Research Output 1968 2019

2019
2 Citations (Scopus)

A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis

Li, X., Patena, W., Fauser, F., Jinkerson, R. E., Saroussi, S., Meyer, M. T., Ivanova, N., Robertson, J. M., Yue, R., Zhang, R., Vilarrasa-Blasi, J., Wittkopp, T. M., Ramundo, S., Blum, S. R., Goh, A., Laudon, M., Srikumar, T., Lefebvre, P. A., Grossman, A. R. & Jonikas, M. C., Apr 1 2019, In : Nature Genetics. 51, 4, p. 627-635 9 p.

Research output: Contribution to journalLetter

Photosynthesis
Genome
Genes
Libraries
Photosynthetic Reaction Center Complex Proteins

Biotic interactions contribute to the geographic range limit of an annual plant: Herbivory and phenology mediate fitness beyond a range margin

Benning, J. W., Eckhart, V. M., Geber, M. A. & Moeller, D., Jun 1 2019, In : American Naturalist. 193, 6, p. 786-797 12 p.

Research output: Contribution to journalArticle

annual plant
herbivory
phenology
fitness
herbivores
3 Citations (Scopus)

BRASSINOSTEROID-SIGNALING KINASE 3, a plasma membrane-associated scaffold protein involved in early brassinosteroid signaling

Ren, H., Willige, B. C., Jaillais, Y., Geng, S., Park, M., Gray, W. M. & Chory, J., Jan 1 2019, In : PLoS genetics. 15, 1, e1007904.

Research output: Contribution to journalArticle

Brassinosteroids
scaffolding proteins
brassinosteroids
Blood Proteins
Membrane Proteins

Carbohydrate metabolism and signaling in squash nectaries and nectar throughout floral maturation

Solhaug, E. M., Johnson, E. & Carter, C. J., Aug 1 2019, In : Plant physiology. 180, 4, p. 1930-1946 17 p.

Research output: Contribution to journalArticle

Open Access
Plant Nectar
Cucurbita
nectar secretion
nectaries
squashes

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

Characterization of a semidominant dwarfing PROCERA allele identified in a screen for CRISPR/Cas9-induced suppressors of loss-of-function alleles

Zhu, Z., Kang, X., Lor, V. S., Weiss, D. & Olszewski, N. E., Feb 1 2019, In : Plant Biotechnology Journal. 17, 2, p. 319-321 3 p.

Research output: Contribution to journalLetter

Clustered Regularly Interspaced Short Palindromic Repeats
Chilo
dwarfing
mutagenesis
Mutagenesis
1 Citation (Scopus)

Chromosome rearrangements shape the diversification of secondary metabolism in the cyclosporin producing fungus Tolypocladium inflatum

Olarte, R., Menke, J. R., Zhang, Y., Sullivan, S., Slot, J. C., Huang, Y., Badalamenti, J., Quandt, A. C., Spatafora, J. W. & Bushley, K. E., Feb 7 2019, In : BMC Genomics. 20, 1, 120.

Research output: Contribution to journalArticle

Secondary Metabolism
Multigene Family
Cyclosporine
Fungi
Chromosomes

Classifying cold-stress responses of inbred maize seedlings using RGB imaging

Enders, T., St. Dennis, S., Oakland, J., Callen, S. T., Gehan, M. A., Miller, N. D., Spalding, E. P., Springer, N. M. & Hirsch, C. D., Jan 1 2019, In : Plant Direct. 3, 1, e00104.

Research output: Contribution to journalArticle

Open Access
Cold-Shock Response
Seedlings
Zea mays
genotype
cold stress

Climate change is predicted to disrupt patterns of local adaptation in wild and cultivated maize

Aguirre-Liguori, J. A., Ramírez-Barahona, S., Tiffin, P. L. & Eguiarte, L. E., Jul 10 2019, In : Proceedings of the Royal Society B: Biological Sciences. 286, 1906

Research output: Contribution to journalArticle

Climate Change
local adaptation
Climate change
Zea mays
maize

Complete genome sequence of a previously undescribed badnavirus occurring in Polyscias fruticosa L. (Ming aralia)

Alvarez-Quinto, R. A., Lockhart, B. E. & Olszewski, N. E., Sep 1 2019, In : Archives of Virology. 164, 9, p. 2371-2374 4 p.

Research output: Contribution to journalArticle

Badnavirus
Aralia
Araliaceae
Ribonuclease H
Genome

Correction: Genotype-by-environment interactions affecting heterosis in maize (PLoS ONE (2018) 13:1 (e0191321) DOI: 10.1371/journal.pone)

Li, Z., Coffey, L., Garfin, J., Miller, N. D., White, M. R., Spalding, E. P., de Leon, N., Kaeppler, S. M., Schnable, P. S., Springer, N. M. & Hirsch, C. N., Jan 1 2019, In : PloS one. 14, 8, e0219528.

Research output: Contribution to journalComment/debate

Open Access
Hybrid Vigor
heterosis
Zea mays
Ear
ears
32 Citations (Scopus)

Cytosine, but not adenine, base editors induce genome-wide off-target mutations in rice

Jin, S., Zong, Y., Gao, Q., Zhu, Z., Wang, Y., Qin, P., Liang, C., Wang, D., Qiu, J. L., Zhang, F. & Gao, C., Jan 1 2019, In : Science. 364, 6437, p. 292-295 4 p.

Research output: Contribution to journalArticle

Cytosine
Adenine
Genome
Mutation
Nucleotides

Determinants of Piper (Piperaceae) climber composition in a lowland tropical rainforest in New Guinea

Lisner, A., Kaina, G., Sisol, M., Fibich, P., Novotný, V., Weiblen, G. D. & Lepš, J., Jan 1 2019, In : Folia Geobotanica.

Research output: Contribution to journalArticle

Piperaceae
Piper
New Guinea
tropical rain forests
rainforest

Direct and indirect effects of climate on richness drive the latitudinal diversity gradient in forest trees

Chu, C., Lutz, J. A., Král, K., Vrška, T., Yin, X., Myers, J. A., Abiem, I., Alonso, A., Bourg, N., Burslem, D. F. R. P., Cao, M., Chapman, H., Condit, R., Fang, S., Fischer, G. A., Gao, L., Hao, Z., Hau, B. C. H., He, Q., Hector, A. & 53 others, Hubbell, S. P., Jiang, M., Jin, G., Kenfack, D., Lai, J., Li, B., Li, X., Li, Y., Lian, J., Lin, L., Liu, Y., Liu, Y., Luo, Y., Ma, K., McShea, W., Memiaghe, H., Mi, X., Ni, M., O'Brien, M. J., de Oliveira, A. A., Orwig, D. A., Parker, G. G., Qiao, X., Ren, H., Reynolds, G., Sang, W., Shen, G., Su, Z., Sui, X., Sun, I. F., Tian, S., Wang, B., Wang, X., Wang, X., Wang, Y., Weiblen, G. D., Wen, S., Xi, N., Xiang, W., Xu, H., Xu, K., Ye, W., Zhang, B., Zhang, J., Zhang, X., Zhang, Y., Zhu, K., Zimmerman, J., Storch, D., Baltzer, J. L., Anderson-Teixeira, K. J., Mittelbach, G. G. & He, F., Feb 1 2019, In : Ecology letters. 22, 2, p. 245-255 11 p.

Research output: Contribution to journalLetter

forest trees
climate
stem
species diversity
stems
plant response
climate
rain
rainfall
fitness

Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development

Zhou, P., Hirsch, C. N., Briggs, S. P. & Springer, N. M., Mar 4 2019, In : Molecular Plant. 12, 3, p. 410-425 16 p.

Research output: Contribution to journalArticle

Zea mays
Gene Expression
gene expression
corn
Genes
2 Citations (Scopus)

Evolution of Portulacineae Marked by Gene Tree Conflict and Gene Family Expansion Associated with Adaptation to Harsh Environments

Wang, N., Yang, Y., Moore, M. J., Brockington, S. F., Walker, J. F., Brown, J. W., Liang, B., Feng, T., Edwards, C., Mikenas, J., Olivieri, J., Hutchison, V., Timoneda, A., Stoughton, T., Puente, R., Majure, L. C., Eggli, U. & Smith, S. A., Jan 1 2019, In : Molecular biology and evolution. 36, 1, p. 112-126 15 p.

Research output: Contribution to journalArticle

Family Conflict
Cactaceae
Didiereaceae
gene
Gene Duplication

Evolution of substrate-specific gene expression and RNA editing in brown rot wood-decaying fungi

Wu, B., Gaskell, J., Zhang, J., Toapanta, C., Ahrendt, S., Grigoriev, I. V., Blanchette, R. A., Schilling, J. S., Master, E., Cullen, D. & Hibbett, D. S., Jun 1 2019, In : ISME Journal. 13, 6, p. 1391-1403 13 p.

Research output: Contribution to journalArticle

RNA Editing
RNA editing
decay fungi
gene expression
RNA

Fluorescence in situ mRNA hybridization for gene expression detection in a wood decay fungus

Zhang, J., Hu, D., Orr, G. & Schilling, J. S., Sep 1 2019, In : International Biodeterioration and Biodegradation. 143, 104731.

Research output: Contribution to journalArticle

Decay (organic)
Fungi
Fluorescence In Situ Hybridization
Gene expression
gene expression
Open Access
Thlaspi arvense
domestication
Thlaspi
genetic variation
single nucleotide polymorphism
1 Citation (Scopus)

Genome-based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Lofgren, L. A., Uehling, J. K., Branco, S., Bruns, T. D., Martin, F. & Kennedy, P. G., Feb 1 2019, In : Molecular ecology. 28, 4, p. 721-730 10 p.

Research output: Contribution to journalArticle

Fungal DNA
DNA Copy Number Variations
Ribosomal DNA
lifestyle
ribosomal DNA

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Wang, J., Li, X., Do Kim, K., Scanlon, M. J., Jackson, S. A., Springer, N. M. & Yu, J., Apr 25 2019, In : Genome biology. 20, 1, 74.

Research output: Contribution to journalArticle

Open Access
domestication
Soybeans
Zea mays
soybean
Nucleotides

Genomic Dissection of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon

Della Coletta, R., Hirsch, C. N., Rouse, M. N., Lorenz, A. J. & Garvin, D. F., Apr 1 2019, In : Molecular Plant-Microbe Interactions. 32, 4, p. 392-400 9 p.

Research output: Contribution to journalArticle

Brachypodium
Brachypodium distachyon
stem rust
Triticum
Dissection
2 Citations (Scopus)

Global patterns in fine root decomposition: climate, chemistry, mycorrhizal association and woodiness

See, C. R., Luke McCormack, M., Hobbie, S. E., Flores Moreno, H., Silver, W. L. & Kennedy, P. G., Jun 1 2019, In : Ecology letters. 22, 6, p. 946-953 8 p.

Research output: Contribution to journalLetter

fine root
chemistry
decomposition
climate
degradation

High specialization and limited structural change in plant-herbivore networks along a successional chronosequence in tropical montane forest

Redmond, C. M., Auga, J., Gewa, B., Segar, S. T., Miller, S. E., Molem, K., Weiblen, G. D., Butterill, P. T., Maiyah, G., Hood, A. S. C., Volf, M., Jorge, L. R., Basset, Y. & Novotný, V., Jan 1 2019, In : Ecography. 42, 1, p. 162-172 11 p.

Research output: Contribution to journalArticle

chronosequences
chronosequence
montane forest
montane forests
structural change
1 Citation (Scopus)
Open Access
oasis
Archean
photosynthesis
thermal spring
oxygen

Idea factory: The maize genomes to fields initiative

Lawrence-Dill, C. J., Schnable, P. S. & Springer, N. M., Jul 1 2019, In : Crop Science. 59, 4, p. 1406-1410 5 p.

Research output: Contribution to journalArticle

Open Access
research support
research and development
factories
education
researchers
1 Citation (Scopus)

Legacy of prior host and soil selection on rhizobial fitness in planta

Burghardt, L. T., Epstein, B. & Tiffin, P. L., Jan 1 2019, In : Evolution.

Research output: Contribution to journalArticle

Plantae
fitness
Soil
soil
Population
1 Citation (Scopus)

Maize Carbohydrate Partitioning Defective33 Encodes an MCTP Protein and Functions in Sucrose Export from Leaves

Tran, T. M., McCubbin, T. J., Bihmidine, S., Julius, B. T., Baker, R. F., Schauflinger, M., Weil, C., Springer, N. M., Chomet, P., Wagner, R., Woessner, J., Grote, K., Peevers, J., Slewinski, T. L. & Braun, D. M., Sep 2 2019, In : Molecular Plant. 12, 9, p. 1278-1293 16 p.

Research output: Contribution to journalArticle

Plasmodesmata
Zea mays
Sucrose
Carbohydrates
sucrose
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

Measuring pectin properties to track cell wall alterations during plant–pathogen interactions

Bethke, G. & Glazebrook, J., Jan 1 2019, Methods in Molecular Biology. Humana Press Inc., p. 55-60 6 p. (Methods in Molecular Biology; vol. 1991).

Research output: Chapter in Book/Report/Conference proceedingChapter

Cell Wall
Plant Cells
Pectins
pectin
Plant Immunity
3 Citations (Scopus)

Melanin mitigates the accelerated decay of mycorrhizal necromass with peatland warming

Fernandez, C. W., Heckman, K., Kolka, R. & Kennedy, P. G., Mar 1 2019, In : Ecology letters. 22, 3, p. 498-505 8 p.

Research output: Contribution to journalLetter

melanin
peatlands
peatland
warming
deterioration

Modulating gene translational control through genome editing

Zhang, F. & Voytas, D. F., May 1 2019, In : National Science Review. 6, 3, 1 p.

Research output: Contribution to journalComment/debate

Open Access
5 Citations (Scopus)

Molecular tools enabling pennycress (Thlaspi arvense) as a model plant and oilseed cash cover crop

McGinn, M., Phippen, W. B., Chopra, R., Bansal, S., Jarvis, B. A., Phippen, M. E., Dorn, K. M., Esfahanian, M., Nazarenus, T. J., Cahoon, E. B., Durrett, T. P., Marks, M. D. & Sedbrook, J. C., Apr 1 2019, In : Plant Biotechnology Journal. 17, 4, p. 776-788 13 p.

Research output: Contribution to journalArticle

Thlaspi
Thlaspi arvense
cash crops
oilseeds
cover crops

Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes

Crisp, P., Noshay, J. M., Anderson, S. N. & Springer, N. M., Mar 4 2019, In : Molecular Plant. 12, 3, p. 282-284 3 p.

Research output: Contribution to journalComment/debate

DNA methylation
DNA Methylation
Genome
genome
crops
1 Citation (Scopus)

Plant-mediated partner discrimination in ectomycorrhizal mutualisms

Bogar, L., Peay, K., Kornfeld, A., Huggins, J., Hortal, S., Anderson, I. & Kennedy, P. G., Mar 1 2019, In : Mycorrhiza. 29, 2, p. 97-111 15 p.

Research output: Contribution to journalArticle

fungus
Fungi
fungi
Suillus
Seedlings

Population Genetics of Calotropis gigantea, a Medicinal and Fiber Resource Plant, as Inferred from Microsatellite Marker Variation in two Native Countries

Islam, M. R., Li, Z. Z., Gichira, A. W., Alam, M. N., Fu, P. C., Hu, G. W., Wang, Q. F. & Chen, L., Aug 1 2019, In : Biochemical Genetics. 57, 4, p. 522-539 18 p.

Research output: Contribution to journalArticle

Calotropis gigantea
Calotropis
Population Genetics
Microsatellite Repeats
population genetics
Open Access
Hot springs
Hot Springs
biosphere
early Earth
hot springs
1 Citation (Scopus)

Reference genes for accurate normalization of gene expression in wood-decomposing fungi

Zhang, J., Mitchell, H. D., Markillie, L. M., Gaffrey, M. J., Orr, G. & Schilling, J. S., Feb 1 2019, In : Fungal Genetics and Biology. 123, p. 33-40 8 p.

Research output: Contribution to journalArticle

Fungi
Gene Expression
Genes
Carbon
Fungal Genes

Seed predation increases from the Arctic to the Equator and from high to low elevations

Hargreaves, A. L., Suárez, E., Mehltreter, K., Myers-Smith, I., Vanderplank, S. E., Slinn, H. L., Vargas-Rodriguez, Y. L., Haeussler, S., David, S., Muñoz, J., Almazán-Núñez, R. C., Loughnan, D., Benning, J. W., Moeller, D., Brodie, J. F., Thomas, H. J. D. & Morales, P. A., Feb 20 2019, In : Science Advances. 5, 2, eaau4403.

Research output: Contribution to journalArticle

Open Access
equators
biological diversity
seeds
productivity
sea level
2 Citations (Scopus)

Sex-biased gene expression in flowers, but not leaves, reveals secondary sexual dimorphism in Populus balsamifera

Sanderson, B. J., Wang, L., Tiffin, P. L., Wu, Z. & Olson, M. S., Jan 1 2019, In : New Phytologist. 221, 1, p. 527-539 13 p.

Research output: Contribution to journalArticle

Populus balsamifera
Populus
Sex Characteristics
sexual dimorphism
flowers

SHB1 and CCA1 interaction desensitizes light responses and enhances thermomorphogenesis

Sun, Q., Wang, S., Xu, G., Kang, X., Zhang, M. & Ni, M., Dec 1 2019, In : Nature communications. 10, 1, 3110.

Research output: Contribution to journalArticle

Open Access
Light
interactions
helices
Temperature
actuators
2 Citations (Scopus)

Snow algae drive productivity and weathering at volcanic rock-hosted glaciers

Havig, J. R. & Hamilton, T., Feb 15 2019, In : Geochimica et Cosmochimica Acta. 247, p. 220-242 23 p.

Research output: Contribution to journalArticle

Volcanic rocks
Glaciers
rock glacier
Algae
Weathering
Open Access
Amaranthus
Climate
Spatial Analysis
Introduced Species
Climate Change
4 Citations (Scopus)

The adaptable use of Brassica NIRS calibration equations to identify pennycress variants to facilitate the rapid domestication of a new winter oilseed crop

Chopra, R., Folstad, N., Lyons, J., Ulmasov, T., Gallaher, C., Sullivan, L., Mcgovern, A., Mitacek, R., Frels, K., Altendorf, K., Killam, A., Ismail, B., Anderson, J. A., Wyse, D. L. & Marks, M. D., Feb 1 2019, In : Industrial Crops and Products. 128, p. 55-61

Research output: Contribution to journalArticle

1 Citation (Scopus)

The evolutionary response of mating system to heterosis

Harkness, A. D., Brandvain, Y. J. & Goldberg, E. E., May 1 2019, In : Journal of Evolutionary Biology. 32, 5, p. 476-490 15 p.

Research output: Contribution to journalArticle

heterosis
outcrossing
mating systems
reproductive strategy
autogamy

The insect-focused classification of fruit syndromes in tropical rain forests: An inter-continental comparison

Dahl, C., Ctvrtecka, R., Gripenberg, S., Lewis, O. T., Segar, S. T., Klimes, P., Sam, K., Rinan, D., Filip, J., Lilip, R., Kongnoo, P., Panmeng, M., Putnaul, S., Reungaew, M., Rivera, M., Barrios, H., Davies, S. J., Bunyavejchewin, S., Wright, J. S., Weiblen, G. D. & 2 others, Novotny, V. & Basset, Y., Jan 1 2019, In : Biotropica. 51, 1, p. 39-49 11 p.

Research output: Contribution to journalArticle

tropical rain forests
fruit
insect
taxonomy
insects
2 Citations (Scopus)
Open Access
Photosynthesis
Oxygen
Chlorophyll
Detoxification
Earth (planet)
25 Citations (Scopus)

The UNITE database for molecular identification of fungi: Handling dark taxa and parallel taxonomic classifications

Nilsson, R. H., Larsson, K. H., Taylor, A. F. S., Bengtsson-Palme, J., Jeppesen, T. S., Schigel, D., Kennedy, P. G., Picard, K., Glöckner, F. O., Tedersoo, L., Saar, I., Kõljalg, U. & Abarenkov, K., Jan 8 2019, In : Nucleic acids research. 47, D1, p. D259-D264

Research output: Contribution to journalArticle

Chemical Databases
Fungi
Databases
Biodiversity
Software
2 Citations (Scopus)

The unreasonable effectiveness of convolutional neural networks in population genetic inference

Flagel, L., Brandvain, Y. J. & Schrider, D. R., Jan 1 2019, In : Molecular biology and evolution. 36, 2, p. 220-238 19 p.

Research output: Contribution to journalArticle

Open Access
Population Genetics
neural networks
population genetics
genomics
Metagenomics