|Steven Roberts||sr320.github.io – ons/sr320|
|Sean Bennett||rpubs/sean80 – genefish/seanb80|
|Mrunmayee Manohar Shete||onsnetwork.org/mrunmayee|
- Environmental influences on DNA methylation patterns in oysters and the relationship with phenotypic variation University of Chicago (Chicago, IL). December 5, 2016
Towards a functional understanding of DNA methylation in shellfish and implications for aquaculture NOAA Northwest Fisheries Science Center (Seattle, WA). November 2, 2016
Hacking the Academy: Open in Action – OA Week @ University of Washington University of Washington (Seattle, WA). October 26, 2016
Environmental Sciences: A Genomic Perspective Commodore Options School (Bainbridge Island, WA). October 20, 2016
Does DNA Methylation Facilitate Phenotypic Plasticity? CNRS Amphitheatre (Moltpellier, France). February 2, 2016.
Open Access Opportunities for Credit, Tenure, and Promotion Claremont College (Claremont, CA). October 15, 2015.
Phenotypic Plasticity and Epigenetics in Invertebrates Centro de Investigación Científica y de Educación Superior de Ensenada, B.C. (CICESE). October 19, 2015.
Genomics on the Half Shell: Environmental Epigenetics, Open Science, and the Oyster Oregon State Unversity (Corvallis, OR). May 4, 2015.
Does DNA Methylation Facilitate Phenotypic Plasticity in Marine Invertebrates? Florida International University (Miami, FL). April 23, 2015.
USDA NRSP-8 – NSA Genomics Resource Coordination Workshop Monterey, CA. March 25, 2015.
Integrating SQLShare into Genomic Workflows UW escience Seminar (Seattle, WA). January 2015.
see also preprints
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.
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 irradians Molecular 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.
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
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
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
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.
Characterizing the effects of ocean acidification in larval and juvenile Manila clam, Ruditapes philippinarum, using a transcriptomic approach. David Metzger. 2012 download