@article{xu_cui_cheng_stomp_2011, title={Production of high-starch duckweed and its conversion to bioethanol}, volume={110}, ISSN={["1537-5110"]}, DOI={10.1016/j.biosystemseng.2011.06.007}, abstractNote={Growing high-starch duckweed for its conversion to bioethanol was investigated as a novel technology to supplement maize-based ethanol production. Under the fall (autumn) climate conditions of North Carolina, the biomass accumulation rate of Spirodela polyrrhiza grown in a pilot-scale culture pond using diluted pig effluent was 12.4 g dry weight m−2 day−1. Through simple transfer of duckweed plants into well water for 10 days, the duckweed starch content increased by 64.9%, resulting in a high annual starch yield of 9.42 × 103 kg ha−1. After enzymatic hydrolysis and yeast fermentation of high-starch duckweed biomass in a 14-l fermentor, 94.7% of the theoretical starch conversion was achieved. The ethanol yield of duckweed reached 6.42 × 103 l ha−1, about 50% higher than that of maize-based ethanol production, which makes duckweed a competitive starch source for fuel ethanol production.}, number={2}, journal={BIOSYSTEMS ENGINEERING}, author={Xu, Jiele and Cui, Weihua and Cheng, Jay J. and Stomp, Anne-M.}, year={2011}, month={Oct}, pages={67–72} }
 @misc{cheng_stomp_2009, title={Growing Duckweed to Recover Nutrients from Wastewaters and for Production of Fuel Ethanol and Animal Feed}, volume={37}, ISSN={["1863-0650"]}, DOI={10.1002/clen.200800210}, abstractNote={Abstract}, number={1}, journal={CLEAN-SOIL AIR WATER}, author={Cheng, Jay J. and Stomp, Anne-M.}, year={2009}, month={Jan}, pages={17–26} }
 @article{xing_bitzer_alexander_vouk_stomp_2009, title={Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation}, volume={37}, ISSN={["1362-4962"]}, DOI={10.1093/nar/gkn917}, abstractNote={We introduce a new approach in this article to distinguish protein-coding sequences from non-coding sequences utilizing a period-3, free energy signal that arises from the interactions of the 3′-terminal nucleotides of the 18S rRNA with mRNA. We extracted the special features of the amplitude and the phase of the period-3 signal in protein-coding regions, which is not found in non-coding regions, and used them to distinguish protein-coding sequences from non-coding sequences. We tested on all the experimental genes from Saccharomyces cerevisiae and Schizosaccharomyces pombe. The identification was consistent with the corresponding information from GenBank, and produced better performance compared to existing methods that use a period-3 signal. The primary tests on some fly, mouse and human genes suggests that our method is applicable to higher eukaryotic genes. The tests on pseudogenes indicated that most pseudogenes have no period-3 signal. Some exploration of the 3′-tail of 18S rRNA and pattern analysis of protein-coding sequences supported further our assumption that the 3′-tail of 18S rRNA has a role of synchronization throughout translation elongation process. This, in turn, can be utilized for the identification of protein-coding sequences.}, number={2}, journal={NUCLEIC ACIDS RESEARCH}, author={Xing, Chuanhua and Bitzer, Donald L. and Alexander, Winser E. and Vouk, Mladen A. and Stomp, Anne-Marie}, year={2009}, month={Feb}, pages={591–601} }
 @inproceedings{chen_yablonski_ernst_stomp_cheng_2007, title={Duckweed: an alternative starch source for bioethanol production}, booktitle={2007 ASABE Regional Annual Conference (Fletcher, North Carolina)}, author={Chen, Y. and Yablonski, M. and Ernst, E. and Stomp, A. -M. and Cheng, J. J.}, year={2007} }
 @misc{stomp_rajbhandari_2007, title={Method for producing stably transformed duckweed using microprojectile bombardment}, volume={7,161,064}, number={2007 Jan. 9}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Stomp, A.-M. and Rajbhandari, N.}, year={2007} }
 @article{starmer_stomp_vouk_bitzer_2006, title={Predicting Shine-Dalgarno sequence locations exposes genome annotation errors}, volume={2}, ISSN={["1553-7358"]}, DOI={10.1371/journal.pcbi.0020057}, abstractNote={In prokaryotes, Shine–Dalgarno (SD) sequences, nucleotides upstream from start codons on messenger RNAs (mRNAs) that are complementary to ribosomal RNA (rRNA), facilitate the initiation of protein synthesis. The location of SD sequences relative to start codons and the stability of the hybridization between the mRNA and the rRNA correlate with the rate of synthesis. Thus, accurate characterization of SD sequences enhances our understanding of how an organism's transcriptome relates to its cellular proteome. We implemented the Individual Nearest Neighbor Hydrogen Bond model for oligo–oligo hybridization and created a new metric, relative spacing (RS), to identify both the location and the hybridization potential of SD sequences by simulating the binding between mRNAs and single-stranded 16S rRNA 3′ tails. In 18 prokaryote genomes, we identified 2,420 genes out of 58,550 where the strongest binding in the translation initiation region included the start codon, deviating from the expected location for the SD sequence of five to ten bases upstream. We designated these as RS+1 genes. Additional analysis uncovered an unusual bias of the start codon in that the majority of the RS+1 genes used GUG, not AUG. Furthermore, of the 624 RS+1 genes whose SD sequence was associated with a free energy release of less than −8.4 kcal/mol (strong RS+1 genes), 384 were within 12 nucleotides upstream of in-frame initiation codons. The most likely explanation for the unexpected location of the SD sequence for these 384 genes is mis-annotation of the start codon. In this way, the new RS metric provides an improved method for gene sequence annotation. The remaining strong RS+1 genes appear to have their SD sequences in an unexpected location that includes the start codon. Thus, our RS metric provides a new way to explore the role of rRNA–mRNA nucleotide hybridization in translation initiation.}, number={5}, journal={PLOS COMPUTATIONAL BIOLOGY}, author={Starmer, J. and Stomp, A. and Vouk, M. and Bitzer, D.}, year={2006}, month={May}, pages={454–466} }
 @inproceedings{sun_adney_bergmann_cheng_decker_freer_himmel_nishimura_skory_stomp_et al._2002, title={Expression of endoglucanase E1 in transgenic duckweed Lemna minor}, ISBN={1588293874}, booktitle={Biotechnology for fuels and chemicals : proceedings of the Twenty-Fourth Symposium on Biotechnology for Fuels and Chemicals, held April 28-May 1, 2002, in Gatlinburg, TN}, author={Sun, Y. and Adney, W. S. and Bergmann, B. A. and Cheng, J. and Decker, S. R. and Freer, S. and Himmel, M. E. and Nishimura, Y. and Skory, C. D. and Stomp, A.-M and et al.}, year={2002} }
 @article{cheng_bergmann_classen_stomp_howard_2002, title={Nutrient recovery from swine lagoon water by Spirodela punctata}, volume={81}, ISSN={["0960-8524"]}, DOI={10.1016/S0960-8524(01)00098-0}, abstractNote={Spirodela punctata 7776, the best duckweed strain in total protein production selected from in vitro screening experiments with synthetic swine lagoon water medium was examined for N and P recovery. It has shown a capability to grow in and to remove N and P from synthetic swine lagoon water with high N (240 mg NH4 N/l) and P (31.0 mg PO4 P/l) levels. A lag period of approximately 96 h was observed before the duckweed started to grow. During the lag period, utilization of N and P by the duckweed was very slow. The rates of N and P uptake, and duckweed growth increased with the increase of the initial N and P concentrations in the medium. The highest rates of N and P uptakes, and duckweed growth observed in this study were 0.955. 0.129 mg/l-h, and 1.33 g/m2-h (or 31.92 g/m2-day), respectively. The N:P ratio in swine lagoon water is adequate for growing the duckweed.}, number={1}, journal={BIORESOURCE TECHNOLOGY}, author={Cheng, JY and Bergmann, BA and Classen, JJ and Stomp, AM and Howard, JW}, year={2002}, month={Jan}, pages={81–85} }
 @article{yamamoto_rajbhandari_lin_bergmann_nishimura_stomp_2001, title={Genetic transformation of duckweed Lemna gibba and Lemna minor}, volume={37}, DOI={10.1007/s11627-001-0062-6}, number={3}, journal={In Vitro Cellular & Developmental Biology. Plant}, author={Yamamoto, Y. T. and Rajbhandari, N. and Lin, X. H. and Bergmann, Ben and Nishimura, Y. and Stomp, A. M.}, year={2001}, pages={349–353} }
 @misc{stomp_rajbhandari_2000, title={Genetically engineered duckweed}, volume={6,040,498}, number={2000 Mar. 21}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Stomp, A.-M. and Rajbhandari, N.}, year={2000} }
 @article{bergmann_cheng_classen_stomp_2000, title={In vitro selection of duckweed geographical isolates for potential use in swine lagoon effluent renovation}, volume={73}, ISSN={["1873-2976"]}, DOI={10.1016/S0960-8524(99)00137-6}, abstractNote={Plant-based systems for nutrient sequestration into valuable biomass have the potential to help avoid the environmental problems associated with the disposal of large volumes of animal waste. The objective of this study was to select superior duckweed (Lemnaceae) genotypes for the utilization of nutrients in animal wastes. A two-step protocol was used to select promising duckweed geographic isolates to be grown on swine lagoon effluent. Forty-one geographic isolates from the worldwide germplasm collection were used in an in vitro screening test, because they were noted to be fast-growing genotypes during routine collection maintenance. In vitro screening was accomplished by growing geographic isolates on a synthetic medium that approximated swine lagoon effluent in terms of nutrient profile, total ionic strength, pH, and buffering capacity. Large differences among geographic isolates were observed for wet weight gain during the 11-day growing period, percent dry weight, and percent protein in dry biomass. Total protein production per culture jar differed 28-fold between the most disparate of the 41 geographic isolates and was the variable used for selection of superior geographic isolates. The challenge of eight of the 41 geographic isolates with full-strength swine lagoon effluent in the greenhouse led to the selection of three that are promising as genotypes to be grown on lagoon effluent.}, number={1}, journal={BIORESOURCE TECHNOLOGY}, author={Bergmann, BA and Cheng, J and Classen, J and Stomp, AM}, year={2000}, month={May}, pages={13–20} }
 @inproceedings{classen_cheng_bergmann_stomp_2000, title={Lemna gibba growth and nutrient uptake in response to different nutrient levels}, ISBN={1892769115}, booktitle={Animal, agricultural, and food processing wastes : proceedings of the Eighth International Symposium, October 9-11, 2000, Des Moines, Iowa}, author={Classen, J. J. and Cheng, J. and Bergmann, B. A. and Stomp, A. M.}, year={2000} }
 @article{cheng_stomp_classen_barker_bergmann_2000, title={Nutrient removal from swine lagoon effluent by duckweed}, volume={43}, DOI={10.13031/2013.2701}, abstractNote={ABSTRACT. Three duckweed geographic isolates were grown on varying concentrations of swine lagoon effluent in a 
greenhouse to determine their ability to remove nutrients from the effluent. Duckweed biomass was harvested every other 
day over a 12-day period. Duckweed biomass production, nutrient loss from the swine lagoon effluent, and nutrient 
content of duckweed biomass were used to identify effluent concentrations/geographic isolate combinations that are 
effective in terms of nutrient utilization from swine lagoon effluent and production of healthy duckweed biomass. When 
Lemna minor geographic isolate 8627 was grown on 50% swine lagoon effluent, respective losses of TKN, NH 3 -N, TP, 
OPO 4 -P, TOC, K, Cu, and Zn were 83, 100, 49, 31, 68, 21, 28, and 67%.}, number={2}, journal={Transactions of the ASAE}, author={Cheng, J. and Stomp, A-M and Classen, J. J. and Barker, J. C. and Bergmann, Ben}, year={2000}, pages={263–269} }
 @inproceedings{cheng_bergmann_classen_stomp_howard_2000, title={Nutrient removal from swine wastewater by duckweed - Spirodela punctata}, volume={1}, ISBN={1900222681}, booktitle={Industrial wastewater and envrironmental contaminants : proceedings of the 1st World Water Congress of the International Water Association, held in Paris, France, 3-7 July 2000}, author={Cheng, J. and Bergmann, B. A. and Classen, J. J. and Stomp, A. M. and Howard, J. W.}, year={2000} }
 @article{house_bergmann_stomp_frederick_1999, title={Combining constructed wetlands and aquatic and soil filters for reclamation and reuse of water}, volume={12}, ISSN={["0925-8574"]}, DOI={10.1016/S0925-8574(98)00052-4}, abstractNote={Reclamation and reuse of water and nutrients at their source provide the opportunity to use simple, less costly technologies and lessens potentials for catastrophic effects due to centralized treatment system failures. The combination of multiple treatment environments within constructed wetlands can provide water quality suitable for reuse. A current project in rural Chatham County, NC, uses simple, aesthetically pleasing treatment components constructed both outdoors and indoors to reclaim domestic sewage for toilet flushing, landscape irrigation and aesthetic water features. A courtyard containing constructed wetlands and a solarium with modular soil filter components and aquatic chambers are designed to treat sewage from within a small business facility and to provide recreational space for its 60 employees. The combination of vertical flow and horizontal flow constructed wetlands with fill and draw controls provides the necessary environments for nitrification–denitrification, removal of organic materials and phosphorus adsorption reactions. The system is designed to treat and reuse 4500 l day−1 (1200 gal day−1) of domestic sewage from the business. Some of the plants used are selectively bred or genetically engineered to maximize their water reclamation potential. Utilization of simple treatment and reuse technology has permitted the business owner to renovate an abandoned and deteriorating school building into a home for two thriving and internationally based businesses and to protect the water quality of a nearby reservoir.}, number={1-2}, journal={ECOLOGICAL ENGINEERING}, author={House, CH and Bergmann, BA and Stomp, AM and Frederick, DJ}, year={1999}, month={Jan}, pages={27–38} }
 @article{moon_stomp_1997, title={Effects of medium components and light on callus induction, growth, and frond regeneration in Lemna gibba (duckweed)}, volume={33}, DOI={10.1007/s11627-997-0035-5}, number={1}, journal={In Vitro Cellular & Developmental Biology. Plant}, author={Moon, H.-K. and Stomp, A.-M.}, year={1997}, pages={20–25} }
 @article{rajbhandari_stomp_1997, title={Embryogenic callus induction in Fraser fir}, volume={32}, number={4}, journal={HortScience}, author={Rajbhandari, N. and Stomp, A. M.}, year={1997}, pages={737–738} }
 @article{bergmann_sun_stomp_1997, title={Harvest time and nitrogen source influence in vitro growth of apical buds from Fraser fir seedlings}, volume={32}, ISSN={["0018-5345"]}, DOI={10.21273/HORTSCI.32.1.125}, abstractNote={Information was obtained concerning appropriate bud harvest time and nitrogen source to be used in the tissue culture of Fraser fir [Abies fraseri (Pursh) Poir] apical buds from 2-year-old seedlings. April was the preferred time to harvest buds for culture, as summer buds had a high contamination frequency, and fall and winter buds did not develop well. Shoot elongation of buds collected in April (1.6 cm) was more than twice that of buds collected in February (0.7 cm) after 100 days in culture; during the same period, shoot fresh mass increased 5-fold (0.21 g in April, 0.04 g in February). Inclusion of a nitrate source reduced the frequency of bud browning, and glutamine was superior to ammonium as a source of reduced nitrogen. Litvay's basal medium containing 10 mm glutamine and 10 mm nitrate was the best nitrogen source combination tested when considering bud browning frequency and shoot fresh mass and length after 100 days in culture.}, number={1}, journal={HORTSCIENCE}, author={Bergmann, BA and Sun, YH and Stomp, AM}, year={1997}, month={Feb}, pages={125–128} }
 @misc{stomp_weissinger_sederoff_1992, title={Ballistic transformation of conifers}, volume={5,122,466}, number={1992 June 16}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Stomp, A. and Weissinger, A. and Sederoff, R.}, year={1992} }
 @article{stomp_weissinger_sederoff_1991, title={Transient expression from microprojectile-mediated DNA transfer in Pinus taeda}, volume={10}, DOI={10.1007/bf00234292}, abstractNote={Transfer of plasmid DNA to Pinus taeda L. (loblolly pine) cotyledon cells by microprojectile bombardment has been demonstrated using beta-glucuronidase (GUS). GUS histochemical staining indicated active enzyme in localized centers (blue spots) 24 hours after bombardment. GUS expression declined during subsequent culture, but remained detectable in meristematic tissue 62 days post-bombardment, however, transgenic shoots were not recovered. Localized GUS expression events resulted predominantly from single-cell events containing one microprojectile. The staining pattern was complex, with indigo found both in the central target cell and in adjacent cells. Cellular damage sustained by GUS-positive cells ranged from undetectable to sufficiently extensive to cause cell death. Microprojectile bombardment provides a useful method to assay transient gene expression in loblolly pine and has potential for the production of transgenic plants in pine.}, number={4}, journal={Plant Cell Reports}, author={Stomp, A. M. and Weissinger, A. and Sederoff, R. R.}, year={1991}, pages={187} }
 @article{stomp_loopstra_chilton_sederoff_moore_1990, title={EXTENDED HOST RANGE OF AGROBACTERIUM-TUMEFACIENS IN THE GENUS PINUS}, volume={92}, ISSN={["0032-0889"]}, DOI={10.1104/pp.92.4.1226}, abstractNote={Two-to 4-month-old seedlings of nine pine species (Pinus eldarica Medw., Pinus elliottii Engelm., Pinus jeffreyi Grev. & Balf., Pinus lambertiana Dougl., Pinus ponderosa Laws., Pinus radiata D. Don, Pinus sylvestris L., Pinus taeda L., Pinus virginiana Mill), Douglas fir (Pseudotsuaa menziesii (Mirb.) Franco) and incense cedar (Libocedrus decurrens Torr.) were inoculated with five strains of Agrobacterium tumefaciens. Transformation occurred in all conifer species tested as determined by gall formation and opine production. The frequency of gall formation varied by host species, by bacterial strain, and was related to the age of the stem when inoculated. Galls were visible 8 to 12 weeks after inoculation and were small (often less than 2.5 millimeters in diameter). Fewer than half (230 of 502) of the galls originally formed on the trees were present after 1 year, and 26 of these grew to diameters greater than 2 centimeters. The majority of these larger galls (18 of 26) were found in P. radiata. Bacterial strain-specific opines were found in 67 of the 81 gall tissues sampled.}, number={4}, journal={PLANT PHYSIOLOGY}, author={STOMP, AM and LOOPSTRA, C and CHILTON, WS and SEDEROFF, RR and MOORE, LW}, year={1990}, month={Apr}, pages={1226–1232} }
 @misc{sederoff_stomp_moore_chilton_1989, title={Method for transforming pine}, volume={4886937}, publisher={Washington, DC: U.S. Patent and Trademark Office}, author={Sederoff, R. R. and Stomp, A.-M. and Moore, L. W. and Chilton, S. W.}, year={1989} }
 @article{stomp_loopstra_sederoff_chilton_fillatti_dupper_tedeschi_kinlaw_1988, title={Development of a DNA transfer system for pines}, ISBN={0306428156}, DOI={10.1007/978-1-4613-1661-9_14}, journal={Genetic manipulation of woody plants}, publisher={New York: Plenum}, author={Stomp, A. M. and Loopstra, C. and Sederoff, R. and Chilton, S. and Fillatti, J. and Dupper, G. and Tedeschi, P. and Kinlaw, C.}, editor={J. W. Hanover and Keathley, D. E.Editors}, year={1988}, pages={231} }