With undergraduate co-authors
  • Undergraduate students are shown in bold.

  • Notre Dame Biological Sciences faculty are hyperlinked.


Mason JA, Cockfield JA, Pape DJ, Meissner H, Sokolowski MT, White TC, Valentín López JC, Liu J, Liu X, Martínez-Reyes I, Chandel NS, Locasale JW, Schafer ZT. SGK1 signaling promotes glucose metabolism and survival in extracellular matrix detached cells. Cell Rep. 2021 Mar 16;34(11):108821. 

Tsegaye MA, He J, McGeehan K, Murphy IM, Nemera M, Schafer ZT. Oncogenic signaling inhibits c-FLIP expression and promotes cancer cell survival during ECM-detachment. Sci Rep. 2021 1118606 (2021).

Rocha, A.V., R. Appel, M.S. Bret-Harte, E. Euskirchen, V. Salmon, and G. Shaver. (2021) Solar position confounds the relationship between ecosystem function and vegetation indices derived from solar and photosynthetically active radiation fluxes. Agricultural and Forest Meteorology. 298-299.

M Poterek, MUG Kraemer, A Watts, K Khan, TA Perkins. Air passenger travel and international surveillance data predict spatiotemporal variation in measles importations to the United States. 2021. Pathogens 10:155.

GM Bron, K Strimbu, H Cecilia, A Lerch, SM Moore, Q Tran, TA Perkins, QA ten Bosch. Over 100 years of Rift Valley fever: a patchwork of data on pathogen spread and spillover. 2021. Pathogens 10:708.

Justin JS Wilcox, John J Lopez-Cotto, Hope Hollocher. Historical contingency, geography and anthropogenic patterns of exposure drive the evolution of host switching in the Blastocystis species-complex. 2021/7, Parasitology, Volume 148, Issue 8, Pages 985-993.

Campbell, L.J., Hobgood, J.S., Jia, M., Boyd, P., Hipp, R.I., and Hyde, D.R. (2021). Notch3 and DeltaB maintain Müller glia quiescence and act as negative regulators of regeneration in the light-damaged zebrafish retina. Glia. 69: 546-566. doi: 10.1002/glia.23912

Lahne, M., Brecker, M., Jones, S.E., and Hyde, D.R. (2021). The regenerating adult zebrafish retina recapitulates developmental fate specification programs. Front. Cell Dev. Biol. doi:10.3389/fcell.2020.617923

Hentig, J., Cloghessy, K., Dunseath, C., and Hyde, D.R. (2021). A scalable model to study the effects of blunt-force injury in adult zebrafish. J. Vis. Exp. (171), e62709, doi:10.3791/62709

Hentig, J., Cloghessy, K., Lahne, M., Jung, Y.J., Petersen, R.A., Morris, A.C., and Hyde, D.R. (2021). Zebrafish blunt‐force TBI induces heterogenous injury pathologies that mimic human TBI and responds with Sonic hedgehog‐dependent cell proliferation across the neuroaxis. Biomedicines 9 (861): biomedicines9080861

Campbell, L.J., Levendusky, J.L., Steines, S.A., and Hyde, D.R. (2021). Retinal regeneration requires dynamic Notch signaling. Neural Regen. Res. in press.

Hao Y, Peng X, Baldwin H, Zhang C, Liu Z, Lu X. Anti-androgen therapy induces transcriptomic reprogramming in metastatic castration-resistant prostate cancer in a murine model. Biochim Biophys Acta Mol Basis Dis. 2021 Jul 1;1867(7):166151.

Zhu Y, Wen J, Huang G, Mittlesteadt J, Wen X, Lu X. CHD1 and SPOP synergistically protect prostate epithelial cells from DNA damage. Prostate. 2021 Jan;81(1):81-88.

Lopez L, Koepfli C. Systematic review of Plasmodium falciparum and Plasmodium vivax polyclonal infections: Impact of prevalence, study population characteristics, and laboratory procedures.
PLoS One. 2021 Jun 11;16(6):e0249382. doi: 10.1371/journal.pone.0249382. eCollection 2021.
PMID: 34115783

Houssein, F.A., K.E. O'Reilly, B.W. Peters, M.A. Brueseke, and G.A. Lamberti. 2021. Nesting bald eagle diet observed using a novel photographic imaging technique. American Midland Naturalist 186:122-135

Bosio, S.F., P.D. Shirey, S.A. Entrekin, T.J. Hoellein, A.H. Moerke, E.J. Rosi, J.L. Tank, and G.A. Lamberti. 2021. Dynamics of large wood added to midwestern USA streams. River Research and Applications 37:843-857



Guldner IH, Wang Q, Yang L, Golomb SM, Zhao A, Lopez JA, Brunory A, Howe EN, Zhang Y, Palakurthi B, Barron M, Gao H, Xuei X, Liu Y, Li J, Chen DZ, Landreth GE, Zhang S. CNS-Native Myeloid Cells Drive Immune Suppression in the Brain Metastatic Niche through Cxcl10. Cell 2020 Nov 25;183(5):1234-1248.e25. doi: 10.1016/j.cell.2020.09.064.

MK Walters, TA Perkins. 2020. Hidden heterogeneity and its influence on dengue vaccination impact. Infectious Disease Modelling 5:783.

BL Bertolet, CR Olson, DK Szydlowski, CT Solomon, SE Jones. 2020. Methane and Primary Productivity in Lakes: Divergence of Temporal and Spatial Relationships. Journal of Geophysical Research: Biogeosciences 125 (9), e2020JG005864

Cheng, Y. Kiene, N. Tatarian A., Eix, E. and Schorey, J.S. (2020) Host Cytosolic RNA Sensing Pathway Promotes T Lymphocyte-mediated Mycobacterial Killing in Macrophages. PLoS Pathogens. May 28;16(5):e1008569.

Montanez-Gonzalez R, Pichler V, Calzetta M, Love RR, Vallera A, Schaecher L, Caputo B, Pombi M, Petrarca V, della Torre A, Besansky NJ (2020) Highly specific PCR-RFLP assays for karyotyping the widespread 2Rb inversion in malaria vectors of the Anopheles gambiae complex. Parasites & Vectors 13: 16.

Boomgarden, A. C., Sheehan, C., D'Souza-Schorey C. (2020). Extracellular Vesicles in the Tumor Microenvironment: Various Implications in Tumor Progression. Advances in Experimental Medicine and Biology, 1259, 155-170.

Howe EN, Burnette MD, Justice ME, Clancy JW, Guldner IH, Schnepp PM, Hendrick V, Aryal UK, Specht AT, Li J, D’Souza-Schorey C., Zartman JZ, and Zhang S. Rab11b-mediated integrin recycling promotes brain metastatic adaptation and outgrowth. Nat Commun. 2020 Jun 15;11(1):3017.

Huang T, Cheng X, Chahoud J, Sarhan A, Tamboli P, Rao P, Guo M, Manyam G, Zhang L, Xiang Y, Han L, Shang X, Deng P, Luo Y, Lu X, Feng S, Ferrer MM, Alan Wang Y, DePinho RA, Pettaway CA, Lu X. Effective combinatorial immunotherapy for penile squamous cell carcinoma. Nat Commun. 2020 May 1;11(1):2124.

Zhang Y, Wilt E, Lu X. Human Isogenic Cell Line Models for Neutrophils and Myeloid-Derived Suppressor Cells. Int J Mol Sci. 2020 Oct 18;21(20).

Luo Y, Medina Bengtsson L, Wang X, Huang T, Liu G, Murphy S, Wang C, Koren J 3rd, Schafer Z, Lu X. UQCRH downregulation promotes Warburg effect in renal cell carcinoma cells. Sci Rep. 2020 Sep 14;10(1):15021.

Hermann, N.T., D.T. Chaloner, B.S. Gerig, and G.A. Lamberti. 2020. Ecological consequences of Great Lakes salmon subsidies for stream-resident brook and brown trout. Canadian Journal of Fisheries and Aquatic Sciences 77:1758-1771

Currier, C.M., D.T. Chaloner, J. Rüegg, S.D. Tiegs, D. D’Amore, and G.A. Lamberti. 2020. Beyond nitrogen and phosphorus subsidies: Pacific salmon (Oncorhynchus spp.) as potential vectors of micronutrients. Aquatic Sciences 82:50



JA Hart, C Vizza, WE West, D.T. Chaloner, SE Jones, GA Lamberti. 2019. Methane Cycling Contributes to Distinct Patterns in Carbon Stable Isotopes of Wetland Detritus. Wetlands 39 (2), 361-370

G España, Y Yao, KB Anderson, MC Fitzpatrick, DL Smith, AC Morrison, A Wilder-Smith, TW Scott, TA Perkins. Model-based assessment of public health impact and cost-effectiveness of dengue vaccination following screening for prior exposure. 2019. PLOS Neglected Tropical Diseases 13:e0007482.

Wilcox, JS, Kerschner, A, Hollocher, H. Indel-informed Bayesian analysis suggests cryptic population structure between Plasmodium knowlesi of humans and long-tailed macaques (Macaca fascicularis) in Malaysian Borneo Infection Genetics and Evolution, Volume75, Article Number103994, DOI10.1016/j.meegid.2019.103994, Published NOV 2019.

Clancy JW, Zhang Y, Sheehan C, D'Souza-Schorey C. (2019) An ARF6-Exportin-5 axis delivers pre-miRNA cargo to tumour microvesicles. Nat Cell Biol. 21(7):856-866. doi: 10.1038/s41556-019-0345-y.

Sheehan C and D’Souza-Schorey C. (2019) Tumor-derived extracellular vesicles: molecular parcels that enable regulation of the immune response. J. Cell. Sci. 132(20). pii:

Clancy J., Tricarico C.J, Marous DR, D'Souza-Schorey C. (2019) Coordinated Regulation of Intracellular Fascin Distribution Governs Tumor Microvesicle Release and Invasive Cell Capacity. Mol Cell Biol. 39(3). pii: e00264-18. doi: 10.1128/MCB.00264-18

Wang Q, Guldner IH, Golomb SM, Sun L, Harris J, Lu X, Zhang S. Single-cell profiling guided combinatorial immunotherapy for fast-evolving CDK4/6 inhibitor resistant HER2-positive breast cancer. Nat Commun. 2019 Aug 23;10(1):3817. doi: 10.1038/s41467-019-11729-1.

Ni Y, Schmidt KR, Werner BA, Koenig JK, Guldner IH, Schnepp PM, Tan X, Jiang L, Host M, Sun L, Howe EN, Wu J, Littlepage LE, Nakshatri H, Zhang S. Death effector domain-containing protein induces vulnerability to cell cycle inhibition in triple-negative breast cancer. Nat Commun. 2019 Jun 28;10(1):2860. doi: 10.1038/s41467-019-10743-7.

Hart, J.A., C. Vizza, W.E. West, D.T. Chaloner, S.E. Jones, and G.A. Lamberti. 2019. Methane cycling contributes to distinct patterns in carbon stable isotopes of wetland detritus. Wetlands 39:361–370

Gerig, B.S., N.T. Hermann, D.T. Chaloner, and G.A. Lamberti. 2019. Using a dynamic bioenergetics-bioaccumulation model to understand mechanisms of uptake and bioaccumulation of salmon-derived contaminants by stream resident fish. Science of the Total Environment 652:633-642



JA Zwart, ZJ Hanson, J Vanderwall, D Bolster, A Hamlet, SE Jones. 2018. Spatially explicit, regional‐scale simulation of lake carbon fluxes.
Global Biogeochemical Cycles 32 (9), 1276-1293

ZJ Hanson, JA Zwart, J Vanderwall, CT Solomon, SE Jones, AF Hamlet, D Bolster. 2018. Integrated, regional‐scale hydrologic modeling of inland lakes.
JAWRA Journal of the American Water Resources Association 54 (6), 1302-1324

Clancy J., Sheehan C., Tricarico C., D’Souza-Schorey C. (2018) Aberrant endocytosis leads to the loss of normal mitotic spindle orientation during epithelial glandular morphogenesis. J. Biol. Chem. jbc.RA117.001640. doi: 10.1074/jbc.RA117.001640.

Lahne, M., Piekos, S.M., O’Neill, J., Ackerman, K.M., and Hyde, D.R. (2018). Photo-regulation of rod precursor cell proliferation. Exp. Eye Res. 178: 148-159

Habig, B., Doellman, M.M., Woods, K., Olansen, J., Archie, E.A. (2018). Social status and parasitism in male and female vertebrates: a meta-analysis. Sci Rep. 8: 3629

Feng S, Cheng X, Zhang L, Lu X, Chaudhary S, Teng R, Frederickson C, Champion MM, Zhao R, Cheng L, Gong Y, Deng H, Lu X. Myeloid-derived suppressor cells inhibit T cell activation through nitrating LCK in mouse cancers. Proc Natl Acad Sci U S A. 2018 Oct 2;115(40):10094-10099.

Gerig, B.S., D.N. Weber, D.T. Chaloner, L.M. McGill, and G.A. Lamberti. 2018. Interactive effects of introduced Pacific salmon and brown trout on native brook trout: an experimental and modeling approach. Canadian Journal of Fisheries and Aquatic Sciences 75: 538-548.

Hawk MA, Gorsuch CL, Fagan P, Lee C, Kim SE, Hamann JC, Mason JA, Weigel KJ, Tsegaye MA, Shen L, Shuff S, Zuo J, Hu S, Jiang L, Chapman S, Leevy WM, DeBerardinis RJ, Overholtzer M, Schafer ZT.
RIPK1-mediated induction of mitophagy compromises the viability of extracellular-matrix-detached cells. Nat Cell Biol. 2018 Mar;20(3):272-284. doi: 10.1038/s41556-018-0034-2.


2017 and earlier

JP Ziegler, EJ Golebie, SE Jones, BC Weidel, CT Solomon. 2017. Social‐ecological outcomes in recreational fisheries: the interaction of lakeshore development and stocking.
Ecological Applications 27 (1), 56-65

C Vizza, WE West, SE Jones, JA Hart, GA Lamberti. 2017.Regulators of coastal wetland methane production and responses to simulated global change.
Biogeosciences 14 (2), 431-446

BC Weidel, K Baglini, SE Jones, PT Kelly, CT Solomon, JA Zwart. 2017. Light climate and dissolved organic carbon concentration influence species-specific changes in fish zooplanktivory.
Inland Waters 7 (2), 210-217

AS Siraj, RJ Oidtman, JH Huber, MUG Kraemer, OJ Brady, MA Johansson, TA Perkins. Temperature modulates dengue virus epidemic growth rates through its effects on reproduction numbers and generation intervals. 2017. PLOS Neglected Tropical Diseases 11:e0005797.

Klegarth AR, Sanders SA, Gloss AD, Lane-deGraaf KE, Jones-Engel L, Fuentes A, Hollocher H.
Investigating biogeographic boundaries of the Sunda shelf: A phylogenetic analysis of two island populations of Macaca fascicularis. American Journal of Physical Anthropology. Volume163, Issue4, Page658-670, DOI10.1002/ajpa.23235, PublishedAUG 2017

Tricarico C., Clancy J., D'Souza-Schorey C. (2017) Biology and Biogenesis of Shed Microvesicles. Small GTPases, 8(4):220-232.

Gorsuch, R.A. Lahne, M., Yarka, C.E., Petravik, M.E., Li, J., and Hyde. D.R. (2017). Sox2 regulates Müller glia reprogramming and proliferation in the regenerating zebrafish retina via Lin28 and Ascl1a. Exp. Eye Res. 161: 174-192.

McGill, L.M., B.S. Gerig, D.T. Chaloner, and G.A. Lamberti. 2017. An ecosystem model for evaluating the effects of introduced Pacific salmon on contaminant burdens of stream-resident fish. Ecological Modelling 355: 39-48.

Mason JA, Hagel KR, Hawk MA, Schafer ZT. Metabolism during ECM Detachment: Achilles Heel of Cancer Cells? Trends Cancer. 2017 Jul;3(7):475-481. doi: 10.1016/j.trecan.2017.04.009.

Mason JA, Davison-Versagli CA, Leliaert AK, Pape DJ, McCallister C, Zuo J, Durbin SM, Buchheit CL, Zhang SSchafer ZT. Oncogenic Ras differentially regulates metabolism and anoikis in extracellular matrix-detached cells. Cell Death Differ. 2016 Aug;23(8):1271-82. doi: 10.1038/cdd.2016.15.

Phytoplankton lipid content influences freshwater lake methanogenesis
WE West, SM McCarthy, SE Jones
Freshwater Biology 60 (11), 2261-2269. 2015

Clancy J.W., Tricarico C.J., D'Souza-Schorey C. (2015) Tumor-derived microvesicles in the tumor microenvironment: How vesicle heterogeneity can shape the future of a rapidly expanding field. Bioessays. 37(12): 1309-16.

Sedgwick A., Clancy J.W., Balmert M., D'Souza-Schorey C. (2015). Extracellular microvesicles and invadopodia mediate non-overlapping modes of tumor cell invasion. Sci Rep 5:14748. doi: 10.1038/srep14748.