Publications
Anthonymuthu TS, Kenny EM, Lamade AM, Gidwani H, Krehel NM, Misse A, Gao X, Amoscato AA, Straub AC, Kagan VE, Dezfulian C, Bayir H. Lipidomics Detection of Brain Cardiolipins in Plasma Is Associated With Outcome After Cardiac Arrest. Crit Care Med. 2019;47(4):e292-e300. Epub 2019/03/12. doi: 10.1097/CCM.0000000000003636. PubMed PMID: 30855329; PMCID: PMC6622168.
Anthonymuthu TS, Kenny EM, Lamade AM, Kagan VE, Bayir H. Oxidized phospholipid signaling in traumatic brain injury. Free Radic Biol Med. 2018;124:493-503. Epub 2018/07/03. doi: 10.1016/j.freeradbiomed.2018.06.031. PubMed PMID: 29964171; PMCID: PMC6098726.
Bayir H, Anthonymuthu TS, Tyurina YY, Patel SJ, Amoscato AA, Lamade AM, Yang Q, Vladimirov GK, Philpott CC, Kagan VE. Achieving Life through Death: Redox Biology of Lipid Peroxidation in Ferroptosis. Cell Chem Biol. 2020;27(4):387-408. Epub 2020/04/11. doi: 10.1016/j.chembiol.2020.03.014. PubMed PMID: 32275865; PMCID: PMC7218794.
Dezfulian C, Kenny E, Lamade A, Misse A, Krehel N, St Croix C, Kelley EE, Jackson TC, Uray T, Rackley J, Kochanek PM, Clark RS, Bayir H. Mechanistic characterization of nitrite-mediated neuroprotection after experimental cardiac arrest. J Neurochem. 2016;139(3):419-31. Epub 2016/10/25. doi: 10.1111/jnc.13764. PubMed PMID: 27507435; PMCID: PMC5247267.
Krainz T, Lamade AM, Du L, Maskrey TS, Calderon MJ, Watkins SC, Epperly MW, Greenberger JS, Bayir H, Wipf P, Clark RSB. Synthesis and Evaluation of a Mitochondria-Targeting Poly(ADP-ribose) Polymerase-1 Inhibitor. ACS Chem Biol. 2018;13(10):2868-79. Epub 2018/09/06. doi: 10.1021/acschembio.8b00423. PubMed PMID: 30184433; PMCID: PMC6402482.
Lamade AM, Anthonymuthu TS, Hier ZE, Gao Y, Kagan VE, Bayir H. Mitochondrial damage & lipid signaling in traumatic brain injury. Exp Neurol. 2020;329:113307. Epub 2020/04/15. doi: 10.1016/j.expneurol.2020.113307. PubMed PMID: 32289317; PMCID: PMC7237325.
Lamade AM, Kenny EM, Anthonymuthu TS, Soysal E, Clark RSB, Kagan VE, Bayir H. Aiming for the target: Mitochondrial drug delivery in traumatic brain injury. Neuropharmacology. 2019;145(Pt B):209-19. Epub 2018/07/17. doi: 10.1016/j.neuropharm.2018.07.014. PubMed PMID: 30009835; PMCID: PMC6309489.
Medina-Rivera M, Centeno-Tablante E, Finkelstein JL, Rayco-Solon P, Peña-Rosas JP, Garcia-Casal MN, Rogers L, Ridwan P, Martinez SS, Andrade J, Layden AJ, Chang J, Zambrano MP, Ghezzi-Kopel K, Mehta S. Presence of Ebola virus in breast milk and risk of mother-to-child transmission: synthesis of evidence. Ann N Y Acad Sci. 2020 Oct 28. doi: 10.1111/nyas.14519. Epub ahead of print. PMID: 33113592.
Layden A, 2018, B-Vitamins and HIV/AIDS, Nutrition and HIV/AIDS.
Layden A, Täse K, Finkelstein J, 2018, Neglected tropical diseases and vitamin B12: a review of the current evidence, Transactions of the Royal Society of Tropical Medicine and Hygiene, 112:423-435.
Finkelstein J, Colt S, Layden A, Krisher J, Stewart-Ibarra A, Polhemus M, Beltrán-Ayala E, Tedesco J, Cárdenas W, Endy T, Mehta S, 2020, Micronutrients, Immunological Parameters, and Dengue Virus Infection in Coastal Ecuador: A Nested Case-Control Study in an Infectious Disease Surveillance Program, The Journal of infectious diseases, 221:91-101.
Ly, M., Foley, L., Manivannan, A., Hitchens, K.T., Richardson, R.M., Modo, M. Mesoscale diffusion magnetic resonance imaging of the ex vivo human hippocampus(2020). Human Brain Mapping.Cover illustration.
Lin, C.*, Ly, M.*, Karim, H.T., Wei, W., Snitz, B.E., Klunk, W.E., Aizenstein, H.J. The longitudinal effect of amyloid on the resting-state functional connectivity in cognitively normal older adults (2020) Alzheimer’s Research & Therapy.12(1): 1-10.*co-first authors.
Ly, M.,Yu, G.Z., Muppidi, N.R., Karim, H.T., Mizuno, A., Klunk, W.E., Aizenstein, H.J. for the Alzheimer’s Disease Neuroimaging Initiative. Improving Brain Age Prediction Models: Incorporation of Amyloid Status in Alzheimer’s Disease (2020) Neurobiology of Aging.87: 44-48.
Raji CA, Ly M, Benzinger TLS. Overview of MR Imaging Volumetric Quantification in Neurocognitive Disorders. Top Magn Reson Imaging. 2019 Dec;28(6):311-315. doi: 10.1097/RMR.0000000000000224. PMID: 31794503.
Wu M, Mennin DS, Ly M, Karim HT, Banihashemi L, Tudorascu DL, Aizenstein HJ, Andreescu C. When worry may be good for you: Worry severity and limbic-prefrontal functional connectivity in late-life generalized anxiety disorder. J Affect Disord. 2019 Oct 1;257:650-657. doi: 10.1016/j.jad.2019.07.022. Epub 2019 Jul 5. PMID: 31357162; PMCID: PMC6711791.
Mizuno A, Ly M, Aizenstein HJ. A Homeostatic Model of Subjective Cognitive Decline. Brain Sci. 2018 Dec 19;8(12):228. doi: 10.3390/brainsci8120228. PMID: 30572628; PMCID: PMC6316074.
Ly M, Andreescu C. Advances and Barriers for Clinical Neuroimaging in Late-Life Mood and Anxiety Disorders. Curr Psychiatry Rep. 2018 Mar 1;20(1):7. doi: 10.1007/s11920-018-0870-6. PMID: 29492705.
Mizuno, A., Karim, H.T., Rangarajan, A., Ly, M., Cohen, A.D., Lopresti, B.J., Mathis, C.A., Klunk, W.E., Aizenstein, H.J., Snitz, B.E. An effect of education on memory-encoding activation in subjective cognitive decline (2021). Journal of Alzheimer’s Disease.
Ly, M.*, Raji, C.A.*, Yu, G., Wang, Q., Wang, Y., Schindler, S., An, H., Samara, A., Eisenstein, S.A., Hershey, T., Smith, G., Klein, S., Ances, B., Morris, J.C., Benzinger, T.L. Obesity and White Matter Neuroinflammation Related Edema in Alzheimer’s Disease Biomarker Negative Cognitively Normal Individuals (2021). Journal of Alzheimer’s Disease. 79(4): 1801-1811. *co-first authors.
Yu, G.Z., Ly, M., Karim, H.T., Muppidi, N., Aizenstein, H.J., Ibinson, J.W. Accelerated brain aging in chronic low back pain (2021). Brain Research. 1755, 147263.
Ly, M., Karim, H.T., Becker, J.T., Lopez, O.L., Aizenstein, H.J., Reynolds, C.F. III., Zmuda, M.D., Butters, M.A. Late-life depression and increased risk of dementia: a longitudinal cohort study (2021). Translational Psychiatry. 11(1): 1-10.
Karim, H.T., Ly, M., Yu, G.Z., Krafty, R., Tudorsacu, D.L., Aizenstein, H.J., Andreescu, C. Aging faster: worry and rumination in late life are associated with greater brain age (2021). Neurobiology of Aging. 101 (13-21).
Mannes PZ, Adams TS, Farsijani S, Barnes CE, Latoche JD, Day KE, Nedrow JR, Ahangari F, Kaminski N, Lee JS, Tavakoli S. Noninvasive assessment of the lung inflammation-fibrosis axis by targeted imaging of CMKLR1. Sci Adv. 2024 Jun 21;10(25):eadm9817. doi: 10.1126/sciadv.adm9817. Epub 2024 Jun 19. PMID: 38896611; PMCID: PMC11186491.
Mannes PZ, Tavakoli S. Imaging Immunometabolism in Atherosclerosis. J Nucl Med. 2021 Jul 1;62(7):896-902. doi: 10.2967/jnumed.120.245407. Epub 2021 May 7. PMID: 33963045; PMCID: PMC8882876.
Mannes PZ, Wang TL, Ma W, Selzer J, Blanco C. Student Substance Use Policies in US Allopathic Medical Schools: A National Study. JAMA Psychiatry. 2021 Dec 1;78(12):1393-1395. doi: 10.1001/jamapsychiatry.2021.2666. PMID: 34586347; PMCID: PMC8482301.
Demirdelen S, Mannes PZ, Aral AM, Haddad J, Leers SA, Gomez D, Tavakoli S. Divergence of acetate uptake in proinflammatory and inflammation-resolving macrophages: implications for imaging atherosclerosis. J Nucl Cardiol. 2021. Epub 2021/01/10. doi: 10.1007/s12350-020-02479-5. PubMed PMID: 33420659.
Wagner S , Sudhamalla B , Mannes P, Sappa S , Kavoosi S , Dey D , Wang S , Islam K . Engineering bromodomains with a photoactive amino acid by engaging 'Privileged' tRNA synthetases. Chem Commun (Camb). 2020 Mar 28;56(25):3641-3644. doi: 10.1039/c9cc09891g. Epub 2020 Feb 28. PMID: 32107512; PMCID: PMC7146825.
Molina L, Zhu J, Trépo E, Bayard Q, Amaddeo G; GENTHEP Consortium; Blanc JF, Calderaro J, Ma X, Zucman-Rossi J, Letouzé E. Bi-allelic hydroxymethylbilane synthase inactivation defines a homogenous clinico-molecular subtype of hepatocellular carcinoma. J Hepatol. 2022 Oct;77(4):1038-1046. doi: 10.1016/j.jhep.2022.05.018. Epub 2022 May 27. PMID: 35636578.
Hu S, Molina L, Tao J, Liu S, Hassan M, Singh S, Poddar M, Bell A, Sia D, Oertel M, Raeman R, Nejak-Bowen K, Singhi A, Luo J, Monga SP, Ko S. NOTCH-YAP1/TEAD-DNMT1 Axis Drives Hepatocyte Reprogramming Into Intrahepatic Cholangiocarcinoma. Gastroenterology. 2022 Aug;163(2):449-465. doi: 10.1053/j.gastro.2022.05.007. Epub 2022 May 10. PMID: 35550144; PMCID: PMC9329208.
Molina LM, Krutsenko Y, Jenkins NEC, Smith MC, Tao J, Wheeler TB, Watkins SC, Watson AM, Monga SP. LiverClear: A versatile protocol for mouse liver tissue clearing. STAR Protoc. 2022 Feb 15;3(1):101178. doi: 10.1016/j.xpro.2022.101178. PMID: 35243370; PMCID: PMC8857608.
Ko S, Kim M, Molina L, Sirica AE, Monga SP. YAP1 activation and Hippo pathway signaling in the pathogenesis and treatment of intrahepatic cholangiocarcinoma. Adv Cancer Res. 2022;156:283-317. doi: 10.1016/bs.acr.2022.02.003. Epub 2022 Mar 9. PMID: 35961703.
Molina L, Nejak-Bowen K, Monga SP. Role of YAP1 Signaling in Biliary Development, Repair, and Disease. Semin Liver Dis. 2022 Feb;42(1):17-33. doi: 10.1055/s-0041-1742277. Epub 2022 Jan 24. PMID: 35073587; PMCID: PMC9372714.
Molina L, Zhu J, Li Q, Pradhan-Sundd T, Krutsenko Y, Sayed K, Jenkins N, Vats R, Bhushan B, Ko S, Hu S, Poddar M, Singh S, Tao J, Sundd P, Singhi A, Watkins S, Ma X, Benos PV, Feranchak A, Michalopoulos G, Nejak-Bowen K, Watson A, Bell A, Monga SP. Compensatory hepatic adaptation accompanies permanent absence of intrahepatic biliary network due to YAP1 loss in liver progenitors. Cell Reports, 2021, Jul 6. PMID: 34233187
Hirsch T*, Pilet J*, Morcrette G*, Roehrig A, Monteiro B, Molina L, Bayard Q, Trépo E, Meunier L, Caruso S, Renault V, Deleuze JF, Fresneau B, Chardot C, Gonzales E, Jacquemin E, Guerin F, Fabre M, Aerts I, Taque S, Laithier V, Branchereau S, Guettier C, Brugières L, Rebouissou S, Letouzé E, Zucman-Rossi J. Integrated genomic analysis identifies driver genes and cisplatin-resistant progenitor phenotype in pediatric liver cancer. Cancer Discovery, 2021, in press. *co-first authors. PMID: 33893148
Bhushan B, Molina L, Koral K, Stoops JW, Mars WM, Banerjee S, Orr A, Paranjpe S, Monga SP, Locker J, Michalopoulos GK. Yap is crucial for CAR-driven hepatocyte proliferation but not for induction of drug metabolism genes in mice. Hepatology, 2020 Aug 13. PMID: 32794202
Ko S, Russell JO, Molina LM, Monga SP. Liver Progenitors and Adult Cell Plasticity in Hepatic Injury and Repair: Knowns and Unknowns. Annu Rev Pathol. 2020 Jan 24;15:23-50. doi: 10.1146/annurev-pathmechdis-012419-032824. Epub 2019 Aug 9.
Bhushan B, Molina L, Koral K, Stoops JW, Mars WM, Banerjee S, Orr A, Paranjpe S, Monga SP, Locker J, Michalopoulos GK. Yap is crucial for CAR-driven hepatocyte proliferation, but not for induction of drug metabolism genes in mice. Hepatology. 2020 Aug 13. doi: 10.1002/hep.31521. Online ahead of print.
Min Q, Molina L, Li J, Adebayo Michael AO, Russell JO, Preziosi ME, Singh S, Poddar M, Matz-Soja M, Ranganathan S, Bell AW, Gebhardt R, Gaunitz F, Yu J, Tao J, Monga SP. β-Catenin and Yes-Associated Protein 1 Cooperate in Hepatoblastoma Pathogenesis. Am J Pathol. 2019 May;189(5):1091-1104. doi: 10.1016/j.ajpath.2019.02.002. Epub 2019 Feb 19.
Molina L, Yang H, Michael AOA, Oertel M, Bell A, Singh S, Chen X, Tao J, Monga SP. Correction: mTOR inhibition affects Yap1-β-catenin-induced hepatoblastoma growth and development. Oncotarget. 2019 Sep 24;10(54):5670. doi: 10.18632/oncotarget.27218. eCollection 2019 Sep 24.
Pradhan-Sundd T, Vats R, Russell JO, Singh S, Michael AA, Molina L, Kakar S, Cornuet P, Poddar M, Watkins SC, Nejak-Bowen KN, Monga SP, Sundd P. Dysregulated Bile Transporters and Impaired Tight Junctions During Chronic Liver Injury in Mice. Gastroenterology. 2018 Oct;155(4):1218-1232.e24. doi: 10.1053/j.gastro.2018.06.048. Epub 2018 Jun 30.
Pradhan-Sundd T, Zhou L, Vats R, Jiang A, Molina L, Singh S, Poddar M, Russell J, Stolz DB, Oertel M, Apte U, Watkins S, Ranganathan S, Nejak-Bowen KN, Sundd P, Monga SP. Dual catenin loss in murine liver causes tight junctional deregulation and progressive intrahepatic cholestasis. Hepatology. 2018 Jun;67(6):2320-2337. doi: 10.1002/hep.29585. Epub 2018 Apr 19.
Molina L, Bell D, Tao J, Preziosi M, Pradhan-Sundd T, Singh S, Poddar M, Luo J, Ranganathan S, Chikina M, Monga SP. Hepatocyte-Derived Lipocalin 2 Is a Potential Serum Biomarker Reflecting Tumor Burden in Hepatoblastoma. Am J Pathol. 2018 Aug;188(8):1895-1909. doi: 10.1016/j.ajpath.2018.05.006. Epub 2018 Jun 18.
van Dinther M, Cunningham KT, Singh SP, White MPJ, Campion T, Ciancia C, van Veelen PA, de Ru AH, González-Prieto R, Mukundan A, Byeon CH, Staggers SR, Hinck CS, Hinck AP, Dijke PT, Maizels RM. CD44 acts as a coreceptor for cell-specific enhancement of signaling and regulatory T cell induction by TGM1, a parasite TGF-β mimic. Proc Natl Acad Sci U S A. 2023 Aug 22;120(34):e2302370120. doi: 10.1073/pnas.2302370120. Epub 2023 Aug 17. PMID: 37590410; PMCID: PMC10450677.
Mukundan A, Byeon CH, Hinck CS, Cunningham K, Campion T, Smyth DJ, Maizels RM, Hinck AP. Convergent evolution of a parasite-encoded complement control protein-scaffold to mimic binding of mammalian TGF-β to its receptors, TβRI and TβRII. J Biol Chem. 2022 Jun;298(6):101994. doi: 10.1016/j.jbc.2022.101994. Epub 2022 Apr 29. PMID: 35500648; PMCID: PMC9163516.
Singh SP, Smyth DJ, Cunningham K, Mukundan A, Byeon CH, Hinck CS, White MPJ, Ciancia C, Wosowska N, Sanders A, Jin R, Lilla S, Zanivan S, Schoenherr C, Inman G, van Dinther M, Ten Dijke P, Hinck AP, Maizels RM. The helminth TGF-β mimic TGM4 is a modular ligand that binds CD44, CD49d and TGF-β receptors to preferentially target myeloid cells. bioRxiv [Preprint]. 2023 Nov 15:2023.11.13.566701. doi: 10.1101/2023.11.13.566701. PMID: 38014296; PMCID: PMC10680678.
White SE, Schwartze TA, Mukundan A, Schoenherr C, Singh SP, van Dinther M, Cunningham KT, White MPJ, Campion T, Pritchard J, Hinck CS, Ten Dijke P, Inman G, Maizels RM, Hinck AP. TGM6, a helminth secretory product, mimics TGF-β binding to TβRII to antagonize TGF-β signaling in fibroblasts. bioRxiv [Preprint]. 2023 Dec 23:2023.12.22.573140. doi: 10.1101/2023.12.22.573140. PMID: 38187573; PMCID: PMC10769414.
Singh SP, Smyth DJ, Cunningham KT, Mukundan A, Byeon CH, Hinck CS, White MPJ, Ciancia C, Wąsowska N, Sanders A, Jin R, White RF, Lilla S, Zanivan S, Schoenherr C, Inman GJ, van Dinther M, Ten Dijke P, Hinck AP, Maizels RM. The TGF-β mimic TGM4 achieves cell specificity through combinatorial surface co-receptor binding. EMBO Rep. 2025 Jan;26(1):218-244. doi: 10.1038/s44319-024-00323-2. Epub 2024 Nov 28. PMID: 39609640; PMCID: PMC11723922.
Nguyen E, Smith KM, Cramer N, Holland RA, Bleimeister IH, Flores-Felix K, Silberberg H, Keller A, Le Pichon CE, Ross SE. Medullary kappa-opioid receptor neurons inhibit pain and itch through a descending circuit. Brain. 2022 Jul 29;145(7):2586-2601. doi: 10.1093/brain/awac189. PMID: 35598161.
Nguyen E, Lim G, Ross SE. Evaluation of Therapies for Peripheral and Neuraxial Opioid-induced Pruritus based on Molecular and Cellular Discoveries. Anesthesiology. 2021 Aug 1;135(2):350-365. doi: 10.1097/ALN.0000000000003844. PMID: 34237130.
Nguyen, E, Lim, G, Ding, H, Hachisuka, J, Ko, M.-C, and Ross, S.E. 2021. Morphine acts on spinal dynorphin neurons to cause itch through disinhibition. Science Translational Medicine.
Nguyen, E, Lim, G, and Ross, S.E. 2021. Mechanistic insights into spinal neurones involved in neuraxial opioid-induced pruritus. British Journal of Anaesthesia.
Chiang MC, Nguyen E, Bustos M, Papale A, and Ross SE. 2020. Divergent neural pathways emanating from the lateral parabrachial nucleus mediate distinct components of the pain response. Neuron.
Fuller A, Parmhans N, Nguyen E, et al. 2020. Identification of Retinal Ganglion Cell Types and Brain Nuclei expressing the transcription factor Brn3c/Pou4f3 using a Cre recombinase knock-in allele. Journal of Comparative Neurology.
Banerjee, H., Nieves-Rosado, HM, Kulkarni, A., Murter, B., McGrath, K. V., Chandran, U. R., . . . Kane, LP. Expression of Tim-3 drives phenotypic and functional changes in Treg cells in secondary lymphoid organs and the tumor microenvironment. Cell Rep; 2021. (PMID 34525351).
Nieves-Rosado HM., Jacobs JL., Naqvi A., Mellors JW., Macatangay BJC., Kane LP. TIM-3 signaling contributes to the suppressive capacity of Tregs from people with HIV on antiretroviral therapy. J Leukoc Biol; 2023. (PMID: 37350502).
Nieves-Rosado, HM., Banerjee, H., Gocher-Demske, A., Manandhar, P., Mehta, I., Ezenwa, O., Xie, B., Murter, B., Das, J., Vignali, DAA., Delgoffe, GM., Kane, LP. Tim-3 is required for Treg-mediated promotion of T cell exhaustion and viral persistence during chronic LCMV infection. Journal of Immunology; 2024.
Peralta, RM., Xie, B., Lontos, K., Nieves-Rosado, HM., Spahr, K., Ford, RB., Quann, K., Frisch, A., Dean, V., Philbin, M., Cillo, AR., Gingras, S., Poholek, AC., Kane, LP., Rivadeneira, DB., Delgoffe GM. Dysfunction of exhausted T cells is enforced by MCT11-mediated lactate metabolism. Nat. Immunol; 2024.
Bain W, Li H, van der Geest R, Moore SR, Olonisakin TF, Ahn B, Papke E, Moghbeli K, DeSensi R, Rapport S, Saul M, Hulver M, Xiong Z, Mallampalli RK, Ray P, Morris A, Ma L, Doi Y, Zhang Y, Kitsios GD, Kulkarni HS, McVerry BJ, Ferreira VP, Nouraie M, Lee JS. Increased Alternative Complement Pathway Function and Improved Survival during Critical Illness. Am J Respir Crit Care Med. 2020;202(2):230-40. Epub 2020/05/07. doi: 10.1164/rccm.201910-2083OC. PubMed PMID: 32374177; PMCID: PMC7365364.
Bain W, Olonisakin T, Yu M, Qu Y, Hulver M, Xiong Z, Li H, Pilewski J, Mallampalli RK, Nouraie M, Ray A, Ray P, Cheng Z, Shanks RMQ, St Croix C, Silverstein RL, Lee JS. Platelets inhibit apoptotic lung epithelial cell death and protect mice against infection-induced lung injury. Blood Adv. 2019;3(3):432-45. Epub 2019/02/09. doi: 10.1182/bloodadvances.2018026286. PubMed PMID: 30733303; PMCID: PMC6373758.
Han S, Olonisakin TF, Pribis JP, Zupetic J, Yoon JH, Holleran KM, Jeong K, Shaikh N, Rubio DM, Lee JS. A checklist is associated with increased quality of reporting preclinical biomedical research: A systematic review. PLoS One. 2017;12(9):e0183591. Epub 2017/09/14. doi: 10.1371/journal.pone.0183591. PubMed PMID: 28902887; PMCID: PMC5597130.
Olonisakin TF, Lee JS. Fighting Bacterial Pathogens in the Lung: Platelets to the Rescue? Am J Respir Cell Mol Biol. 2018;58(3):282-3. Epub 2018/03/02. doi: 10.1165/rcmb.2017-0349ED. PubMed PMID: 29493323; PMCID: PMC5854961.
Olonisakin TF, Li H, Xiong Z, Kochman EJ, Yu M, Qu Y, Hulver M, Kolls JK, St Croix C, Doi Y, Nguyen MH, Shanks RM, Mallampalli RK, Kagan VE, Ray A, Silverstein RL, Ray P, Lee JS. CD36 Provides Host Protection Against Klebsiella pneumoniae Intrapulmonary Infection by Enhancing Lipopolysaccharide Responsiveness and Macrophage Phagocytosis. J Infect Dis. 2016;214(12):1865-75. Epub 2016/09/30. doi: 10.1093/infdis/jiw451. PubMed PMID: 27683817; PMCID: PMC5142085.
Olonisakin TF, Suber T, Gonzalez-Ferrer S, Xiong Z, Penaloza HF, van der Geest R, Xiong Y, Osei-Hwedieh DO, Tejero J, Rosengart MR, Mars WM, Van Tyne D, Perlegas A, Brashears S, Kim-Shapiro DB, Gladwin MT, Bachman MA, Hod EA, St Croix C, Tyurina YY, Kagan VE, Mallampalli RK, Ray A, Ray P, Lee JS. Stressed erythrophagocytosis induces immunosuppression during sepsis through heme-mediated STAT1 dysregulation. J Clin Invest. 2021;131(1). Epub 2020/09/18. doi: 10.1172/JCI137468. PubMed PMID: 32941182; PMCID: PMC7773401.
Qu Y, Olonisakin T, Bain W, Zupetic J, Brown R, Hulver M, Xiong Z, Tejero J, Shanks RM, Bomberger JM, Cooper VS, Zegans ME, Ryu H, Han J, Pilewski J, Ray A, Cheng Z, Ray P, Lee JS. Thrombospondin-1 protects against pathogen-induced lung injury by limiting extracellular matrix proteolysis. JCI Insight. 2018;3(3). Epub 2018/02/09. doi: 10.1172/jci.insight.96914. PubMed PMID: 29415890; PMCID: PMC5821195.
Zhao Y, Olonisakin TF, Xiong Z, Hulver M, Sayeed S, Yu MT, Gregory AD, Kochman EJ, Chen BB, Mallampalli RK, Sun M, Silverstein RL, Stolz DB, Shapiro SD, Ray A, Ray P, Lee JS. Thrombospondin-1 restrains neutrophil granule serine protease function and regulates the innate immune response during Klebsiella pneumoniae infection. Mucosal Immunol. 2015;8(4):896-905. Epub 2014/12/11. doi: 10.1038/mi.2014.120. PubMed PMID: 25492474; PMCID: PMC4465063.
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.
Ibarra AJ, Lopa SH, Phan BN, Himes K, Butters MA, Beck S, Catov JM. Novel Approach to Identify Severe Maternal Morbidity Clusters: A Latent Class Analysis. Am J Perinatol. 2024 Oct 8. doi: 10.1055/a-2418-9955. Epub ahead of print. PMID: 39379025.
Ibarra AJ, Lopa SH, Phan BN, Himes K, Butters MA, Beck S, Catov JM. Novel Approach to Identify Severe Maternal Morbidity Clusters: A Latent Class Analysis. Am J Perinatol. 2024 Oct 8. doi: 10.1055/a-2418-9955. Epub ahead of print. PMID: 39379025.
Ramamurthy E, Agarwal S, Toong N, Sestili H, Kaplow IM, Chen Z, Phan B, Pfenning AR. Regression convolutional neural network models implicate peripheral immune regulatory variants in the predisposition to Alzheimer's disease. PLoS Comput Biol. 2024 Aug 26;20(8):e1012356. doi: 10.1371/journal.pcbi.1012356. PMID: 39186798; PMCID: PMC11389932.
Wirthlin ME, Schmid TA, Elie JE, Zhang X, Kowalczyk A, Redlich R, Shvareva VA, Rakuljic A, Ji MB, Bhat NS, Kaplow IM, Schäffer DE, Lawler AJ, Wang AZ, Phan BN, Annaldasula S, Brown AR, Lu T, Lim BK, Azim E; Zoonomia Consortium; Clark NL, Meyer WK, Pond SLK, Chikina M, Yartsev MM, Pfenning AR, Andrews G, Armstrong JC, Bianchi M, Birren BW, Bredemeyer KR, Breit AM, Christmas MJ, Clawson H, Damas J, Di Palma F, Diekhans M, Dong MX, Eizirik E, Fan K, Fanter C, Foley NM, Forsberg-Nilsson K, Garcia CJ, Gatesy J, Gazal S, Genereux DP, Goodman L, Grimshaw J, Halsey MK, Harris AJ, Hickey G, Hiller M, Hindle AG, Hubley RM, Hughes GM, Johnson J, Juan D, Kaplow IM, Karlsson EK, Keough KC, Kirilenko B, Koepfli KP, Korstian JM, Kowalczyk A, Kozyrev SV, Lawler AJ, Lawless C, Lehmann T, Levesque DL, Lewin HA, Li X, Lind A, Lindblad-Toh K, Mackay-Smith A, Marinescu VD, Marques-Bonet T, Mason VC, Meadows JRS, Meyer WK, Moore JE, Moreira LR, Moreno-Santillan DD, Morrill KM, Muntané G, Murphy WJ, Navarro A, Nweeia M, Ortmann S, Osmanski A, Paten B, Paulat NS, Pfenning AR, Phan BN, Pollard KS, Pratt HE, Ray DA, Reilly SK, Rosen JR, Ruf I, Ryan L, Ryder OA, Sabeti PC, Schäffer DE, Serres A, Shapiro B, Smit AFA, Springer M, Srinivasan C, Steiner C, Storer JM, Sullivan KAM, Sullivan PF, Sundström E, Supple MA, Swofford R, Talbot JE, Teeling E, Turner-Maier J, Valenzuela A, Wagner F, Wallerman O, Wang C, Wang J, Weng Z, Wilder AP, Wirthlin ME, Xue JR, Zhang X. Vocal learning-associated convergent evolution in mammalian proteins and regulatory elements. Science. 2024 Mar 29;383(6690):eabn3263. doi: 10.1126/science.abn3263. Epub 2024 Mar 29. PMID: 38422184; PMCID: PMC11313673.
Phan BN, Ray MH, Xue X, Fu C, Fenster RJ, Kohut SJ, Bergman J, Haber SN, McCullough KM, Fish MK, Glausier JR, Su Q, Tipton AE, Lewis DA, Freyberg Z, Tseng GC, Russek SJ, Alekseyev Y, Ressler KJ, Seney ML, Pfenning AR, Logan RW. Single nuclei transcriptomics in human and non-human primate striatum in opioid use disorder. Nat Commun. 2024 Jan 31;15(1):878. doi: 10.1038/s41467-024-45165-7. PMID: 38296993; PMCID: PMC10831093.
Chen HY, Phan BN, Shim G, Hamersky GR, Sadowski N, O'Donnell TS, Sripathy SR, Bohlen JF, Pfenning AR, Maher BJ. Psychiatric risk gene Transcription Factor 4 (TCF4) regulates the density and connectivity of distinct inhibitory interneuron subtypes. Mol Psychiatry. 2023 Nov;28(11):4679-4692. doi: 10.1038/s41380-023-02248-z. Epub 2023 Sep 28. PMID: 37770578; PMCID: PMC11144438.
Gayden J, Puig S, Srinivasan C, Phan BN, Abdelhady G, Buck SA, Gamble MC, Tejeda HA, Dong Y, Pfenning AR, Logan RW, Freyberg Z. Integrative multi-dimensional characterization of striatal projection neuron heterogeneity in adult brain. bioRxiv [Preprint]. 2023 Oct 21:2023.05.04.539488. doi: 10.1101/2023.05.04.539488. PMID: 37205475; PMCID: PMC10187292.
Kaplow IM, Lawler AJ, Schäffer DE, Srinivasan C, Sestili HH, Wirthlin ME, Phan BN, Prasad K, Brown AR, Zhang X, Foley K, Genereux DP; Zoonomia Consortium**; Karlsson EK, Lindblad-Toh K, Meyer WK, Pfenning AR. Relating enhancer genetic variation across mammals to complex phenotypes using machine learning. Science. 2023 Apr 28;380(6643):eabm7993. doi: 10.1126/science.abm7993. Epub 2023 Apr 28. PMID: 37104615; PMCID: PMC10322212.
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wang C, Wallerman O, Xue J, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler A, Keough KC, Zheng Z, Zeng J, Wray NR, Li Y, Johnson J, Chen J; Zoonomia Consortium§; Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging base-pair mammalian constraint to understand genetic variation and human disease. Science. 2023 Apr 28;380(6643):eabn2937. doi: 10.1126/science.abn2937. Epub 2023 Apr 28. PMID: 37104612; PMCID: PMC10259825.
Christmas MJ, Kaplow IM, Genereux DP, Dong MX, Hughes GM, Li X, Sullivan PF, Hindle AG, Andrews G, Armstrong JC, Bianchi M, Breit AM, Diekhans M, Fanter C, Foley NM, Goodman DB, Goodman L, Keough KC, Kirilenko B, Kowalczyk A, Lawless C, Lind AL, Meadows JRS, Moreira LR, Redlich RW, Ryan L, Swofford R, Valenzuela A, Wagner F, Wallerman O, Brown AR, Damas J, Fan K, Gatesy J, Grimshaw J, Johnson J, Kozyrev SV, Lawler AJ, Marinescu VD, Morrill KM, Osmanski A, Paulat NS, Phan BN, Reilly SK, Schäffer DE, Steiner C, Supple MA, Wilder AP, Wirthlin ME, Xue JR; Zoonomia Consortium§; Birren BW, Gazal S, Hubley RM, Koepfli KP, Marques-Bonet T, Meyer WK, Nweeia M, Sabeti PC, Shapiro B, Smit AFA, Springer MS, Teeling EC, Weng Z, Hiller M, Levesque DL, Lewin HA, Murphy WJ, Navarro A, Paten B, Pollard KS, Ray DA, Ruf I, Ryder OA, Pfenning AR, Lindblad-Toh K, Karlsson EK. Evolutionary constraint and innovation across hundreds of placental mammals. Science. 2023 Apr 28;380(6643):eabn3943. doi: 10.1126/science.abn3943. Epub 2023 Apr 28. PMID: 37104599; PMCID: PMC10250106.
Sullivan PF, Meadows JRS, Gazal S, Phan BN, Li X, Genereux DP, Dong MX, Bianchi M, Andrews G, Sakthikumar S, Nordin J, Roy A, Christmas MJ, Marinescu VD, Wallerman O, Xue JR, Li Y, Yao S, Sun Q, Szatkiewicz J, Wen J, Huckins LM, Lawler AJ, Keough KC, Zheng Z, Zeng J, Wray NR, Johnson J, Chen J; Zoonomia Consortium; Paten B, Reilly SK, Hughes GM, Weng Z, Pollard KS, Pfenning AR, Forsberg-Nilsson K, Karlsson EK, Lindblad-Toh K. Leveraging Base Pair Mammalian Constraint to Understand Genetic Variation and Human Disease. bioRxiv [Preprint]. 2023 Mar 10:2023.03.10.531987. doi: 10.1101/2023.03.10.531987. Update in: Science. 2023 Apr 28;380(6643):eabn2937. doi: 10.1126/science.abn2937. PMID: 36945512; PMCID: PMC10028973.
Desai DD, Yu SE, Salvatore B, Goldberg Z, Bowers EMR, Moore JA, Phan B, Lee SE. Olfactory and neurological outcomes of SARS-CoV-2 from acute infection to recovery. Front Allergy. 2022 Oct 26;3:1019274. doi: 10.3389/falgy.2022.1019274. PMID: 36389036; PMCID: PMC9644087.
Morris J, Olonisakin TF, Moore JA, Phan B, Parker DM, Uribe BA, Barel SJ, Bowers EMR, Buchheit KM, Laidlaw TM, Lee SE. Inhibiting the type 2 inflammatory pathway with dupilumab is associated with an increase in interleukin-4 and interleukin-18 production. Int Forum Allergy Rhinol. 2022 Oct;12(10):1313-1316. doi: 10.1002/alr.23003. Epub 2022 Apr 29. PMID: 35394682.
Lawler AJ, Ramamurthy E, Brown AR, Shin N, Kim Y, Toong N, Kaplow IM, Wirthlin M, Zhang X, Phan BN, Fox GA, Wade K, He J, Ozturk BE, Byrne LC, Stauffer WR, Fish KN, Pfenning AR. Machine learning sequence prioritization for cell type-specific enhancer design. Elife. 2022 May 16;11:e69571. doi: 10.7554/eLife.69571. PMID: 35576146; PMCID: PMC9110026.
Xue X, Zong W, Glausier JR, Kim SM, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Seney ML, Logan RW. Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder. Transl Psychiatry. 2022 Mar 26;12(1):123. doi: 10.1038/s41398-022-01894-1. PMID: 35347109; PMCID: PMC8960783.
Ramnauth AD, Maynard KR, Kardian AS, Phan BN, Tippani M, Rajpurohit S, Hobbs JW, Page SC, Jaffe AE, Martinowich K. Induction of Bdnf from promoter I following electroconvulsive seizures contributes to structural plasticity in neurons of the piriform cortex. Brain Stimul. 2022 Mar-Apr;15(2):427-433. doi: 10.1016/j.brs.2022.02.003. Epub 2022 Feb 17. PMID: 35183789; PMCID: PMC8957536.
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 Oct 27;41(43):9008-9030. doi: 10.1523/JNEUROSCI.2534-20.2021. Epub 2021 Aug 30. PMID: 34462306; PMCID: PMC8549541.
Seney ML, Kim SM, Glausier JR, Hildebrand MA, Xue X, Zong W, Wang J, Shelton MA, Phan BN, Srinivasan C, Pfenning AR, Tseng GC, Lewis DA, Freyberg Z, Logan RW. Transcriptional Alterations in Dorsolateral Prefrontal Cortex and Nucleus Accumbens Implicate Neuroinflammation and Synaptic Remodeling in Opioid Use Disorder. Biol Psychiatry. 2021 Oct 15;90(8):550-562. doi: 10.1016/j.biopsych.2021.06.007. Epub 2021 Jun 12. PMID: 34380600; PMCID: PMC8463497.
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. Correction to: SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor‑powered RNA‑seq analyses. BMC Bioinformatics. 2021 Jul 22;22(1):381. doi: 10.1186/s12859-021-04283-5. Erratum for: BMC Bioinformatics. 2021 May 1;22(1):224. doi: 10.1186/s12859-021-04142-3. PMID: 34294043; PMCID: PMC8299680.
Eagles NJ, Burke EE, Leonard J, Barry BK, Stolz JM, Huuki L, Phan BN, Serrato VL, Gutiérrez-Millán E, Aguilar-Ordoñez I, Jaffe AE, Collado-Torres L. SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses. BMC Bioinformatics. 2021 May 1;22(1):224. doi: 10.1186/s12859-021-04142-3. Erratum in: BMC Bioinformatics. 2021 Jul 22;22(1):381. doi: 10.1186/s12859-021-04283-5. PMID: 33932985; PMCID: PMC8088074.
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. PMID: 30710716.
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. PMID: 30467002.