Philip N Benfey

Summary

Affiliation: Duke University Medical Center
Country: USA

Publications

  1. pmc Intergenic and genic sequence lengths have opposite relationships with respect to gene expression
    Juliette Colinas
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina, USA
    PLoS ONE 3:e3670. 2008
  2. pmc High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype
    Rosangela Sozzani
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina, USA
    Genome Biol 12:219. 2011
  3. pmc Toward a systems analysis of the root
    P N Benfey
    Department of Biology, Duke Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
    Cold Spring Harb Symp Quant Biol 77:91-6. 2012
  4. pmc Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana
    Ana Pop
    Computer Science Department, Princeton University, Princeton, NJ, USA
    BMC Syst Biol 4:180. 2010
  5. pmc From genotype to phenotype: systems biology meets natural variation
    Philip N Benfey
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 320:495-7. 2008
  6. pmc Developmental networks
    Philip N Benfey
    Biology Department, Duke University, Durham, North Carolina 27708, USA
    Plant Physiol 138:548-9. 2005
  7. doi request reprint Taking a developmental perspective on systems biology
    Philip N Benfey
    Biology Department and IGSP Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Dev Cell 21:27-8. 2011
  8. pmc Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research
    Philip N Benfey
    Department of Biology, Institute for Genome Sciences and Policy, Center for Systems Biology, Duke University, Durham, NC, USA
    Plant J 61:992-1000. 2010
  9. ncbi request reprint An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants
    Hongchang Cui
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Science 316:421-5. 2007
  10. doi request reprint Cell identity mediates the response of Arabidopsis roots to abiotic stress
    JOSE R DINNENY
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 320:942-5. 2008

Detail Information

Publications83

  1. pmc Intergenic and genic sequence lengths have opposite relationships with respect to gene expression
    Juliette Colinas
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina, USA
    PLoS ONE 3:e3670. 2008
    ..These findings could shed light on the role and influence of noncoding sequences on gene expression...
  2. pmc High-throughput phenotyping of multicellular organisms: finding the link between genotype and phenotype
    Rosangela Sozzani
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina, USA
    Genome Biol 12:219. 2011
    ..Here we highlight promising technologies for 'phenome-scale' analyses in multicellular organisms...
  3. pmc Toward a systems analysis of the root
    P N Benfey
    Department of Biology, Duke Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
    Cold Spring Harb Symp Quant Biol 77:91-6. 2012
    ..Finally, the genetic basis for the physical network of different roots that constitutes root system architecture is being dissected using automated imaging of growing root systems. ..
  4. pmc Integrated functional networks of process, tissue, and developmental stage specific interactions in Arabidopsis thaliana
    Ana Pop
    Computer Science Department, Princeton University, Princeton, NJ, USA
    BMC Syst Biol 4:180. 2010
    ..Arabidopsis thaliana, a versatile model organism, represents an opportunity to evaluate the predictive power of biological network inference for plant functional genomics...
  5. pmc From genotype to phenotype: systems biology meets natural variation
    Philip N Benfey
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 320:495-7. 2008
    ..Mapping genes to their function is called the "genotype-to-phenotype problem," where phenotype is whatever is changed in the organism when a gene's function is altered...
  6. pmc Developmental networks
    Philip N Benfey
    Biology Department, Duke University, Durham, North Carolina 27708, USA
    Plant Physiol 138:548-9. 2005
  7. doi request reprint Taking a developmental perspective on systems biology
    Philip N Benfey
    Biology Department and IGSP Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Dev Cell 21:27-8. 2011
    ..These insights need to be more widely applied to systems biology. Another challenge is to incorporate real-time imaging and develop computational approaches to model biological phenomena in four dimensions...
  8. pmc Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research
    Philip N Benfey
    Department of Biology, Institute for Genome Sciences and Policy, Center for Systems Biology, Duke University, Durham, NC, USA
    Plant J 61:992-1000. 2010
    ..Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology...
  9. ncbi request reprint An evolutionarily conserved mechanism delimiting SHR movement defines a single layer of endodermis in plants
    Hongchang Cui
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Science 316:421-5. 2007
    ..Our studies with SHR and SCR homologs from rice suggest that this mechanism is evolutionarily conserved, providing a plausible explanation why nearly all plants have a single layer of endodermis...
  10. doi request reprint Cell identity mediates the response of Arabidopsis roots to abiotic stress
    JOSE R DINNENY
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 320:942-5. 2008
    ..By performing a similar analysis using iron deprivation, we identified common cell-type-specific stress responses and revealed the crucial role the environment plays in defining the transcriptional outcome of cell-fate decisions...
  11. pmc Interplay between SCARECROW, GA and LIKE HETEROCHROMATIN PROTEIN 1 in ground tissue patterning in the Arabidopsis root
    Hongchang Cui
    Biology Department and Institute for Genome Sciences and Policy, Center for Systems Biology, Duke University, Box 90338, Durham, NC 27708, USA
    Plant J 58:1016-27. 2009
    ..Together, these results suggest that epigenetic regulation is probably the common basis for SCR and GA activity in cortex cell proliferation...
  12. pmc Oscillating gene expression determines competence for periodic Arabidopsis root branching
    Miguel A Moreno-Risueno
    Department of Biology and Institute for Genome Sciences and Policy Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Science 329:1306-11. 2010
    ..This molecular mechanism has characteristics that resemble molecular clock-driven activities in animal species...
  13. pmc Cell identity regulators link development and stress responses in the Arabidopsis root
    ANJALI S IYER-PASCUZZI
    Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Dev Cell 21:770-82. 2011
    ..These results reveal surprising linkages between stress and development at cellular resolution, and show the power of multiple genome-wide data sets to elucidate biological processes...
  14. ncbi request reprint Cell type-specific expression profiling in plants via cell sorting of protoplasts from fluorescent reporter lines
    Kenneth Birnbaum
    Department of Biology, New York University, 100 Washington Square East, New York, New York 10003, USA
    Nat Methods 2:615-9. 2005
  15. ncbi request reprint A high-resolution root spatiotemporal map reveals dominant expression patterns
    Siobhan M Brady
    Department of Biology, Duke University, Durham, NC 27708, USA
    Science 318:801-6. 2007
    ..Methods that combine these profiles demonstrate transcriptionally rich and complex programs that define Arabidopsis root development in both space and time...
  16. pmc Transcriptional profile of the Arabidopsis root quiescent center
    Tal Nawy
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Cell 17:1908-25. 2005
    ..Mutations in all enriched transcription factor genes including AGL42 exhibited no detectable root phenotype, raising the possibility of a high degree of functional redundancy in the QC...
  17. pmc Combining expression and comparative evolutionary analysis. The COBRA gene family
    Siobhan M Brady
    Department of Biology and The Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    Plant Physiol 143:172-87. 2007
    ..Regulation of expression of the Arabidopsis COB gene family members has highly diversified in comparison to that of the maize COB gene superfamily members. We also identify BRITTLE STALK 2-LIKE 3 as a putative ortholog of AtCOB...
  18. pmc 3D phenotyping and quantitative trait locus mapping identify core regions of the rice genome controlling root architecture
    Christopher N Topp
    Department of Biology, Duke University, Durham, NC 27708, USA
    Proc Natl Acad Sci U S A 110:E1695-704. 2013
    ..Our imaging and analytical platform provides a means to identify genes with high potential for improving root traits and agronomic qualities of crops...
  19. pmc Whole-genome analysis of the SHORT-ROOT developmental pathway in Arabidopsis
    Mitchell P Levesque
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina, USA
    PLoS Biol 4:e143. 2006
    ..Taken together, our results not only identify the first nodes in the SHR pathway and a new function for SHR in the development of the vascular tissue but also reveal the global architecture of this developmental pathway...
  20. doi request reprint Manipulating large-scale Arabidopsis microarray expression data: identifying dominant expression patterns and biological process enrichment
    David A Orlando
    Department of Biology, Duke University, Durham, NC, USA
    Methods Mol Biol 553:57-77. 2009
    ..Using these new methods we can begin to understand the biological information contained within large-scale expression data sets...
  21. pmc Transcriptional and posttranscriptional regulation of transcription factor expression in Arabidopsis roots
    Ji Young Lee
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Proc Natl Acad Sci U S A 103:6055-60. 2006
    ..This study provides a systematic overview of regulation of TF expression at a cellular level...
  22. pmc High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability
    Paul A Ingram
    GrassRoots Biotechnology, Durham, NC, USA
    Philos Trans R Soc Lond B Biol Sci 367:1559-69. 2012
    ..This work lays the foundation for future identification of important genetic components of RSA traits under nutrient limitation using a mapping population derived from these two accessions...
  23. pmc Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data
    Song Li
    Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA
    Genome Res 23:1730-9. 2013
    ..An analysis of small-RNA sequencing data showed that ∼4% of cis-NAT pairs produce putative cis-NAT-induced siRNAs. Taken together, our data and analyses illustrate the potential for multifaceted regulatory roles of plant cis-NATs. ..
  24. pmc The protein expression landscape of the Arabidopsis root
    Jalean J Petricka
    Department of Biology, Duke Center for Systems Biology, and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA
    Proc Natl Acad Sci U S A 109:6811-8. 2012
    ..Finally, among our root hair-specific proteins we identified two unique regulators of root hair development...
  25. pmc Systems approaches to identifying gene regulatory networks in plants
    Terri A Long
    1Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Annu Rev Cell Dev Biol 24:81-103. 2008
    ..Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed...
  26. doi request reprint Fluorescence-activated cell sorting in plant developmental biology
    ANJALI S IYER-PASCUZZI
    Department of Biology and NIH Center for Systems Biology, Duke University, Durham, NC, USA
    Methods Mol Biol 655:313-9. 2010
    ..In addition to gene expression, downstream applications of FACS include proteomic and metabolite analysis. This is a powerful method to examine biological functions of specific cell types and tissues with a systems biology approach...
  27. ncbi request reprint A broad competence to respond to SHORT ROOT revealed by tissue-specific ectopic expression
    Giovanni Sena
    NYU, Department of Biology, The Silver Center, Room 1009, 100 Washington Square East, New York, NY 10003, USA
    Development 131:2817-26. 2004
    ..The spatial distribution of competence to respond to SHR highlights the importance of tightly regulated movement in generating the root radial pattern...
  28. pmc Intercellular communication during plant development
    Jaimie M Van Norman
    Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Cell 23:855-64. 2011
    ..Finally, a novel temporal mechanism for lateral root positioning and the implications for intercellular signaling are considered...
  29. pmc Both the conserved GRAS domain and nuclear localization are required for SHORT-ROOT movement
    Kimberly L Gallagher
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Plant J 57:785-97. 2009
    ..Finally, we provide evidence that movement requires both cytoplasmic and nuclear localization, strongly suggesting a mechanistic link between nuclear transport and cell-to-cell movement...
  30. pmc POWRS: position-sensitive motif discovery
    Ian W Davis
    GrassRoots Biotechnology, Durham, North Carolina, United States of America
    PLoS ONE 7:e40373. 2012
    ..This provides a foundation for future efforts to rationally engineer gene expression in plants, a problem of great importance in developing biotech crop varieties...
  31. ncbi request reprint Quantification of transcription factor expression from Arabidopsis images
    Daniel L Mace
    Institute for Genome Science and Policy, Duke University, Durham, NC 27708, USA
    Bioinformatics 22:e323-31. 2006
    ....
  32. ncbi request reprint Transcriptional regulation of ROS controls transition from proliferation to differentiation in the root
    Hironaka Tsukagoshi
    Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Cell 143:606-16. 2010
    ..This pathway functions independently of auxin and cytokinin plant hormonal signaling. Comparison to ROS-regulated growth control in animals suggests that a similar mechanism is used in plants and animals...
  33. doi request reprint Patterning the primary root in Arabidopsis
    Heidi M Cederholm
    Department of Biology and Center for Systems Biology, Duke University, Durham, NC, USA
    Wiley Interdiscip Rev Dev Biol 1:675-91. 2012
    ..In this article, we provide a broad overview of the major events controlling embryonic and post-embryonic development within each major tissue and cell type in the primary root of Arabidopsis...
  34. pmc Control of Arabidopsis root development
    Jalean J Petricka
    Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Annu Rev Plant Biol 63:563-90. 2012
    ..Future refinement of these models will lead to a more complete description of the complex molecular interactions that give rise to a simple growing root...
  35. pmc Cell type-specific transcriptional profiling: implications for metabolite profiling
    Eric D Rogers
    Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Plant J 70:5-17. 2012
    ..Advancements in the isolation of single-cell populations will be highlighted, and the potential application towards generating detailed metabolic profiles will be discussed...
  36. ncbi request reprint Mechanisms regulating SHORT-ROOT intercellular movement
    Kimberly L Gallagher
    Department of Biology, Duke University, Durham, NC 27708, USA
    Curr Biol 14:1847-51. 2004
    ..Thus, in contrast to proteins that move by a process resembling diffusion, a cytoplasmic pool of SHR is not sufficient for movement...
  37. pmc High-resolution experimental and computational profiling of tissue-specific known and novel miRNAs in Arabidopsis
    Natalie W Breakfield
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Genome Res 22:163-76. 2012
    ..Knockdown of three of the newly identified miRNAs results in altered root growth phenotypes, confirming that novel miRNAs predicted by PIPmiR have functional relevance...
  38. pmc Detecting separate time scales in genetic expression data
    David A Orlando
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, NC, USA
    BMC Genomics 11:381. 2010
    ..This issue is particularly relevant to developmental biologists, who are interested in processes such as growth, segmentation and differentiation, which can all take place simultaneously, but on different time scales...
  39. pmc Information processing without brains--the power of intercellular regulators in plants
    Wolfgang Busch
    Department of Biology, Institute of Genome Sciences and Policy, Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Development 137:1215-26. 2010
    ..Together, these mechanisms coherently coordinate developmental decisions with resource allocation and growth...
  40. pmc COBRA, an Arabidopsis extracellular glycosyl-phosphatidyl inositol-anchored protein, specifically controls highly anisotropic expansion through its involvement in cellulose microfibril orientation
    Francois Roudier
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Cell 17:1749-63. 2005
    ..Our observations suggest that COB, through its involvement in cellulose microfibril orientation, is an essential factor in highly anisotropic expansion during plant morphogenesis...
  41. pmc The bHLH transcription factor POPEYE regulates response to iron deficiency in Arabidopsis roots
    Terri A Long
    Department of Biology and Institute for Genome Science and Policy Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Cell 22:2219-36. 2010
    ..PYE and BTS expression is also tightly coregulated. We propose that interactions among PYE, PYE homologs, and BTS are important for maintaining iron homeostasis under low iron conditions...
  42. ncbi request reprint Transcription factors and hormones: new insights into plant cell differentiation
    Terri A Long
    Department of Biology and Institute for Genome Sciences and Policy, Duke University, Durham, NC 27710, USA
    Curr Opin Cell Biol 18:710-4. 2006
    ..Several recent studies provide new insight into how transcription factors and phytohormones interact within meristems to control cell proliferation and differentiation...
  43. pmc Periodic root branching in Arabidopsis requires synthesis of an uncharacterized carotenoid derivative
    Jaimie M Van Norman
    Department of Biology, Duke Center for Systems Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708
    Proc Natl Acad Sci U S A 111:E1300-9. 2014
    ..These results indicate that developmental prepatterning of LRs requires an uncharacterized carotenoid-derived molecule. We propose that this molecule functions non-cell-autonomously in establishment of the LR prepattern. ..
  44. pmc HEC of a Job Regulating Stem Cells
    Erin E Sparks
    Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Dev Cell 28:349-50. 2014
    ..HEC1 acts antagonistically with other factors, integrating multiple cues to provide a balance between cellular differentiation and proliferation. ..
  45. ncbi request reprint To branch or not to branch: the role of pre-patterning in lateral root formation
    Jaimie M Van Norman
    Department of Biology, Duke Center for Systems Biology and Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
    Development 140:4301-10. 2013
    ..In addition, we compare the development of lateral root primordia with in vitro plant regeneration and discuss possible common molecular mechanisms. ..
  46. pmc Genotypic recognition and spatial responses by rice roots
    Suqin Fang
    Department of Biology, Duke Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Proc Natl Acad Sci U S A 110:2670-5. 2013
    ..This finding suggests that root tips act as local sensors that integrate rhizosphere information into global root architectural changes...
  47. ncbi request reprint A gene expression map of the Arabidopsis root
    Kenneth Birnbaum
    Department of Biology, New York University, New York, NY 10003, USA
    Science 302:1956-60. 2003
    ..Chromosomal clustering defined some coregulated genes. This expression map correlates groups of genes to specific cell fates and should serve to guide reverse genetics...
  48. pmc Transcriptional switches direct plant organ formation and patterning
    Miguel A Moreno-Risueno
    Department of Biology and Duke Center for Systems Biology, Duke University, Durham, North Carolina, USA
    Curr Top Dev Biol 98:229-57. 2012
    ..Finally, a dynamic transcriptional mechanism for lateral organ positioning that integrates spatial and temporal information into a repeating pattern is summarized...
  49. pmc High-throughput RNA isolation technologies. New tools for high-resolution gene expression profiling in plant systems
    Ji Young Lee
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Physiol 138:585-90. 2005
  50. pmc Unraveling the dynamic transcriptome
    Siobhan M Brady
    Department of Biology and Institute for Genome Sciences and Policy Duke University Durham, NC 27708, USA
    Plant Cell 18:2101-11. 2006
  51. ncbi request reprint Plant stem cell niches: standing the test of time
    JOSE R DINNENY
    Department of Biology, Duke University, Durham, NC 27708, USA
    Cell 132:553-7. 2008
    ..Recent work using computer modeling and live imaging is helping to elucidate some of the mechanisms responsible for the specification and maintenance of stem cells in the root and shoot...
  52. pmc A stele-enriched gene regulatory network in the Arabidopsis root
    Siobhan M Brady
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Mol Syst Biol 7:459. 2011
    ..Remarkably, molecular phenotypes were identified for 65% of the TFs, but morphological phenotypes were associated with only 16%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered...
  53. pmc Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems
    ANJALI S IYER-PASCUZZI
    Department of Biology, Institute for Genome Sciences and Policy Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Physiol 152:1148-57. 2010
    ..This work enables the automatic phenotyping of RSA of individuals within mapping populations, providing an integrative framework for quantitative trait loci analysis of RSA...
  54. pmc Symmetry breaking in plants: molecular mechanisms regulating asymmetric cell divisions in Arabidopsis
    Jalean J Petricka
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA
    Cold Spring Harb Perspect Biol 1:a000497. 2009
    ..These examples occur in early embryogenesis, stomatal development, and ground tissue formation in the root...
  55. pmc Omics meet networks - using systems approaches to infer regulatory networks in plants
    Miguel A Moreno-Risueno
    Duke University, Department of Biology and Center for Systems Biology, USA
    Curr Opin Plant Biol 13:126-31. 2010
    ..Ultimately, the integration of diverse and massive datasets into coherent models will improve our understanding of the molecular networks that underlie biological processes...
  56. pmc Root layers: complex regulation of developmental patterning
    Jalean J Petricka
    Biology Department, IGSP Center for Systems Biology, Duke University, 124 Science Drive, FFSC 4101, Durham, NC 27708, United States
    Curr Opin Genet Dev 18:354-61. 2008
    ..As a result, future research advances in this field will require tissue-specific information at both the single gene and global level...
  57. pmc Spatiotemporal signalling in plant development
    Erin Sparks
    1 Department of Biology and Center for Systems Biology, Duke University, Durham, North Carolina 27708, USA 2
    Nat Rev Genet 14:631-44. 2013
    ..In some cases, we also address the evolutionary context of mechanisms and discuss possible links between the lifestyle of plants and selection for different signalling mechanisms. ..
  58. doi request reprint High-throughput, noninvasive imaging of root systems
    ANJALI S IYER-PASCUZZI
    Department of Biology, Duke University, Durham, NC, USA
    Methods Mol Biol 959:177-87. 2013
    ..The platform is relatively inexpensive, high-throughput, and is ideally suited for researchers aiming to understand the genetic control of root architecture. Here we describe the application of this method to rice and maize root systems...
  59. pmc Integrative systems biology: an attempt to describe a simple weed
    Louisa M Liberman
    Department of Biology and Duke Center for Systems Biology, Duke University, Durham, NC, USA
    Curr Opin Plant Biol 15:162-7. 2012
    ..In this review we propose that 'triangulation' among transcriptomics, proteomics and metabolomics is a meaningful approach for beginning this integrative analysis and uncovering a systems level perspective of Arabidopsis biology...
  60. pmc Maturation of the ground tissue of the root is regulated by gibberellin and SCARECROW and requires SHORT-ROOT
    Alice J Paquette
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Plant Physiol 138:636-40. 2005
  61. pmc A microfluidic device and computational platform for high-throughput live imaging of gene expression
    Wolfgang Busch
    Department of Biology, Duke University, Durham, North Carolina, USA
    Nat Methods 9:1101-6. 2012
    ..We tracked hundreds of roots to capture detailed expression patterns of 12 transgenic reporter lines under different conditions...
  62. doi request reprint From lab to field, new approaches to phenotyping root system architecture
    Jinming Zhu
    GrassRoots Biotechnology, Durham, NC, USA
    Curr Opin Plant Biol 14:310-7. 2011
    ..Improvements in phenotyping will facilitate the genetic analysis of RSA and aid in the identification of the genetic loci underlying useful agronomic traits...
  63. ncbi request reprint Signals that regulate stem cell activity during plant development
    Teva Vernoux
    DCMB Group, Department of Biology, Duke University, Box 91000, Research Drive, Durham, NC 27708, USA
    Curr Opin Genet Dev 15:388-94. 2005
    ....
  64. ncbi request reprint Not just another hole in the wall: understanding intercellular protein trafficking
    Kimberly L Gallagher
    Department of Biology, Duke University, Durham, NC 27708, USA
    Genes Dev 19:189-95. 2005
    ..Here we review recent developments in cell-to-cell trafficking of macromolecules in plants and animals...
  65. pmc Arabidopsis thaliana as a model organism in systems biology
    Jaimie M Van Norman
    Department of Biology, Duke University, Durham, North Carolina 27708, USA
    Wiley Interdiscip Rev Syst Biol Med 1:372-9. 2009
    ..Further investigation of plant systems will require data gathering from specific cells and tissues, continued improvement in metabolic technologies, and novel computational methods for data visualization and modeling...
  66. ncbi request reprint Stem cell research goes underground: the RETINOBLASTOMA-RELATED gene in root development
    JOSE R DINNENY
    Department of Biology, Duke University, Durham, NC 27708, USA
    Cell 123:1180-2. 2005
    ..In this issue of Cell, it is revealed that a canonical retinoblastoma pathway plays a crucial role in regulating the balance between differentiation and renewal of plant root stem cells...
  67. ncbi request reprint Trait-to-gene: a computational method for predicting the function of uncharacterized genes
    Mitchell Levesque
    New York University, 1009 Main Building, 100 Washington Square East, 10003, New York, NY, USA
    Curr Biol 13:129-33. 2003
    ..We observed a motility phenotype for two of these three genes. Thus, these algorithms allow for high-throughput functional prediction of genes beyond that provided by simple orthology-based annotation endeavors...
  68. ncbi request reprint A common switch used by plants and animals
    Philip N Benfey
    Biology Department, Duke University, Durham, NC 27708, USA
    Cell 116:4-5. 2004
    ..The discovery that a kinase of the MAPKK class plays a key role in cell specification at the first division of the Arabidopsis embryo suggests that there may be similarities based on a common logic...
  69. pmc GiA Roots: software for the high throughput analysis of plant root system architecture
    Taras Galkovskyi
    Department of Mathematics, Duke University, Durham, NC, USA
    BMC Plant Biol 12:116. 2012
    ..Identifying RSA-associated genes also represents an underexplored opportunity for crop improvement. Software tools are needed to accelerate the pace at which quantitative traits of RSA are estimated from images of root networks...
  70. pmc The COBRA family of putative GPI-anchored proteins in Arabidopsis. A new fellowship in expansion
    Francois Roudier
    Department of Biology, New York University, New York, NY 10003, USA
    Plant Physiol 130:538-48. 2002
    ..Together, these results indicate that COB family members are likely to be important new players at the plasma membrane-cell wall interface...
  71. pmc Transcriptional networks in root cell fate specification
    ANJALI S IYER-PASCUZZI
    Department of Biology, Duke University, Durham NC 27708, USA
    Biochim Biophys Acta 1789:315-25. 2009
    ..A new, high resolution root expression map detailing the transciptome of nearly all cell types in the Arabidopsis root across developmental timepoints will provide a framework for understanding these networks...
  72. pmc Reconstructing regulatory network transitions
    Jalean J Petricka
    Department of Biology and IGSP Center for Systems Biology, Duke University, Durham, NC 27708, USA
    Trends Cell Biol 21:442-51. 2011
    ..We describe recent regulatory network reconstructions in a variety of organisms, and discuss the success they share in identifying new regulatory components, shared relationships and phenotypic outcomes...
  73. pmc Using cauliflower to find conserved non-coding regions in Arabidopsis
    Juliette Colinas
    Department of Biology, 1009 Main Building, New York University, 100 Washington Square East, New York, NY 10003, USA
    Plant Physiol 129:451-4. 2002
  74. ncbi request reprint Systems biology
    Mitchell P Levesque
    Biology Department, Duke University, Box 91000, Durham, North Carolina 27708, USA
    Curr Biol 14:R179-80. 2004
  75. ncbi request reprint Auxin action: slogging out of the swamp
    Philip N Benfey
    Biology Department, New York University, 1009 Main Building, 100 Washington Square East, New York, NY 10003, USA
    Curr Biol 12:R389-90. 2002
    ....
  76. ncbi request reprint Development and ecology in the time of systems biology
    Philip N Benfey
    Biology Department, Duke University, Durham, NC 27708, USA
    Dev Cell 7:329-30. 2004
  77. pmc Conservation and diversification of SCARECROW in maize
    Jun Lim
    Department of Molecular Biotechnology, Konkuk University, 143 701 Seoul, Korea
    Plant Mol Biol 59:619-30. 2005
    ..We found SCL23 to be the most closely related to SCR in both eudicots and monocots, suggesting that a gene duplication resulting in SCR and SCL23 predates the divergence of dicots and monocots...
  78. pmc Two new loci, PLEIADE and HYADE, implicate organ-specific regulation of cytokinesis in Arabidopsis
    Sabine Muller
    Center of Applied Genetics, University of Agricultural Sciences Vienna, Muthgasse 18, A 1190 Vienna, Austria
    Plant Physiol 130:312-24. 2002
    ..hya/hya seedlings and double mutants point to a role of PLE and HYA in the same process. These mutants provide tools to elucidate the regulation of nuclear cytoskeletal interactions during cell division and cytokinesis...
  79. ncbi request reprint Receptor-like kinase ACR4 restricts formative cell divisions in the Arabidopsis root
    Ive De Smet
    Department of Plant Systems Biology, Flanders Institute for Biotechnology VIB, B 9052 Ghent, Belgium
    Science 322:594-7. 2008
    ..Thus, ACR4 function reveals a common mechanism of formative cell division control in the main root tip meristem and during lateral root initiation...
  80. ncbi request reprint Molecular biology: microRNA is here to stay
    Philip N Benfey
    Nature 425:244-5. 2003
  81. ncbi request reprint Network building: transcriptional circuits in the root
    Kenneth Birnbaum
    New York University, 1009 Main Building, 100 Washington Square East, New York, New York 10003, USA
    Curr Opin Plant Biol 7:582-8. 2004
    ..A map of gene expression in the Arabidopsis root has identified many new candidate genes that feed into and out of these transcriptional controls...
  82. pmc Signaling in and out: control of cell division and differentiation in the shoot and root
    Keiji Nakajima
    Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916 5 Takayama, Ikoma, Nara 630 0101, Japan
    Plant Cell 14:S265-76. 2002
  83. pmc Beyond Arabidopsis. Translational biology meets evolutionary developmental biology
    Vivian F Irish
    Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA
    Plant Physiol 135:611-4. 2004
    ..The possibility of applying comparative genomics approaches to Arabidopsis and related species promises profound new insights into the interplay of evolution and development...