Publications
Eddens T, Parks OB, Williams JV. Neonatal Immune Responses to Respiratory Viruses. Front Immunol. 2022 Apr 14;13:863149. doi: 10.3389/fimmu.2022.863149. PMID: 35493465; PMCID: PMC9047724.
Lin X, Gaudino SJ, Jang KK, Bahadur T, Singh A, Banerjee A, Beaupre M, Chu T, Wong HT, Kim CK, Kempen C, Axelrad J, Huang H, Khalid S, Shah V, Eskiocak O, Parks OB, Berisha A, McAleer JP, Good M, Hoshino M, Blumberg R, Bialkowska AB, Gaffen SL, Kolls JK, Yang VW, Beyaz S, Cadwell K, Kumar P. IL-17RA-signaling in Lgr5+ intestinal stem cells induces expression of transcription factor ATOH1 to promote secretory cell lineage commitment. Immunity. 2022 Feb 8;55(2):237-253.e8. doi: 10.1016/j.immuni.2021.12.016. Epub 2022 Jan 25. PMID: 35081371; PMCID: PMC8895883.
Mihi B, Gong Q, Nolan LS, Gale SE, Goree M, Hu E, Lanik WE, Rimer JM, Liu V, Parks OB, Lewis AN, Agrawal P, Laury ML, Kumar P, Huang E, Bidani SS, Luke CJ, Kolls JK, Good M. Interleukin-22 signaling attenuates necrotizing enterocolitis by promoting epithelial cell regeneration. Cell Rep Med. 2021 Jun 15;2(6):100320. doi: 10.1016/j.xcrm.2021.100320. PMID: 34195684; PMCID: PMC8233697.
Chen HC, Polisetty TS, Zhu K, Phan BN, Durr NJ, Tian J, Mahoney NR. A quantitative analysis of factors influencing lower lid retraction and involutional ectropion. J Plast Reconstr Aesthet Surg. 2019 Jan;72(1):137-171. doi: 10.1016/j.bjps.2018.10.020. Epub 2018 Nov 2. PubMed PMID: 30467002.
Perez JL, Ozpinar A, Kano H, Phan B, Niranjan A, Lunsford LD. Salvage Stereotactic Radiosurgery in Breast Cancer Patients with Multiple Brain Metastases. World Neurosurg. 2019 May;125:e479-e486. doi: 10.1016/j.wneu.2019.01.108. Epub 2019 Jan 31. PubMed PMID: 30710716.
Phan, B.N., Bohlen, J.F., Davis, B.A. et al. A myelin-related transcriptomic profile is shared by Pitt–Hopkins syndrome models and human autism spectrum disorder. Nat Neurosci 23, 375–385 (2020). https://doi.org/10.1038/s41593-019-0578-x
Srinivasan C*, Phan BN*, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology. bioRxiv 2020.09.29.318329; doi: https://doi.org/10.1101/2020.09.29.318329. In review
Seney ML, Moon-Kim S, Glausier JR, Hildebrand MA, XiangningXue, Zong W, Wang J, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Freyberg Z, Logan RW. Transcriptional alterations in opioid use disorder reveal an interplay between neuroinflammation and synaptic remodeling.bioRxiv 2020.09.14.296707; doi: https://doi.org/10.1101/2020.09.14.296707. In review
Phan BN, Bohlen JF, Davis BA, Ye Z, Chen HY, Mayfield B, Sripathy SR, Cerceo Page S, Campbell MN, Smith HL, Gallop D, Kim H, Thaxton CL, Simon JM, Burke EE, Shin JH, Kennedy AJ, Sweatt JD, Philpot BD, Jaffe AE, Maher BJ. A myelin-related transcriptomic profile is shared by Pitt-Hopkins syndrome models and human autism spectrum disorder. Nat Neurosci. 2020 Feb 3;. doi: 10.1038/s41593-019-0578-x. [Epub ahead of print] PubMed PMID: 32015540.
Burke EE, Chenoweth JG, Shin JH, Collado-Torres L, Kim SK, Micali N, Wang Y, Colantuoni C, Straub RE, Hoeppner DJ, Chen HY, Sellers A, Shibbani K, Hamersky GR, Diaz Bustamante M, Phan BN, Ulrich WS, Valencia C, Jaishankar A, Price AJ, Rajpurohit A, Semick SA, Bürli RW, Barrow JC, Hiler DJ, Page SC, Martinowich K, Hyde TM, Kleinman JE, Berman KF, Apud JA, Cross AJ, Brandon NJ, Weinberger DR, Maher BJ, McKay RDG, Jaffe AE. Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs. Nat Commun. 2020 Jan 23;11(1):462. doi: 10.1038/s41467-019-14266-z. PubMed PMID: 31974374; PubMed Central PMCID: PMC6978526.
Maynard KR, Tippani M, Takahashi Y, Phan BN, Hyde TM, Jaffe AE, Martinowich K. dotdotdot: an automated approach to quantify multiplex single molecule fluorescent in situ hybridization (smFISH) images in complex tissues. Nucleic Acids Research, Volume 48, Issue 11, 19 June 2020, Page e66, https://doi.org/10.1093/nar/gkaa312
Srinivasan C, Phan BN, Lawler AJ, Ramamurthy E, Kleyman M, Brown AR, Kaplow IM, Wirthlin ME, Pfenning AR. Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology. J Neurosci. 2021 Aug 30:JN-RM-2534-20. doi: 10.1523/JNEUROSCI.2534-20.2021. Epub ahead of print. PMID: 34462306.
Rashid R, Copelli S, Silverstein JC, Becich MJ. REDCap and the National Mesothelioma Virtual Bank-a scalable and sustainable model for rare disease biorepositories. J Am Med Inform Assoc. 2023 Jul 24:ocad132. doi: 10.1093/jamia/ocad132. Epub ahead of print. PMID: 37487555.
Rasero J, Sentis AI, Yeh FC, Verstynen T. Integrating across neuroimaging modalities boosts prediction accuracy of cognitive ability. PLoS Comput Biol. 2021 Mar 5;17(3):e1008347. doi: 10.1371/journal.pcbi.1008347. PMID: 33667224; PMCID: PMC7984650.
Ortega-Gonzalez P, Taylor G, Jangra RK, Tenorio R, Fernandez de Castro I, Mainou BA, Orchard RC, Wilen CB, Brigleb PH, Sojati J, Chandran K, Sachse M, Risco C, Dermody TS. Reovirus infection is regulated by NPC1 and endosomal cholesterol homeostasis. PLoS Pathog. 2022 Mar 9;18(3):e1010322. doi: 10.1371/journal.ppat.1010322. PMID: 35263388; PMCID: PMC8906592.
Parks O.B., Eddens T.J., Sojati J., Lan J., Zhang Y., Oury T.D., Ramsey M.J., Erickson J.J., Byersdorfer C., Williams J.V. “Terminally exhausted CD8+ T cells contribute to age-dependent severity of respiratory virus infection. Immunity and Ageing 20, 40 (2023). https://doi.org/10.1186/s12979-023-00365-5
Sojati J, Murali A, Pressimone C, Dakroub A. A Cross-Sectional Factor Analysis of COVID-19 and Influenza Vaccination Decisions in a Racially Diverse Western Pennsylvania Community. J Prim Care Community Health. 2023 Jan-Dec;14:21501319231212287. doi: 10.1177/21501319231212287.
Murali A,* Sojati J,* Levochkina M, Pressimone C, Griffith K, Fan E, Dakroub A. A Cross-Sectional Analysis of Community Perceptions of Flu and COVID-19 Vaccines at Turtle Creek Primary Care Center. Community Health Equity Res Policy. 2023 Oct 14:2752535X231205665. doi: 10.1177/2752535X231205665.
Zhang Y, Xu J, Miranda-Katz M, Sojati J, Tollefson SJ, Manni ML, Alcorn JF, Sarkar SN, Williams JV. Distinct roles for type I and type III interferons in virulent human metapneumovirus pathogenesis. PLoS Pathog. 2024 Feb 5;20(2):e1011840. doi: 10.1371/journal.ppat.1011840.
Sojati J, Murali A, Rapsinski G, Williams JV. Do Not Throw Away Your Shot: Pilot Study in Improving Medical School Curricula Through Focused Vaccine Education. AJPM Focus. 2023 Dec 23;3(2):100178. doi: 10.1016/j.focus.2023.100178.
Sojati J, Zhang Y, Williams JV. Clinical human metapneumovirus isolates show distinct pathogenesis and inflammatory profiles but similar CD8+ T cell impairment. mSphere. 2024 Jan 30;9(1):e0057023. doi: 10.1128/msphere.00570-23. Epub 2024 Jan 10.
Abou-Daya KI, Tieu R, Zhao D, Rammal R, Sacirbegovic F, Williams AL, Shlomchik WD, Oberbarnscheidt MH, Lakkis FG. Resident memory T cells form during persistent antigen exposure leading to allograft rejection. Sci Immunol. 2021 Mar 19;6(57):eabc8122. doi: 10.1126/sciimmunol.abc8122. PMID: 33741656; PMCID: PMC8103522.
Hughes AD, Zhao D, Dai H, Abou-Daya KI, Tieu R, Rammal R, Williams AL, Landsittel DP, Shlomchik WD, Morelli AE, Oberbarnscheidt MH, Lakkis FG. Cross-dressed dendritic cells sustain effector T cell responses in islet and kidney allografts. J Clin Invest. 2020 Jan 2;130(1):287-294. doi: 10.1172/JCI125773. PMID: 31763998; PMCID: PMC6934226.
Vignali, P.D.A., DePeaux, K., Watson, M.J. et al. Hypoxia drives CD39-dependent suppressor function in exhausted T cells to limit antitumor immunity. Nat Immunol (2022). https://doi.org/10.1038/s41590-022-01379-9
Ford BR*, Vignali PDA*, Rittenhouse NL, Scharping NE, Peralta R, Lontos K, Frisch AT, Delgoffe GM, Poholek AC. Tumor microenvironmental signals reshape chromatin landscapes to limit the functional potential of exhausted T cells. Sci Immunol. 2022 Aug 5;7(74):eabj9123. doi: 10.1126/sciimmunol.abj9123. Epub 2022 Aug 5. PMID: 35930654. *co-first author https://doi.org/10.1126/sciimmunol.abj9123
Jayaprakash P*, Vignali PDA*, Delgoffe GM, Curran MA. Hypoxia Reduction Sensitizes Refractory Cancers to Immunotherapy. Annu Rev Med. 2022 Jan 27;73:251-265. doi: 10.1146/annurev-med-060619-022830. Epub 2021 Oct 26. PMID: 34699264. https://doi.org/10.1146/annurev-med-060619-022830 *co-first author
Watson MJ, Vignali PDA, Mullett SJ, Overacre-Delgoffe AE, Peralta R, Grebinowski S, Menk AV, Rittenhouse NL, DePeaux K, Whetstone RD, Vignali DAA, Hand TW, Poholek AC, Morrison BM, Rothstein JD, Wendell SG, Delgoffe GM. (2021). Regulatory T cell functional identity is sustained by a glucose:lactate axis that is exploited in the tumor microenvironment. Nature. doi: https://doi.org/10.1038/s41586-020-03045-2
Scharping NE, Rivadeneria DB*, Menk AV*, Vignali PDA, Rittenhouse NL, Ford RB, Ronal P, DePeaux K, Poholek AC, Delgoffe GM. (2021). Metabolic stress induced by continuous stimulation under hypoxia rapidly promotes a terminally exhausted T cell state. Nature Immunology. doi: https://doi.org/10.1038/s41590-020-00834-9.
Karim HT, Wang M, Andreescu C, Tudorascu D, Butters MA, Karp JF, Reynolds CF 3rd, Aizenstein HJ. Acute trajectories of neural activation predict remission to pharmacotherapy in late-life depression. Neuroimage Clin. 2018 Jun 8;19:831-839. doi: 10.1016/j.nicl.2018.06.006. PMID: 30013927; PMCID: PMC6024196.
Karim, H. T.*, Wang, M. B.*, Andreescu, C., Tudorascu, D., Butters, M. A., Karp, J. F., ... & Aizenstein, H. J. (2018). Acute trajectories of neural activation predict remission to pharmacotherapy in late-life depression. NeuroImage: Clinical, PubMed PMID: 30013927 (*: equal contribution)
Palacios E., Owen J., Yuh E., Wang M. B., Vassar M., Ferguson A., … & Mukherjee P. (2020). The Evolution of White Matter Changes After Mild Traumatic Brain Injury. Science Advances, PubMed PMID: 32821816
Payabvash S., Palacios E., Owen J., Wang M. B., Tavassoli T., … & Marco, E. (2019). White Matter Connectome Correlates of Auditory Over-Responsivity: Edge Density Imaging and Machine-learning Classifiers. Frontiers in Integrative Neuroscience, PubMed PMID: 30983979
Payabvash, S., Palacios, E. M., Owen, J. P., Wang, M. B., Tavassoli, T., Gerdes, M., ... & Mukherjee, P. (2019). Diffusion tensor tractography in children with sensory processing disorder: Potentials for devising machine learning classifiers. NeuroImage: Clinical, 23, 101831., PMID: 31035231
Payabvash, S., Palacios, E. M., Owen, J. P., Wang, M. B., Tavassoli, T., Gerdes, M., ... & Mukherjee, P. (2019). White matter connectome edge density in children with autism spectrum disorders: potential imaging biomarkers using machine-learning models. Brain connectivity, 9(2), 209-220., PMID: 30661372
Kaminski N, Wondisford AR, Kwon Y, Lynskey ML, Bhargava R, Barroso-González J, García-Expósito L, He B, Xu M, Mellacheruvu D, Watkins SC, Modesti M, Miller KM, Nesvizhskii AI, Zhang H, Sung P, O'Sullivan RJ. RAD51AP1 regulates ALT-HDR through chromatin-directed homeostasis of TERRA. Mol Cell. 2022 Nov 3;82(21):4001-4017.e7. doi: 10.1016/j.molcel.2022.09.025. Epub 2022 Oct 19. PMID: 36265488; PMCID: PMC9713952.
Prokhorova E, Agnew T, Wondisford AR, Tellier M, Kaminski N, Beijer D, Holder J, Groslambert J, Suskiewicz MJ, Zhu K, Reber JM, Krassnig SC, Palazzo L, Murphy S, Nielsen ML, Mangerich A, Ahel D, Baets J, O'Sullivan RJ, Ahel I. Unrestrained poly-ADP-ribosylation provides insights into chromatin regulation and human disease. Mol Cell. 2021 Jun 17;81(12):2640-2655.e8. doi: 10.1016/j.molcel.2021.04.028. Epub 2021 May 20. PMID: 34019811; PMCID: PMC8221567.
Hoang SM, Kaminski N, Bhargava R, Barroso-González J, Lynskey ML, García-Expósito L, Roncaioli JL, Wondisford AR, Wallace CT, Watkins SC, James DI, Waddell ID, Ogilvie D, Smith KM, da Veiga Leprevost F, Mellacharevu D, Nesvizhskii AI, Li J, Ray-Gallet D, Sobol RW, Almouzni G, O'Sullivan RJ. Regulation of ALT-associated homology-directed repair by polyADP-ribosylation. Nat Struct Mol Biol. 2020 Dec;27(12):1152-1164. doi: 10.1038/s41594-020-0512-7. Epub 2020 Oct 12. PMID: 33046907.
Buck TM, Zeng X, Cantrell PS, Cattley RT, Hasanbasri Z, Yates ME, Nguyen D, Yates NA, Brodsky JL. The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation. Mol Cell Proteomics. 2020 Nov;19(11):1896-1909. doi: 10.1074/mcp.RA120.002050. Epub 2020 Aug 31. PubMed PMID: 32868373; PubMed Central PMCID: PMC7664122.
Koppes EA, Redel BK, Johnson MA, Skvorak KJ, Ghaloul-Gonzalez L, Yates ME, Lewis DW, Gollin SM, Wu YL, Christ SE, Yerle M, Leshinski A, Spate LD, Benne JA, Murphy SL, Samuel MS, Walters EM, Hansen SA, Wells KD, Lichter-Konecki U, Wagner RA, Newsome JT, Dobrowolski SF, Vockley J, Prather RS, Nicholls RD. A porcine model of phenylketonuria generated by CRISPR/Cas9 genome editing. JCI Insight. 2020 Oct 15;5(20). doi: 10.1172/jci.insight.141523. PubMed PMID: 33055427; PubMed Central PMCID: PMC7605535.