Publications

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Recent Papers

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Less Recent Papers (2020 and older)

Shelly A. Wanamaker , Kaitlyn R. Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B. Timmins-Schiffman & Steven B. Roberts. (2020) Temporal proteomic profiling reveals insight into critical developmental processes and temperature-influenced physiological response differences in a bivalve mollusc BMC Genomics 21, 723 doi:10.1186/s12864-020-07127-3

Yong-Kian Lim, Khan Cheung, Xin Dang, Steven B. Roberts, Xiaotong Wang, Vengatesen Thiyagarajan (2020) DNA methylation changes in response to ocean acidification at the time of larval metamorphosis in the edible oyster, Crassostrea hongkongensis Marine Environmental Research, Volume 163 doi:10.1016/j.marenvres.2020.105214

Downey-Wall Alan M., Cameron Louise P., Ford Brett M., McNally Elise M., Venkataraman Yaamini R., Roberts Steven B., Ries Justin B., Lotterhos Katie E (2020) Ocean Acidification Induces Subtle Shifts in Gene Expression and DNA Methylation in Mantle Tissue of the Eastern Oyster (Crassostrea virginica) Frontiers in Marine Science v7 p828 doi:10.3389/fmars.2020.566419

Cristian Gallardo-Escárate; Valentina Valenzuela-Muñoz; Gustavo Núñez-Acuña; Diego Valenzuela-Miranda; Bárbara P. Benaventel; Constanza Sáez-Vera; Homero Urrutia; Beatriz Novoa; Antonio Figueras; Steven Roberts; Paulina Assmann; Marta Bravo (2020) The wastewater microbiome: A novel insight for COVID-19 surveillance Science of The Total Environment Page: 142867 doi:10.1016/j.scitotenv.2020.142867

Bonnie J. Becker, Michael D. Behrens, Brian Allen, Megan Hintz, Hannah Parker, Michelle M. McCartha, and Sarah M. White (2020) Spatial and Temporal Distribution of the Early Life History Stages of the Native Olympia Oyster Ostrea lurida (Carpenter, 1864) in a Restoration Site in Northern Puget Sound, Wa Journal of Shellfish Research 39(1), 43-58. doi:/10.2983/035.039.0105

Emma Timmins-Schiffman, José M. Guzmán, Rhonda Elliott Thompson, Brent Vadopalas, Benoit Eudeline and Steven B. Roberts (2020) Larval Geoduck (Panopea generosa) Proteomic Response to Ciliates Scientific Reports 10, 6042. doi:10.1038/s41598-020-63218-x

Venkataraman Yaamini R., Downey-Wall Alan M., Ries Justin, Westfield Isaac, White Samuel J., Roberts Steven B., Lotterhos Kathleen E (2020) General DNA Methylation Patterns and Environmentally-Induced Differential Methylation in the Eastern Oyster (Crassostrea virginica) Frontiers in Marine Science, Volume 7, Page 225. doi:10.3389/fmars.2020.00225

Gurr SJ, Vadopalas B, Roberts SB, Putnam HM (2020) Metabolic recovery and compensatory shell growth of juvenile Pacific geoduck Panopea generosa following short-term exposure to acidified seawater Conservation Physiology, Volume 8, Issue 1, coaa024. doi:10.1093/conphys/coaa024

Spencer, LH, Venkataraman, YR, Crim R, Ryan S, Horwith MJ, and Roberts SB (2020) Carryover effects of temperature and pCO2 across multiple Olympia oyster populations. Ecological Applications 00( 00):e02060. doi:10.1002/eap.2060

Dimond JL and Roberts SB. (2020) Convergence of DNA Methylation Profiles of the Reef Coral Porites astreoides in a Novel Environment Frontiers in Marine Science. vol 6. doi:10.3389/fmars.2019.00792

Venkataraman YR, Spencer LH, Roberts SB. (2019) Larval Response to Parental Low pH Exposure in the Pacific Oyster Crassostrea gigas Journal of Shellfish Research, 38(3), 743-750. doi:10.2983/035.038.0325

Timmins‐Schiffman E, Guzmán JM, Elliott Thompson R, Vadopalas B, Eudeline B, Roberts SB. (2019) Dynamic response in the larval geoduck (Panopea generosa) proteome to elevated pCO2. Ecol Evol.00: 1– 13. doi:10.1002/ece3.5885

Gallardo-Escárate C, Valenzuela-Muñoz V, Núñez-Acuña , Carrera C, Gonçalves AT, Valenzuela-Miranda D, Benavente BP, Roberts SB. (2019) Catching the complexity of salmon-louse interactions Fish & Shellfish Immunology. doi:10.1016/j.fsi.2019.04.065

Spencer LH, Horwith M, Lowe AT, Venkataraman YR, Timmins-Schiffman E, Nunn BL, Roberts SB. (2019) Pacific geoduck (Panopea generosa) resilience to natural pH variation Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. doi:10.1016/j.cbd.2019.01.010 bioRxiv

Venkataraman YR, Timmins-Schiffman E, Horwith MJ, Lowe AT, Nunn B, Vadopalas B, Spencer LH, Roberts SB. (2019) Characterization of Pacific oyster Crassostrea gigas proteomic response to natural environmental differences Mar Ecol Prog Ser 610:65-81. doi:10.3354/meps12858 bioRxiv

Juárez, O., Lafarga-De la Cruz, F., Leyva-Valencia, I., López-Landavery, E., García-Esquivel, Z., Díaz, F., Re-Araujo, D., Vadopalas, B., and C. Galindo-Sánchez. (2018). Transcriptomic and metabolic response to chronic and acute thermal exposure of juvenile geoduck clams Panopea globosa. Marine Genomics. doi:10.1016/j.margen.2018.09.003

Javier A. Rodriguez‐Casariego, Mark C. Ladd, Andrew A. Shantz, Christian Lopes, Manjinder S. Cheema, Bohyun Kim, Steven B. Roberts, James W. Fourqurean, Juan Ausio, Deron E. Burkepile, and Jose M. Eirin‐Lopez. (2018) Coral epigenetic responses to nutrient stress: Histone H2A.X phosphorylation dynamics and DNA methylation in the staghorn coral Acropora cervicornis Ecol Evol. 2018;00:1–15. doi:10.1002/ece3.4678 pdf

Roberts SB, Gavery MR. (2018) Opportunities in Functional Genomics: A Primer on Lab and Computational Aspects Journal of Shellfish Research 37(4):747-754. doi:10.2983/035.037.0406

Silliman KE, Bowyer TK, Roberts SB. (2018) Consistent differences in fitness traits across multiple generations of Olympia oysters Scientific Reports volume 8, Article number:6080. doi:10.1038/s41598-018-24455-3

Heare JE, White SJ, Vadopalas B, Roberts SB. (2018) Differential response to stress in Ostrea lurida as measured by gene expression PeerJ 6:e4261. doi: 10.7717/peerj.4261

Goetz FW, Jasonowicz AJ, Roberts SB. (2017) What goes up must come down: Diel vertical migration in the deep-water sablefish (Anoplopoma fimbria) revealed by pop-up satellite archival tags Fish Oceanogr. 2017;00:1–16. doi: 10.1111/fog.12239

Gavery MR, Roberts SB. (2017) Epigenetic considerations in aquaculture PeerJ 5:e4147 doi: 10.7717/peerj.4147

Jake Emerson Heare, Brady Blake, Jonathan P Davis, Brent Vadopalas, Steven Roberts (2017) Evidence of Ostrea lurida Carpenter, 1864 population structure in Puget Sound, WA Marine Ecology 38:e12458 doi: 10.1111/maec.12458

Megan Hintz, Katherine Gratz, Bonnie Becker, Brent Vadopalas, and Steven Roberts (2017) A Nonlethal Anesthesia Protocol for Accessing the Mantle Cavity of Olympia Oysters in the Laboratory or Field Journal of Shellfish Research 2017 36 (2), 353-357 doi: 10.2983/035.036.0207

Samuel J. White, Brent Vadopalas, Katherine Silliman & Steven B. Roberts (2017) Genotoype-by-sequencing of three geographically distinct populations of Olympia oysters, Ostrea lurida Scientific Data 4, Article number: 170130 doi: 10.1038/sdata.2017.130

Dimond JL, Gamblewood SK, Roberts SB. (2017) Genetic and epigenetic insight into morphospecies in a reef coral Molecular Ecology. 00:1–12. doi: 10.1111/mec.14252

Emma B. Timmins-Schiffman, Grace A Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn and Steven Roberts (2017) Integrating discovery-driven proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation Journal of Proteome Research doi: 10.1021/acs.jproteome.7b00288 pdf

C. Gallardo-Escárate V. Valenzuela-Muñoz S. Boltaña G. Nuñez-Acuña D. Valenzuela-Miranda A.T. Gonçalves C. Détrée E. Tarifeño-Saldivia R. Farlora S. Roberts H.M. Putnam (2017) The Caligus rogercresseyi miRNome: Discovery and transcriptome profiling during the sea lice ontogeny AgriGene doi: 10.1016/j.aggene.2017.03.002 eprint

The Aquaculture Genomics, Genetics and Breeding Workshop (2017) Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research BMC Genomics 18:191. doi: 10.1186/s12864-017-3557-1

Detree C, Núñez-Acuña G, Roberts S, Gallardo-Escárate C (2016) Uncovering the Complex Transcriptome Response of Mytilus chilensis against Saxitoxin: Implications of Harmful Algal Blooms on Mussel Populations PLoS ONE 11(10): e0165231. doi:10.1371/journal.pone.0165231

Dimond JL and Roberts SB (2016), Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change Molecular Ecology doi:10.1111/mec.13414 preprint

Jasonowicz AJ, Goetz FW, Goetz GW, Nichols KM (2016) Love the one you’re with: Genomic evidence of panmixia in the sablefish (Anoplopoma fimbria) Canadian Journal of Fisheries and Aquatic Sciences doi: 10.1139/cjfas-2016-0012

Froehlich HE, Roberts SB, Essington TE (2015) Evaluating hypoxia-inducible factor-1α mRNA expression in a pelagic fish, Pacific herring Clupea pallasii, as a biomarker for hypoxia exposure Comparative Biochemistry and Physiology - Part A: Molecular and Integrative Physiology doi:10.1016/j.cbpa.2015.07.016

Cook MA, Massee KC, Wade TH, Oden SM, Jensen C, Jasonowicz A, Immerman DA, Goetz FW (2015) Culture of sablefish (Anoplopoma fimbria) larvae in four experimental tank designs Aquacultural Engineering doi:10.1016/j.aquaeng.2015.09.003

Fuess LE, Eisenlord ME, Closek CJ, Tracy AM, Mauntz R, Gignoux-Wolfsohn S, Moritsch MM, Yoshioka R, Burge CA, Harvell CD, Friedman CS, Hewson I, Hershberger PK, Roberts SB (2015) Up in Arms: Immune and Nervous System Response To Sea Star Wasting Disease PLoS ONE doi:10.1371/journal.pone.0133053

Timmins-Schiffman E, Coffey WD, Hua W, Nunn BL, Dickinson GH and Roberts SB. (2014). Shotgun proteomics reveals physiological response to ocean acidification in Crassostrea gigas BMC Genomics 2014, 15:951 doi:10.1186/1471-2164-15-951

Immerman DA and Goetz FW (2014). The activation and cryopreservation of sablefish (Anoplopoma fimbria) sperm Aquaculture doi:10.1016/j.aquaculture.2014.04.010

Olson CE and Roberts SB. (2014). Genome-wide profiling of DNA methylation and gene expression in Crassostrea gigas male gametes Frontiers in Physiology. 5:224. doi: 10.3389/fphys.2014.0022

Gavery MR and Roberts SB. (2014) A context specific role for DNA methylation in bivalves Briefings in Functional Genomics. doi:10.1093/bfgp/elt054 (pdf)

Gavery MR and Roberts SB. (2013) Predominant intragenic methylation is associated with gene expression characteristics in a bivalve mollusc PeerJ 1:e215. doi:10.7717/peerj.215

Garcia-Vedrenne AE, Groner M, Page-Karjian A, Siegmund G-F, Singhal S, Sziklay J and Roberts SB. (2013) Development of Genomic Resources for a thraustochytrid Pathogen and Investigation of Temperature Influences on Gene Expression PLoS ONE 8(9): e74196. doi:10.1371/journal.pone.0074196

Storer CS, Quinn TP and Roberts SB. (2013) Quantitative PCR analysis used to characterize physiological changes in brain tissue of senescent sockeye salmon Biogerontology. doi:10.1007/s10522-013-9448-1 (pdf)

Burge CA, Mouchka ME, Harvell CD and Roberts SB. (2013) Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing Frontiers in Physiology 4:180. doi:10.3389/fphys.2013.00180

Timmins-Schiffman EB, Nunn BL, Goodlett DR and Roberts SB. (2013) Shotgun proteomics as a viable approach for biological discovery in the Pacific oyster Conservation Physiology. doi:10.1093/conphys/cot009

Timmins-Schiffman EB, Friedman CS, Metzger DC, White SJ and Roberts SB. (2013) Genomic resource development for shellfish of conservation concern Molecular Ecology Resources. doi:10.1111/1755-0998.12052

Timmins-Schiffman EB and Roberts SB. (2012) Characterization of genes involved in ceramide metabolism in the Pacific oyster Crassostrea gigas BMC Research Notes 5:502. doi:10.1186/1756-0500-5-502

Storer CG, Pascal CE, Roberts SB, Templin WD, Seeb LW and Seeb JE. (2012) Rank and Order: Evaluating the Performance of SNPs for Individual Assignment in a Non-Model Organism PLoS ONE 7(11): e49018. doi:10.1371/journal.pone.0049018

Timmins-Schiffman EB, O’Donnell M, Friedman CS, and Roberts SB. (2012) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas Marine Biology. doi:10.1007/s00227-012-2055-x pdf

Burge CA, Douglas N, Conti-Jerpe I, Weil E, Roberts SB, Friedman CS and CD Harvell. (2012) Friend or foe: the association of Labyrinthulomycetes with the Caribbean sea fan, Gorgonia ventalina Diseases of Aquatic Organisms 101:1-12. doi:10.3354/dao02487

Metzger DC, Pratt P and Roberts SB. (2012) Characterizing the effects of heavy metal and Vibrio exposure on hsp70 expression in Crassostrea gigas gill tissue Journal of Shellfish Research 31(3):627-630. doi:10.2983/035.031.0305 pdf

Roberts SB, Hauser L, Seeb LW and Seeb JE (2012) Development of genomic resources for Pacific herring through targeted transcriptome pyrosequencing PLoS ONE 7(2): e30908. doi:10.1371/journal.pone.0030908

Roberts SB and Gavery MR (2012) Is there a relationship between DNA methylation and phenotypic plasticity in invertebrates? Frontiers in Physiology 2:116. doi:10.3389/fphys.2011.00116

Gavery MR and Roberts SB (2012) Characterizing short read sequencing for gene discovery and RNA-Seq analysis in Crassostrea gigas Comparative Biochemistry and Physiology Part D: Genomics and Proteomics 7:2 94-99. doi:10.1016/j.cbd.2011.12.003

Morera D, Roher N, Ribas L, Balasch JC, Doñate C, Callol A, Boltaña A, Roberts SB, Goetz G, Goetz FW and Mackenzie SA. (2011) RNA-Seq reveals an integrated immune response in nucleated erythrocytes PLoS ONE 6(10): e26998. doi:10.1371/journal.pone.0026998

Roberts SB, Sunila I, and Wikfors G. (2011) Immune response and mechanical stress susceptibility in diseased oysters, Crassostrea virginica Journal of Comparative Physiology B 182:1 41-48. doi:10.1007/s00360-011-0605-z

Seeb JE, Carvalho G, Hauser L, Naish K, Roberts SB and Seeb LW. (2011) Single-nucleotide polymorphism (SNP) discovery and applications of SNP genotyping in nonmodel organisms Molecular Ecology Resources 11 1–8. doi:10.1111/j.1755-0998.2010.02979.x

Seeb JE, Pascal CE, Graue ED, Seeb LW, Templin WD, Harkins T and Roberts SB. (2010) Transcriptome sequencing and high-resolution melt analysis advance single nucleotidepolymorphism discovery in duplicated salmonids Molecular Ecology Resources. doi: 10.1111/j.1755-0998.2010.02936.x

Gavery MR and Roberts SB. (2010) DNA methylation patterns provide insight into epigenetic regulation in the Pacific oyster (Crassostrea gigas) BMC Genomics 11:483. doi:10.1186/1471-2164-11-483

Mathger L, Roberts SB, and Hanlon R. (2010) Evidence for distributed light sensing in the skin of cuttlefish, Sepia officinalis Biology Letters. doi: 10.1098/rsbl.2010.0223

Goetz FW, Rosauer D, Sitar S, Goetz G, Simchick C, Roberts SB, Johnson R, Murphy C, Bronte C, and Mackenzie S. (2010) A genetic basis for the phenotypic differentiation between siscowet and lean lake trout (Salvelinus namaycush) Molecular Ecology 19 176–196.

Defaveri J*, Smolowitz R, and Roberts S (2009) Development and validation of a real-time quantitative PCR assay for the detection and quantification of Perkinsus marinus in the Eastern oyster, Crassostrea virginica Journal of Shellfish Research Vol. 28 No. 3 459-464. eprint

Roberts SB, Goetz G, White S, and Goetz F (2009) Analysis of genes isolated from plated hemocytes of the Pacific Oyster, Crassostrea gigas Marine Biotechnology 11:24-44. doi: 10.1007/s10126-008-9117-6

Roberts SB, Gueguen Y, de Lorgeril J, and Goetz F. (2008) Rapid accumulation of an interleukin 17 homolog transcript in Crassostrea gigas hemocytes following bacterial exposure Developmental and Comparative Immunology 32, 1099-1104. doi: 10.1016/j.dci.2008.02.006

Lyons MM*, Lau Y-T, Carden WE, Ward JE, Roberts SB, Smolowitz R, Vallino J, and Allam B. (2007) Characteristics of marine aggregates in shallow-water ecosystems: Implications for disease ecology EcoHealth 4, 406–420.

Weiss E, Bennie M, Hodgins-Davis A, Roberts SB, and Gerlach G. (2007) Characterization of new SSR-EST markers in cod, Gadus morhua Molecular Ecology Notes 7: 866–867. doi: 10.1111/j.1471-8286.2007.01731.x

Hodgins-Davis A*, Roberts SB, Cowan D, Atema J, Avolio C, Defaveri J, and Gerlach G. (2007) Characterization of SSRs from the American lobster, Homarus americanus Molecular Ecology Notes 7:330-332.

Rodgers BD, Roalson EH, Weber GM, Roberts SB, Goetz FW. (2007) A Proposed Nomenclature Consensus for the Myostatin Gene Family AJP- Endocrinology and Metabolism 292(2):E371-2.

Lyons MM*, Smolowitz R, Dungan C, and Roberts SB. (2006) Development of a real-time quantitative PCR assay for the hard clam pathogen, Quahog Parasite Unknown (QPX) Diseases of Aquatic Organisms 72(1):45-52.

Biga PR, Roberts SB, Iliev DB, McCauley LA, Moon JS, Collodi P, and Goetz FW. (2005) The isolation, characterization, and expression of a novel GDF11 gene and a second myostatin form in zebrafish, Danio rerio. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 141: 218-230.

Roberts SB, Romano C, and Gerlach G. (2005) Characterization of EST derived SSRs from the bay scallop, Argopectens irradiansMolecular Ecology Notes 5: 567-568.

Jentoft S, Topp N, Seeliger M, Malison JA, Barry TP, Held JA, Roberts SB, and Goetz FW. (2005) Lack of growth enhancement by exogenous growth hormone treatment in yellow perch in four separate experiments Aquaculture 250:471-479.

Hollis DM, Goetz FW, Roberts SB, and Boyd SK. (2004) Acute neurosteroid modulation and subunit isolation of the GABAa receptor in the bullfrog, Rana catesbeiana Journal of Molecular Endocrinology 32(3):921-34.

Biga PR, Cain KD, Hardy RW, Schelling GT, Overturf K, Roberts SB, Goetz FW, Ott TL. (2004) Growth hormone differentially regulates muscle myostatin1 and -2 and increases circulating cortisol in rainbow trout Oncorhynchus mykiss General and Comparative Endocrinology Vol 138(1):32-41.

Roberts SB, McCauley LAR, Devlin RH, Goetz FW. (2004) Transgenic salmon over-expressing growth hormone exhibit decreased myostatin transcript and protein expression Journal of Experimental Biology 207(Pt 21):3741-8.

Kim H-W, Mykles DL, Goetz FW, Roberts SB. (2004) Characterization of an invertebrate myostatin homologue from the bay scallop, Argopecten irradians BBA – Gene Structure and Expression 1679(2):174-9.

Roberts SB, Barry T, Malison J, Goetz FW. (2004) Production of a recombinantly-derived growth hormone antibody and the characterization of growth hormone levels in yellow perch Aquaculture Vol.232/1-4: 591-602.

Roberts SB, Goetz FW. (2003) Expressed sequence tag analysis of genes expressed in the bay scallop, Argopecten irradians Biological Bulletin 205: 227-228.

Roberts SB, Goetz FW. (2003) Myostatin protein and mRNA transcript levels in adult and developing brook trout Molecular and Cellular Endocrinology 210(1-2): 9-20.

Roberts SB, Goetz FW. (2001) Differential skeletal muscle expression of myostatin across teleost species, and the isolation of multiple myostatin isoformsFEBS Letters Vol 49:3,212-216.

Roberts SB, Langenau DM, Goetz FW. (2000) Cloning and characterization of prostaglandin endoperoxide synthase-1 and -2 from the brook trout ovary Molecular and Cellular Endocrinology 160(1-2):89-97.

Moser ML, Roberts SB. (2000) Effects of nonindigenous ictalurids and recreational electrofishing on the ictalurid community of the Cape Fear River drainage, North Carolina in Catfish 2000: Proceedings of the International Ictalurid Symposium; ER Irwin, WA Hubert, CF Rabeni, HL Schramm, Jr., and T Coon, editors. Davenport, IA. June 23-25, 1998. pp 479-485.

Roberts SB, Langenau DM, Goetz FW. (2000) Isolation through cloning of fish prostaglandin endoperoxide synthase (cyclooxygenase) in Proceedings of the 6th International Symposium on the Reproductive Physiology of Fish; B Norberg, OS Kjesbu, GL Taranger, E Andersson, and SO Stefansson, editors. Bergen, Norway. July 4-9, 1999. p 197.

Langenau DM, Goetz FW, Roberts SB. (1999) The upregulation of messenger ribonucleic acids during 17a, 20b-dihydroxy-4-pregnen-3-one-induced ovulation in the perch ovary Journal of Molecular Endocrinology 23(2):137-52.

Roberts SB, Jackson LF, King WK, Taylor RG, Grier HJ, Sullivan CV. (1999) Annual reproductive cycle of the common snook: Endocrine correlates of maturation Transactions of the American Fisheries Society 128:426-445.

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Book Chapters

Moreira Sanmartín R, Roberts SB, Figueras A. (2016) Molluscs. pages 223-245, in Genomics in Aquaculture. Editors: Simon A. MacKenzie and Sissel Jentoft. ISBN: 978-0-12-801418-9

Gavery, M., & Roberts, S. (2018). Genetics & Epigenetics in Life History and Reproduction: Oysters. In M. K. Skinner (Ed.), Encyclopedia of Reproduction. vol. 6, pp. 736–742. Academic Press: Elsevier. doi: 10.1016/B978-0-12-809633-8.20621-3 pdf

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Preprints

Shelly A Wanamaker , Kaitlyn R Mitchell, Rhonda Elliott Thompson, Benoit Eudeline, Brent Vadopalas, Emma B Timmins-Schiffman, Steven B Roberts (2020). Temporal proteomic profiling reveals insight into critical devleopmental processes and temperature-influenced physiological response differences in a bivalve mollusc. bioRxiv. https://doi.org/10.1101/2020.06.05.137059

Emma B. Timmins-Schiffman, Grace A. Crandall, Brent Vadopalas, Michael E. Riffle, Brook L. Nunn, Steven B. Roberts (2016) Integrating proteomics and selected reaction monitoring to develop a non-invasive assay for geoduck reproductive maturation. bioRxiv doi: https://doi.org/10.1101/094615

Heare JE, White SJ, Roberts SB. (2015) Differential response to stress in Ostrea lurida (Carpenter 1864) as measured by gene expression. PeerJ PrePrints 3:e1595v1 https://doi.org/10.7287/peerj.preprints.1595v1

Gavery MR, Delrow J, Basom R, Roberts SB. (2015) Influence of 17α-ethinylestradiol on DNA Methylation in Oysters. GitHub / Zenodo https://github.com/sr320/paper-Oyster-EE2

Heare JE, Blake B, Davis JP, Vadopalas B, Roberts SB. (2014) Evidence of Ostrea lurida (Carpenter 1894) population structure in Puget Sound, WA. PeerJ PrePrints 2:e704v1 http://dx.doi.org/10.7287/peerj.preprints.704v1

Claire E. Olson, Steven B. Roberts. Indication of family-specific DNA methylation patterns in developing oysters bioRxiv doi: http://dx.doi.org/10.1101/012831

Roberts et al. Sequence Data that never made it. https://www.authorea.com/users/3858/articles/3989/_show_article

David C. Metzger, Paul McElhany, Shallin Busch, Carolyn S. Friedman, Steven B. Roberts (preprint) Underlying impact of ocean acidification on Manila clam (Ruditapes philippinarum) larvae revealed through RNA-Seq analysis. Status: Available for Comment peer reviews: BMC, MB

David C. Metzger, Carolyn S. Friedman, Emma B. Timmins-Schiffman and Steven B. Roberts (preprint) Thermal tolerance and gene expression characterization in Manila clams (Ruditapes philippinarum) exposed to elevated carbon dioxide. Status: Available for Comment peer reviews: AB

Storer C, Goetz F, Roberts S. (preprint) Transcriptional variation in lake trout (Salvelinus namaycush) ecotypes raised under constant environmental conditions. Status: Available for Comment

Steven Roberts, Roxanna Smolowitz, Richard Karney, Mackenzie Gavery et al. (preprint) Disease tolerance in the eastern oyster. Status: Available for Comment

Roberts et al. (preprint) Hard clam gene expression analysis. Status: Available for Comment

Archived

Dimond JL and Roberts SB (2015) Germline DNA methylation in reef corals: patterns and potential roles in response to environmental change UW ResearchWorks Archive uri:http://hdl.handle.net/1773/34298

Mackenzie Gavery and Steven Roberts (preprint) A context specific role for DNA methylation in bivalves. Status: Archived download (Revised and later accepted at Briefings in Functional Genomics 10.1093/bfgp/elt054

Emma Timmins-Schiffman, Carolyn Friedman, Steven Roberts, Sam White, Dave Metzger (preprint) Genomic resource development of shellfish of conservation concern. Status: on figshare (published - Molecular Ecology Resources)

Timmins-Schiffman E, O’Donnell M, Friedman C, and Roberts S. (preprint) Elevated pCO2 causes developmental delay in early larval Pacific oysters, Crassostrea gigas Status: on figshare (published - Marine Biology)

Lyons, Dungan, and Roberts – Thraustochytrid-like isolates from marine bivalve mollusks

Smolowitz, Schaff, DeFaveri, Roberts - Renal Trematodiasis of Largemouth Bass and Development of PCR Methods

White SJ and Roberts S. (preprint) Identification of myostatin interacting proteins using a yeast-two hybrid approach. Status: Available for Comment

Gavery MR, White SJ, Roberts S (preprint) Characterization of prostaglandin endoperoxide synthase from the Pacific oyster, Crassostrea gigas. Status: Available for Comment

Thompson R and Roberts SB (preprint) Influence of carbon dioxide-induced acidification and mechanical stress on gene expression and microbial community composition in oysters. Status: Available for Comment

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Theses

Developing Tools and Resources for Maturation Control in Bivalvia. Olivia Cattau. 2023 http://hdl.handle.net/1773/50826

Patterns, dynamics, and potential roles of DNA methylation in reef corals and their allies. James Dimond. 2019 http://hdl.handle.net/1773/44815

Response of Olympia oysters (Ostrea lurida) to changing environmental conditions. Jake Heare. 2015 http://hdl.handle.net/1773/35206

Genomic signatures of natural selection and population structure in West Coast and Alaskan sablefish (Anoplopoma fimbria). Andrew Jasonowicz. 2014 http://hdl.handle.net/1773/33907

DNA methylation variation in gametes and larvae of the Pacific oyster, Crassostrea gigas. Claire Ellis Olson. 2014 http://hdl.handle.net/1773/27478

Epigenomic and transcriptomic regulation of environmental responses in the Pacific oyster, Crassostrea gigas. Mackenzie Gavery. 2014. http://hdl.handle.net/1773/25984

The Effects of Ocean Acidification on Multiple Life History Stages of the Pacific Oyster, Crassostrea gigas: Implications for Physiological Trade-offs. Emma Timmins-Schiffman. 2014. http://hdl.handle.net/1773/25413

Sablefish (Anoplopoma fimbria) sperm: The physiology of activation and the development of a cryopreservation protocol. Doug Immerman. 2014. http://hdl.handle.net/1773/25414

Genetic and phenotypic diversity in sockeye salmon, Oncorhynchus nerka. Caroline Storer. 2012. figshare. http://dx.doi.org/10.6084/m9.figshare.661720

Characterizing the effects of ocean acidification in larval and juvenile Manila clam, Ruditapes philippinarum, using a transcriptomic approach. David Metzger. 2012 download

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Notebooks

Person	Notebook	Commitment
Steven Roberts	sr320.github.io
Sam White	robertslab.github.io
Matt George	mattgeorgephd.github.io
Aspen Coyle	aspencoyle.github.io
Ariana Huffmyer	ahuffmyer.github.io
Chris Mantegna	chrismantegna.github.io/cmlabsite
Zach Bengtsson	zbengt.github.io
Celeste Valdivia	valeste.github.io
Larken Root	larkenr.github.io
Grace Crandall	grace-ac.github.io
Kathleen Durkin	shedurkin.github.io

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Recent Presentations

2024

• Pycnopodia helianthoides immune response to Sea Star Wasting Disease. Grace Crandall. Society of Integrative and Comparative Biology. January 2024.

• Thermal stress reduces photosynthate metabolism and disrupts nitrogen cycling in coral larvae. Ariana S. Huffmyer. Society of Integrative and Comparative Biology. January 2024.

• Biodiversity Survey Methods: Using eDNA Metabarcoding to Complement Existing Methods. Chris Mantegna. Society of Integrative and Comparative Biology. January 2024.

• Comparative analyses of long non-coding RNA activity in three coral species. Zachary Bengtsson. Society of Integrative and Comparative Biology. January 2024.

2023

• Pycnopodia helianthoides immune response to Sea Star Wasting Disease. Grace Crandall. Western Society of Naturalists, Monterey, California. November 2023.

• Genomic Applications in Sustainable Aquaculture. Steven Roberts. 1er Congreso de Biología Experimental y Aplicada, CICESE, Ensenada, Mexico. October 2023

• Development of an Alternative Sterility Method for Shellfish Aquaculture: Identification of Candidate Genes Involved in Germ Cell Specification Mackenzie Gavery (NOAA Fisheries - NW Fisheries Science Center), Lauren Saunders, Lauren Vandepas, Brent Vadopalas, Adam Luckenbach, Cole Trapnell, Steven Roberts. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023

• Environmental Priming for Ocean Acidification: Potential hatchery practices to build resilience for clam aquaculture in the Puget Sound Larken Root (Univeristy of Washington/NOAA), Mackenzie Gavery, Ryan Crim. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023

• Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following heatwaves Matthew George (University of Washington), Olivia Cattau, Mollie A. Middleton, Delaney Lawson, Brent Vadopalas, Mackenzie Gavery, Steven Roberts. Pacific Coast Shellfish Growers Association (PCSGA) and the National Shellfisheries Association Pacific Coast Section (NSA-PCS) Meeting. Seaside Civic & Convention Center, Seaside, OR. September 19-21, 2023

• Triploid Pacific oysters experience enhanced mortality following marine heatwaves Presentation. National Shellfish Association Annual Meeting, Baltimore, MD, March 30, 2023.

• DNA Methylaiton in Bivalves Keynote at Epigenomics in Aquaculture - January 25 2023, University of Concepcion, Chile

• Ploidy mediates the stress response of Pacific oysters following marine heatwave exposure Presentation. Plant and Animal Genome Conference, San Diego, CA, January 14, 2023.

• Triploid Pacific oysters exhibit stress response dysregulation and elevated mortality following marine heatwaves Presentation. NOAA Fisheries Northwest Fisheries Science Center Physiology Group Meeting, Seattle, WA, January 11, 2023.

2022

• Mechanisms of tilapia salinity tolerance at the limits of osmoregulation Presentation. NOAA physiology program monthly meeting, Virtual, March 3, 2022.

• Yellow Island Intertidal Ecological Monitoring Presentation. NWStraits Commission meeting, Virtual, August 12, 2022.

• Comparative Response of Littleneck and Manila Clams from the Puget Sound to Ocean Acidification Conditions: Year 1 Presentation. Pacific Coast Shellfish Growers Association (PCSGA) annual meeting, Wenatchee, September 20, 2022.

• Using aquaculture to turn the tide on aquatic ecosystem collapse Presentation. University of Puget Sound Weekly Science Seminar, Thompson Hall, September 29, 2022.

• Physiological and multi-omic signatures of shifts in symbiotic nutritional exchange in reef-building coral early life history Presentation. Benthic Ecology Meeting. Portsmouth, New Hampshire. March 2022.

• Understanding shifts in symbiotic and physiological state in reef- building corals across developmental and environmental gradients Virtual seminar. Old Dominion University. December 2022.

• Multi-omic approaches to understand reef coral development and symbiosis Virtual seminar. University of Washington eScience Institute Postdoctoral Seminar Series. November 2022.

• The contribution of summer heatwaves to ‘triploid mortality’ events observed during commercial pacific oyster production in Washington State Presentation. The Society of Integrative and Comparative Biology, Virtual, January 4, 2022.

2021

• Diversity in animal response to environmental change Presentation. Academic Data Science Alliance (ADSA) 2021 Data Science Coast to Coast Seminar Series, Virtual May 19, 2021 3pm.

• Exploring the tolerance of Pacific geoduck to low pH through comparative physiology, genomics, and DNA methylation Presentation. The Society for Integrative and Comparative Biology (SICB) 2021 Annual Meeting, Virtual January - February 2021

• A perspective on DNA methylation in bivalves Presentation. The Society for Integrative and Comparative Biology (SICB) 2021 Annual Meeting, Virtual January - February 2021

• How do dynamic conditions shape coral symbiosis and metabolism and drive energetic-epigenetic linkages? Presentation. 2021 Moorea Coral Reef Long Term Ecological Research All Invesitgator Meeting. November 2021.

2020

• Harnessing the power of single-cell RNA sequencing to control reproductive development in bivalves 74th Annual Pacific Coast Shellfish Growers Association Conference, Virtual October 2020

• Carryover effects of winter warming in the Olympia oyster. Presentation. 74th Annual Pacific Coast Shellfish Growers Association Conference, Virtual October 2020

• Oysters, Ocean Acidification, and -Omics Presentation, Friday Harbor Laboratories Summer Seminar Series, June 2020

• Influence of ocean acidification on eastern (Crassostrea virginica) and Pacific oyster (Crassostrea gigas) DNA methylation Poster, Ocean Sciences Meeting 2020, San Diego, CA February 2020

• DNA methylation associations with growth rate in Olympia oyster populations presentation, Aquaculture America 2020, Honolulu, HI, February 2020

• Influence of ocean acidification on DNA methylation patterns in geoduck Presentation, The Plant and Animal Genome XXVII Conference (PAG), San Diego, CA, January 2020