Research Output 1968 2019

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Review article
2019

Challenges of Translating Gene Regulatory Information into Agronomic Improvements

Springer, N. M., de León, N. & Grotewold, E., Jan 1 2019, In : Trends in Plant Science.

Research output: Contribution to journalReview article

regulator genes
regulatory sequences
genome
quantitative traits
agronomic traits
1 Citation (Scopus)

Making a Murderer: The Evolutionary Framing of Hybrid Gamete-Killers

Sweigart, A. L., Brandvain, Y. J. & Fishman, L., Apr 1 2019, In : Trends in Genetics. 35, 4, p. 245-252 8 p.

Research output: Contribution to journalReview article

Germ Cells
Population Genetics
Molecular Biology
History
Alleles
2 Citations (Scopus)
Open Access
Photosynthesis
Oxygen
Chlorophyll
Detoxification
Earth (planet)
2018
1 Citation (Scopus)

Harnessing fungi to mitigate CH 4 in natural and engineered systems

Oliver, J. P. & Schilling, J. S., Sep 1 2018, In : Applied Microbiology and Biotechnology. 102, 17, p. 7365-7375 11 p.

Research output: Contribution to journalReview article

Fungi
Biofilms
Natural Gas
Methane
Bioreactors
3 Citations (Scopus)
DNA Transposable Elements
Trans-Activators
Genes
Alleles
Mothers
10 Citations (Scopus)

Practical considerations for plant phylogenomics

McKain, M. R., Johnson, M. G., Uribe-Convers, S., Eaton, D. & Yang, Y., Mar 1 2018, In : Applications in Plant Sciences. 6, 3, e1038.

Research output: Contribution to journalReview article

genome
polyploidy
herbarium
herbaria
researchers
1 Citation (Scopus)

Response to comment on “plant diversity increases with the strength of negative density dependence at the global scale”

LaManna, J. A., Mangan, S. A., Alonso, A., Bourg, N. A., Brockelman, W. Y., Bunyavejchewin, S., Chang, L. W., Chiang, J. M., Chuyong, G. B., Clay, K., Cordell, S., Davies, S. J., Furniss, T. J., Giardina, C. P., Nimal Gunatilleke, I. A. U., Savitri Gunatilleke, C. V., He, F., Howe, R. W., Hubbell, S. P., Hsieh, C. F. & 29 others, Inman-Narahari, F. M., Janík, D., Johnson, D. J., Kenfack, D., Korte, L., Král, K., Larson, A. J., Lutz, J. A., McMahon, S. M., McShea, W. J., Memiaghe, H. R., Nathalang, A., Novotny, V., Ong, P. S., Orwig, D. A., Ostertag, R., Parker, G. G., Phillips, R. P., Sack, L., Sun, I. F., Sebastián Tello, J., Thomas, D. W., Turner, B. L., Vela Díaz, D. M., Vrška, T., Weiblen, G. D., Wolf, A., Yap, S. & Myers, J. A., May 25 2018, In : Science. 360, 6391, eaar5245.

Research output: Contribution to journalReview article

1 Citation (Scopus)

Response to Comment on “Plant diversity increases with the strength of negative density dependence at the global scale”

LaManna, J. A., Mangan, S. A., Alonso, A., Bourg, N. A., Brockelman, W. Y., Bunyavejchewin, S., Chang, L. W., Chiang, J. M., Chuyong, G. B., Clay, K., Cordell, S., Davies, S. J., Furniss, T. J., Giardina, C. P., Nimal Gunatilleke, I. A. U., Savitri Gunatilleke, C. V., He, F., Howe, R. W., Hubbell, S. P., Hsieh, C. F. & 29 others, Inman-Narahari, F. M., Janík, D., Johnson, D. J., Kenfack, D., Korte, L., Král, K., Larson, A. J., Lutz, J. A., McMahon, S. M., McShea, W. J., Memiaghe, H. R., Nathalang, A., Novotny, V., Ong, P. S., Orwig, D. A., Ostertag, R., Parker, G. G., Phillips, R. P., Sack, L., Sun, I. F., Sebastián Tello, J., Thomas, D. W., Turner, B. L., Vela Díaz, D. M., Vrška, T., Weiblen, G. D., Wolf, A., Ya, S. & Myers, J. A., May 25 2018, In : Science. 360, 6391, eaar3824.

Research output: Contribution to journalReview article

Artifacts
1 Citation (Scopus)

Review: Plant immune signaling from a network perspective

Katagiri, F., Nov 1 2018, In : Plant Science. 276, p. 14-21 8 p.

Research output: Contribution to journalReview article

Information Services
Vulnerable Populations
information networks
topology
immune response
2017
12 Citations (Scopus)

Accelerating silphium domestication: An opportunity to develop new crop ideotypes and breeding strategies informed by multiple disciplines

Van Tassel, D. L., Albrecht, K. A., Bever, J. D., Boe, A. A., Brandvain, Y., Crews, T. E., Gansberger, M., Gerstberger, P., González-Paleo, L., Hulke, B. S., Kane, N. C., Johnson, P. J., Pestsova, E. G., Picasso Risso, V. D., Prasifka, J. R., Ravetta, D. A., Schlautman, B., Sheaffer, C. C., Smith, K. P., Speranza, P. R. & 4 others, Turner, M. K., Vilela, A. E., von Gehren, P. & Wever, C., Jan 1 2017, In : Crop Science. 57, 3, p. 1274-1284 11 p.

Research output: Contribution to journalReview article

Silphium
ideotypes
Silphium perfoliatum
new crops
domestication
38 Citations (Scopus)

Exploiting induced and natural epigenetic variation for crop improvement

Springer, N. M. & Schmitz, R. J., Sep 1 2017, In : Nature Reviews Genetics. 18, 9, p. 563-575 13 p.

Research output: Contribution to journalReview article

Epigenomics
Alleles
27 Citations (Scopus)

Microbial ecology of mountain glacier ecosystems: biodiversity, ecological connections and implications of a warming climate

Hotaling, S., Hood, E. & Hamilton, T. L., Aug 1 2017, In : Environmental microbiology. 19, 8, p. 2935-2948 14 p.

Research output: Contribution to journalReview article

Ice Cover
microbial ecology
Biodiversity
glaciers
Ecology
28 Citations (Scopus)

Review: Nectar biology: From molecules to ecosystems

Roy, R., Schmitt, A. J., Thomas, J. B. & Carter, C. J., Sep 1 2017, In : Plant Science. 262, p. 148-164 17 p.

Research output: Contribution to journalReview article

Plant Nectar
nectar
Ecosystem
Biological Sciences
ecosystems
13 Citations (Scopus)

Sulfur and carbon isotopic evidence for metabolic pathway evolution and a four-stepped Earth system progression across the Archean and Paleoproterozoic

Havig, J. R., Hamilton, T., Bachan, A. & Kump, L. R., Nov 1 2017, In : Earth-Science Reviews. 174, p. 1-21 21 p.

Research output: Contribution to journalReview article

Archean
sulfur
oxidation
carbon
sulfite
1 Citation (Scopus)

Vacuolar convolution: Possible mechanisms and role of phosphatidylinositol 3,5-bisphosphate

Pérez Koldenkova, V. & Hatsugai, N., Jan 1 2017, In : Functional Plant Biology. 44, 8, p. 751-760 10 p.

Research output: Contribution to journalReview article

phosphatidylinositols
vacuoles
organelles
bubbles
cytoskeleton
44 Citations (Scopus)

Will seasonally dry tropical forests be sensitive or resistant to future changes in rainfall regimes?

Allen, K., Dupuy, J. M., Gei, M. G., Hulshof, C., Medvigy, D., Pizano, C., Salgado-Negret, B., Smith, C. M., Trierweiler, A., Van Bloem, S. J., Waring, B. G., Xu, X. & Powers, J. S., Feb 3 2017, In : Environmental Research Letters. 12, 2, 023001.

Research output: Contribution to journalReview article

Drought
dry forest
tropical forest
Rain
Droughts
2016
116 Citations (Scopus)

Dimensions of biodiversity in the Earth mycobiome

Peay, K. G., Kennedy, P. G. & Talbot, J. M., Jun 14 2016, In : Nature Reviews Microbiology. 14, 7, p. 434-447 14 p.

Research output: Contribution to journalReview article

Biodiversity
Animal Structures
Plant Structures
DNA Sequence Analysis
Ecosystem
3 Citations (Scopus)

Exploring structural variants in environmentally sensitive gene families

Young, N. D., Zhou, P. & Silverstein, K. A., Apr 1 2016, In : Current Opinion in Plant Biology. 30, p. 19-24 6 p.

Research output: Contribution to journalReview article

genome assembly
genome
genes
multigene family
phosphotransferases (kinases)
133 Citations (Scopus)

Learning the Languages of the Chloroplast: Retrograde Signaling and beyond

Chan, K. X., Phua, S. Y., Crisp, P., McQuinn, R. & Pogson, B. J., Apr 29 2016, In : Annual Review of Plant Biology. 67, p. 25-53 29 p.

Research output: Contribution to journalReview article

Chloroplasts
communication (human)
Language
learning
chloroplasts
107 Citations (Scopus)

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

Crisp, P., Ganguly, D., Eichten, S. R., Borevitz, J. O. & Pogson, B. J., Feb 1 2016, In : Science Advances. 2, 2, e1501340.

Research output: Contribution to journalReview article

Epigenomics
RNA
DNA Methylation
Genomics
RNA Interference
50 Citations (Scopus)

The decomposition of ectomycorrhizal fungal necromass

Fernandez, C. W., Langley, J. A., Chapman, S., McCormack, M. L. & Koide, R. T., Feb 1 2016, In : Soil Biology and Biochemistry. 93, p. 38-49 12 p.

Research output: Contribution to journalReview article

Intrinsic Factor
decomposition
Ecosystem
degradation
Research
30 Citations (Scopus)

The Limits of Natural Selection in a Nonequilibrium World

Brandvain, Y. J. & Wright, S. I., Apr 1 2016, In : Trends in Genetics. 32, 4, p. 201-210 10 p.

Research output: Contribution to journalReview article

Genetic Selection
Population
Population Density
Genetic Recombination
Metagenomics
2015
6 Citations (Scopus)

An ecological role of fungal endophytes to ameliorate plants under biotic stress

Chadha, N., Mishra, M., Rajpal, K., Bajaj, R., Choudhary, D. K. & Varma, A., Sep 18 2015, In : Archives of Microbiology. 197, 7, p. 869-881 13 p.

Research output: Contribution to journalReview article

Endophytes
Pathogens
Ecosystems
Crops
DNA
26 Citations (Scopus)

Applying developmental threshold models to evolutionary ecology

Donohue, K., Burghardt, L., Runcie, D., Bradford, K. J. & Schmitt, J., Feb 1 2015, In : Trends in Ecology and Evolution. 30, 2, p. 66-77 12 p.

Research output: Contribution to journalReview article

phenology
ecology
genotype
fitness
pleiotropy
33 Citations (Scopus)

Creating order from chaos: Epigenome dynamics in plants with complex genomes

Springer, N. M., Lisch, D. & Li, Q., Feb 1 2015, In : Plant Cell. 28, 2, p. 314-325 12 p.

Research output: Contribution to journalReview article

DNA Transposable Elements
transposons
Chromatin
Genome
chromatin
15 Citations (Scopus)

Nutrient addition effects on tropical dry forests: A mini-review from microbial to ecosystem scales

Powers, J. S., Becklund, K. K., Gei, M. G., Iyengar, S. B., Meyer, R. L., O’Connell, C. S., Schilling, E. M., Smith, C. M., Waring, B. & Werden, L. K., Jun 30 2015, In : Frontiers in Earth Science. 3, 34.

Research output: Contribution to journalReview article

dry forest
tropical forest
nutrient
ecosystem
element mobility
4 Citations (Scopus)

Paramutation in evolution, population genetics and breeding

Springer, N. M. & McGinnis, K. M., Aug 1 2015, In : Seminars in Cell and Developmental Biology. 44, p. 33-38 6 p.

Research output: Contribution to journalReview article

Population Genetics
Breeding
Alleles
Epigenomics
Genome
11 Citations (Scopus)

Phylogenomics and evolution of secondary metabolism in plant-associated fungi

Spatafora, J. W. & Bushley, K. E., Aug 1 2015, In : Current Opinion in Plant Biology. 26, p. 37-44 8 p.

Research output: Contribution to journalReview article

ecological function
fungi
metabolism
multigene family
Ascomycota
289 Citations (Scopus)

Redefining fine roots improves understanding of below-ground contributions to terrestrial biosphere processes

McCormack, M. L., Dickie, I. A., Eissenstat, D. M., Fahey, T. J., Fernandez, C. W., Guo, D., Helmisaari, H. S., Hobbie, E. A., Iversen, C. M., Jackson, R. B., Leppälammi-Kujansuu, J., Norby, R. J., Phillips, R. P., Pregitzer, K. S., Pritchard, S. G., Rewald, B. & Zadworny, M., Aug 1 2015, In : New Phytologist. 207, 3, p. 505-518 14 p.

Research output: Contribution to journalReview article

Ecosystem
Fungi
Soil
Carbon
Food
36 Citations (Scopus)

Regulation of the plasma membrane proton pump (H+-ATPase) by phosphorylation

Haruta, M., Gray, W. M. & Sussman, M. R., Dec 1 2015, In : Current Opinion in Plant Biology. 28, p. 68-75 8 p.

Research output: Contribution to journalReview article

proton pump
H-transporting ATP synthase
phosphorylation
plasma membrane
Plantae
93 Citations (Scopus)

SAUR Proteins as Effectors of Hormonal and Environmental Signals in Plant Growth

Ren, H. & Gray, W. M., Aug 3 2015, In : Molecular Plant. 8, 8, p. 1153-1164 12 p., 134.

Research output: Contribution to journalReview article

plant growth
RNA
Indoleacetic Acids
Growth
Plant Development
70 Citations (Scopus)

The scope of Baker's law

Pannell, J. R., Auld, J. R., Brandvain, Y., Burd, M., Busch, J. W., Cheptou, P. O., Conner, J. K., Goldberg, E. E., Grant, A. G., Grossenbacher, D. L., Hovick, S. M., Igic, B., Kalisz, S., Petanidou, T., Randle, A. M., de Casas, R. R., Pauw, A., Vamosi, J. C. & Winn, A. A., Jan 1 2015, In : New Phytologist. 208, 3, p. 656-667 12 p.

Research output: Contribution to journalReview article

Islands
selfing
Self-Fertilization
dioecy
Reproduction
13 Citations (Scopus)

Uncultivated thermophiles: Current status and spotlight on 'Aigarchaeota'

Hedlund, B. P., Murugapiran, S. K., Alba, T. W., Levy, A., Dodsworth, J. A., Goertz, G. B., Ivanova, N. & Woyke, T., Jun 1 2015, In : Current Opinion in Microbiology. 25, p. 136-145 10 p.

Research output: Contribution to journalReview article

Korarchaeota
Hot Temperature
Metagenomics
Meta-Analysis
2014
110 Citations (Scopus)

Advances and limits of using population genetics to understand local adaptation

Tiffin, P. L. & Ross-Ibarra, J., Dec 1 2014, In : Trends in Ecology and Evolution. 29, 12, p. 673-680 8 p.

Research output: Contribution to journalReview article

local adaptation
population genetics
loci
complement
species diversity
8 Citations (Scopus)

Functions of novel symbiotic fungus - Piriformospora indica

Varma, A., Sowjanya Sree, K., Arora, M., Bajaj, R., Prasad, R. & Kharkwal, A. C., Jan 1 2014, In : Proceedings of the Indian National Science Academy. 80, 2, p. 429-441 13 p.

Research output: Contribution to journalReview article

fungi
Fungi
deserts
Growth
germination
6 Citations (Scopus)

Gene interactions in the evolution of genomic imprinting

Wolf, J. B. & Brandvain, Y. J., Jan 1 2014, In : Heredity. 113, 2, p. 129-137 9 p.

Research output: Contribution to journalReview article

Genomic Imprinting
Alleles
Genes
Genotype
Sex Chromosomes
40 Citations (Scopus)

Impact of single-cell genomics and metagenomics on the emerging view of extremophile “microbial dark matter”

Hedlund, B. P., Dodsworth, J. A., Murugapiran, S. K., Rinke, C. & Woyke, T., Sep 1 2014, In : Extremophiles. 18, 5, p. 865-875 11 p.

Research output: Contribution to journalReview article

Metagenomics
Genomics
Archaea
Korarchaeota
Ecosystem
34 Citations (Scopus)

New approaches to facilitate rapid domestication of a wild plant to an oilseed crop: Example pennycress (Thlaspi arvense L.)

Sedbrook, J. C., Phippen, W. B. & Marks, M. D., Jan 1 2014, In : Plant Science. 227, p. 122-132 11 p.

Research output: Contribution to journalReview article

Thlaspi
Thlaspi arvense
oilseed crops
wild plants
domestication
2013
9 Citations (Scopus)

Energy, ecology and the distribution of microbial life

Macalady, J. L., Hamilton, T. L., Grettenberger, C. L., Jones, D. S., Tsao, L. E. & Burgos, W. D., Jul 19 2013, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 368, 1622

Research output: Contribution to journalReview article

energy resources
Energy resources
Ecology
ecologists
microbial communities
60 Citations (Scopus)

Epigenetics and crop improvement

Springer, N. M., Apr 1 2013, In : Trends in Genetics. 29, 4, p. 241-247 7 p.

Research output: Contribution to journalReview article

Epigenomics
Developmental Genes
Transgenes
Gene Expression
157 Citations (Scopus)

Progress toward understanding heterosis in crop plants

Schnable, P. S. & Springer, N. M., Apr 1 2013, In : Annual Review of Plant Biology. 64, p. 71-88 18 p.

Research output: Contribution to journalReview article

Hybrid Vigor
heterosis
crops
loci
Agriculture
1059 Citations (Scopus)

Towards a unified paradigm for sequence-based identification of fungi

Kõljalg, U., Nilsson, R. H., Abarenkov, K., Tedersoo, L., Taylor, A. F. S., Bahram, M., Bates, S. T., Bruns, T. D., Bengtsson-Palme, J., Callaghan, T. M., Douglas, B., Drenkhan, T., Eberhardt, U., Dueñas, M., Grebenc, T., Griffith, G. W., Hartmann, M., Kirk, P. M., Kohout, P., Larsson, E. & 22 others, Lindahl, B. D., Lücking, R., Martín, M. P., Matheny, P. B., Nguyen, N. H., Niskanen, T., Oja, J., Peay, K. G., Peintner, U., Peterson, M., Põldmaa, K., Saag, L., Saar, I., Schüßler, A., Scott, J. A., Senés, C., Smith, M. E., Suija, A., Taylor, D. L., Telleria, M. T., Weiss, M. & Larsson, K. H., Nov 1 2013, In : Molecular ecology. 22, 21, p. 5271-5277 7 p.

Research output: Contribution to journalReview article

internal transcribed spacers
Names
Fungi
Chemical Databases
fungus
2012
39 Citations (Scopus)

Light-regulated stomatal aperture in Arabidopsis

Chen, C., Xiao, Y., Li, X. & Ni, M., Jan 1 2012, In : Molecular Plant. 5, 3, p. 566-572 7 p.

Research output: Contribution to journalReview article

phytochrome
blue light
Arabidopsis
Phytochrome
stomatal movement
17 Citations (Scopus)

Radical AdoMet enzymes in complex metal cluster biosynthesis

Duffus, B. R., Hamilton, T. L., Shepard, E. M., Boyd, E. S., Peters, J. W. & Broderick, J. B., Nov 1 2012, In : Biochimica et Biophysica Acta - Proteins and Proteomics. 1824, 11, p. 1254-1263 10 p.

Research output: Contribution to journalReview article

S-Adenosylmethionine
Biosynthesis
Coordination Complexes
Enzymes
Iron
25 Citations (Scopus)

Scaling up: Examining the macroecology of ectomycorrhizal fungi

Kennedy, P. G., Matheny, P. B., Ryberg, K. M., Henkel, T. W., Uehling, J. K. & Smith, M. E., Sep 1 2012, In : Molecular ecology. 21, 17, p. 4151-4154 4 p.

Research output: Contribution to journalReview article

macroecology
fungal communities
Fungi
fungus
ecology
2011
24 Citations (Scopus)

Demography, kinship, and the evolving theory of genomic imprinting

Brandvain, Y., Van Cleve, J., Úbeda, F. & Wilkins, J. F., Jul 1 2011, In : Trends in Genetics. 27, 7, p. 251-257 7 p.

Research output: Contribution to journalReview article

Genomic Imprinting
Demography
Genetic Selection
Interpersonal Relations
Natural History
134 Citations (Scopus)

The role of vacuole in plant cell death

Hara-Nishimura, I. & Hatsugai, N., Jan 1 2011, In : Cell Death and Differentiation. 18, 8, p. 1298-1304 7 p.

Research output: Contribution to journalReview article

Plant Cells
Vacuoles
Cell Death
Membrane Fusion
Proteasome Endopeptidase Complex
2010
38 Citations (Scopus)

Chloroplast-to-nucleus communication: Current knowledge, experimental strategies and relationship to drought stress signaling

Chan, K. X., Crisp, P. A., Estavillo, G. M. & Pogson, B. J., Dec 1 2010, In : Plant Signaling and Behavior. 5, 12

Research output: Contribution to journalReview article

water stress
chloroplasts
organelles
cells
environmental factors
307 Citations (Scopus)

Comparing signaling mechanisms engaged in pattern-triggered and effector-triggered immunity

Tsuda, K. & Katagiri, F., Aug 1 2010, In : Current Opinion in Plant Biology. 13, 4, p. 459-465 7 p.

Research output: Contribution to journalReview article

immunity
pathogens
immune response
microorganisms
293 Citations (Scopus)

Ecological opportunity and the origin of adaptive radiations

Yoder, J. B., Clancey, E., Des Roches, S., Eastman, J. M., Gentry, L., Godsoe, W., Hagey, T. J., Jochimsen, D., Oswald, B. P., Robertson, J., Sarver, B. A. J., Schenk, J. J., Spear, S. F. & Harmon, L. J., Aug 1 2010, In : Journal of Evolutionary Biology. 23, 8, p. 1581-1596 16 p.

Research output: Contribution to journalReview article

adaptive radiation
Radiation
Population
Anolis
Lizards