@article{rajab_andersen_kenter_berlinsky_borski_mcginty_ashwell_ferket_daniels_reading_2024, title={Combinatorial metabolomic and transcriptomic analysis of muscle growth in hybrid striped bass (female white bass <i>Morone chrysops</i> x male striped bass <i>M. saxatilis</i>)}, volume={25}, ISSN={["1471-2164"]}, DOI={10.1186/s12864-024-10325-y}, abstractNote={Understanding growth regulatory pathways is important in aquaculture, fisheries, and vertebrate physiology generally. Machine learning pattern recognition and sensitivity analysis were employed to examine metabolomic small molecule profiles and transcriptomic gene expression data generated from liver and white skeletal muscle of hybrid striped bass (white bass Morone chrysops x striped bass M. saxatilis) representative of the top and bottom 10 % by body size of a production cohort.}, number={1}, journal={BMC GENOMICS}, author={Rajab, Sarah A. S. and Andersen, Linnea K. and Kenter, Linas W. and Berlinsky, David L. and Borski, Russell J. and McGinty, Andrew S. and Ashwell, Christopher M. and Ferket, Peter R. and Daniels, Harry V. and Reading, Benjamin J.}, year={2024}, month={Jun} }
 @article{andersen_reading_2024, title={A supervised machine learning workflow for the reduction of highly dimensional biological data}, volume={5}, ISSN={["2667-3185"]}, DOI={10.1016/j.ailsci.2023.100090}, abstractNote={Recent technological advancements have revolutionized research capabilities across the biological sciences by enabling the collection of large data that provides a broader picture of systems from the cellular to ecosystem level at a more refined resolution. The rapid rate of generating these data has exacerbated bottlenecks in study design and data analysis approaches, especially as conventional methods that incorporate traditional statistical tests and assumptions are not suitable or sufficient for highly dimensional data (i.e., more than 1,000 variables). The application of machine learning techniques in large data analysis is one promising solution that is increasingly popular. However, limitations in expertise such that the results from machine learning models can be interpreted to gain meaningful biological insight pose a great challenge. To address this challenge, a user-friendly machine learning workflow that can be applied to a wide variety of data types to reduce these large data to those variables (attributes) most determinant of experimental and/or observed conditions is provided, as well as a general overview of data analysis and machine learning approaches and considerations thereof. The workflow presented here has been beta-tested with great success and is recommended to be incorporated into analysis pipelines of large data as a standardized approach to reduce data dimensionality. Moreover, the workflow is flexible, and the underlying concepts and steps can be modified to best suit user needs, objectives, and study parameters.}, journal={ARTIFICIAL INTELLIGENCE IN THE LIFE SCIENCES}, author={Andersen, Linnea K. and Reading, Benjamin J.}, year={2024}, month={Jun} }
 @article{andersen_abernathy_berlinsky_bolton_booker_borski_brown_cerino_ciaramella_clark_et al._2021, title={The status of striped bass, <scp><i>Morone saxatilis</i>,</scp> as a commercially ready species for U.S. marine aquaculture}, volume={52}, ISSN={0893-8849 1749-7345}, url={http://dx.doi.org/10.1111/jwas.12812}, DOI={10.1111/jwas.12812}, abstractNote={AbstractStriped bass, Morone saxatilis, is an anadromous fish native to the North American Atlantic Coast and is well recognized as one of the most important and highly regarded recreational fisheries in the United States. Decades of research have been conducted on striped bass and its hybrid (striped bass × white bass Morone chrysops) and culture methods have been established, particularly for the hybrid striped bass, the fourth largest finfish aquaculture industry in the United States (US $50 million). Domesticated striped bass have been developed since the 1990s and broodstock are available from the government for commercial fry production using novel hormone‐free methods along with traditional hormone‐induced tank and strip spawning. No commercial‐scale intensive larval rearing technologies have been developed at present and current fingerling production is conducted in fertilized freshwater ponds. Larval diets have not been successfully used as first feeds; however, they have been used for weaning from live feeds prior to metamorphosis. Striped bass can be grown out in marine (32 ppt) or freshwater (<5 ppt); however, they require high hardness (200+ ppm) and some salinity (8–10 ppt) to offset handling stress. Juveniles must be 1–10 g/fish prior to stocking into marine water. Commercially available fingerling, growout, and broodstock feeds are available from several vendors. Striped bass may reach 1.36 kg/fish in recirculating aquaculture by 18 months and as much as 2.27 kg/fish by 24 months. Farm gate value of striped bass has not been determined, although seasonally available wild‐harvested striped bass are valued at about US $6.50 to US $10.14 per kg and cultured hybrid striped bass are valued at about US $8.45 to US $9.25 per kg whole; the farm gate value for cultured striped bass may be as much as US $10.00 or more per kg depending on demand and market. The ideal market size is between 1.36 and 2.72 kg/fish, which is considerably larger than the traditional 0.68 to 0.90 kg/fish for the hybrid striped bass market.}, number={3}, journal={Journal of the World Aquaculture Society}, publisher={Wiley}, author={Andersen, Linnea K. and Abernathy, Jason and Berlinsky, David L. and Bolton, Greg and Booker, Matthew M. and Borski, Russell J. and Brown, Travis and Cerino, David and Ciaramella, Michael and Clark, Robert W. and et al.}, year={2021}, month={May}, pages={710–730} }
 @article{andersen_clark_hopper_hodson_schilling_daniels_woods_kovach_berlinsky_kenter_et al._2021, title={Methods of domestic striped bass (Morone saxatilis) spawning that do not require the use of any hormone induction}, volume={533}, ISSN={["1873-5622"]}, DOI={10.1016/j.aquaculture.2020.736025}, abstractNote={Nineteen batch spawning trials were conducted using 5th and 6th generation domestic striped bass (Morone saxatilis) to demonstrate the ability of these fish to volitionally spawn in large tanks to produce larvae using only photothermal and salinity conditioning. The findings described are the first report of multiple striped bass successfully batch spawning in captivity without exogenous hormone administration. The results of these trials indicate that an approximately 1:1 ratio of female to male striped bass in a single batch spawning unit is more favorable for production, that a minimum of at least 10 fish of each sex is required to elicit this particular spawning behavior, and that using 25 fish of each sex will yield commercially scalable larval production. This batch spawning method has been employed to effectively and consistently spawn over half of the female striped bass in the National Program for Genetic Improvement and Selective Breeding for the Hybrid Striped Bass Industry (N = 202 of 334 female fish over five years) to produce 44,608,181 swim-up larvae (26.6% hatching rate). Microsatellite genotyping and parentage assignment demonstrates that females will reproduce with between 2 and 18 males and that males will reproduce with between 1 and 6 females. Moreover, the effective broodstock size (Nb) of these batch spawning units is 33 and when accounting for multiple partners and unequal family sizes (Nbv) is 28. Lastly, the reported results include the successful spawning of female striped bass staged at and beyond 15 Bayless hours, or those that would have previously been considered ineligible for spawning even with the use of exogenous hormone treatment.}, journal={AQUACULTURE}, author={Andersen, L. K. and Clark, R. W. and Hopper, M. S. and Hodson, R. G. and Schilling, J. and Daniels, H. V. and Woods, L. C., III and Kovach, A. I. and Berlinsky, D. L. and Kenter, L. W. and et al.}, year={2021}, month={Feb} }
 @article{andersen_clark_mcginty_hopper_kenter_salger_schilling_hodson_kovach_berlinsky_et al._2021, title={Volitional tank spawning of domestic striped bass (Morone saxatilis) using human chorionic gonadotropin (hCG) and gonadotropin releasing hormone analogue (GnRHa)- induced 'pace-setting' females}, volume={532}, ISSN={["1873-5622"]}, DOI={10.1016/j.aquaculture.2020.735967}, abstractNote={Seventy-one tank spawning trials were conducted to evaluate the efficacy of exogenous hormone compounds and a novel "pace-set" strategy for inducing volitional tank spawning behavior in 5th generation domestic striped bass. Female fish (4.74 ± 0.73 kg; mean ± standard deviation) were treated with human chorionic gonadotropin (hCG; 29 trials), gonadotropin releasing hormone analog (GnRHa; 39 trials) or received no hormone treatment (control; 3 trials). Spawning trials were conducted using single females placed in spawning tanks with two (12 trials) or three (38 trials) males or with paired females placed in spawning tanks with three (4 trials) males. Significant differences in egg production, fry production, hatching rate, and fry/kg female body weight were generally not observed between exogenous hormone treatment groups (alpha = 0.05), with the exception of egg production differing between paired females spawning with three males (Student's t-test, p = 0.0255). However, a trend suggesting that increasing the number of males or females within the tanks improves yield of larvae (fry/kg female body weight) was observed. The untreated control females failed to spawn within 7 days. The pace-set spawning was conducted whereby one female treated with either hCG (7 trials) or GnRHa (7 trials) was placed in a spawning tank with one untreated female and multiple males. The results of these trials show for the first time that a hormone-induced female striped bass can be used to stimulate successful volitional spawning of an untreated female in the same tank with fry/kg female body weight production similar to that of hormone-treated fish. Microsatellite-based parentage of select tank spawns and four additional trials conducted with an increased number of males (19 trials total) showed that female striped bass typically spawn with at least two males; a single pair mating was only observed for one spawning trial. These data allowed for the determination of effective broodstock size (Nb) of each tank spawning trial at between 2.00 and 5.60 when considering all male contributions. The Nb generally increased as the number of males and female fish in the tank increased (from 2.53 for one female and two males to 5.52 for two females and six males). These results indicate that domestic striped bass are promiscuous and will generally reproduce in captivity using tank spawning procedures that allow for a high level of genetic diversity to be retained among the offspring. The pace-set method reduces hormone use and may be applied to commercial striped bass production as well as captive spawning of other fish species.}, journal={AQUACULTURE}, author={Andersen, L. K. and Clark, R. W. and McGinty, A. S. and Hopper, M. S. and Kenter, L. W. and Salger, S. A. and Schilling, J. and Hodson, R. G. and Kovach, A. I. and Berlinsky, D. L. and et al.}, year={2021}, month={Feb} }