Publications

Featured Publications

Multiomics profiling of mouse polycystic kidney disease progression at a single-cell resolution.
Muto Y, Yoshimura Y, Wu H, Chang-Panesso M, Ledru N, Woodward OM, Outeda P, Cheng T, Mahjoub MR, Watnick, TJ, Humphreys BD. Proceedings of the National Academy of Sciences of the United States of America, 2024, 121, e2410830121

Epigenetic reprogramming driving successful and failed repair in acute kidney injury.
Muto Y, Dixon EE, Yoshimura Y, Ledru N, Kirita Y, Wu H, Humphreys BD. Science Advances, 2024 Aug 9;10(32): eado284

Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis.
Muto Y, Dixon EE, Yoshimura Y, Wu H, Omachi K, Wilson PC, King AJ, Olson EN, Gunawan MG, Kuo JJ, Cox J, Miner JH, Seliger SL, Woodward OM, Welling PA, Watnick TJ, Humphreys BD. Nature Communications, 2022 Oct 30;13(1):6497.

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney.
Muto Y, Wilson PC, Ledru N, Wu H, Dimke H, Waikar SS, Humphreys BD. Nature Communications. 2021 Apr 13;12(1):2190

Disruption of FBXL5-mediated cellular iron homeostasis promotes liver carcinogenesis.
Muto Y, Moroishi T, Ichihara K, Nishiyama M, Shimizu H, Eguchi H, Moriya K, Koike K, Mimori K, Mori M, Katayama Y, Nakayama KI. Journal of Experimental Medicine, 2019 Apr 1;216(4):950-965

Essential role of FBXL5-mediated cellular iron homeostasis in maintenance of hematopoietic stem cells.
Muto Y, Nita A, Nishiyama M, Moroishi T, Nakayama KI. Nature Communications, 2017 Jul 17;8:16114.

Multiomics profiling of mouse polycystic kidney disease progression at a single-cell resolution

Muto Y, Yoshimura Y, Wu H, Chang-Panesso M, Ledru N, Woodward OM, Outeda P, Cheng T, Mahjoub MR, Watnick TJ, Humphreys BD 2024 Oct Proceedings of the National Academy of Sciences of the United States of America 121

Epigenetic reprogramming driving successful and failed repair in acute kidney injury

Muto Y, Dixon EE, Ledru N, Kirita Y, Wu H, Humphreys BD 2024 Aug Science advances 10

Injury-induced Foxm1 expression in the mouse kidney drives epithelial proliferation by a cyclin F-dependent mechanism

Noonan ML, Muto Y, Yoshimura Y, Leckie-Harre A, Wu H, Kalinichenko VV, Humphreys BD, Chang-Panesso M 2024 Jun JCI insight 9

Multi-omics profiling of mouse polycystic kidney disease progression at a single cell resolution

Muto Y, Yoshimura Y, Wu H, Chang-Panesso M, Ledru N, Woodward OM, Outeda P, Cheng T, Mahjoub MR, Watnick TJ, Humphreys BD 2024 May bioRxiv : the preprint server for biology

TNIK depletion induces inflammation and apoptosis in injured renal proximal tubule epithelial cells

Bradford ST, Wu H, Kirita Y, Chen C, Malvin NP, Yoshimura Y, Muto Y, Humphreys BD 2024 May American Journal of Physiology - Renal Physiology 326 F827-F838

Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing

Ledru N, Wilson PC, Muto Y, Yoshimura Y, Wu H, Li D, Asthana A, Tullius SG, Waikar SS, Orlando G, Humphreys BD 2024 Feb Nature communications 15

Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease

Wilson PC, Verma A, Yoshimura Y, Muto Y, Li H, Malvin NP, Dixon EE, Humphreys BD 2024 Jan Genome biology 25

Leveraging multimodal chromatin profiling to identify a new potential driver of diabetic kidney disease

Muto Y, Humphreys BD 2024 Jan Kidney international 105 25-27

Elucidating the Proximal Tubule HNF4A Gene Regulatory Network in Human Kidney Organoids

Yoshimura Y, Muto Y, Omachi K, Miner JH, Humphreys BD 2023 Oct Journal of the American Society of Nephrology 34 1672-1686

A single-cell multiomic analysis of kidney organoid differentiation

Yoshimura Y, Muto Y, Ledru N, Wu H, Omachi K, Miner JH, Humphreys BD 2023 May Proceedings of the National Academy of Sciences of the United States of America 120

Tubular Epithelial Cell HMGB1 Promotes AKI-CKD Transition by Sensitizing Cycling Tubular Cells to Oxidative Stress: A Rationale for Targeting HMGB1 during AKI Recovery

Zhao ZB, Marschner JA, Iwakura T, Li C, Motrapu M, Kuang M, Popper B, Linkermann A, Klocke J, Enghard P, Muto Y, Humphreys BD, Harris HE, Romagnani P, Anders HJ 2023 Mar Journal of the American Society of Nephrology 34 394-411

Quality assessment and refinement of chromatin accessibility data using a sequence-based predictive model

Han SK, Muto Y, Wilson PC, Humphreys BD, Sampson MG, Chakravarti A, Lee D 2022 Dec Proceedings of the National Academy of Sciences of the United States of America 119

Defining cellular complexity in human autosomal dominant polycystic kidney disease by multimodal single cell analysis

Muto Y, Dixon EE, Yoshimura Y, Wu H, Omachi K, Ledru N, Wilson PC, King AJ, Eric Olson N, Gunawan MG, Kuo JJ, Cox JH, Miner JH, Seliger SL, Woodward OM, Welling PA, Watnick TJ, Humphreys BD 2022 Dec Nature communications 13

Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

Wilson PC, Muto Y, Wu H, Karihaloo A, Waikar SS, Humphreys BD 2022 Dec Nature communications 13

Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model

Dixon EE, Wu H, Muto Y, Wilson PC, Humphreys BD 2022 Feb Journal of the American Society of Nephrology 33

Single Cell Transcriptomics

Muto Y, Li H, Humphreys BD 2022 Jan 87-102

Single cell transcriptional and chromatin accessibility profiling redefine cellular heterogeneity in the adult human kidney

Muto Y, Wilson PC, Ledru N, Wu H, Dimke H, Waikar SS, Humphreys BD 2021 Dec Nature communications 12

Recent advances in lineage tracing for the kidney

Muto Y, Humphreys BD 2021 Dec Kidney international 100 1179-1184

Nita A, Muto Y, Katayama Y, Matsumoto A, Nishiyama M, Nakayama KI 2021 Feb Cell Reports 34

Skp2 contributes to cell cycle progression in trophoblast stem cells and to placental development

Yamauchi Y, Nita A, Nishiyama M, Muto Y, Shimizu H, Nakatsumi H, Nakayama KI 2020 Jun Genes to Cells 25 427-438

Disruption of FBXL5-mediated cellular iron homeostasis promotes liver carcinogenesis

Muto Y, Moroishi T, Ichihara K, Nishiyama M, Shimizu H, Eguchi H, Moriya K, Koike K, Mimori K, Mori M, Katayama Y, Nakayama KI 2019 Apr Journal of Experimental Medicine 216 950-965

A conditionally immortalized Gli1-positive kidney mesenchymal cell line models myofibroblast transition

Ó Hainmhire E, Wu H, Muto Y, Donnelly EL, Machado FG, Fan LX, Chang-Panesso M, Humphreys BD 2019 Jan American Journal of Physiology - Renal Physiology 316 F63-F75

Essential role of FBXL5-mediated cellular iron homeostasis in maintenance of hematopoietic stem cells

Muto Y, Nishiyama M, Nita A, Moroishi T, Nakayama KI 2017 Jul Nature communications 8

FBXL12 regulates T-cell differentiation in a cell-autonomous manner

Nita A, Nishiyama M, Muto Y, Nakayama KI 2016 May Genes to Cells 21 517-524

A case of cell-free and concentrated ascites reinfusion therapy effective for refractory ascites in spontaneous bacterial peritonitis in a renal transplant patient

Maeda A, Takeda K, Tsuruya K, Miura S, Toyonaga J, Nakashita S, Furushou M, Mukai H, Muto Y, Komaki T, Takae K, Yasunaga C 2012 Sep Case reports in nephrology and urology 2 138-44

Repeated Epstein-Barr virus-associated hemophagocytic syndrome in a lupus nephritis patient

Miura S, Takeda K, Muto Y, Mukai H, Furusho M, Nakashita S, Maeda A, Kimura H 2012 Jan Clinical Nephrology 77 71-74

Development of Wernicke's encephalopathy during initiation of hemodialysis in an elderly non-alcoholic patient

Kimura H, Takeda K, Muto Y, Mukai H, Furusho M, Nakashita S, Miura S, Maeda A, Tsuruya K 2012 Clinical Nephrology 78 487-491

Percutaneous renal artery embolization in a patient with severe nephrotic syndrome which continued after the introduction of hemodialysis

Maeda A, Takeda K, Kondou H, Kimura H, Miura S, Nakashita S, Furushou M, Mukai H, Mutou Y, Uesugi N 2011 Dec Internal Medicine 50 2899-2904

Left ventricular mass index is an independent determinant of diastolic dysfunction in patients on chronic hemodialysis: A tissue doppler imaging study

Kimura H, Takeda K, Tsuruya K, Mukai H, Muto Y, Okuda H, Furusho M, Ueno T, Nakashita S, Miura S, Maeda A, Kondo H 2010 Dec Nephron - Clinical Practice 117 c67-c73