- Rouressol L, Briseno J, Vijayan N, Chen G Y, Rischard E A, Sanchez G, Nyholm SV, McFall-Ngai MJ, Simakov O. (2023) “Emergence of novel genomic regulatory regions associated with light-organ development in the bobtail squid.” iScience
- Mcanulty SJ, Kerwin AH, Koch E, Nuttall B, Schleicher TR, Rader BA, Nyholm SV, Collins AJ. (2023) “ Failure To Launch ” : Development of a Reproductive Organ Linked to Symbiotic Bacteria. mBio
- Kerwin, A. H., McAnulty, S. J., Nyholm, S. V. (2021) Development of the Accessory Nidamental Gland and Associated Bacterial Community in the Hawaiian Bobtail Squid, Euprymna scolopes. Biological Bulletin
- Nyholm, S. V. (2020) In the beginning: egg–microbe interactions and consequences for animal hosts. Phil. Trans. R. Soc
- Kerwin, A. H., Gromek, S. M., Suria, A. M., Samples, R. M., Deoss, D. J., O’Donnell, K., Frasca Jr., S., Sutton, D. A. Wiederhold, N. P., Balunas, M. J., Nyholm, S. V. (2019) Shielding the Next Generation: Symbtiontic Bacteria from a Reproductive Organ Protective Bobtail Squid Eggs from Fungal Fouling. mBio
- Lynch, J. B., Schwartzman, J. A., Bennett, B. D., McAnulty, S. J., Knop, M. Nyholm, S. V., Ruby, E. G. (2019) Ambient pH Alters the Protein Content of Outer Membrane Vesicles, Driving Host Development in a Beneficial Symbiosis. Journal of Bacteriology
- Baker, L. J., Freed, L. L., Easson, C. G., Lopez, J. V., Fenolio, D., Sutton, T. T., Nyholm, S. V., Hendry, T. A. (2019) Diverse deep-sea anglerfishes share a geneticall reduced luminous symbtion that is acquired from the environment. eLife
- Rader, B., McAnulty S. J., Nyholm, S. V. (2019) Persistent symbiont colonization leads to a maturation of hemocyte response in the Euprymna sclolopes / Vibrio fischeri symbiosis. Microbiology Open
- Belcaid, M., Casaburi, C., McAnulty M. J., Schmidbaur, H., Suria, A. M., Moriano-Gutierrez, S., Pankey, M. S., Oakley, T. H., Kremer, N., Koch, E.J., Collins, A. J., Nguyen, H., Lek, S., Goncharenko-Foster, I., Minx, P., Sodergren, E., Weinstock, G., Rokhsar, D., McFall-Ngai, M., Simakov, O., Foster, J. S., Nyholm, S. V. (2019) Symbiotic organs shaped by distinct modes of genome evolution in cephalopods. PNAS
- Kerwin, A. H., Nyholm S.V. (2018). Reproductive System Symbiotic Bacteria Are Conserved between Two Distinct Populations of Euprymna scolopes from Oahu, Hawaii. mSphere
- Kerwin, A. H., Nyholm S. V., (2017). Symbiotic bacteria associated with a bobtail squid reproductive system are detectable in the environment, and stable in the host and in eggs throughout development. Environmental microbiology
- McAnulty, S. J., Nyholm, S. V., (2017) The Role of Hemocytes in the Hawaiian Bobtail squid, Euprymna scolopes: A Model Organism for Studying Beneficial Host-Microbe Interactions. Front. Microbiol.
- Gromek, S. M., Suria A. M., Fullmer M.S., Garcia, J.L., Gogarten, J.P., Nyholm S. V., Balunas, M.J. (2016). Leisingera sp. JC1, a Bacterial isolate from Hawaiian Bobtail Squid Eggs, Produces Indigoidine and Differentially Inhibits Vibrios. Front. Microbiol.
- Collins, A. J., Fullmer S. M. , Gogarten, J. P., Nyholm, S. V. Comparative genomics of Roseobacter clase bacteria isolated from the accessory nidamental gland of Euprymna scolopes. Frontiers Microbiology. 6:123.
- Schleicher, T. R., VerBerkmoes, N. C., Shah, M., & Nyholm, S. V. (2014). Colonization state influences the hemocyte proteome in a beneficial squid-vibrio symbiosis. Molecular & Cellular Proteomics : MCP, 1–46.
- Beinart, R. A., Nyholm, S. V, Dubilier, N., & Girguis, P. R. (2014). Intracellular Oceanospirillales inhabit the gills of the hydrothermal vent snail Alviniconcha with chemosynthetic , γ -Proteobacterial symbionts. doi:10.1111/1758-2229.12183
- Albertin, C. B., Bonnaud, L., Brown, C. T., Crookes-Goodson, W. J., da Fonseca, R. R., Di Cristo, C., … Ragsdale, C. W. (2012). Cephalopod genomics: A plan of strategies and organization. Standards in Genomic Sciences, 7(1), 175–88. doi:10.4056/sigs.3136559
- Rader, B. A., & Nyholm, S. V. (2012). Host/microbe interactions revealed through “omics” in the symbiosis between the Hawaiian bobtail squid Euprymna scolopes and the bioluminescent bacterium Vibrio fischeri. The Biological Bulletin, 223(1), 103–11. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/22983036
- Nyholm, S. V, & Graf, J. (2012). Knowing your friends: invertebrate innate immunity fosters beneficial bacterial symbioses. Nature Reviews. Microbiology, 10(12), 815–27. doi:10.1038/nrmicro2894
- Nyholm, S. V, Song, P., Dang, J., Bunce, C., & Girguis, P. R. (2012). Expression and putative function of innate immunity genes under in situ conditions in the symbiotic hydrothermal vent tubeworm Ridgeia piscesae. PloS One, 7(6), e38267. doi:10.1371/journal.pone.0038267
- Collins, A. J., LaBarre, B. a, Won, B. S. W., Shah, M. V, Heng, S., Choudhury, M. H., Nyholm, S. V. (2012). Diversity and partitioning of bacterial populations within the accessory nidamental gland of the squid Euprymna scolopes. Applied and Environmental Microbiology, 78(12), 4200–8. doi:10.1128/AEM.07437-11
- Fidopiastis, P. M., Rader, B. a, Gerling, D. G., Gutierrez, N. a, Watkins, K. H., Frey, M. W., S.V. Nyholm Whistler, C. a. (2012). Characterization of a Vibrio fischeri aminopeptidase and evidence for its influence on an early stage of squid colonization. Journal of Bacteriology, 194(15), 3995–4002. doi:10.1128/JB.00108-12
- Collins, A. J., Schleicher, T. R., Rader, B. a, & Nyholm, S. V. (2012). Understanding the role of host hemocytes in a squid/vibrio symbiosis using transcriptomics and proteomics. Frontiers in Immunology, 3(May), 91. doi:10.3389/fimmu.2012.00091
- Collins AJ, Nyholm SV (2011) Draft genome of Phaeobacter gallaeciensis ANG1; a dominant member of the accessory nidamental gland of Euprymna scolopes. J. Bacteriol. 193:3397-3398.
- Schleicher, T. R., & Nyholm, S. V. (2011). Characterizing the host and symbiont proteomes in the association between the Bobtail squid, Euprymna scolopes, and the bacterium, Vibrio fischeri. PloS One, 6(10), e25649. doi:10.1371/journal.pone.0025649
- Collins AJ, Nyholm SV (2010) Obtaining Hemocytes from the Hawaiian Bobtail Squid Euprymna scolopes and Observing their Adherence to Symbiotic and Non-Symbiotic Bacteria.JoVE. 36. http://www.jove.com/index/details.stp?id=1714, doi: 10.3791/1714
- Wier AM, Nyholm SV, Mandel MJ, Massengo-Tiassé RP, Schaefer AL, Koroleva I, Splinter-Bondurant S, Brown B, Manzella L, Snir E, Almabrazi H, Scheetz TE, Bonaldo Mde F,Casavant TL, Soares MB, Cronan JE, Reed JL, Ruby EG, McFall-Ngai MJ. (2010) Transcriptional patterns in both host and bacterium underlie a daily rhythm of anatomical and metabolic change in a beneficial symbiosis. Proc. Nat. Acad. Sci., USA, 107, 2259-64
- McFall-Ngai MJ, Nyholm SV, Castillo MG (2009) The role of the immune system in the initiation and persistence of the Euprymna scolopes-Vibrio fischeri symbiosis. Semin.Immunol. 22: 48-53.
- Nyholm SV, Stewart JJ, Ruby EG, McFall-Ngai MJ (2009) Recognition between symbiotic Vibrio fischeri and the haemocytes of Euprymna scolopes. Environ. Microbiol. 11:483-93.
- Nyholm, SV (2009) Peptidoglycan monomer release and Vibrio fischeri. J. Bacteriol. 191:1997-1999.
- Nyholm SV, Nishiguchi MK (2008) The evolutionary ecology of a sepiolid squid-Vibrio association: from cell to environment. Vie et Milieu 58: 175-184.
- Spencer V. Nyholm, Julie Robidart and Peter R. Girguis. 2008. Coupling metabolite flux to transcriptomics: insights into the molecular mechanisms underlying primary productivity by the hydrothermal vent tubeworm Ridgeia piscesae. Biol. Bull. 214: 255-265. Symbiosis
- Nyholm, S.V. and M. J. McFall-Ngai. 2004. The Winnowing: Establishing the Squid-Vibrio Symbiosis. Nature Rev. Microbiol. 2: 632-642.
- Nyholm, S. V. and M. J. McFall-Ngai. 2003. Dominance of Vibrio fischeri in secreted mucus outside the light organ of Euprymna scolopes: the first site of symbiont specificity. Appl. Environ. Microbiol. 69: 3932-7.
- Nyholm, S. V., B. Deplancke, H. R. Gaskins, M. A. Apicella, and M. J. McFall-Ngai. 2002. Roles of nonsymbiotic and symbiotic bacteria in the dynamics of mucus secretion during symbiont colonization of the Euprymna scolopes light organ. Appl. Environ. Microbiol. 68:5113-5122.
- Nyholm, S. V., E. V. Stabb, E. G. Ruby, and M. J. McFall-Ngai. 2000 Establishment of an animal-bacterial association: recruiting symbiotic vibrios from the environment. Proc. Nat. Acad. Sci., USA 97:10231-10235.
- Nyholm, S. V. and M. J. McFall-Ngai. 1998. Sampling the light-organ microenvironment of Euprymna scolopes: description of a population of host cells in association with the bacterial symbiont Vibrio fischeri. Biol. Bull. 195: 89-97.