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The tumour microenvironment shapes innate lymphoid cells in patients with hepatocellular carcinoma.
Heinrich B, Gertz EM, Schäffer AA, Craig A, Ruf B, Subramanyam V, McVey JC, Diggs LP, Heinrich S, Rosato U, Ma C, Yan C, Hu Y, Zhao Y, Shen TW, Kapoor V, Telford W, Kleiner DE, Stovroff MK, Dhani HS, Kang J, Fishbein T, Wang XW, Ruppin E, Kroemer A, Greten TF, Korangy F. Heinrich B, et al. Among authors: zhao y. Gut. 2022 Jun;71(6):1161-1175. doi: 10.1136/gutjnl-2021-325288. Epub 2021 Aug 2. Gut. 2022. PMID: 34340996 Free PMC article.
Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
Fang LT, Zhu B, Zhao Y, Chen W, Yang Z, Kerrigan L, Langenbach K, de Mars M, Lu C, Idler K, Jacob H, Zheng Y, Ren L, Yu Y, Jaeger E, Schroth GP, Abaan OD, Talsania K, Lack J, Shen TW, Chen Z, Stanbouly S, Tran B, Shetty J, Kriga Y, Meerzaman D, Nguyen C, Petitjean V, Sultan M, Cam M, Mehta M, Hung T, Peters E, Kalamegham R, Sahraeian SME, Mohiyuddin M, Guo Y, Yao L, Song L, Lam HYK, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Jensen RV, Pirooznia M, Li Z, Xiao C, Sherry ST, Kusko R, Moos M, Donaldson E, Tezak Z, Ning B, Tong W, Li J, Duerken-Hughes P, Catalanotti C, Maheshwari S, Shuga J, Liang WS, Keats J, Adkins J, Tassone E, Zismann V, McDaniel T, Trent J, Foox J, Butler D, Mason CE, Hong H, Shi L, Wang C, Xiao W; Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium. Fang LT, et al. Among authors: zhao y. Nat Biotechnol. 2021 Sep;39(9):1151-1160. doi: 10.1038/s41587-021-00993-6. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504347 Free PMC article.
Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.
Zhao Y, Fang LT, Shen TW, Choudhari S, Talsania K, Chen X, Shetty J, Kriga Y, Tran B, Zhu B, Chen Z, Chen W, Wang C, Jaeger E, Meerzaman D, Lu C, Idler K, Ren L, Zheng Y, Shi L, Petitjean V, Sultan M, Hung T, Peters E, Drabek J, Vojta P, Maestro R, Gasparotto D, Kõks S, Reimann E, Scherer A, Nordlund J, Liljedahl U, Foox J, Mason CE, Xiao C, Hong H, Xiao W. Zhao Y, et al. Sci Data. 2021 Nov 9;8(1):296. doi: 10.1038/s41597-021-01077-5. Sci Data. 2021. PMID: 34753956 Free PMC article.
Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures.
Latt KZ, Heymann J, Jessee JH, Rosenberg AZ, Berthier CC, Arazi A, Eddy S, Yoshida T, Zhao Y, Chen V, Nelson GW, Cam M, Kumar P, Mehta M, Kelly MC, Kretzler M; Nephrotic Syndrome Study Network (NEPTUNE); Accelerating Medicines Partnership in Rheumatoid Arthritis and Systemic Lupus Erythematosus (AMP RA/SLE) Consortium; Ray PE, Moxey-Mims M, Gorman GH, Lechner BL, Regunathan-Shenk R, Raj DS, Susztak K, Winkler CA, Kopp JB. Latt KZ, et al. Among authors: zhao y. Kidney Int Rep. 2021 Nov 25;7(2):289-304. doi: 10.1016/j.ekir.2021.11.005. eCollection 2022 Feb. Kidney Int Rep. 2021. PMID: 35155868 Free PMC article.
HIV viral protein R induces loss of DCT1-type renal tubules.
Latt KZ, Yoshida T, Shrivastav S, Abedini A, Reece JM, Sun Z, Lee H, Okamoto K, Dagur P, Heymann J, Zhao Y, Chung JY, Hewitt S, Jose PA, Lee K, He JC, Winkler CA, Knepper MA, Kino T, Rosenberg AZ, Susztak K, Kopp JB. Latt KZ, et al. Among authors: zhao y. bioRxiv [Preprint]. 2023 Nov 13:2023.02.02.526686. doi: 10.1101/2023.02.02.526686. bioRxiv. 2023. PMID: 36945458 Free PMC article. Preprint.
APOL1 kidney risk variants in glomerular diseases modeled in transgenic mice.
Yoshida T, Latt KZ, Santo BA, Shrivastav S, Zhao Y, Fenaroli P, Chung JY, Hewitt SM, Tutino VM, Sarder P, Rosenberg AZ, Winkler CA, Kopp JB. Yoshida T, et al. Among authors: zhao y. bioRxiv [Preprint]. 2023 Mar 27:2023.03.27.534273. doi: 10.1101/2023.03.27.534273. bioRxiv. 2023. PMID: 37090576 Free PMC article. Preprint.
Tumor biology and immune infiltration define primary liver cancer subsets linked to overall survival after immunotherapy.
Budhu A, Pehrsson EC, He A, Goyal L, Kelley RK, Dang H, Xie C, Monge C, Tandon M, Ma L, Revsine M, Kuhlman L, Zhang K, Baiev I, Lamm R, Patel K, Kleiner DE, Hewitt SM, Tran B, Shetty J, Wu X, Zhao Y, Shen TW, Choudhari S, Kriga Y, Ylaya K, Warner AC, Edmondson EF, Forgues M, Greten TF, Wang XW. Budhu A, et al. Among authors: zhao y. Cell Rep Med. 2023 Jun 20;4(6):101052. doi: 10.1016/j.xcrm.2023.101052. Epub 2023 May 23. Cell Rep Med. 2023. PMID: 37224815 Free PMC article.
Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.
Xiao W, Ren L, Chen Z, Fang LT, Zhao Y, Lack J, Guan M, Zhu B, Jaeger E, Kerrigan L, Blomquist TM, Hung T, Sultan M, Idler K, Lu C, Scherer A, Kusko R, Moos M, Xiao C, Sherry ST, Abaan OD, Chen W, Chen X, Nordlund J, Liljedahl U, Maestro R, Polano M, Drabek J, Vojta P, Kõks S, Reimann E, Madala BS, Mercer T, Miller C, Jacob H, Truong T, Moshrefi A, Natarajan A, Granat A, Schroth GP, Kalamegham R, Peters E, Petitjean V, Walton A, Shen TW, Talsania K, Vera CJ, Langenbach K, de Mars M, Hipp JA, Willey JC, Wang J, Shetty J, Kriga Y, Raziuddin A, Tran B, Zheng Y, Yu Y, Cam M, Jailwala P, Nguyen C, Meerzaman D, Chen Q, Yan C, Ernest B, Mehra U, Jensen RV, Jones W, Li JL, Papas BN, Pirooznia M, Chen YC, Seifuddin F, Li Z, Liu X, Resch W, Wang J, Wu L, Yavas G, Miles C, Ning B, Tong W, Mason CE, Donaldson E, Lababidi S, Staudt LM, Tezak Z, Hong H, Wang C, Shi L. Xiao W, et al. Among authors: zhao y. Nat Biotechnol. 2021 Sep;39(9):1141-1150. doi: 10.1038/s41587-021-00994-5. Epub 2021 Sep 9. Nat Biotechnol. 2021. PMID: 34504346 Free PMC article.
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