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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.


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

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

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 ppecies 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.


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

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

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. Epub ahead of print. 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. Epub ahead of print.  Abstract


Arsenault AB, Gunsalus KTW, Laforce-Nesbitt SS, Przystac L, DeAngelis EJ, Hurley ME, Vorel ES, Tucker R, Matthan NR, Lichtenstein AH, Kumamoto CA, Bliss JM. 2018. Dietary supplementation with medium-chain triglycerides reduces Candida gastrointestinal colonization in preterm infants. Pediatr Infect Dis. Epub ahead of print. Abstract

Kfoury N, Morimoto J, Kern A, Scott ER, Orians CM, Ahmed S, Griffin T, Cash SB, Stepp JR, Xue D, Long C, Robbat A Jr. 2018. Striking changes in tea metabolites due to elevational effects. Food Chem. 264: 334-341. Abstract

Koch MR, House NCM, Cosetta CM, Jong RM, Salomon CG, Joyce CE, Philips EA, Su XA, Freudenreich CH. 2018. The chromatin remodeler Isw1 prevents CAG repeat expansions during transcription in Saccharomyces cerevisiae. Genetics Epub ahead of print. Abstract

Mekdara PJ, Schwalbe MAB, Coughlin LL, Tytell ED. 2018. The effects of lateral line ablation and regeneration in schooling giant danios. J Exp Biol. 221(Pt 8). pii: jeb175166. doi: 10.1242/jeb.175166. Abstract

Melón L, Hammond R, Lewis M, Maguire J. 2018. A Novel, synthetic, neuroactive steroid is effective at decreasing depression-like behaviors and improving maternal care in preclinical models of postpartum depression. Front Endocrinol. 9: 703. Abstract

Melón LC, Nasman JT, John AS, Mbonu K, Maguire JL. 2018. Interneuronal δ-GABAA receptors regulate binge drinking and are necessary for the behavioral effects of early withdrawal. Neuropsychopharmacology Epub ahead of print. Abstract

Pirone A, Alexander JM, Koenig JB, Cook-Snyder DR, Palnati M, Wickham RJ, Eden L, Shrestha N, Reijmers L, Biederer T, Miczek KA, Dulla CG, Jacob MH. 2018. Social stimulus causes aberrant activation of the medial prefrontal cortex in a mouse model with autism-like behaviors. Fron Synaptic Neurosci. Epub ahead of print.  Abstract

Whalen C, Tuohy C, Tallo T, Kaufman JW, Moore C, Kuehner JN. 2018. RNA Polymerase II transcription attenuation at the yeast DNA repair gene, DEF1, involves Sen1-dependent and polyadenylation site-dependent termination. G3 8: 2043-2058. Abstract

Wise TN, Schwalbe MAB, Tytell ED. 2018. Hydrodynamics of linear acceleration in bluegill sunfish, Lepomis macrochirus. J Exp Biol. 221(Pt 23). pii: jeb190892. doi: 10.1242/jeb.190892. Abstract


Breindel JL, Skibinski A, Sedic M, Wronski-Campos A, Zhou W, Keller PJ, Mills J, Bradner J, Onder T, Kuperwasser C. 2017. Epigenetic reprogramming of lineage-committed human mammary epithelial cells requires DNMT3A and loss of DOT1L. Stem Cell Reports. Epub ahead of print.  Abstract

Kuehner JN, Kaufman JW, Moore C. 2017. Stimulation of RNA Polymerase II ubiquitination and degradation by yeast mRNA 3'-end processing factors is a conserved DNA damage response in eukaryotes. DNA Repair 57:151-160. Abstract

Heggeness ML, Gunsalus KT, Pacas J, McDowell G. 2017. The new face of US science. Science 541: 21-23. Abstract

Hodul M, Dahlberg CL, Juo P. 2017. Function of the deubiquitinating enzyme USP46 in the nervous system and its regulation by WD40-repeat proteins. Front Synaptic Neurosci. 9:16. Abstract

Killpack TL, Ballesteros M, Bunnell SC, Bedugnis A, Kobzik L, Hu LT, Petnicki-Ocwieja T. 2017. Phagocytic receptors activate Syk and Src signaling during Borrelia burgdorferi phagocytosis. Infec Immun Epub ahead of print.  Abstract

Kim JC, Harris ST, Dinter T, Shah KA, Mirkin SM. 2017. The role of break-induced replication in large-scale expansions of (CAG)n/(CTG)n repeats. Nat Struct Mol Biol. 24: 55-60.  Abstract

Melón LC, Hooper A, Yang X, Moss SJ, Maguire J. 2017. Inability to suppress the stress-induced activation of the HPA axis during the peripartum period engenders deficits in postpartum behaviors in mice. Psychoneuroendocrinology Epub ahead of print. Abstract

Neil AJ, Kim JC, Mirkin SM. 2017. Precarious maintenance of simple DNA repeats in eukaryotes. Bioessasy Epub ahead of print. Abstract

Regan H, Scaduto C, Hirakawa MP, Gunsalus K, Correia-Mesquita TO, Sun Y, Chen Y, Kumamoto CA, Bennett R, Whiteway M. 2017. Negative regulation of filamentous growth in Candida albicans by Dig1p. Mol Microbiol. Epub ahead of print. Abstract

Smith EE, Zhang W, Schiele NR, Khademhosseini A, Kuo CK, Yelick PC. 2017. Developing a biomimetic tooth bud model. J Tissue Eng Regen Med. Epub ahead of print. Abstract

Tsutakawa SE, Thompson MJ, Arvai AS, Neil AJ, Shaw SJ, Algasaier SI, Kim JC, Finger LD, Jardine E, Gotham VJB, Sarker AH, Her MZ, Rashid F, Hamdan SM, Mirkin SM, Grasby JA, Tainer JA. 2017. Nat Comm. 8: 15855. Abstract

Yang X, Hartman MR, Harrington KT, Etson CM, Fierman MB, Slonim DK, Walt DR. 2017. Using next-generation sequencing to explore genetics and race in the high school classroom. CBE Lif Sic Educ. 16: pii: ar22. doi: 10.1187/cbe.16-09-0281.  Abstract


Blair L, Labitigan R, Liu Z, Zheng D, Pearson E, Nazeer F, Cao J, Rines R, Mackintosh S, Moore C, Li W, Tian B, Tackett A, Yan Q. 2016. KDM5 lysine demethylases are involved in maintenance of 3’ UTR length. Science Advances 2:e1501662. Abstract

Byrnes JJ, Gleason ED, Schoen MK, Lovelock DF, Carini LM, Byrnes EM, Bridges RS. 2016. Corrigendum to "Accelerated maternal responding following intra-VTA pertussis toxin treatment." Behav Brain Res. 303: 238. Abstract

Melón LC, Maguire J. 2016. GABAergic regulation of the HPA and HPG axes and the impact of stress on reproductive function. J Steroid Biochem Mol Biol. 160: 196-203. Abstract

Gunsalus KT, Kumamoto CA. 2016. Transcriptional profiling of Candida albicans in the host. Methods Mol Biol. 1356:17-29.   Abstract

Hartman MR, Harrington KT, Etson CM, Fierman MB, Slonim DK, Walt DR. 2016. Personal microbiomes and next-generation sequencing for laboratory-based education. FEMS Microbiol Lett. Epub ahead of print.   Abstract

Killpack TL, Melón LC. 2016. Toward inclusive STEM classrooms: What personal role do faculty play? CBE Life Sci Educ. Fall 15 (3).  Abstract

Kim JC, Harris ST, Dinter T, Shah KA, Mirkin SM. 2016. The role of break-induced replication in large-scale expansions of (CAG)n/(CTG)n repeats. Nat Struct Mol Biol. Epub ahead of print.  Abstract

MacKenzie G, O'Toole KK, Maguire J. 2016. Compromised GABAergic inhibition contributes to tumor-associated epilepsy. Epilespy Res 126:185-196. Abstract

Marturano JE, Schiele NR, Schiller ZA, Galassi TV, Stoppato M, Kuo CK. 2016. Embryonically inspired scaffolds regulate tenogenically differentiating cells. J Biomech. 49: 3281-3288.  Abstract

Moss BJ, Park L, Dahlberg CL, Juo P. 2016. The CaM kinase CMK-1 mediates a negative feedback mechanism coupling the C. elegans glutamate receptor GLR-1 with its own transcription. PLoS Genet. 12: e1006180. Abstract

Ng FS, Sengupta S, Huang Y, Yu AM, You S, Roberts MA, Iyer LK, Yang Y, Jackson FR. 2016. TRAP-seq profiling and RNAi-based genetic screens identify conserved glial genes required for adult Drosophila behavior. Front Mol Neurosci. 9: 146.  Abstract

Stoppel WL, Gao AE, Greaney AM, Partlow BP, Bretherton RC, Kaplan DL, Black LD 3rd. 2016. Elastic, silk-cardiac extracellular matrix hydrogels exhibit time-dependent stiffening that modulates cardiac fibroblast response. J Biomed Mater Res A 104: 3058-3072.  Abstract

Stoppel WL, Kaplan DL, Black LD 3rd. 2016. Electrical and mechanical stimulation of cardiac cells and tissue constructs. Adv Drug Deliv Rev. 96: 135-155.   Abstract


Brown JP, Galassi TV, Stoppato M, Schiele NR, Kuo CK 2015. Comparative analysis of mesenchymal stem cell and embryonic tendon progenitor cell response to embryonic tendon biochemical and mechanical factors. Stem Cell Res Ther. 6: 89. Abstract

Bouillaut L, McBride S, Sorg JA, Schmidt DJ, Suarez JM, Tzipori S, Mascio C, Chesnel L, Sonenshein AL. 2015. Effects of surotomycin on Clostridium difficile viability and tPLosoxin production in vitro. Antimicrob Agents Chemother. 59: 4199-4205. Abstract

Cantu D, Walker K, Andresen L, Taylor-Weiner A, Hampton D, Tesco G, Dulla CG. 2015. Traumatic brain injury increases cortical glutamate network activity by compromising GABAergic control. Cereb Cortex 25: 2306-2320. Abstract

Cook-Snyder DR, Jones A, Reijmers LG. 2015. A retrograde adeno-associated virus for collecting ribosome-bound mRNA from anatomically defined projection neurons. Front Mol Neurosci. 8: 56. Abstract

Garafalo SD, Luth ES, Moss BJ, Monteiro MI, Malkin E, Juo P. 2015. The AP2 clathrin adaptor protein complex regulates the abundance of GLR-1 glutamate receptors in the ventral nerve cord of C. elegans. Mol Biol Cell. 26: 1887-1900. Abstract

Gunsalus KT, Tornberg-Belanger SN, Matthan NR, Lichtenstein AH, Kumamoto CA.. 2015. Manipulation of host diet to reduce gastrointestinal colonization by the opportunistic pathogen Candida albicans. mSphere 1: pii: e00020-15.  Abstract

Hanson E, Armbruster M, Cantu D, Andresen L, Taylor A, Danbolt NC, Dulla CG. 2015. Astrocytic glutamate uptake is slow and does not limit neuronal NMDA receptor activation in the neonatal neocortex. Glia 63: 1784-1796. Abstract

Kim JC, Mirkin SM. 2015. Putting the brakes on Huntington Disease in a mouse experimental model. PLoS Genet. 11: e1005409. Abstract

Kwon H, Rainbow RS, Sun L, Hui CK, Cairns DM, Preda RC, Kaplan DL, Zeng L. 2015. Scaffold structure and fabrication method affect pro-inflammatory milieu in 3D-cultured chondrocytes. J Biomed Mater Res A 103: 534-544. Abstract

Leahy AA, Esfahani SA, Foote AT, Hui CK, Rainbow RS, Nakamura DS, Tracey BH, Mahmood U, Zeng L. 2015. Following the trajectory of osteoarthritis development through serial near infrared fluorescence imaging of MMP activities. Arthritis Rheumatol. 67: 443-453. Abstract

Li C, Luo T, Zheng Z, Murphy AR, Wang X, Kaplan DL. 2015. Curcumin-functionalized silk materials for enhancing adipogenic differentiation of bone marrow-derived human mesenchymal stem cells. Acta Biomater. 11: 222-232. Abstract

McGehee AM, Moss BJ, Juo P. 2015. The DAF-7/TGF-β signaling pathway regulates abundance of the Caenorhabditis elegans glutamate receptor GLR-1. Mol Cell Neurosci. 67: 66-74. Abstract

Petnicki-Ocwieja T, Kern A, Killpack TL, Bunnell SC, Hu LT. 2015. Adaptor protein-3-mediated trafficking of TLR2 ligands controls specificity of inflammatory responses but not adaptor complex assembly. J Immunol. 195: 4331-4340. Abstract

Schiele NR, von Flotow F, Tochka ZL, Hockaday LA, Marturano JE, Thibodeau JJ, Kuo CK. 2015. Actin cytoskeleton contributes to the elastic modulus of embryonic tendon during early development. J Orthop Res. 33: 874-881. Abstract

Shainheit MG, Valentino MD, Gilmore MS, Camilli A. 2015. Mutations in pneumococcal cpsE generated via in vitro serial passaging reveals a potential mechanism of reduced encapsulation utilized by a conjunctival isolate. J Bacteriol. 197: 1781-1791. Abstract

Stoppel WL, Hu D, Domian IJ, Kaplan DL, Black LD. 2015. Anisotropic silk biomaterials containing cardiac extracellular matrix for cardiac tissue engineering. Biomed Mater. 10: 034105. Abstract

Stoppel WL, Ghezzi CE, McNamara SL, Black III LD, Kaplan DL. 2015. Clinical applications of naturally derived biopolymer-based scaffolds for regenerative medicine. Ann Biomed Eng. 43: 657-680. Abstract

Williams C, Budina E, Stoppel WL, Sullivan KE, Emani S, Emani SM, Black LD 3rd. 2015. Cardiac extracellular matrix-fibrin hybrid scaffolds with tunable properties for cardiovascular tissue engineering. Acta Biomater. 14: 84-89. Abstract