Scholar Publications

Publication in peer-reviewed journals is an integral part of Tufts IRACDA training. Publications by our trainees over the past five years are listed below.


Davis KP, Morales Y, Ende RJ, Peters R, McCabe AL, Mecsas J, Aldridge BB.. 2024. Critical role of growth medium for detecting drug interactions in Gram-negative bacteria that model in vivo responses. mBio. 2024 Feb 16:e0015924. doi: 10.1128/mbio.00159-24. Abstract

Draganova EB, Wang H, Wu M, Liao S, Vu A, Gonzalez-Del Pino GL, Zhou ZH, Roller RJ, Heldwein EE. 2024. The universal suppressor mutation restores membrane budding defects in the HSV-1 nuclear egress complex by stabilizing the oligomeric lattice. PLoS Pathog. Jan 16;20(1):e1011936. doi: 10.1371/journal.ppat.1011936. Abstract


Blaney G, Fernandez C, Sassaroli A, Fantini S. 2023. Dual-slope imaging of cerebral hemodynamics with frequency-domain near-infrared spectroscopy. Neurophotonics. Jan;10(1):013508. doi: 10.1117/1.NPh.10.1.013508.  Abstract

Blaney G, Ivich F, Sassarolia A, Niedre M, Fantini S. 2023. Dual-ratio approach for detection of point fluorophores in biological tissue. J Biomed Opt. 2023 Jul;28(7):077001. Abstract

Foster O, Shaidani S, Theodossiou SK, Falcucci T, Hiscox D, Smiley BM, Romano C, Kaplan DL. 2023. Sudan Black B pretreatment to suppress autofluorescence in silk fibroin scaffolds. ACS Biomater Sci Eng. Jun 12;9(6):3193-3205. doi: 10.1021/acsbiomaterials.3c00145. Abstract

Gildawie KR, Wang K, Budge KE, Byrnes EM. 2023. Effects of maternal separation on effort-based responding for sucrose are associated with c-Fos expression in the nucleus accumbens core. Neuroscience. Nov 28:S0306-4522(23)00531-6. doi: 10.1016/j.neuroscience.2023.11.030.  Abstract

Kuehnemann C, Wiley CD. 2023. Senescent cells at the crossroads of aging, disease, and tissue homeostasis. Aging Cell. Sep 20:e13988. doi: 10.1111/acel.13988. Abstract

Kuehnemann C, Wiley CD. 2023. Cholesterol drives inflammatory senescence. Nat Metab. Mar 2. doi: 10.1038/s42255-023-00758-2. Abstract

Kuehnemann C, Hughes JB, Desprez PY, Melov S, Wiley CD, Campisi J. 2023. Antiretroviral protease inhibitors induce features of cellular senescence that are reversible upon drug removal. Aging Cell. Jan;22(1):e13750. doi: 10.1111/acel.13750. Abstract

Liaudanskaya V, Fiore NJ, Zhang Y, Milton Y, Kelly MF, Coe M, Barreiro A, Rose VK, Shapiro MR, Mullis AS, Shevzov-Zebrun A, Blurton-Jones M, Whalen MJ, Symes AJ, Georgakoudi I, Nieland TJF, Kaplan DL. 2023. Mitochondria dysregulation contributes to secondary neurodegeneration progression post-contusion injury in human 3D in vitro triculture brain tissue model. Cell Death Dis. 2023 Aug 3;14(8):496. doi: 10.1038/s41419-023-05980-0. Abstract

Mullis AS, Kaplan DL. 2023. Functional bioengineered tissue models of neurodegenerative diseases. Biomaterials. May 2;298:122143. doi: 10.1016/j.biomaterials.2023.122143. Abstract

Mullis AS, Broderick SR, Phadke KS, Peroutka-Bigus N, Bellaire BH, Rajan K, Narasimhan B. 2023. Data analytics-guided rational design of antimicrobial nanomedicines against opportunistic, resistant pathogens. Nanomedicine. Feb;48:102647. doi: 10.1016/j.nano.2022.102647. Abstract

Rennich BJ, Luth ES, Hofer J, Juo P. 2023. Low-Density Lipoprotein Receptor LRP-2 regulates GLR-1 glutamate receptors and glutamatergic behavior in C. elegans. MicroPubl Biol. Apr 26;2023:10.17912/micropub.biology.000837. doi: 10.17912/micropub.biology.000837. Abstract

Ribis JW, Melo L, Shrestha S, Giacalone D, Rodriguez EE, Shen A, Rohlfing A. 2023. Single-spore germination analyses reveal that calcium released during Clostridioides difficile germination functions in a feedforward loop. mSphere. Jun 20:e0000523. doi: 10.1128/msphere.00005-23. Abstract

Romo JA, Tomihiro M, Kumamoto CA.2023. Pre-colonization with the fungus Candida glabrata exacerbates infection by the bacterial pathogen Clostridioides difficile in a murine model. mSphere. Jun 26:e0012223. doi: 10.1128/msphere.00122-23. Abstract

Sanchez S, Ng WL. 2023. Motility control as a possible link between quorum sensing to surface attachment in Vibrio species. Adv Exp Med Biol. 1404:65-75. doi: 10.1007/978-3-031-22997-8_4. Abstract

Sassaroli A, Blaney G, Fantini S. 2023. Novel data types for frequency-domain diffuse optical spectroscopy and imaging of tissues: characterization of sensitivity and contrast-to-noise ratio for absorption perturbations. Biomed Opt Express. Apr 18;14(5):2091-2116. doi: 10.1364/BOE.485651. Abstract


Ayaz H, Baker WB, Blaney G, Boas DA, Bortfeld H, Brady K, Brake J, Brigadoi S, Buckley EM, Carp SA, Cooper RJ, Cowdrick KR, Culver JP, Dan I, Dehghani H, Devor A, Durduran T, Eggebrecht AT, Emberson LL, Fang Q, Fantini S, Franceschini MA, Fischer JB, Gervain J, Hirsch J, Hong KS, Horstmeyer R, Kainerstorfer JM, Ko TS, Licht DJ, Liebert A, Luke R, Lynch JM, Mesquida J, Mesquita RC, Naseer N, Novi SL, Orihuela-Espina F, O'Sullivan TD, Peterka DS, Pifferi A, Pollonini L, Sassaroli A, Sato JR, Scholkmann F, Spinelli L, Srinivasan VJ, St Lawrence K, Tachtsidis I, Tong Y, Torricelli A, Urner T, Wabnitz H, Wolf M, Wolf U, Xu S, Yang C, Yodh AG, Yücel MA, Zhou W. 2022.Optical imaging and spectroscopy for the study of the human brain: status report. Neurophotonics. Aug;9(Suppl 2):S24001. doi: 10.1117/1.NPh.9.S2.S24001. Abstract

Blaney G, Bottoni M, Sassaroli A, Fernandez C, Fantini S. 2022. Broadband diffuse optical spectroscopy of two-layered scattering media containing oxyhemoglobin, deoxyhemoglobin, water, and lipids. J Innov Opt Health Sci. May;15(3):2250020. doi: 10.1142/s1793545822500201. Abstract 

Gonzalez-Del Pino GL, Heldwein EE. 2022. Well put together-A guide to accessorizing with the herpesvirus gH/gL complexes. Viruses. Jan 30;14(2):296. doi: 10.3390/v14020296. Abstract

Johnson MA, Klickstein JA, Khanna R, Gou Y; Cure VCP Disease Research Consortium, Raman M. 2022. The Cure VCP Scientific Conference 2021: Molecular and clinical insights into neurodegeneration and myopathy linked to multisystem proteinopathy-1 (MSP-1). Neurobiol Dis. Apr 8:105722. doi: 10.1016/j.nbd.2022.105722.

Kuehnemann C, Hu KQ, Butera K, Patel SK, Bons J, Schilling B, Aguayo-Mazzucato C, Wiley CD. 2022. Extracellular nicotinamide phosphoribosyltransferase is a component of the senescence-associated secretory phenotype. Front Endocrinol. Jul 14;13:935106. doi: 10.3389/fendo.2022.935106. Abstract

Lamisere H, Bhalchandra S, Kane AV, Zeng XL, Mo D, Adams W, Estes MK, Ward HD. 2022. Differential response to the course of Cryptosporidium parvum infection and its impact on epithelial integrity in differentiated versus undifferentiated human intestinal enteroids. Infect Immun. Oct 26:e0039722. doi: 10.1128/iai.00397-22. Abstract

Martin SK, McVey M. 2022. BRCA1 protest against its own fragility. Mol Cell. Oct 20;82(20):3757-3759. doi: 10.1016/j.molcel.2022.09.023. Abstract

Mekdara PJ, Tirmizi S, Schwalbe MAB, Tytell ED. 2022. Comparison of aminoglycoside antibiotics and cobalt chloride for ablation of the lateral line system in giant danios. Integr Org Biol. Mar 21;4(1):obac012. doi: 10.1093/iob/obac012. Abstract

Mortensen JC, Damjanovic J, Miao J, Hui T, Lin YS. 2022. A backbone-dependent rotamer library with high (ϕ, ψ) coverage using metadynamics simulations. Protein Sci. Dec;31(12):e4491. doi: 10.1002/pro.4491. Abstract

Pereira MJ, Wager B, Garrigues RJ, Gerlach E, Quinn JD, Dowdell AS, Osburne MS, Zückert WR, Kraiczy P, Garcia BL, Leong JM. 2022. Lipoproteome screening of the Lyme disease agent identifies inhibitors of antibody-mediated complement killing. Proc Natl Acad Sci USA. Mar 29;119(13):e2117770119. doi: 10.1073/pnas.2117770119. Abstract

Porter EC, Stoppel WL, Kudej RK, Black LD 3rd. 2022. Right ventricular outflow tract surgical resection in young, large animal model for the study of alternative cardiovascular patches. Methods Mol Bio. 2485:299-309. doi: 10.1007/978-1-0716-2261-2_20. Abstract

Rojas-Rodriguez R, Price, LL, Somogie J, Hauguel-de Mouzon S, Kalhan SC, Catalano PM. 2-22. Maternal lipid metabolism is associated with neonatal adiposity: A longitudinal study. J Clin Endocrinol Metab. Aug 18;107(9):e3759-e3768.doi: 10.1210/clinem/dgac360. Abstract

Romo JA, Rokop ME. 2022. A novel undergraduate seminar course celebrating scientific contributions by scientists from historically marginalized communities. J Microbiol Biol Educ. Oct 31;23(3):e00123-22. doi: 10.1128/jmbe.00123-22. Abstract

Romo JA, Kumamoto CA. 2022. Characterization of the effects of Candida gastrointestinal colonization on Clostridioides difficile infection in a murine model. Methods Mol Biol. 2022;2542:271-285. doi: 10.1007/978-1-0716-2549-1_20. Abstract

Romo JA, Arsenault AB, Laforce-Nesbitt SS, Bliss JM, Kumamoto CA. 2022. Minimal effects of medium-chain triglyceride supplementation on the intestinal microbiome composition of premature infants: A single-center pilot study. Nutrients. 14(10):2159. doi: 10.3390/nu14102159. Abstract

Silveira IA, Mullis AS, Cairns DM, Shevzov-Zebrun A, Whalen J, Galuppo A, Walsh KG, Kaplan DL. 2022. Screening neuroprotective compounds in herpes-induced Alzheimer's disease cell and 3D tissue models. Free Radic Biol Med. 2022 Jun;186:76-92. doi: 10.1016/j.freeradbiomed.2022.05.002. Abstract

Thorsen MK, Draganova EB, Heldwein EE. 2022. The nuclear egress complex of Epstein-Barr virus buds membranes through an oligomerization-driven mechanism. PLoS Pathog. Jul 8;18(7):e1010623. doi: 10.1371/journal.ppat.1010623. Abstract

Watson MC, Williams C, Wang RM, Perreault LR, Sullivan KE, Stoppel WL, Black LD 3rd. 2022. Extracellular matrix and cyclic stretch alter fetal cardiomyocyte proliferation and maturation in a rodent model of heart hypoplasia. Front Cardiovasc Med. Nov 28;9:993310. doi: 10.3389/fcvm.2022.993310. Abstract<

Wickham RJ, Genné-Bacon EA, Jacob MH. 2021. The spine lab: A short-duration, fully-remote course-based undergraduate research experience. J Undergrad Neurosci Educ. 20(1):A28-A39. Abstract

Wu J, Shaidani S, Theodossiou SK, Hartzell EJ, Kaplan DL. 2022. Localized, on-demand, sustained drug delivery from biopolymer-based materials. Expert Opin Drug Deliv. Oct;19(10):1317-1335. doi: 10.1080/17425247.2022.2110582. Abstract

Ye X, Lee YC, Gates ZP, Ling Y, Mortensen JC, Yang FS, Lin YS, Pentelute BL. 2022. Binary combinatorial scanning reveals potent poly-alanine-substituted inhibitors of protein-protein interactions. Commun Chem. Oct 14;5(1):128. doi: 10.1038/s42004-022-00737-w. Abstract

Yuen JSK Jr, Stout AJ, Kawecki NS, Letcher SM, Theodossiou SK, Cohen JM, Barrick BM, Saad MK, Rubio NR, Pietropinto JA, DiCindio H, Zhang SW, Rowat AC, Kaplan DL. 2022. Perspectives on scaling production of adipose tissue for food applications. Biomaterials. Jan;280:121273. doi: 10.1016/j.biomaterials.2021.121273. Abstract


Antonoudiou P, Colmers PLW, Walton NL, Weiss GL, Smith AC, Nguyen DP, Lewis M, Quirk MC, Barros L, Melón LC, Maguire JL. 2021. Allopregnanolone mediates affective switching through modulation of oscillatory states in the basolateral amygdala. Biol Psychiatry. Jul 27:S0006-3223(21)01470-0. doi: 10.1016/j.biopsych.2021.07.017. Abstract

Draganova EB, Valentin J, Heldwein EE. 2021. The ins and outs of herpesviral capsids: Divergent structures and assembly mechanisms across the three subfamilies. Viruses. 13(10):1913. doi: 10.3390/v13101913. Abstract

Draganova EB, Thorsen MK, Heldwein EE. 2021. Nuclear egress. Curr Issues Mol Biol. 41: 125-170. Abstract

Draganova EB, Heldwein EE. 2021. Virus-derived peptide inhibitors of the herpes simplex virus type 1 nuclear egress complex. Sci Rep. 11(1):4206. doi: 10.1038/s41598-021-83402-x. Abstract

Etson CM, Todorov P, Shatery Nejad N, Shrestha N, Walt DR. 2021. Single-molecule dwell-time analysis of restriction endonuclease-mediated DNA cleavage. J Vis Exp. Feb 7;(168). doi: 10.3791/62112. Abstract

Hodul M, Rennich BJ, Luth ES, Dahlberg CL, Juo P. 2021. The WD40-repeat protein WDR-20 and the deubiquitinating enzyme USP-46 promote cell surface levels of glutamate receptors. J Neurosci. Feb 22:JN-RM-1074-20. doi: 10.1523/JNEUROSCI.1074-20.2021. Abstract

Kumamoto CA, Romo JA. 2021. Debaryomyces, the Achilles heel of wound repair. Cell Host Microbe. 29: 740-741. Abstract

Luth ES, Hodul M, Rennich BJ, Riccio C, Hofer J, Markoja K, Juo P. 2021. VER/VEGF receptors regulate AMPA receptor surface levels and glutamatergic behavior. PLoS Genet. 17(2):e1009375. doi: 10.1371/journal.pgen.1009375. Abstract

Park L, Luth ES, Jones K, Hofer J, Nguyen I, Watters KE, Juo P. 2021. The Snail transcription factor CES-1 regulates glutamatergic behavior in C. elegans. PLoS One 16(2):e0245587. doi: 10.1371/journal.pone.0245587. Abstract

Rodrigues CF, Romo JA. 2021. Fungal biofilms 2020. J Fungi 7: 603. Abstract


Adams W, Bhowmick R, Bou Ghanem EN, Wade K, Shchepetov M, Weiser JN, McCormick BA, Tweten RK, Leong JM. 2020. Pneumolysin induces 12-lipoxygenase-dependent neutrophil migration during Streptococcus pneumoniae infection. J Immunol.204: 101-111. Abstract

Cantu D, Croker D, Shacham S, Tamir S, Dulla C. 2020. In vivo KPT-350 treatment decreases cortical hyperexcitability following traumatic brain injury. Brain Inj. 27:1-8.  Abstract

Donnelly ML, Forster ER, Rohlfing AE, Shen A. 2020. Differential effects of "resurrecting" Csp pseudoproteases during Clostridioides difficile spore germination. Biochem J. pii: BCJ20190875. doi: 10.1042/BCJ20190875. Abstract

Draganova EB, Zhang J, Zhou ZH, Heldwein EE. 2020. Structural basis for capsid recruitment and coat formation during HSV-1 nuclear egress. Elife. 9: e56627. Abstract

Jackson FR, You S, Crowe LB. 2019. Regulation of rhythmic behaviors by astrocytes. Wiley Interdiscip Rev Dev Biol. Dec 15:e372. doi: 10.1002/wdev.372. Abstract

Kuperberg GR, Brothers T, Wlotko EW. 2020. A tale of two positivities and the N400: Distinct neural signatures are evoked by confirmed and violated predictions at different levels of representation. J Cogn Neurosci. 32: 12-35. Abstract

Donnelly ML, Forster ER, Rohlfing AE, Shen A. 2020. Differential effects of "resurrecting" Csp pseudoproteases during Clostridioides difficile spore germination. Biochem J. pii: BCJ20190875. doi: 10.1042/BCJ20190875. Abstract

Markey L, Hooper A, Melon LC, Baglot S, Hill MN, Maguire J, Kumamoto CA. 2020. Colonization with the commensal fungus Candida albicans perturbs the gut-brain axis through dysregulation of endocannabinoid signaling. Psychoneuroendocrinology 121: 104808. Abstract

Paczosa MK, Silver RJ, McCabe AL, Tai AK, McLeish CH, Lazinski DW, Mecsas J. 2020. Transposon mutagenesis screen of Klebsiella pneumoniae identifies multiple genes important for resisting antimicrobial activities of neutrophils in mice. 88: e00034-20. Abstract

Romo JA, Kumamoto CA. 2020. On commensalism of Candida. J Fungi. 6(1). pii: E16. doi: 10.3390/jof6010016. Abstract

Romo JA, Markey L, Kumamoto CA. 2020. Lipid species in the GI tract are increased by the commensal fungus Candida albicans and decrease the virulence of Clostridioides difficile. J Fungi pii: E100. doi: 10.3390/jof6030100.

Schwalbe MAB, Boden AL, Wise TN, Tytell ED. 2020. Red muscle activity in bluegill sunfish Lepomis macrochirus during forward accelerations. Sci Rep. 9(1):8088. doi: 10.1038/s41598-019-44409-7. Abstract


Ahmed S, Griffin TS, Kraner D, Schaffner MK, Sharma D, Hazel M, Leitch AR, Orians CM, Han W, Stepp JR, Robbat A, Matyas C, Long C, Xue D, Houser RF, Cash SB. 2019. Environmental factors variably impact tea secondary metabolites in the context of climate change. Front Plant Sci. 10:939. doi: 10.3389/fpls.2019.00939. Abstract

Bouillaut L, Dubois T, Francis MB, Daou N, Monot M, Sorg JA, Sonenshein AL, Dupuy B. 2019. Role of the Global Regulator Rex in Control of NAD+ -Regeneration in Clostridioides (Clostridium) difficile. Mol Microbiol. Epub ahead of print.  Abstract

Cassidy D, Epiney D, Salameh C, Zhou LT, Salomon RN, Schirmer AE, McVey M, Bolterstein E. 2019. Exp Gerontol. 10:110733. Abstract

Darnieder LM, Melón LC, Do T, Walton NL, Miczek KA, Maguire JL. 2019. Female-specific decreases in alcohol binge-like drinking resulting from GABAA receptor delta-subunit knockdown in the VTA. Sci Rep. 9: 8102. Abstract

Gross KM*, Zhou W*, Breindel JL, Ouyang J, Jin DX, Sokol ES, Gupta PB, Huber K, Zou L, Kuperwasser C. 2019. Loss of Slug compromises DNA damage repair and accelerates stem cell aging in mammary epithelium. Cell Rep. 28: 394-407. (equal contribution) Abstract

Huang H, Kfoury N, Orians CM, Griffin T, Ahmed S, Cash SB, Stepp JR, Xue D, Long C, Robbat A Jr. 2019. 2014-2016 seasonal rainfall effects on metals in tea (Camelia sinensis (L.) Kuntze). Chemosphere 219: 796-803. Abstract

Jackson FR, You S, Crowe LB. 2019. Regulation of rhythmic behaviors by astrocytes. Wiley Interdiscip Rev Dev Biol. Dec 15:e372. doi: 10.1002/wdev.372. Abstract

Koenig JB, Cantu D, Low C, Sommer M, Noubary F, Croker D, Whalen M, Kong D, Dulla CG. 2019. Glycolytic inhibitor 2-deoxyglucose prevents cortical hyperexcitability after traumatic brain injury. JCI Insight 5. pii: 126506. doi: 10.1172/jci.insight.126506. Abstract

Kfoury N, Scott ER, Orians CM, Ahmed S, Cash SB, Griffin T, Matyas C, Stepp JR, Han W, Xue D, Long C, Robbat A Jr. 2019. Plant-climate interaction effects: Changes in the relative distribution and concentration of the volatile tea leaf metabolome in 2014-2016. Front Plan Sci. 10:1518. doi: 10.3389/fpls.2019.01518. eCollection. Abstract

Li J, Stoppato M, Schiele NR, Graybeal KL, Nguyen PK, Kuo CK. 2019. Embryonic and postnatal tendon cells respond differently to interleukin-1β. Ann NY Acad Sci. 1442: 118-127. Abstract

López Barreiro D, Martín-Moldes Z, Yeo J, Shen S, Hawker MJ, Martin-Martinez FJ, Kaplan DL, Buehler MJ. 2019. Conductive silk-based composites using biobased carbon Materials. Adv Mater. 31(44):e1904720. doi: 10.1002/adma.201904720. Abstract

McKay TB, Parker RN, Hawker MJ, McGill M, Kaplan DL. 2019. Silk-based therapeutics targeting Pseudomonas aeruginosa. J Funct Biomater. 10(3). pii: E41. doi: 10.3390/jfb10030041. Abstract

Melón LC, Nasman JT, John AS, Mbonu K, Maguire JL. 2019. Interneuronal δ-GABAA receptors regulate binge drinking and are necessary for the behavioral effects of early withdrawal. Neuropsychopharmacology 44: 425-434. Abstract

Nguyen GT, McCabe AL, Fasciano AC, Mecsas J. 2019. Detection of cells translocated with Yersinia Yops in infected tissues using β-lactamase fusions. Methods Mol Biol. 2010: 117-139. Abstract

Rohlfing AE, Eckenroth BE, Forster ER, Kevorkian Y, Donnelly ML, Benito de la Puebla H, Doublié S, Shen A. 2019. The CspC pseudoprotease regulates germination of Clostridioides difficile spores in response to multiple environmental signals. PLoS Genet. 15: e1008224. Abstract

Schwalbe MAB, Boden AL, Wise TN, Tytell ED. 2019. Red muscle activity in bluegill sunfish Lepomis macrochirus during forward accelerations. Sci Rep. 9(1):8088. doi: 10.1038/s41598-019-44409-7. Abstract

Silver RJ, Paczosa MK, McCabe AL, Balada-Llasat JM, Baleja JD, Mecsas J. 2019. Amino acid biosynthetic pathways are required for Klebsiella pneumoniae growth in immunocompromised lungs and are druggable targets during infection. Antimicrob Agents Chemother. 63: e02674-18. Abstract

Stewart D, Romo JA, Lamendella R, Kumamoto CA. 2019. The role of fungi in C. difficile infection: An underappreciated transkingdom interaction. Fungal Genet Biol. 129: 1-6. Abstract

Sengupta S, Crowe LB, You S, Roberts MA, Jackson FR. 2019. A secreted Ig-domain protein required in both astrocytes and neurons for regulation of Drosophila night sleep. Curr Biol. 29(15):2547-2554.e2. doi: 10.1016/j.cub.2019.06.055. Abstract

Wickham RJ, Alexander JM, Eden LW, Valencia-Yang M, Llamas J, Aubrey JR, Jacob MH. 2019. Learning impairments and molecular changes in the brain caused by β-catenin loss. Hum Mol Genet. 28: 2965-2975. doi: 10.1093/hmg/ddz115.  Abstract