Research Output 1975 2019

2014

Sequencing and assembly of the transgenic papaya genome

VanBuren, R. & Ming, R. R., Jan 1 2014, Genetics and Genomics of Papaya. Springer New York, p. 187-203 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
papayas
genetically modified organisms
Genome
genome

Sex Determination: Why So Many Ways of Doing It?

Bachtrog, D., Mank, J. E., Peichel, C. L., Kirkpatrick, M., Otto, S. P., Ashman, T. L., Hahn, M. W., Kitano, J., Mayrose, I., Ming, R., Perrin, N., Ross, L., Valenzuela, N., Vamosi, J. C., Mank, J. E., Peichel, C. L., Ashman, T. L., Blackmon, H., Goldberg, E. E., Hahn, M. W. & 8 others, Kirkpatrick, M., Kitano, J., Mayrose, I., Ming, R., Pennell, M. W., Perrin, N., Valenzuela, N. & Vamosi, J. C., Jan 1 2014, In : PLoS biology. 12, 7, p. 1-13 13 p., e1001899.

Research output: Contribution to journalArticle

Chromosomes
Animals
Genes
Earth (planet)
gender

Sex determination in flowering plants: Papaya as a model system

Aryal, R. & Ming, R. R., Mar 1 2014, In : Plant Science. 217-218, p. 56-62 7 p.

Research output: Contribution to journalReview article

Carica
papayas
Angiospermae
Sex Chromosomes
gender

Sex specific expression and distribution of small RNAs in papaya

Aryal, R., Jagadeeswaran, G., Zheng, Y., Yu, Q., Sunkar, R. & Ming, R., Jan 13 2014, In : BMC genomics. 15, 1, 20.

Research output: Contribution to journalArticle

Carica
MicroRNAs
RNA
Y Chromosome
X Chromosome

Simultaneous improvement in productivity, water use, and albedo through crop structural modification

Drewry, D. T., Kumar, P. & Long, S. P., Jun 2014, In : Global change biology. 20, 6, p. 1955-1967 13 p.

Research output: Contribution to journalArticle

Crops
water use
albedo
Productivity
canopy
forest regeneration
lowland forests
carbon sequestration
tropical forests
tropical forest

Spatiotemporal variation in the origin of C4 grasses: δ13C analysis of grass pollen from the southeastern United States

Nelson, D. M., Urban, M. A. & Hu, F. S., Feb 15 2014, In : Palaeogeography, Palaeoclimatology, Palaeoecology. 396, p. 227-231 5 p.

Research output: Contribution to journalArticle

Southeastern United States
pollen
grass
grasses
Eocene

Species ages in neutral biodiversity models

Chisholm, R. A. & O'Dwyer, J. P., May 2014, In : Theoretical Population Biology. 93, p. 85-94 10 p.

Research output: Contribution to journalArticle

biodiversity
biogeography
forest trees
symmetry
prediction

The bench scientist’s guide to statistical analysis of RNA-seq data

Yendrek, C. R., Ainsworth, E. & Thimmapuram, J., Jan 1 2014, Bioinformatics: The Impact of Accurate Quantification on Proteomic and Genetic Analysis and Research. Apple Academic Press, p. 1-20 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Statistical Analysis
Statistical methods
RNA
Differential Expression
Reproducibility

The biophysical link between climate, water, and vegetation in bioenergy agro-ecosystems

Bagley, J. E., Davis, S. C., Georgescu, M., Hussain, M. Z., Miller, J., Nesbitt, S., VanLoocke, A. & Bernacchi, C., Dec 1 2014, In : Biomass and Bioenergy. 71, p. 187-201 15 p.

Research output: Contribution to journalReview article

bioenergy
Gas emissions
Greenhouse gases
Land use
Ecosystems

The Carboxy-terminus of BAK1 regulates kinase activity and is required for normal growth of Arabidopsis

Oh, M. H., Wang, X., Kim, S. Y., Wu, X., Clouse, S. D. & Huber, S. C., Feb 4 2014, In : Frontiers in Plant Science. 5, FEB, 16.

Research output: Contribution to journalArticle

phosphotransferases (kinases)
Arabidopsis
receptors
brassinosteroids
growth retardation

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., Aury, J. M., Bento, P., Bernard, M., Bocs, S., Campa, C., Cenci, A., Combes, M. C., Crouzillat, D., Da Silva, C., Daddiego, L. & 44 others, De Bellis, F., Dussert, S., Garsmeur, O., Gayraud, T., Guignon, V., Jahn, K., Jamilloux, V., Joët, T., Labadie, K., Lan, T., Leclercq, J., Lepelley, M., Leroy, T., Li, L. T., Librado, P., Lopez, L., Muñoz, A., Noel, B., Pallavicini, A., Perrotta, G., Poncet, V., Pot, D., Priyono, Rigoreau, M., Rouard, M., Rozas, J., Tranchant-Dubreuil, C., VanBuren, R., Zhang, Q., Andrade, A. C., Argout, X., Bertrand, B., De Kochko, A., Graziosi, G., Henry, R. J., Jayarama, Ming, R., Nagai, C., Rounsley, S., Sankoff, D., Giuliano, G., Albert, V. A., Wincker, P. & Lashermes, P., Sep 5 2014, In : Science. 345, 6201, p. 1181-1184 4 p.

Research output: Contribution to journalArticle

Coffee
Caffeine
Genome
Methyltransferases
Coffea

The effects of gibberellic acid on sex expression and secondary sexual characteristics in papaya

Han, J., Murray, J. E., Yu, Q., Moore, P. H. & Ming, R. R., Mar 2014, In : HortScience. 49, 3, p. 378-383 6 p.

Research output: Contribution to journalArticle

papayas
gibberellic acid
gibberellins
gender
Carica papaya

The theoretical limit to plant productivity

Delucia, E. H., Gomez-Casanovas, N., Greenberg, J., Hudiburg, T. W., Kantola, I. B., Long, S. P., Miller, A. D., Ort, D. R. & Parton, W. J., Aug 19 2014, In : Environmental Science and Technology. 48, 16, p. 9471-9477 7 p.

Research output: Contribution to journalArticle

net primary production
Biomass
Productivity
productivity
Crops

Threshold dynamics in soil carbon storage for bioenergy crops

Woo, D. K., Quijano, J. C., Kumar, P., Chaoka, S. & Bernacchi, C., Oct 21 2014, In : Environmental Science and Technology. 48, 20, p. 12090-12098 9 p.

Research output: Contribution to journalArticle

bioenergy
soil carbon
carbon sequestration
Crops
Nitrogen

Ticked off

Berenbaum, M. R., Jan 1 2014, In : American Entomologist. 60, 3, p. 131-134 4 p.

Research output: Contribution to journalArticle

Transcriptional reprogramming and stimulation of leaf respiration by elevated CO2 concentration is diminished, but not eliminated, under limiting nitrogen supply

Markelz, R. J. C., Lai, L. X., Vosseler, L. N. & Leakey, A., Apr 1 2014, In : Plant, Cell and Environment. 37, 4, p. 886-898 13 p.

Research output: Contribution to journalArticle

cell respiration
Respiration
Nitrogen
nitrogen
leaves

Transcriptional responses indicate maintenance of photosynthetic proteins as key to the exceptional chilling tolerance of C4 photosynthesis in Miscanthus × giganteus

Spence, A. K., Boddu, J., Wang, D., James, B., Swaminathan, K., Moose, S. P. & Long, S. P., Jul 2014, In : Journal of experimental botany. 65, 13, p. 3737-3747 11 p.

Research output: Contribution to journalArticle

Miscanthus giganteus
C4 photosynthesis
Photosynthesis
Chlorophyll Binding Proteins
cold tolerance

Tree of Sex: A database of sexual systems

Ashman, T. L., Bachtrog, D., Blackmon, H., Goldberg, E. E., Hahn, M. W., Kirkpatrick, M., Kitano, J., Mank, J. E., Mayrose, I., Ming, R., Otto, S. P., Peichel, C. L., Pennell, M. W., Perrin, N., Ross, L., Valenzuela, N. & Vamosi, J. C., Jun 24 2014, In : Scientific Data. 1, 140015.

Research output: Contribution to journalArticle

Chromosomes
Fish
Animals
Testing
Chromosome

Using leaf optical properties to detect ozone effects on foliar biochemistry

Ainsworth, E., Serbin, S. P., Skoneczka, J. A. & Townsend, P. A., Feb 1 2014, In : Photosynthesis research. 119, 1-2, p. 65-76 12 p.

Research output: Contribution to journalArticle

Biochemistry
Ozone
optical properties
ozone
biochemistry

Variation in chilling tolerance for photosynthesis and leaf extension growth among genotypes related to the C4 grass Miscanthus ×giganteus

Głowacka, K., Adhikari, S., Peng, J., Gifford, J., Juvik, J. A., Long, S. P. & Sacks, E. J., Oct 1 2014, In : Journal of experimental botany. 65, 18, p. 5267-5278 12 p.

Research output: Contribution to journalArticle

Miscanthus giganteus
Photosynthesis
Poaceae
cold tolerance
Genotype
Photosynthesis
Biotechnology
biotechnology
Breeding
Oryza sativa

Yields of Miscanthus × giganteus and Panicum virgatum decline with stand age in the Midwestern USA

Arundale, R. A., Dohleman, F. G., Heaton, E. A., Mcgrath, J. M., Voigt, T. B. & Long, S. P., Jan 2014, In : GCB Bioenergy. 6, 1, p. 1-13 13 p.

Research output: Contribution to journalArticle

Miscanthus giganteus
Panicum virgatum
Cellulosic ethanol
Linear regression
Agriculture
2013

Aflatoxin B1: Toxicity, bioactivation and detoxification in the polyphagous caterpillar Trichoplusia ni

Zeng, R. S., Wen, Z., Niu, G. & Berenbaum, M. R., Jun 1 2013, In : Insect Science. 20, 3, p. 318-328 11 p.

Research output: Contribution to journalArticle

Detoxification
Aflatoxin B1
Trichoplusia ni
aflatoxin B1
caterpillar

A hierarchical Bayesian approach to the classification of C3 and C4 grass pollen based on SPIRAL δ13C data

Urban, M. A., Nelson, D. M., Kelly, R., Ibrahim, T., Dietze, M., Pearson, A. & Hu, F. S., Nov 15 2013, In : Geochimica et Cosmochimica Acta. 121, p. 168-176 9 p.

Research output: Contribution to journalArticle

Isotopes
pollen
grass
isotope
Sediments

Altered Belowground Carbon Cycling Following Land-Use Change to Perennial Bioenergy Crops

Anderson-Teixeira, K. J., Masters, M. D., Black, C. K., Zeri, M., Hussain, M. Z., Bernacchi, C. & Delucia, E. H., Jan 7 2013, In : Ecosystems. 16, 3, p. 508-520 13 p.

Research output: Contribution to journalArticle

energy crops
bioenergy
Land use
land use change
Crops

Altered dynamics of forest recovery under a changing climate

Anderson-Teixeira, K. J., Miller, A. D., Mohan, J. E., Hudiburg, T. W., Duval, B. D. & DeLucia, E. H., Jul 1 2013, In : Global change biology. 19, 7, p. 2001-2021 21 p.

Research output: Contribution to journalReview article

Recovery
Climate change
Ecosystems
climate
Feedback
intercropping
meta-analysis
Meta-Analysis
shade
Greenhouse Effect

Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.)

VanBuren, R., Walters, B., Ming, R. R. & Min, X. J., Sep 24 2013, In : Plant OMICS. 6, 4, p. 311-317 7 p.

Research output: Contribution to journalArticle

Nelumbo nucifera
Lotus
alternative splicing
expressed sequence tags
genes

An emerging understanding of mechanisms governing insect herbivory under elevated CO2

Zavala, J. A., Nabity, P. D. & DeLucia, E. H., Jan 7 2013, In : Annual Review of Entomology. 58, p. 79-97 19 p.

Research output: Contribution to journalReview article

herbivory
herbivores
insect
insects
chemistry

A new, prairie-restricted species of Anacampsis Curtis (Lepidoptera: Gelechiidae) from Illinois

Harrison, T. L. & Berenbaum, M. R., Nov 26 2013, In : Zootaxa. 3741, 1, p. 194-200 7 p.

Research output: Contribution to journalArticle

Gelechiidae
prairies
prairie
Amorpha canescens
Lepidoptera

A new, prairie-restricted species of Filatima Busck (Lepidoptera: Gelechiidae) from Illinois

Harrison, T. L. & Berenbaum, M. R., Nov 7 2013, In : Zootaxa. 3734, 4, p. 469-476 8 p.

Research output: Contribution to journalArticle

Amorpha canescens
Gelechiidae
overwintering
shelter
prairies

Artefacts of the pot environment on soil nutrient availability: Implications for the interpretation of ecological studies

Dalling, J. W., Winter, K., Andersen, K. M. & Turner, B. L., Feb 11 2013, In : Plant Ecology. 214, 2, p. 329-338 10 p.

Research output: Contribution to journalArticle

nutrient availability
soil nutrient
soil nutrients
artifact
soil conditioners

A taxonomic comparison of local habitat niches of tropical trees

Baldeck, C. A., Kembel, S. W., Harms, K. E., Yavitt, J. B., John, R., Turner, B. L., Chuyong, G. B., Kenfack, D., Thomas, D. W., Madawala, S., Gunatilleke, N., Gunatilleke, S., Bunyavejchewin, S., Kiratiprayoon, S., Yaacob, A., Nur Supardi, M. N., Valencia, R., Navarrete, H., Davies, S. J., Hubbell, S. P. & 1 others, Dalling, J. W., Dec 1 2013, In : Oecologia. 173, 4, p. 1491-1498 8 p.

Research output: Contribution to journalArticle

niche
niches
habitat
habitats
niche overlap

Automated pollen identification system for forensic geo-historical location applications

Hwang, G. M., Riley, K. C., Christou, C. T., Jacyna, G. M., Woodard, J. P., Ryan, R. M., Bush, M. B., Valencia, B. G., McMichael, C. N. H., Punyasena, S. W. & Masters, D. L., Dec 1 2013, 2013 IEEE International Conference on Technologies for Homeland Security, HST 2013. p. 297-303 7 p. 6699018. (2013 IEEE International Conference on Technologies for Homeland Security, HST 2013).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

agricultural product
attribution
expert
Values

Carbon partitioning in sugarcane (Saccharum species)

Wang, J., Nayak, S., Koch, K. & Ming, R., Jun 18 2013, In : Frontiers in Plant Science. 4, JUN, 201.

Research output: Contribution to journalReview article

Saccharum
sugarcane
sucrose
carbon
cell walls

Chronic ozone exacerbates the reduction in photosynthesis and acceleration of senescence caused by limited N availability in Nicotiana sylvestris

Yendrek, C. R., Leisner, C. P. & Ainsworth, E., Oct 1 2013, In : Global change biology. 19, 10, p. 3155-3166 12 p.

Research output: Contribution to journalArticle

Photosynthesis
Ozone
senescence
Crops
photosynthesis

Classification of grass pollen through the quantitative analysis of surface ornamentation and texture

Mander, L., Li, M., Mio, W., Fowlkes, C. C. & Punyasena, S. W., Sep 18 2013, In : Proceedings of the Royal Society B: Biological Sciences. 280, 1770, 20131905.

Research output: Contribution to journalArticle

ornamentation
Pollen
Poaceae
quantitative analysis
pollen

Climate refugia: From the last glacial maximum to the twenty-first century

Hampe, A., Rodríguez-Sánchez, F., Dobrowski, S., Hu, F. S. & Gavin, D. G., Jan 1 2013, In : New Phytologist. 197, 1, p. 16-18 3 p.

Research output: Contribution to journalArticle

Plant Physiological Phenomena
ecosystem resilience
Phylogeography
Global Warming
Physiological Adaptation

Climatic and land cover influences on the spatiotemporal dynamics of Holocene boreal fire regimes

Barrett, C. M., Kelly, R., Higuera, P. E. & Hu, F. S., Feb 1 2013, In : Ecology. 94, 2, p. 389-402 14 p.

Research output: Contribution to journalArticle

fire regime
land cover
Holocene
charcoal
boreal forests

CO2 uptake and ecophysiological parameters of the grain crops of midcontinent North America: Estimates from flux tower measurements

Gilmanov, T. G., Wylie, B. K., Tieszen, L. L., Meyers, T. P., Baron, V. S., Bernacchi, C. J., Billesbach, D. P., Burba, G. G., Fischer, M. L., Glenn, A. J., Hanan, N. P., Hatfield, J. L., Heuer, M. W., Hollinger, S. E., Howard, D. M., Matamala, R., Prueger, J. H., Tenuta, M. & Young, D. G., Jan 1 2013, In : Agriculture, Ecosystems and Environment. 164, p. 162-175 14 p.

Research output: Contribution to journalArticle

grain crops
cereal
photosynthesis
uptake mechanisms
respiration

Creationist hit or myth

Berenbaum, M. R., Jan 1 2013, In : American Entomologist. 59, 3, p. 132-134 3 p.

Research output: Contribution to journalArticle

myth

Cytochrome P450 Genes from the Sacred Lotus Genome

Nelson, D. R. & Schuler, M. A., Sep 1 2013, In : Tropical Plant Biology. 6, 2-3, p. 138-151 14 p.

Research output: Contribution to journalArticle

Nelumbo
Lotus
cytochrome P-450
Cytochrome P-450 Enzyme System
Genome

DDT-the persistent pesticide (onscreen)

Berenbaum, M. R., Dec 1 2013, In : American Entomologist. 59, 4, p. 196-198 3 p.

Research output: Contribution to journalArticle

DDT (pesticide)
DDT
pesticides
pesticide

Detecting tropical forest biomass dynamics from repeated airborne lidar measurements

Meyer, V., Saatchi, S. S., Chave, J., Dalling, J. W., Bohlman, S., Fricker, G. A., Robinson, C., Neumann, M. & Hubbell, S., Aug 26 2013, In : Biogeosciences. 10, 8, p. 5421-5438 18 p.

Research output: Contribution to journalArticle

lidar
tropical forests
tropical forest
biomass
sensors (equipment)

Detection of Switchgrass mosaic virus in Miscanthus and other grasses

Agindotan, B., Okanu, N., Oladeinde, A., Voigt, T. B., Long, S. P., Gray, M. & Bradley, C., Jan 1 2013, In : Canadian Journal of Plant Pathology. 35, 1, p. 81-86 6 p.

Research output: Contribution to journalArticle

Miscanthus
Panicum virgatum
grasses
viruses
Marafivirus

Differential lysine acetylation profiles of Erwinia amylovora strains revealed by proteomics

Wu, X., Vellaichamy, A., Wang, D., Zamdborg, L., Kelleher, N. L., Huber, S. C. & Zhao, Y., Feb 1 2013, In : Journal of Proteomics. 79, p. 60-71 12 p.

Research output: Contribution to journalArticle

Erwinia amylovora
Acetylation
Proteomics
Lysine
Virulence

Differential seed germination responses to the ratio of red to far-red light in temperate and tropical species

Tiansawat, P. & Dalling, J. W., May 1 2013, In : Plant Ecology. 214, 5, p. 751-764 14 p.

Research output: Contribution to journalArticle

far-red light
germination
seed germination
seed
seeds

Dispersal patterns in space and time: A case study of apiaceae subfamily apioideae

Banasiak, Ł., Piwczyński, M., Uliński, T., Downie, S. R., Watson, M. F., Shakya, B. & Spalik, K., Jul 1 2013, In : Journal of Biogeography. 40, 7, p. 1324-1335 12 p.

Research output: Contribution to journalArticle

Apiaceae
Eurasia
Neotropical Kingdom
space and time
case studies