Publications

Trainee: Current

Faculty Member: Matthew Smith, PhD

Publications:

Johnston R, Snyder AC, Khanna SB, Issar D, Smith MA. The eyes reflect an internal cognitive state hidden in the population activity of cortical neurons. Cereb Cortex. 2022 Jul 21;32(15):3331-3346. doi: 10.1093/cercor/bhab418. PMID: 34963140; PMCID: PMC9340396.

Issar D, Williamson RC, Khanna SB, Smith MA. A neural network for online spike classification that improves decoding accuracy. J Neurophysiol. 2020 Apr 1;123(4):1472-1485. doi: 10.1152/jn.00641.2019. Epub 2020 Feb 26. PMID: 32101491; PMCID: PMC7191521.

Snyder AC, Issar D, Smith MA. What does scalp electroencephalogram coherence tell us about long-range cortical networks? Eur J Neurosci. 2018 Oct;48(7):2466-2481. doi: 10.1111/ejn.13840. Epub 2018 Feb 13. PMID: 29363843; PMCID: PMC6497452.

Trainee Name: Jeffrey (Yong Joon) Kim, PhD

Trainee: Current

Faculty Member: Angela Gronenborn, PhD

Publications:

Xie Y, Clarke BP, Kim YJ, Ivey AL, Hill PS, Shi Y, Ren Y. Cryo-EM structure of the yeast TREX complex and coordination with the SR-like protein Gbp2. Elife. 2021 Mar 31;10:e65699. doi: 10.7554/eLife.65699. PMID: 33787496; PMCID: PMC8043747.

Sun D, Sang Z, Kim YJ, Xiang Y, Cohen T, Belford AK, Huet A, Conway JF, Sun J, Taylor DJ, Schneidman-Duhovny D, Zhang C, Huang W, Shi Y. Potent neutralizing nanobodies resist convergent circulating variants of SARS-CoV-2 by targeting diverse and conserved epitopes. Nat Commun. 2021 Aug 3;12(1):4676. doi: 10.1038/s41467-021-24963-3. PMID: 34344900; PMCID: PMC8333356.

Yong Joon Kim J, Sang Z, Xiang Y, Shen Z, Shi Y. Nanobodies: Robust miniprotein binders in biomedicine. Adv Drug Deliv Rev. 2023 Apr;195:114726. doi: 10.1016/j.addr.2023.114726. Epub 2023 Feb 7. PMID: 36754285.

Krzysiak TC, Choi YJ, Kim YJ, Yang Y, DeHaven C, Thompson L, Ponticelli R, Mermigos MM, Thomas L, Marquez A, Sipula I, Kemper JK, Jurczak M, Thomas G, Gronenborn AM. Inhibitory protein-protein interactions of the SIRT1 deacetylase are choreographed by post-translational modification. Protein Sci. 2024 Apr;33(4):e4938. doi: 10.1002/pro.4938. PMID: 38533551; PMCID: PMC10966392.

Trainee Name: Anna Kirillova

Trainee: Current

Faculty Member: Stephen Chan, MD, PhD, FAHA

Publications:

Kirillova A, Sethuraman M, Dong X, Kirdar A, Speyer G, Al Aaraj Y, Watson A, Schneider LK, Creager MD, Lafyatis R, Okawa S, Kim S, Chan SY. Reversal of inflammatory reprogramming by vasodilator agents in pulmonary hypertension. ERJ Open Res. 2025;11(1):00486-2024. PMCID: PMC11726584.

Kirillova A, Chan SY. miR-roring Changes in Blood: miR-210 Reflects Hypoxic Disease Dynamics in Obstructive Sleep Apnea. Am J Respir Crit Care Med. 2023; 207(3):240-242. PMCID: PMC9896649.

Harvey LD, Alotaibi M, Tai YY, Tang Y, Kim HJ, Kelly NJ, Sun W, Woodcock CC, Arshad S, Culley MK, El Khoury W, Xie R, Al Aaraj Y, Zhao J, Hafeez N, Rao RJ, Jiang S, Negi V, Kirillova A,…Chan SY. Lysosomal dysfunction and inflammatory sterol metabolism in pulmonary arterial hypertension. Science. 2025 Jan 24;387(6732):eadn7277. PMID: 39847635.

Kelly NJ, Newhouse D, Chapagain H, Patel A, Tang Y, Howard A, Kirillova A…Chan SY. Omics and Extreme Phenotyping Reveal Longitudinal Association Between Left Atrial Size and Pulmonary Vascular Resistance in Group 2 Pulmonary Hypertension. J Am Heart Assoc. 2023;12(23):e031746. PMCID: PMC10727316.

Hafeez N, Kirillova A…Sun W, Chan SY. Single Nucleotide Polymorphism rs9277336 Controls the Nuclear Alpha Actinin 4-Human Leukocyte Antigen-DPA1 Axis and Pulmonary Endothelial Pathophenotypes in Pulmonary Arterial Hypertension. J Am Heart Assoc. 2023;12(7):e027894; PMCID: PMC10122886.

Kirillova A, Han L, Liu H, Kühn B. Polyploid cardiomyocytes: implications for heart regeneration. Development. 2021; 148(14):dev199401. PMCID: PMC8326922.

Trainee Name: Danica Lee

Trainee: Current

Faculty Member: Daniella Schwartz, MD

Publications:

Anthony-Gonda K, Ray A, Su H, Wang Y, Xiong Y, Lee D, Block A, Chilunda V, Weiselberg J, Zemelko L, Wang YY, Kleinsorge-Block S, Reese JS, de Lima M, Ochsenbauer C, Kappes JC, Dimitrov DS, Orentas R, Deeks SG, Rutishauser RL, Berman JW, Goldstein H, Dropulić B. In vivo killing of primary HIV-infected cells by peripheral-injected early memory-enriched anti-HIV duoCAR T cells. JCI Insight. 2022 Nov 8;7(21):e161698. doi: 10.1172/jci.insight.161698. PMID: 36345941; PMCID: PMC9675454.

Trainee Name: Brandon Lehrich, PhD

Trainee: Current

Faculty Member: Pal Monga, MD

Publications:

Lehrich BM, Delgado ER, Yasaka TM, Liu S, Cao C, Liu Y, Taheri M, Guan X, Koeppen H, Singh S, Liu JJ, Singh-Varma A, Krutsenko Y, Poddar M, Hitchens TK, Foley LM, Liang B, Rialdi A, Rai RP, Patel P, Riley M, Bell A, Raeman R, Dadali T, Luke JJ, Guccione E, Ebrahimkhani MR, Lujambio A, Chen X, Maier M, Wang Y, Broom W, Tao J, Monga SP. Precision targeting of β-catenin induces tumor reprogramming and immunity in hepatocellular cancers. Res Sq [Preprint]. 2024 Dec 12:rs.3.rs-5494074. doi: 10.21203/rs.3.rs-5494074/v1. PMID: 39711542; PMCID: PMC11661417.

Lehrich BM, Tao J, Liu S, Hirsch TZ, Yasaka TM, Cao C, Delgado ER, Guan X, Lu S, Pan L, Liu Y, Singh S, Poddar M, Bell A, Singhi AD, Zucman-Rossi J, Wang Y, Monga SP. Development of mutated β-catenin gene signature to identify CTNNB1 mutations from whole and spatial transcriptomic data in patients with HCC. JHEP Rep. 2024 Aug 20;6(12):101186. doi: 10.1016/j.jhepr.2024.101186. PMID: 39583094; PMCID: PMC11582745.

Lehrich BM, Delgado ER. Lipid Nanovesicle Platforms for Hepatocellular Carcinoma Precision Medicine Therapeutics: Progress and Perspectives. Organogenesis. 2024 Dec 31;20(1):2313696. doi: 10.1080/15476278.2024.2313696. Epub 2024 Feb 15. PMID: 38357804; PMCID: PMC10878025.

Zhao L, Qiu Z, Yang Z, Xu L, Pearce TM, Wu Q, Yang K, Li F, Saulnier O, Fei F, Yu H, Gimple RC, Varadharajan V, Liu J, Hendrikse LD, Fong V, Wang W, Zhang J, Lv D, Lee D, Lehrich BM, Jin C, Ouyang L, Dixit D, Wu H, Wang X, Sloan AE, Wang X, Huan T, Mark Brown J, Goldman SA, Taylor MD, Zhou S, Rich JN. Lymphatic endothelial-like cells promote glioblastoma stem cell growth through cytokine-driven cholesterol metabolism. Nat Cancer. 2024 Jan;5(1):147-166. doi: 10.1038/s43018-023-00658-0. Epub 2024 Jan 3. PMID: 38172338.

Lehrich BM, Zhang J, Monga SP, Dhanasekaran R. Battle of the biopsies: Role of tissue and liquid biopsy in hepatocellular carcinoma. J Hepatol. 2024 Mar;80(3):515-530. doi: 10.1016/j.jhep.2023.11.030. Epub 2023 Dec 15. PMID: 38104635; PMCID: PMC10923008.

Lehrich BM, Monga SP. Learning human liver biology in humanized mice. Cell Res. 2024 Jan;34(1):9-10. doi: 10.1038/s41422-023-00877-1. PMID: 37730939; PMCID: PMC10770126.

Lehrich BM, Abiri A, Nguyen TV, Bitner BF, Tong CCL, Kuan EC. Mutational landscape and predictors of survival in head and neck mucosal melanoma. Int Forum Allergy Rhinol. 2024 Apr;14(4):858-861. doi: 10.1002/alr.23267. Epub 2023 Sep 7. PMID: 37676479; PMCID: PMC10918024.

Trainee Name: Michael Leone

Trainee: Current

Faculty Member: Andreas Pfenning, PhD

Publications:

Arokiaraj CM, Leone MJ, Kleyman M, Chamessian A, Noh MC, Phan BN, Lopes BC, Corrigan KA, Cherupally VK, Yeramosu D, Franusich ME, Podder R, Lele S, Shiers S, Kang B, Kennedy MM, Chen V, Chen Z, Mathys H, Dum RP, Lewis DA, Qadri Y, Price TJ, Pfenning AR, Seal RP. Spatial, transcriptomic, and epigenomic analyses link dorsal horn neurons to chronic pain genetic predisposition. Cell Rep. 2024 Nov 26;43(11):114876. doi: 10.1016/j.celrep.2024.114876. Epub 2024 Oct 24. PMID: 39453813; PMCID: PMC11801220.

Trainee Name: Anna Li

Trainee: Current

Faculty Member: Vaughn Cooper, PhD

Publications:

Nordstrom HR, Griffith MP, Rangachar Srinivasa V, Wallace NR, Li A, Cooper VS, Shields RK, Van Tyne D. Harnessing the Diversity of Burkholderia spp. Prophages for Therapeutic Potential. Cells. 2024 Feb 29;13(5):428. doi: 10.3390/cells13050428. PMID: 38474392; PMCID: PMC10931425.

Nordstrom HR, Griffith MP, Srinivasa VR, Wallace NR, Li A, Cooper VS, Shields RK, Van Tyne D. Harnessing the diversity of Burkholderia spp. prophages for therapeutic potential. bioRxiv [Preprint]. 2024 Jan 25:2024.01.24.577087. doi: 10.1101/2024.01.24.577087. Update in: Cells. 2024 Feb 29;13(5):428. doi: 10.3390/cells13050428. PMID: 38328162; PMCID: PMC10849711.

Trainee Name: Andrew Liu, PhD

Trainee: Current

Faculty Member: Daniel Kaplan, MD, PhD

Publications:

Liu AW, Zhang YR, Chen CS, Edwards TN, Ozyaman S, Ramcke T, McKendrick LM, Weiss ES, Gillis JE, Laughlin CR, Randhawa SK, Phelps CM, Kurihara K, Kang HM, Nguyen SN, Kim J, Sheahan TD, Ross SE, Meisel M, Sumpter TL, Kaplan DH. Scratching promotes allergic inflammation and host defense via neurogenic mast cell activation. Science. 2025 Jan 31;387(6733):eadn9390. doi: 10.1126/science.adn9390. Epub 2025 Jan 31. PMID: 39883751.

Liu AW, Gillis JE, Sumpter TL, Kaplan DH. Neuroimmune interactions in atopic and allergic contact dermatitis. J Allergy Clin Immunol. 2023 May;151(5):1169-1177. doi: 10.1016/j.jaci.2023.03.013. PMID: 37149370; PMCID: PMC10167546.

Kazi R, Evankovich MR, Liu R, Liu A, Moorhead A, Ferris LK, Falo LD Jr, English JC 3rd. Utilization of Asynchronous and Synchronous Teledermatology in a Large Health Care System During the COVID-19 Pandemic. Telemed J E Health. 2021 Jul;27(7):771-777. doi: 10.1089/tmj.2020.0299. Epub 2020 Oct 19. PMID: 33074786.

Cohen JA, Edwards TN, Liu AW, Hirai T, Jones MR, Wu J, Li Y, Zhang S, Ho J, Davis BM, Albers KM, Kaplan DH. Cutaneous TRPV1⁺ Neurons Trigger Protective Innate Type 17 Anticipatory Immunity. Cell. 2019 Aug 8;178(4):919-932.e14. doi: 10.1016/j.cell.2019.06.022. Epub 2019 Jul 25. PMID: 31353219; PMCID: PMC6788801.

Trainee Name: Joseph Maggiore, PhD

Trainee: Current

Faculty Member: Neil Hukriede, PhD

Publications:

Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR. Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids. Cell Syst. 2021 Jan 20;12(1):41-55.e11. doi: 10.1016/j.cels.2020.11.002. Epub 2020 Dec 7. PMID: 33290741; PMCID: PMC8164844.

Montalbetti N, Przepiorski AJ, Shi S, Sheng S, Baty CJ, Maggiore JC, Carattino MD, Vanichapol T, Davidson AJ, Hukriede NA, Kleyman TR. Functional characterization of ion channels expressed in kidney organoids derived from human induced pluripotent stem cells. Am J Physiol Renal Physiol. 2022 Oct 1;323(4):F479-F491. doi: 10.1152/ajprenal.00365.2021. Epub 2022 Aug 18. PMID: 35979965; PMCID: PMC9529267.

Al-Bataineh MM, Kinlough CL, Marciszyn A, Lam T, Ye L, Kidd K, Maggiore JC, Poland PA, Kmoch S, Bleyer A, Bain DJ, Montalbetti N, Kleyman TR, Hughey RP, Ray EC. Influence of glycoprotein MUC1 on trafficking of the Ca²⁺-selective ion channels, TRPV5 and TRPV6, and on in vivo calcium homeostasis. J Biol Chem. 2023 Mar;299(3):102925. doi: 10.1016/j.jbc.2023.102925. Epub 2023 Jan 20. PMID: 36682497; PMCID: PMC9996365.

Maggiore JC, LeGraw R, Przepiorski A, Velazquez J, Chaney C, Streeter E, Silva-Barbosa A, Franks J, Hislop J, Hill A, Wu H, Pfister K, Howden SE, Watkins SC, Little M, Humphreys BD, Watson A, Stolz DB, Kiani S, Davidson AJ, Carroll TJ, Cleaver O, Sims-Lucas S, Ebrahimkhani MR, Hukriede NA. Genetically engineering endothelial niche in human kidney organoids enables multilineage maturation, vascularization and de novo cell types. bioRxiv [Preprint]. 2023 May 30:2023.05.30.542848. doi: 10.1101/2023.05.30.542848. Update in: Kidney Int. 2024 Jun 18:S0085-2538(24)00407-1. doi: 10.1016/j.kint.2024.05.026. PMID: 37333155; PMCID: PMC10274893.

Kaverina N, Schweickart RA, Chan GC, Maggiore JC, Eng DG, Zeng Y, McKinzie SR, Perry HS, Ali A, O'Connor C, Pereira BMV, Theberge AB, Vaughan JC, Loretz CJ, Chang A, Hukriede NA, Bitzer M, Pippin JW, Wessely O, Shankland SJ. Inhibiting NLRP3 signaling in aging podocytes improves their life- and health-span. Aging (Albany NY). 2023 Jul 23;15(14):6658-6689. doi: 10.18632/aging.204897. Epub 2023 Jul 23. PMID: 37487005; PMCID: PMC10415579.

Veloso Pereira BM, Zeng Y, Maggiore JC, Schweickart RA, Eng DG, Kaverina N, McKinzie SR, Chang A, Loretz CJ, Thieme K, Hukriede NA, Pippin JW, Wessely O, Shankland SJ. Podocyte injury at young age causes premature senescence and worsens glomerular aging. Am J Physiol Renal Physiol. 2024 Jan 1;326(1):F120-F134. doi: 10.1152/ajprenal.00261.2023. Epub 2023 Oct 19. PMID: 37855038; PMCID: PMC11198990.

Molinari L, Rio-Pertuz GD, Priyanka P, Smith A, Maggiore JC, Kennedy J, Gomez H, Seymour CW, Kellum JA; ProCESS and ProGReSS-AKI Investigators. Distribution of Acute and Chronic Kidney Disease Across Clinical Phenotypes for Sepsis. Chest. 2024 Sep;166(3):480-490. doi: 10.1016/j.chest.2024.03.006. Epub 2024 Mar 8. PMID: 38462074.

Maggiore JC, LeGraw R, Przepiorski A, Velazquez J, Chaney C, Vanichapol T, Streeter E, Almuallim Z, Oda A, Chiba T, Silva-Barbosa A, Franks J, Hislop J, Hill A, Wu H, Pfister K, Howden SE, Watkins SC, Little MH, Humphreys BD, Kiani S, Watson A, Stolz DB, Davidson AJ, Carroll T, Cleaver O, Sims-Lucas S, Ebrahimkhani MR, Hukriede NA. A genetically inducible endothelial niche enables vascularization of human kidney organoids with multilineage maturation and emergence of renin expressing cells. Kidney Int. 2024 Jun 18:S0085-2538(24)00407-1. doi: 10.1016/j.kint.2024.05.026. Epub ahead of print. PMID: 38901605.

Trainee Name: Varun Mandi

Trainee: Current

Faculty Member: Vijay Yechoor, PhD

Publications:

Negi V, Lee J, Mandi V, Danvers J, Liu R, Perez-Garcia EM, Li F, Jagannathan R, Yang P, Filingeri D, Kumar A, Ma K, Moulik M, Yechoor VK. Bromodomain Protein Inhibition Protects β-Cells from Cytokine-Induced Death and Dysfunction via Antagonism of NF-κB Pathway. Cells. 2024 Jun 26;13(13):1108. doi: 10.3390/cells13131108. PMID: 38994961; PMCID: PMC11240345.

Espinosa-Diez C, Mandi V, Du M, Liu M, Gomez D. Smooth muscle cells in atherosclerosis: clones but not carbon copies. JVS Vasc Sci. 2021 May 15;2:136-148. doi: 10.1016/j.jvssci.2021.02.002. PMID: 34617064; PMCID: PMC8489213.