary reference for plant biology.
Genome biology 2008;9(3):402.
2007: Jansen Robert K; Cai Zhengqiu; Raubeson Linda A; Daniell Henry; Depamphilis Claude W; Leebens-Mack James; Müller Kai F; Guisinger-Bellian Mary; Haberle Rosemarie C; Hansen Anne K; Chumley Timothy W; Lee Seung-Bum; Peery Rhiannon; McNeal Joel R; Kuehl Jennifer V; Boore Jeffrey L
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(49):19369-74.
2007: Barakat Abdelali; Wall Kerr; Leebens-Mack Jim; Wang Yunjiao J; Carlson John E; Depamphilis Claude W
Large-scale identification of microRNAs from a basal eudicot (Eschscholzia californica) and conservation in flowering plants.
The Plant journal : for cell and molecular biology 2007;51(6):991-1003.
2007: Soltis Douglas E; Ma Hong; Frohlich Michael W; Soltis Pamela S; Albert Victor A; Oppenheimer David G; Altman Naomi S; dePamphilis Claude; Leebens-Mack Jim
The floral genome: an evolutionary history of gene duplication and shifting patterns of gene expression.
Trends in plant science 2007;12(8):358-67.
2007: Kong Hongzhi; Landherr Lena L; Frohlich Michael W; Leebens-Mack Jim; Ma Hong; dePamphilis Claude W
Patterns of gene duplication in the plant SKP1 gene family in angiosperms: evidence for multiple mechanisms of rapid gene birth.
The Plant journal : for cell and molecular biology 2007;50(5):873-85.
2007: Barakat Abdelali; Wall Phillip K; Diloreto Scott; Depamphilis Claude W; Carlson John E
Conservation and divergence of microRNAs in Populus.
BMC genomics 2007;8():481.
2007: Barkman Todd J; McNeal Joel R; Lim Seok-Hong; Coat Gwen; Croom Henrietta B; Young Nelson D; Depamphilis Claude W
Mitochondrial DNA suggests at least 11 origins of parasitism in angiosperms and reveals genomic chimerism in parasitic plants.
BMC evolutionary biology 2007;7():248.
2007: McNeal Joel R; Arumugunathan Kathiravetpilla; Kuehl Jennifer V; Boore Jeffrey L; Depamphilis Claude W
Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae).
BMC biology 2007;5():55.
2006: Carlson John E; Leebens-Mack James H; Wall P Kerr; Zahn Laura M; Mueller Lukas A; Landherr Lena L; Hu Yi; Ilut Daniel C; Arrington Jennifer M; Choirean Stephanie; Becker Annette; Field Dawn; Tanksley Steven D; Ma Hong; dePamphilis Claude W
EST database for early flower development in California poppy (Eschscholzia californica Cham., Papaveraceae) tags over 6,000 genes from a basal eudicot.
Plant molecular biology 2006;62(3):351-69.
2006: McNeal Joel R; Leebens-Mack James H; Arumuganathan Kathiravetpillai; Kuehl Jennifer V; Boore Jeffrey L; DePamphilis Claude W
Using partial genomic fosmid libraries for sequencing complete organellar genomes.
BioTechniques 2006;41(1):69-73.
2006: Cui Liying; Wall P Kerr; Leebens-Mack James H; Lindsay Bruce G; Soltis Douglas E; Doyle Jeff J; Soltis Pamela S; Carlson John E; Arumuganathan Kathiravetpilla; Barakat Abdelali; Albert Victor A; Ma Hong; dePamphilis Claude W
Widespread genome duplications throughout the history of flowering plants.
Genome research 2006;16(6):738-49.
2006: Duarte Jill M; Cui Liying; Wall P Kerr; Zhang Qing; Zhang Xiaohong; Leebens-Mack Jim; Ma Hong; Altman Naomi; dePamphilis Claude W
Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
Molecular biology and evolution 2006;23(2):469-78.
2006: Zahn Laura M; Leebens-Mack James H; Arrington Jennifer M; Hu Yi; Landherr Lena L; dePamphilis Claude W; Becker Annette; Theissen Günter; Ma Hong
Conservation and divergence in the AGAMOUS subfamily of MADS-box genes: evidence of independent sub- and neofunctionalization events.
Evolution & development 2006;8(1):30-45.
2006: Cui Liying; Veeraraghavan Narayanan; Richter Alexander; Wall Kerr; Jansen Robert K; Leebens-Mack Jim; Makalowska Izabela; dePamphilis Claude W
ChloroplastDB: the Chloroplast Genome Database.
Nucleic acids research 2006;34(Database issue):D692-6.
2006: Cai Zhengqiu; Penaflor Cynthia; Kuehl Jennifer V; Leebens-Mack James; Carlson John E; dePamphilis Claude W; Boore Jeffrey L; Jansen Robert K
Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids.
BMC evolutionary biology 2006;6():77.
2006: Leebens-Mack Jim; Vision Todd; Brenner Eric; Bowers John E; Cannon Steven; Clement Mark J; Cunningham Clifford W; dePamphilis Claude; deSalle Rob; Doyle Jeff J; Eisen Jonathan A; Gu Xun; Harshman John; Jansen Robert K; Kellogg Elizabeth A; Koonin Eugene V; Mishler Brent D; Philippe Hervé; Pires J Chris; Qiu Yin-Long; Rhee Seung Y; Sjölander Kimmen; Soltis Douglas E; Soltis Pamela S; Stevenson Dennis W; Wall Kerr; Warnow Tandy; Zmasek Christian
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA).
Omics : a journal of integrative biology 2006;10(2):231-7.
2006: Cui Liying; Leebens-Mack Jim; Wang Li-San; Tang Jijun; Rymarquis Linda; Stern David B; dePamphilis Claude W
Adaptive evolution of chloroplast genome structure inferred using a parametric bootstrap approach.
BMC evolutionary biology 2006;6():13.
2005: Sampedro Javier; Lee Yi; Carey Robert E; dePamphilis Claude; Cosgrove Daniel J
Use of genomic history to improve phylogeny and understanding of births and deaths in a gene family.
The Plant journal : for cell and molecular biology 2005;44(3):409-19.
2005: Leebens-Mack Jim; Raubeson Linda A; Cui Liying; Kuehl Jennifer V; Fourcade Matthew H; Chumley Timothy W; Boore Jeffrey L; Jansen Robert K; depamphilis Claude W
Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one's way out of the Felsenstein zone.
Molecular biology and evolution 2005;22(10):1948-63.
2005: Zahn L M; Leebens-Mack J; DePamphilis C W; Ma H; Theissen G
To B or Not to B a flower: the role of DEFICIENS and GLOBOSA orthologs in the evolution of the angiosperms.
The Journal of heredity 2005;96(3):225-40.
2005: Zahn Laura M; Kong Hongzhi; Leebens-Mack James H; Kim Sangtae; Soltis Pamela S; Landherr Lena L; Soltis Douglas E; Depamphilis Claude W; Ma Hong
The evolution of the SEPALLATA subfamily of MADS-box genes: a preangiosperm origin with multiple duplications throughout angiosperm history.
Genetics 2005;169(4):2209-23.
2005: Parkinson Christopher L; Mower Jeffrey P; Qiu Yin-Long; Shirk Andrew J; Song Keming; Young Nelson D; DePamphilis Claude W; Palmer Jeffrey D
Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae.
BMC evolutionary biology 2005;5():73.
2005: Wang Ji-Ping Z; Lindsay Bruce G; Cui Liying; Wall P Kerr; Marion Josh; Zhang Jiaxuan; dePamphilis Claude W
Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries.
BMC bioinformatics 2005;6():300.
2005: Jansen Robert K; Raubeson Linda A; Boore Jeffrey L; dePamphilis Claude W; Chumley Timothy W; Haberle Rosemarie C; Wyman Stacia K; Alverson Andrew J; Peery Rhiannon; Herman Sallie J; Fourcade H Matthew; Kuehl Jennifer V; McNeal Joel R; Leebens-Mack James; Cui Liying
Methods for obtaining and analyzing whole chloroplast genome sequences.
Methods in enzymology 2005;395():348-84.
2005: Albert Victor A; Soltis Douglas E; Carlson John E; Farmerie William G; Wall P Kerr; Ilut Daniel C; Solow Teri M; Mueller Lukas A; Landherr Lena L; Hu Yi; Buzgo Matyas; Kim Sangtae; Yoo Mi-Jeong; Frohlich Michael W; Perl-Treves Rafael; Schlarbaum Scott E; Bliss Barbara J; Zhang Xiaohong; Tanksley Steven D; Oppenheimer David G; Soltis Pamela S; Ma Hong; DePamphilis Claude W; Leebens-Mack James H
Floral gene resources from basal angiosperms for comparative genomics research.
BMC plant biology 2005;5():5.
2005: Young Nelson D; dePamphilis Claude W
Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function.
BMC evolutionary biology 2005;5(1):16.
2004: Wang Ji-Ping Z; Lindsay Bruce G; Leebens-Mack James; Cui Liying; Wall Kerr; Miller Webb C; dePamphilis Claude W
EST clustering error evaluation and correction.
Bioinformatics (Oxford, England) 2004;20(17):2973-84.
2004: Wang Guanfang; Kong Hongzhi; Sun Yujin; Zhang Xiaohong; Zhang Wei; Altman Naomi; DePamphilis Claude W; Ma Hong
Genome-wide analysis of the cyclin family in Arabidopsis and comparative phylogenetic analysis of plant cyclin-like proteins.
Plant physiology 2004;135(2):1084-99.
2004: Kong Hongzhi; Leebens-Mack Jim; Ni Weimin; dePamphilis Claude W; Ma Hong
Highly heterogeneous rates of evolution in the SKP1 gene family in plants and animals: functional and evolutionary implications.
Molecular biology and evolution 2004;21(1):117-28.
2003: Nam Jongmin; dePamphilis Claude W; Ma Hong; Nei Masatoshi
Antiquity and evolution of the MADS-box gene family controlling flower development in plants.
Molecular biology and evolution 2003;20(9):1435-47.
2002: Maul Jude E; Lilly Jason W; Cui Liying; dePamphilis Claude W; Miller Webb; Harris Elizabeth H; Stern David B
The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats.
The Plant cell 2002;14(11):2659-79.
2002: Leebens-Mack Jim; DePamphilis Claude
Power analysis of tests for loss of selective constraint in cave crayfish and nonphotosynthetic plant lineages.
Molecular biology and evolution 2002;19(8):1292-302.
2002: Soltis Douglas E; Soltis Pamela S; Albert Victor A; Oppenheimer David G; dePamphilis Claude W; Ma Hong; Frohlich Michael W; Theissen Günter;
Missing links: the genetic architecture of flowers [correction of flower] and floral diversification.
Trends in plant science 2002;7(1):22-31; dicussion 31-4.
2000: Young N D; dePamphilis C W
Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants.
Molecular biology and evolution 2000;17(12):1933-41.
2000: Barkman T J; Chenery G; McNeal J R; Lyons-Weiler J; Ellisens W J; Moore G; Wolfe A D; dePamphilis C W
Independent and combined analyses of sequences from all three genomic compartments converge on the root of flowering plant phylogeny.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(24):13166-71.
1998: Wolfe A D; dePamphilis C W
The effect of relaxed functional constraints on the photosynthetic gene rbcL in photosynthetic and nonphotosynthetic parasitic plants.
Molecular biology and evolution 1998;15(10):1243-58.
1997: dePamphilis C W; Young N D; Wolfe A D
Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(14):7367-72.
1997: Wolfe A D; dePamphilis C W
Alternate paths of evolution for the photosynthetic gene rbcL in four nonphotosynthetic species of Orobanche.
Plant molecular biology 1997;33(6):965-77.
1996: Bowe L M; dePamphilis C W
Effects of RNA editing and gene processing on phylogenetic reconstruction.
Molecular biology and evolution 1996;13(9):1159-66.

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Claude dePamphilis

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