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RFX6 Maintains Gene Expression and Function of Adult Human Islet α-Cells. Coykendall VMN, Qian MF, Tellez K, Bautista A, Bevacqua RJ, Gu X, Hang Y, Neukam M, Zhao W, Chang C, MacDonald PE, Kim SK. Diabetes. 2024 Mar 1;73(3):448-460. doi: 10.2337/db23-0483. PMID: 38064570; PMCID: PMC10882151.

Multiplexed CRISPR gene editing in primary human islet cells with Cas9 ribonucleoprotein. Bevacqua RJ, Zhao W, Merheb E, Kim SH, Marson A, Gloyn AL, Kim SK. iScience. 2023 Dec 8;27(1):108693. doi: 10.1016/j.isci.2023.108693. PMID: 38205242; PMCID: PMC10777115.

HNF1α maintains pancreatic α and β cell functions in primary human islets. Qian MF, Bevacqua RJ, Coykendall VM, Liu X, Zhao W, Chang CA, Gu X, Dai XQ, MacDonald PE, Kim SK. JCI Insight. 2023 Dec 22;8(24):e170884. doi: 10.1172/jci.insight.170884. PMID: 37943614; PMCID: PMC10807710.

Digital health application integrating wearable data and behavioral patterns improves metabolic health. Zahedani AD, McLaughlin T, Veluvali A, Aghaeepour N, Hosseinian A, Agarwal S, Ruan J, Tripathi S, Woodward M, Hashemi N, Snyder M. NPJ Digit Med. 2023 Nov 25;6(1):216. doi: 10.1038/s41746-023-00956-y. Erratum in: NPJ Digit Med. 2024 Jan 12;7(1):9. doi: 10.1038/s41746-024-00996-y. PMID: 38001287; PMCID: PMC10673832.

Dynamic lipidome alterations associated with human health, disease and ageing. Hornburg D, Wu S, Moqri M, Zhou X, Contrepois K, Bararpour N, Traber GM, Su B, Metwally AA, Avina M, Zhou W, Ubellacker JM, Mishra T, Schüssler-Fiorenza Rose SM, Kavathas PB, Williams KJ, Snyder MP. Nat Metab. 2023 Sep;5(9):1578-1594. doi: 10.1038/s42255-023-00880-1. Epub 2023 Sep 11. PMID: 37697054; PMCID: PMC10513930.

A single-cell CRISPRi platform for characterizing candidate genes relevant to metabolic disorders in human adipocytes. Bielczyk-Maczynska E, Sharma D, Blencowe M, Saliba Gustafsson P, Gloudemans MJ, Yang X, Carcamo-Orive I, Wabitsch M, Svensson KJ, Park CY, Quertermous T, Knowles JW, Li J. Am J Physiol Cell Physiol. 2023 Sep 1;325(3):C648-C660. doi: 10.1152/ajpcell.00148.2023. Epub 2023 Jul 24. PMID: 37486064; PMCID: PMC10635647.

Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing. Henn D, Zhao D, Sivaraj D, Trotsyuk A, Bonham CA, Fischer KS, Kehl T, Fehlmann T, Greco AH, Kussie HC, Moortgat Illouz SE, Padmanabhan J, Barrera JA, Kneser U, Lenhof HP, Januszyk M, Levi B, Keller A, Longaker MT, Chen K, Qi LS, Gurtner GC. Nat Commun. 2023 Aug 7;14(1):4729. doi: 10.1038/s41467-023-40519-z. PMID: 37550295; PMCID: PMC10406832.

Organism-wide, cell-type-specific secretome mapping of exercise training in mice. Wei W, Riley NM, Lyu X, Shen X, Guo J, Raun SH, Zhao M, Moya-Garzon MD, Basu H, Sheng-Hwa Tung A, Li VL, Huang W, Wiggenhorn AL, Svensson KJ, Snyder MP, Bertozzi CR, Long JZ. Cell Metab. 2023 Jul 11;35(7):1261-1279.e11. doi: 10.1016/j.cmet.2023.04.011. Epub 2023 May 3. PMID: 37141889; PMCID: PMC10524249.

Single-cell transcriptome dataset of human and mouse in vitro adipogenesis models. Li J, Jin C, Gustafsson S, Rao A, Wabitsch M, Park CY, Quertermous T, Bielczyk-Maczynska E, Knowles JW. bioRxiv [Preprint]. 2023 Mar 29:2023.03.27.534456. doi: 10.1101/2023.03.27.534456. Update in: Sci Data. 2023 Jun 16;10(1):387. doi: 10.1038/s41597-023-02293-x. PMID: 37034809; PMCID: PMC10081256.

Macrophage inflammatory and regenerative response periodicity is programmed by cell cycle and chromatin state. Daniel B, Belk JA, Meier SL, Chen AY, Sandor K, Czimmerer Z, Varga Z, Bene K, Buquicchio FA, Qi Y, Kitano H, Wheeler JR, Foster DS, Januszyk M, Longaker MT, Chang HY, Satpathy AT. Mol Cell. 2023 Jan 5;83(1):121-138.e7. doi: 10.1016/j.molcel.2022.11.017. Epub 2022 Dec 14. PMID: 36521490; PMCID: PMC9831293.

Divergent clonal differentiation trajectories of T cell exhaustion. Daniel B, Yost KE, Hsiung S, Sandor K, Xia Y, Qi Y, Hiam-Galvez KJ, Black M, J Raposo C, Shi Q, Meier SL, Belk JA, Giles JR, Wherry EJ, Chang HY, Egawa T, Satpathy AT. Nat Immunol. 2022 Nov;23(11):1614-1627. doi: 10.1038/s41590-022-01337-5. Epub 2022 Oct 26. PMID: 36289450; PMCID: PMC11225711.

Single-cell sequencing unveils distinct immune microenvironments with CCR6-CCL20 crosstalk in human chronic pancreatitis. Lee B, Namkoong H, Yang Y, Huang H, Heller D, Szot GL, Davis MM, Husain SZ, Pandol SJ, Bellin MD, Habtezion A. Gut. 2022 Sep;71(9):1831-1842. doi: 10.1136/gutjnl-2021-324546. Epub 2021 Oct 26. PMID: 34702715; PMCID: PMC9105403.

Robust identification of temporal biomarkers in longitudinal omics studies. Metwally AA, Zhang T, Wu S, Kellogg R, Zhou W, Contrepois K, Tang H, Snyder M. Bioinformatics. 2022 Aug 2;38(15):3802-3811. doi: 10.1093/bioinformatics/btac403. PMID: 35762936; PMCID: PMC9344853.

Generating human artery and vein cells from pluripotent stem cells highlights the arterial tropism of Nipah and Hendra viruses. Ang LT, Nguyen AT, Liu KJ, Chen A, Xiong X, Curtis M, Martin RM, Raftry BC, Ng CY, Vogel U, Lander A, Lesch BJ, Fowler JL, Holman AR, Chai T, Vijayakumar S, Suchy FP, Nishimura T, Bhadury J, Porteus MH, Nakauchi H, Cheung C, George SC, Red-Horse K, Prescott JB, Loh KM. Cell. 2022 Jul 7;185(14):2523-2541.e30. doi: 10.1016/j.cell.2022.05.024. Epub 2022 Jun 22. PMID: 35738284; PMCID: PMC9617591.

Lymph node colonization induces tumor-immune tolerance to promote distant metastasis. Reticker-Flynn NE, Zhang W, Belk JA, Basto PA, Escalante NK, Pilarowski GOW, Bejnood A, Martins MM, Kenkel JA, Linde IL, Bagchi S, Yuan R, Chang S, Spitzer MH, Carmi Y, Cheng J, Tolentino LL, Choi O, Wu N, Kong CS, Gentles AJ, Sunwoo JB, Satpathy AT, Plevritis SK, Engleman EG. Cell. 2022 May 26;185(11):1924-1942.e23. doi: 10.1016/j.cell.2022.04.019. Epub 2022 May 6. PMID: 35525247; PMCID: PMC9149144.

Genome-wide identification of the genetic basis of amyotrophic lateral sclerosis. Zhang S, Cooper-Knock J, Weimer AK, Shi M, Moll T, Marshall JNG, Harvey C, Nezhad HG, Franklin J, Souza CDS, Ning K, Wang C, Li J, Dilliott AA, Farhan S, Elhaik E, Pasniceanu I, Livesey MR, Eitan C, Hornstein E, Kenna KP; Project MinE ALS Sequencing Consortium, Veldink JH, Ferraiuolo L, Shaw PJ, Snyder MP. Neuron. 2022 Mar 16;110(6):992-1008.e11. doi: 10.1016/j.neuron.2021.12.019. Epub 2022 Jan 18. PMID: 35045337; PMCID: PMC9017397.

Invariant natural killer T-cell subsets have diverse graft-versus-host-disease-preventing and antitumor effects. Maas-Bauer K, Lohmeyer JK, Hirai T, Ramos TL, Fazal FM, Litzenburger UM, Yost KE, Ribado JV, Kambham N, Wenokur AS, Lin PY, Alvarez M, Mavers M, Baker J, Bhatt AS, Chang HY, Simonetta F, Negrin RS. Blood. 2021 Sep 9;138(10):858-870. doi: 10.1182/blood.2021010887. PMID: 34036317; PMCID: PMC8432044.

Xenogeneic skin transplantation promotes angiogenesis and tissue regeneration through activated Trem2+ macrophages. Henn D, Chen K, Fehlmann T, Trotsyuk AA, Sivaraj D, Maan ZN, Bonham CA Jr, Barrera JA, Mays CJ, Greco AH, Moortgat Illouz SE, Lin JQ, Steele SR, Foster DS, Padmanabhan J, Momeni A, Nguyen D, Wan DC, Kneser U, Januszyk M, Keller A, Longaker MT, Gurtner GC. Sci Adv. 2021 Dec 3;7(49):eabi4528. doi: 10.1126/sciadv.abi4528. Epub 2021 Dec 1. PMID: 34851663; PMCID: PMC8635426.

Integrated spatial multiomics reveals fibroblast fate during tissue repair. Foster DS, Januszyk M, Yost KE, Chinta MS, Gulati GS, Nguyen AT, Burcham AR, Salhotra A, Ransom RC, Henn D, Chen K, Mascharak S, Tolentino K, Titan AL, Jones RE, da Silva O, Leavitt WT, Marshall CD, des Jardins-Park HE, Hu MS, Wan DC, Wernig G, Wagh D, Coller J, Norton JA, Gurtner GC, Newman AM, Chang HY, Longaker MT. Proc Natl Acad Sci U S A. 2021 Oct 12;118(41):e2110025118. doi: 10.1073/pnas.2110025118. PMID: 34620713; PMCID: PMC8521719.

Multi-omic profiling reveals widespread dysregulation of innate immunity and hematopoiesis in COVID-19. Wilk AJ, Lee MJ, Wei B, Parks B, Pi R, Martínez-Colón GJ, Ranganath T, Zhao NQ, Taylor S, Becker W; Stanford COVID-19 Biobank; Jimenez-Morales D, Blomkalns AL, O'Hara R, Ashley EA, Nadeau KC, Yang S, Holmes S, Rabinovitch M, Rogers AJ, Greenleaf WJ, Blish CA. J Exp Med. 2021 Aug 2;218(8):e20210582. doi: 10.1084/jem.20210582. Epub 2021 Jun 15. PMID: 34128959; PMCID: PMC8210586.

Pre-clinical development and molecular characterization of an engineered type 1 regulatory T-cell product suitable for immunotherapy. Liu JM, Chen P, Uyeda MJ, Cieniewicz B, Sayitoglu EC, Thomas BC, Sato Y, Bacchetta R, Cepika AM, Roncarolo MG. Cytotherapy. 2021 Nov;23(11):1017-1028. doi: 10.1016/j.jcyt.2021.05.010. Epub 2021 Aug 15. PMID: 34404616; PMCID: PMC8546780.

Alloantigen-specific type 1 regulatory T cells suppress through CTLA-4 and PD-1 pathways and persist long-term in patients. Chen PP, Cepika AM, Agarwal-Hashmi R, Saini G, Uyeda MJ, Louis DM, Cieniewicz B, Narula M, Amaya Hernandez LC, Harre N, Xu L, Thomas BC, Ji X, Shiraz P, Tate KM, Margittai D, Bhatia N, Meyer E, Bertaina A, Davis MM, Bacchetta R, Roncarolo MG. Sci Transl Med. 2021 Oct 27;13(617):eabf5264. doi: 10.1126/scitranslmed.abf5264. Epub 2021 Oct 27. PMID: 34705520; PMCID: PMC9451143.

Evolution of Cytomegalovirus-Responsive T Cell Clonality following Solid Organ Transplantation. Higdon LE, Schaffert S, Huang H, Montez-Rath ME, Lucia M, Jha A, Saligrama N, Margulies KB, Martinez OM, Davis MM, Khatri P, Maltzman JS. J Immunol. 2021 Oct 15;207(8):2077-2085. doi: 10.4049/jimmunol.2100404. Epub 2021 Sep 22. PMID: 34551964; PMCID: PMC8492537.

Functional Consequences of Memory Inflation after Solid Organ Transplantation. Higdon LE, Schaffert S, Cohen RH, Montez-Rath ME, Lucia M, Saligrama N, Margulies KB, Martinez OM, Tan JC, Davis MM, Khatri P, Maltzman JS. J Immunol. 2021 Oct 15;207(8):2086-2095. doi: 10.4049/jimmunol.2100405. Epub 2021 Sep 22. PMID: 34551963; PMCID: PMC8492533.

Disrupting biological sensors of force promotes tissue regeneration in large organisms. Chen K, Kwon SH, Henn D, Kuehlmann BA, Tevlin R, Bonham CA, Griffin M, Trotsyuk AA, Borrelli MR, Noishiki C, Padmanabhan J, Barrera JA, Maan ZN, Dohi T, Mays CJ, Greco AH, Sivaraj D, Lin JQ, Fehlmann T, Mermin-Bunnell AM, Mittal S, Hu MS, Zamaleeva AI, Keller A, Rajadas J, Longaker MT, Januszyk M, Gurtner GC. Nat Commun. 2021 Sep 6;12(1):5256. doi: 10.1038/s41467-021-25410-z. PMID: 34489407; PMCID: PMC8421385.

Discovery of ciliary G protein-coupled receptors regulating pancreatic islet insulin and glucagon secretion. Wu CT, Hilgendorf KI, Bevacqua RJ, Hang Y, Demeter J, Kim SK, Jackson PK. Genes Dev. 2021 Sep 1;35(17-18):1243-1255. doi: 10.1101/gad.348261.121. Epub 2021 Aug 12. PMID: 34385262; PMCID: PMC8415323.

Longitudinal linked-read sequencing reveals ecological and evolutionary responses of a human gut microbiome during antibiotic treatment. Roodgar M, Good BH, Garud NR, Martis S, Avula M, Zhou W, Lancaster SM, Lee H, Babveyh A, Nesamoney S, Pollard KS, Snyder MP. Genome Res. 2021 Aug;31(8):1433-1446. doi: 10.1101/gr.265058.120. Epub 2021 Jul 22. PMID: 34301627; PMCID: PMC8327913.

Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging. Rovira-Clavé X, Jiang S, Bai Y, Zhu B, Barlow G, Bhate S, Coskun AF, Han G, Ho CK, Hitzman C, Chen SY, Bava FA, Nolan GP. Nat Commun. 2021 Jul 30;12(1):4628. doi: 10.1038/s41467-021-24822-1. PMID: 34330905; PMCID: PMC8324837.

Skeletal stem and progenitor cells maintain cranial suture patency and prevent craniosynostosis. Menon S, Salhotra A, Shailendra S, Tevlin R, Ransom RC, Januszyk M, Chan CKF, Behr B, Wan DC, Longaker MT, Quarto N. Nat Commun. 2021 Jul 30;12(1):4640. doi: 10.1038/s41467-021-24801-6. PMID: 34330896; PMCID: PMC8324898.

An inflammatory aging clock (iAge) based on deep learning tracks multimorbidity, immunosenescence, frailty and cardiovascular aging. Sayed N, Huang Y, Nguyen K, Krejciova-Rajaniemi Z, Grawe AP, Gao T, Tibshirani R, Hastie T, Alpert A, Cui L, Kuznetsova T, Rosenberg-Hasson Y, Ostan R, Monti D, Lehallier B, Shen-Orr SS, Maecker HT, Dekker CL, Wyss-Coray T, Franceschi C, Jojic V, Haddad F, Montoya JG, Wu JC, Davis MM, Furman D. Nat Aging. 2021 Jul;1:598-615. doi: 10.1038/s43587-021-00082-y. Epub 2021 Jul 12. PMID: 34888528; PMCID: PMC8654267.

Pancreatic Pseudoislets: An Organoid Archetype for Metabolism Research. Friedlander MSH, Nguyen VM, Kim SK, Bevacqua RJ. Diabetes. 2021 May;70(5):1051-1060. doi: 10.2337/db20-1115. Epub 2021 May 4. PMID: 33947722; PMCID: PMC8343609.