5 Works

Data from: Phytochrome diversity in green plants and the origin of canonical plant phytochromes

Fay-Wei Li, Michael Melkonian, Carl J. Rothfels, Juan Carlos Villarreal, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer & Sarah Mathews
Phytochromes are red/far-red photoreceptors that play essential roles in diverse plant morphogenetic and physiological responses to light. Despite their functional significance, phytochrome diversity and evolution across photosynthetic eukaryotes remain poorly understood. Using newly available transcriptomic and genomic data we show that canonical plant phytochromes originated in a common ancestor of streptophytes (charophyte algae and land plants). Phytochromes in charophyte algae are structurally diverse, including canonical and non-canonical forms, whereas in land plants, phytochrome structure is...

Data from: Phylogenetic relationships in Asarum (Aristolochiaceae): effect of data partitioning and a revised classification

Brandon T. Sinn, Lawrence M. Kelly & John V. Freudenstein
Premise of the study: Generic boundaries and infrageneric relationships among the charismatic temperate magnoliid Asarum sensu lato have long been uncertain. Previous molecular phylogenetic analyses used either plastid or nuclear loci alone and varied greatly in their taxonomic implications for the genus. We analyze additional molecular markers from the nuclear and plastid genomes, reevaluate the possibility of a derived loss of autonomous self-pollination, and investigate the topological effects of matrix partitioning scheme choice. Methods: We...

Data from: Cell signaling-based classifier predicts response to induction therapy in elderly patients with acute myeloid leukemia

Alessandra Cesano, Cheryl L. Willman, Kenneth J. Kopecky, Urte Gayko, Santosh Putta, Brent Louie, Matt Westfall, Norman Purvis, David C. Spellmeyer, Carol Marimpietri, Aileen C. Cohen, James Hackett, Jing Shi, Michael G. Walker, Zhuoxin Sun, Elisabeth Paietta, Martin S. Tallman, Larry D. Cripe, Susan Atwater, Frederick R. Appelbaum & Jerald P. Radich
Single-cell network profiling (SCNP) data generated from multi-parametric flow cytometry analysis of bone marrow (BM) and peripheral blood (PB) samples collected from patients >55 years old with non-M3 AML were used to train and validate a diagnostic classifier (DXSCNP) for predicting response to standard induction chemotherapy (complete response [CR] or CR with incomplete hematologic recovery [CRi] versus resistant disease [RD]). SCNP-evaluable patients from four SWOG AML trials were randomized between Training (N = 74 patients...

Data from: Resolving relationships within the palm subfamily Arecoideae (Arecaceae) using next-gen derived plastid sequences

Jason R. Comer, Wendy B. Zomlefer, Craig F. Barrett, Jerrold I. Davis, Dennis W. Stevenson, Karolina Heyduk & James H. Leebens-Mack
Premise of the study: Several studies have incorporated molecular and morphological data to study the phylogeny of the palms (Arecaceae), but some relationships within the family remain ambiguous—particularly those within Arecoideae, the most diverse subfamily including coconut and oil palm. Here, two next-generation, targeted plastid-enrichment methods were compared and used to elucidate Arecoideae phylogeny. Methods: Next-generation sequencing techniques were used to generate a plastid genome data set. Long range PCR and hybrid gene capture were...

Data from: The evolutionary history of ferns inferred from 25 low-copy nuclear genes

Carl J. Rothfels, Fay-Wei Li, Erin M. Sigel, Layne Huiet, Anders Larsson, Dylan O. Burge, Markus Ruhsam, Michael Deyholos, Douglas E. Soltis, , Shane W. Shaw, Lisa Pokorny, Tao Chen, Claude DePamphilis, Lisa DeGironimo, Li Chen, Xiaofeng Wei, Xiao Sun, Petra Korall, Dennis W. Stevenson, Sean W. Graham, Gane Ka-Shu Wong, Kathleen M. Pryer, C. Neal Stewart, Gane K-S. Wong … & Claude De Pamphilis
Premise of the study: Understanding fern (monilophyte) phylogeny and its evolutionary timescale is critical for broad investigations of the evolution of land plants, and for providing the point of comparison necessary for studying the evolution of the fern sister group, seed plants. Molecular phylogenetic investigations have revolutionized our understanding of fern phylogeny, however, to date, these studies have relied almost exclusively on plastid data. Methods: Here we take a curated phylogenomics approach to infer the...

Registration Year

  • 2015

Resource Types

  • Dataset


  • The Bronx Defenders
  • Duke University
  • University of Alberta
  • University of California, Berkeley
  • Royal Botanic Garden Edinburgh
  • University of British Columbia
  • Fred Hutchinson Cancer Research Center
  • Stanford University
  • University of Cologne
  • The Ohio State University