Research Output 1971 2019

Filter
Chapter
2018

Bioinformatics for prohormone and neuropeptide discovery

Southey, B. R., Romanova, E. V., Rodriguez-Zas, S. L. & Sweedler, J. V., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 71-96 26 p. (Methods in Molecular Biology; vol. 1719).

Research output: Chapter in Book/Report/Conference proceedingChapter

Computational Biology
Neuropeptides
Peptide Hormones
Post Translational Protein Processing
Proteomics

Use of in vitro kernel culture to study maize nitrogen and carbohydrate metabolism

Seebauer, J. R. & Below, F. E., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 3-13 11 p. (Methods in Molecular Biology; vol. 1676).

Research output: Chapter in Book/Report/Conference proceedingChapter

Carbohydrate Metabolism
Zea mays
Nitrogen
Growth
Ear
2017

Applications of genomics in weed science

Gaines, T. A., Tranel, P. J., Fleming, M. B., Patterson, E. L., Küpper, A., Ravet, K., Giacomini, D. A., Gonzalez, S. & Beffa, R., Jan 1 2017, Biology, Physiology and Molecular Biology of Weeds. Jugulam, M. (ed.). CRC Press, p. 185-218 34 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

weed science
Sugar Phosphates
Thymine
Cytosine
Guanine

Chapter 3: Microplate-based Comet Assay

Wagner, E. D. & Plewa, M. J., Jan 1 2017, The Comet Assay in Toxicology, 2nd Edition. Anderson, D. & Dhawan, A. (eds.). 30 ed. Royal Society of Chemistry, p. 93-111 19 p. (Issues in Toxicology; vol. 2017-January, no. 30).

Research output: Chapter in Book/Report/Conference proceedingChapter

Comet Assay
Disinfection
Byproducts
Assays
Drinking Water

Chapter 4: The Use of Higher Plants in the Comet Assay

Gichner, T., Znidar, I., Wagner, E. D. & Plewa, M. J., Jan 1 2017, The Comet Assay in Toxicology, 2nd Edition. 30 ed. Royal Society of Chemistry, Vol. 2017-January. p. 112-133 22 p. (Issues in Toxicology; vol. 2017-January, no. 30).

Research output: Chapter in Book/Report/Conference proceedingChapter

Comet Assay
Assays
Environmental Pollutants
Xenobiotics
Pesticides

Crop selectivity and herbicide safeners: Historical perspectives and development, safener-regulated gene expression, signaling, and new research directions

Riechers, D. E. & Green, J. M., Jan 1 2017, Biology, Physiology and Molecular Biology of Weeds. Jugulam, M. (ed.). CRC Press, p. 123-143 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

herbicide safeners
Herbicides
Gene expression
Crops
herbicides

IR Spectroscopy, Soil Analysis Applications

Margenot, A. J., Calderón, F. J., Goyne, K. W., Mukome, F. N. D. & Parikh, S. J., Jan 1 2017, Encyclopedia of Spectroscopy and Spectrometry. Elsevier Inc., p. 448-454 7 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Infrared spectroscopy
soils
Soils
infrared spectroscopy
Fourier transform infrared spectroscopy

The compressed vocabulary of the proteins of archaea

Caetano-Anolles, G., Minhas, B. F., Aziz, F., Mughal, F., Shahzad, K., Tal, G., Mittenthal, J. E., Caetano-Anollés, D., Koç, I., Nasir, A., Caetano-Anollés, K. & Kim, K. M., Sep 27 2017, Biocommunication of Archaea. Springer International Publishing, p. 147-174 28 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Vocabulary
Archaea
Proteins
proteins
2016

Oomycete diseases of cucurbits: History, significance, and management

Babadoost, M., Jan 1 2016, Horticultural Reviews. John Wiley and Sons Inc., p. 279-314 36 p. (Horticultural Reviews; vol. 44).

Research output: Chapter in Book/Report/Conference proceedingChapter

Oomycetes
Pythium
Cucurbitaceae
Phytophthora
History

The phylogenomic roots of translation

Caetano-Anollés, D. & Caetano-Anolles, G., Jan 1 2016, Evolution of the Protein Synthesis Machinery and Its Regulation. Springer International Publishing, p. 9-30 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Transfer RNA
ribosomes
Ribosomes
translation (genetics)
Genetic Code

Transcriptomic profiling of central nervous system regions in three species of honey bee during dance communication behavior

Sarma, M. S., Rodriguez-Zas, S. L., Hong, F., Zhong, S. & Robinson, G. E., Apr 19 2016, Animal Behavior: An Evolutionary Approach. Apple Academic Press, p. 210-230 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

bee dances
Honey
Bees
Neurology
transcriptomics
2015

Analysis, occurrence, and toxicity of haloacetaldehydes in drinking waters: Iodoacetaldehyde as an emerging disinfection by-product

Postigo, C., Jeong, C. H., Richardson, S. D., Wagner, E. D., Plewa, M. J., Simmons, J. E. & Barcelo, D., Jan 1 2015, Recent Advances in Disinfection By-Products. Xie, Y., Mitch, B., Karanfil, T. & Westerhoff, P. (eds.). American Chemical Society, p. 25-43 19 p. (ACS Symposium Series; vol. 1190).

Research output: Chapter in Book/Report/Conference proceedingChapter

Disinfection
Potable water
Drinking Water
Byproducts
Toxicity

Charting a new path to resolve the adverse health effects of DBPs

Plewa, M. J. & Wagner, E. D., Jan 1 2015, Recent Advances in Disinfection By-Products. Xie, Y., Mitch, B., Karanfil, T. & Westerhoff, P. (eds.). American Chemical Society, p. 3-23 21 p. (ACS Symposium Series; vol. 1190).

Research output: Chapter in Book/Report/Conference proceedingChapter

Disinfection
Byproducts
Health
Potable water
Drinking Water

NC-140 peach rootstock testing in thirteen U.S. states

Reighard, G., Bridges, W., Archbold, D., Wolfe, D., Atucha, A., Pokharel, R., Autio, W., Beckman, T., Black, B., Lindstrom, T., Coneva, E., Day, K., Johnson, R. S., Kushad, M. M., Parker, M., Robinson, T., Schupp, J. & Warmund, M., May 20 2015, VIII International Peach Symposium. Inglese, P., Xiloyannis, C. & Montanaro, G. (eds.). International Society for Horticultural Science, p. 225-232 8 p. (Acta Horticulturae; vol. 1084).

Research output: Chapter in Book/Report/Conference proceedingChapter

Prunus americana
peaches
rootstocks
fruit maturity
testing

Phytophthora blight (Phytophthora capsici) of pepper and its management

Babadoost, M., Pavon, C., Islam, S. Z. & Tian, D., Dec 23 2015, XXIX International Horticultural Congress on Horticulture: Sustaining Lives, Livelihoods and Landscapes (IHC2014): International Symposia on Innovative Plant Protection in Horticulture, Biosecurity, Quarantine Pests, and Market Access. Hale, C., Hunter, D., Roberts, W., Ikin, R. & McMaugh, S. (eds.). International Society for Horticultural Science, p. 61-66 6 p. (Acta Horticulturae; vol. 1105).

Research output: Chapter in Book/Report/Conference proceedingChapter

Phytophthora capsici
Phytophthora
blight
pepper
cultivars

Sisal/agave

Davis, S. C. & Long, S. P., Jan 1 2015, Industrial Crops: Breeding for Bioenergy and Bioproducts. Springer New York, p. 335-349 15 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Agave
sisal
feedstocks
Biofuels
biofuels

Successful Technologies and Approaches Used to Develop and Manage Resistance Against Crop Diseases and Pests

Hartman, G. L., Pawlowski, M. L., Chang, H. X. & Hill, C. B., Dec 4 2015, Emerging Technologies for Promoting Food Security: Overcoming the World Food Crisis. Elsevier Inc., p. 43-66 24 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Crops
Genes
pests
Pathogens
Technology
2014

An alternative sigma factor cascade regulates expression of type III secretion system in Erwinia amylovora

Zhao, Y., Ancona, V., Li, W. & Lee, J. H., Oct 29 2014, XIII International Workshop on Fire Blight. Smits, T. H. M., Holliger, E. & Rezzonico, F. (eds.). International Society for Horticultural Science, p. 155-160 6 p. (Acta Horticulturae; vol. 1056).

Research output: Chapter in Book/Report/Conference proceedingChapter

sigma factors
type III secretion system
Erwinia amylovora
DNA-directed RNA polymerase
gene expression

Cloning major genes controlling fruit flesh color in papaya

Aryal, R. & Ming, R. R., Jan 1 2014, Genetics and Genomics of Papaya. Springer New York, p. 341-353 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
papayas
major genes
Organism Cloning
molecular cloning

Genomics of erwinia amylovora and related erwinia species associated with pome fruit trees

Zhao, Y., Apr 1 2014, Genomics of Plant-Associated Bacteria. Springer-Verlag Berlin Heidelberg, Vol. 9783642553783. p. 1-36 36 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Erwinia amylovora
Erwinia
Pathogens
Fruits
Genomics

Genomics of papaya sex chromosomes

VanBuren, R. & Ming, R. R., Jan 1 2014, Genetics and Genomics of Papaya. Springer New York, p. 309-326 18 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
Sex Chromosomes
sex chromosomes
papayas
Genomics

Insights into the Common Ancestor of Eudicots

Li, J., Tang, H., Bowers, J. E., Ming, R. R. & Paterson, A. H., 2014, Advances in Botanical Research. Academic Press Inc., p. 137-174 38 p. (Advances in Botanical Research; vol. 69).

Research output: Chapter in Book/Report/Conference proceedingChapter

ancestry
genome
Angiospermae
stems

Molecular genetic mapping of papaya

Han, J. & Ming, R. R., Jan 1 2014, Genetics and Genomics of Papaya. Springer New York, p. 143-155 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
papayas
molecular genetics
chromosome mapping
Molecular Biology

Physical mapping of papaya sex chromosomes

Wang, J., Na, J. K. & Ming, R. R., Jan 1 2014, Genetics and Genomics of Papaya. Springer New York, p. 329-340 12 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
Sex Chromosomes
physical chromosome mapping
sex chromosomes
papayas

Plants in changing environmental conditions of the anthropocene

Leakey, A., Jan 1 2014, Ecology and the Environment. Springer New York, p. 533-572 40 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Productivity
environmental factors
Ecosystems
Ozone
Drought

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

Soil chemical insights provided through vibrational spectroscopy

Parikh, S. J., Goyne, K. W., Margenot, A. J., Mukome, F. N. D. & Calderón, F. J., 2014, Advances in Agronomy. Academic Press Inc., p. 1-148 148 p. (Advances in Agronomy; vol. 126).

Research output: Chapter in Book/Report/Conference proceedingChapter

spectroscopy
Raman spectroscopy
Fourier transform infrared spectroscopy
soil science
FTIR spectroscopy

Switchgrass and giant Miscanthus agronomy

Lee, D., Parrish, A. S. & Voigt, T. B., Oct 1 2014, Engineering and Science of Biomass Feedstock Production and Provision. Springer New York, Vol. 9781489980144. p. 37-59 23 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Panicum
Miscanthus
Panicum virgatum
agronomy
feedstocks

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 GrrSA-Csr global regulatory system plays a critical role in Erwinia amylovora virulence

Ancona, V. & Zhao, Y., Oct 29 2014, XIII International Workshop on Fire Blight. Smits, T. H. M., Holliger, E. & Rezzonico, F. (eds.). International Society for Horticultural Science, p. 207-212 6 p. (Acta Horticulturae; vol. 1056).

Research output: Chapter in Book/Report/Conference proceedingChapter

type III secretion system
Erwinia amylovora
virulence
mutants
phenotype
2013

Bridging classical and molecular genetics of sorghum plant stature and maturity

Brown, P. J. & Paterson, A. H., Jan 1 2013, Genomics of the Saccharinae. Springer New York, p. 333-345 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Sorghum
Sorghum (Poaceae)
molecular genetics
Molecular Biology
Phytochrome B

Genomic Changes in Response to 110 Cycles of Selection for Seed Protein and Oil Concentration in Maize

Lucas, C. J., Zhao, H., Schneerman, M. & Moose, S. P., Feb 5 2013, Seed Genomics. Wiley Blackwell, p. 217-236 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Zea mays
Seeds
Oils
genomics
oils

Molecular Clock

Wang, M. & Caetano-Anolles, G., Feb 27 2013, Brenner's Encyclopedia of Genetics: Second Edition. Elsevier Inc., p. 461-462 2 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Molecular Evolution
Clocks
Macromolecules

RNA World

Caetano-Anolles, G., Feb 27 2013, Brenner's Encyclopedia of Genetics: Second Edition. Elsevier Inc., p. 298-300 3 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA
Biochemistry
Molecules
Transcription
Metabolism

The gene pool of Miscanthus species and its improvement

Sacks, E. J., Juvik, J. A., Lin, Q., Ryan Stewart, J. & Yamada, T., Jan 1 2013, Genomics of the Saccharinae. Springer New York, p. 73-101 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Gene Pool
Miscanthus
Renewable Energy
Biomass
Crops

Underutilized Grasses

Boe, A., Springer, T., Lee, D., Rayburn, A. L. & Gonzalez-Hernandez, J., Apr 25 2013, Bioenergy Feedstocks: Breeding and Genetics. John Wiley and Sons, p. 173-205 33 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Spartina pectinata
Tripsacum dactyloides
breeding methods
Poaceae
grasses
2012

Papaya genome and genomics

Ming, R. R., Yu, Q. & Moore, P. H., Nov 1 2012, Genomics of Tree Crops. Springer New York, Vol. 9781461409205. p. 241-259 19 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
papayas
Genomics
Genome
genomics

Papaya sex chromosomes

Gschwend, A. R. & Ming, R. R., Feb 2012, New Insights on Plant Sex Chromosomes. Nova Science Publishers, Inc., p. 51-66 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Carica
Sex Chromosomes
sex chromosomes
papayas
X Chromosome

Tissue-Specific Regulation of Gene Expression by siRNAs in Soybean

Vodkin, L. O., Zabala, G., Campos, E., Tuteja, J. & Jones, S. I., Jan 10 2012, Designing Soybeans for 21st Century Markets. Elsevier Inc., p. 111-127 17 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Gene Expression Regulation
Soybeans
Gene expression
Small Interfering RNA
RNA
2011

Elucidation of General and Condition-Dependent Gene Pathways Using Mixture Models and Bayesian Networks

Rodriguez-Zas, S. L. & Ko, Y., Apr 21 2011, Applied Statistics for Network Biology: Methods in Systems Biology. Wiley-VCH, Vol. 1. p. 91-103 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Bayesian networks
Genes

Global change and photosynthesis

Bernacchi, C., Calfapietra, C., Centritto, M. & Valladares, F., Jan 1 2011, Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 537-545 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Photosynthesis
global change
photosynthesis
Planets
Biota

Measurement of chloroplast ATP synthesis activity in Arabidopsis

Grennan, A. K. & Ort, D. R., Oct 24 2011, Chloroplast Research in Arabidopsis: Methods and Protocols, Volume II. Vol. 775. p. 343-355 13 p. (Methods in Molecular Biology; vol. 775).

Research output: Chapter in Book/Report/Conference proceedingChapter

Chloroplasts
Arabidopsis
Adenosine Triphosphate
Thylakoids
Luciferases

Photosynthetic responses to high temperature

Sharkey, T. D. & Bernacchi, C., Jan 1 2011, Terrestrial Photosynthesis in a Changing Environment a Molecular, Physiological and Ecological Approach. Cambridge University Press, p. 290-298 9 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Temperature
Photosynthesis
temperature
photosynthesis
Droughts

Tropical maize: Exploiting maize genetic diversity to develop a novel annual crop for lignocellulosic biomass and sugar production

White, W. G., Moose, S. P., Weil, C. F., McCann, M. C., Carpita, N. C. & Below, F. E., Dec 1 2011, Routes to Cellulosic Ethanol. Springer New York, p. 167-179 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Fructose
Biomass
Zea mays
Crops
Sucrose
2010

Advances in Coffea Genomics

Kochko, A. D., Campa, C., Guyot, R., Hamon, P., Poncet, V., Tranchant-Dubreuil, C., Hamon, S., Akaffou, S., Andrade, A. C., Crouzillat, D., Ming, R. R. & Mueller, L. A., Jan 1 2010, Advances in Botanical Research. C ed. p. 23-63 41 p. (Advances in Botanical Research; vol. 53, no. C).

Research output: Chapter in Book/Report/Conference proceedingChapter

Coffea
genomics
Coffea canephora
genome
microsatellite repeats

Direct Effects of Rising Atmospheric Carbon Dioxide and Ozone on Crop Yields

Ainsworth, E. & McGrath, J. M., Jan 1 2010, Advances in Global Change Research. Springer International Publishing, p. 109-130 22 p. (Advances in Global Change Research; vol. 37).

Research output: Chapter in Book/Report/Conference proceedingChapter

crop yield
carbon dioxide
ozone
crop
air

Efforts to deregulate Rainbow papaya in Japan: Molecular characterization of transgene and vector inserts

Suzuki, J. Y., Tripathi, S., Fermín, G. A., Jan, F. J., Hou, S., Saw, J. H., Ackerman, C. M., Yu, Q., Schatz, M. C., Pitz, K. Y., Yépes, M., Fitch, M. M. M., Manshardt, R. M., Slightom, J. L., Ferreira, S. A., Salzberg, S. L., Alam, M., Ming, R. R., Moore, P. H. & Gonsalves, D., Jan 31 2010, Acta Horticulturae. International Society for Horticultural Science, p. 235-240 6 p. (Acta Horticulturae; vol. 851).

Research output: Chapter in Book/Report/Conference proceedingChapter

papayas
transgenes
Japan
plasmids
imports

Genomics of Glyphosate Resistance

Stewart, C. N., Peng, Y., Abercrombie, L. G., Halfhill, M. D., Rao, M. R., Ranjan, P., Hu, J., Sammons, R. D., Heck, G. R., Tranel, P. J. & Yuan, J. S., Jul 21 2010, Glyphosate Resistance in Crops and Weeds: History, Development, and Management. John Wiley and Sons, p. 149-164 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

glyphosate
genomics

Miscanthus. A Promising Biomass Crop

Heaton, E. A., Dohleman, F. G., Miguez, A. F., Juvik, J. A., Lozovaya, V., Widholm, J., Zabotina, O. A., McIsaac, G. F., David, M. B., Voigt, T. B., Boersma, N. N. & Long, S. P., 2010, Advances in Botanical Research. C ed. Academic Press Inc., p. 75-137 63 p. (Advances in Botanical Research; vol. 56, no. C).

Research output: Chapter in Book/Report/Conference proceedingChapter

Miscanthus
energy crops
Miscanthus giganteus
crops
fuel production

Phylogenetic Utility of RNA Structure: Evolution's Arrow and Emergence of Early Biochemistry and Diversified Life

Sun, F. J., Harish, A. & Caetano-Anolles, G., Jul 12 2010, Evolutionary Genomics and Systems Biology. John Wiley and Sons, p. 329-360 32 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biochemistry
RNA