Publications
2024
2023
- Jingyi Zheng, Shasha Wu, Mao Tang, Shaoyan Xi, Yanchen Wang, Jun Ren, Hao Luo, Pengchao Hu, Liangzhan Sun, Yuyang Du, Hui Yang, Fenfen Wang, Han Gao, Ziwei Dai, Xijun Ou, Yan Li. USP39 promotes hepatocellular carcinogenesis through regulating alternative splicing in cooperation with SRSF6/HNRNPC. Cell Death & Disease 14 (10), 670.
- Sixian Zhou, Fengli Zhao, Danling Zhu, Qiqi Zhang, Ziwei Dai, Zhe Wu. Coupling of co-transcriptional splicing and 3’end Pol II pausing during termination in Arabidopsis.Genome Biology 24 (1), 206.
2022
- Ziwei Dai, Weiyan Zheng, Jason W Locasale.Amino acid variability, tradeoffs and optimality in human diet.Nature communications 13 (1), 6683.
- Simon Zhongyuan Tian, Guoliang Li, Duo Ning, Kai Jing, Yewen Xu, Yang Yang, Melissa J Fullwood, Pengfei Yin, Guangyu Huang, Dariusz Plewczynski, Jixian Zhai, Ziwei Dai, Wei Chen, Meizhen Zheng. MCIBox: a toolkit for single-molecule multi-way chromatin interaction visualization and micro-domains identification. Briefings in Bioinformatics 23 (6), bbac380.
- Shuaishi Gao, Ziwei Dai, Hanyu Xu, Luhua Lai.Pinpointing Cancer Sub-Type Specific Metabolic Tasks Facilitates Identification of Anti-cancer Targets.Frontiers in Medicine 9, 872024.
2021
- Michael A Reid, Shree Bose, Kristin M Pladna, Rebecca Anderson, Peter G Mikhael, Zhengtao Xiao, Ziwei Dai, Shiyu Liu, Juan Liu, Timothy S Pardee, Jason W Locasale.
Predictive targeting of mitochondrial metabolism in Acute Myeloid Leukemia patients with a lipoic acid analog. medRxiv [Preprint]. 2021.06. 03.21257935.
- Z Dai, JW Locasale. Amino acid variability, tradeoffs and optimality in human diet. bioRxiv [Preprint]. 2021 June 16.
- Hwang I, Uchida H, Dai Z, Li F, Sanchez T, Locasale JW, Cantley LC, Zheng H, Paik J. Cellular stress signaling activates type-I IFN response through FOXO3-regulated lamin posttranslational modification. Nat Commun. 2021 Jan 28;12(1):640.
2020
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Dai Z, Ramesh V, Locasale JW. The evolving metabolic landscape of chromatin
biology and epigenetics. Nat Rev Genet. 2020 Dec;21(12):737-753.
-
Liu S, Dai Z, Cooper DE, Kirsch DG, Locasale JW. Quantitative Analysis of the
Physiological Contributions of Glucose to the TCA Cycle. Cell Metab. 2020 Oct 6;32(4):619-628.e21.
-
Dai Z, Locasale JW. Cooperative virus propagation underlies COVID-19
transmission dynamics.
medRxiv [Preprint]. 2020 May 7:2020.05.05.20092361.
- Lin KH, Rutter JC, Xie A, Pardieu B, Winn ET, Bello RD, Forget A, Itzykson R, Ahn YR, Dai Z,
Sobhan RT, Anderson GR, Singleton KR, Decker AE, Winter PS, Locasale JW, Crawford L, Puissant A, Wood
KC. Using
antagonistic pleiotropy to design a chemotherapy-induced evolutionary trap to target drug resistance
in
cancer. Nat Genet. 2020 Apr;52(4):408-417.
- Xiao Z, Locasale JW, Dai Z. Metabolism in the tumor microenvironment:
insights from single-cell analysis. Oncoimmunology. 2020 Feb 9;9(1):1726556.
- Quek LE, Krycer JR, Ohno S, Yugi K, Fazakerley DJ, Scalzo R, Elkington SD, Dai Z, Hirayama A,
Ikeda S, Shoji F, Suzuki K, Locasale JW, Soga T, James DE, Kuroda S. Dynamic
13C Flux Analysis Captures the Reorganization of Adipocyte Glucose Metabolism in Response
to Insulin. iScience. 2020 Feb 21;23(2):100855.
- Liberti MV, Allen AE, Ramesh V, Dai Z, Singleton KR, Guo Z, Liu JO, Wood KC, Locasale JW. Evolved
resistance to partial GAPDH inhibition results in loss of the Warburg effect and in a different
state of
glycolysis. J Biol Chem. 2020 Jan 3;295(1):111-124.
2019
- Dai Z, Yang S, Xu L, Hu H, Liao K, Wang J, Wang Q, Gao S, Li B, Lai L. Identification of
Cancer-associated metabolic vulnerabilities by modeling multi-objective optimality in
metabolism. Cell
Commun Signal. 2019 Oct 10;17(1):124.
- Sanderson SM, Gao X, Dai Z, Locasale JW. Methionine metabolism in
health and cancer: a nexus of
diet and precision medicine. Nat Rev Cancer. 2019 Nov;19(11):625-637.
- Xiao Z, Dai Z, Locasale JW. Metabolic landscape of the tumor
microenvironment at single cell
resolution. Nat Commun. 2019 Aug 21;10(1):3763.
- Gao X, Sanderson SM, Dai Z, Reid MA, Cooper DE, Lu M, Richie JP Jr, Ciccarella A, Calcagnotto A,
Mikhael PG, Mentch SJ, Liu J, Ables G, Kirsch DG, Hsu DS, Nichenametla SN, Locasale JW. Dietary
methionine
influences therapy in mouse cancer models and alters human metabolism. Nature. 2019
Aug;572(7769):397-401.
- Sanderson SM, Mikhael PG, Ramesh V, Dai Z, Locasale JW. Nutrient
availability shapes methionine
metabolism in p16/MTAP-deleted cells. Sci Adv. 2019 Jun 26;5(6):eaav7769.
2018
- Reid MA, Allen AE, Liu S, Liberti MV, Liu P, Liu X, Dai Z, Gao X, Wang Q, Liu Y, Lai L, Locasale
JW.
Serine synthesis through PHGDH coordinates nucleotide levels by maintaining
central carbon metabolism.
Nat Commun. 2018 Dec 21;9(1):5442.
- Dai Z, Locasale JW. Thermodynamic constraints on the regulation of
metabolic fluxes. J Biol Chem.
2018
Dec 21;293(51):19725-19739.
- Meng H , Dai Z , Zhang W , Liu Y , Lai L . Molecular mechanism of
15-lipoxygenase allosteric
activation
and inhibition. Phys Chem Chem Phys. 2018 May 30;20(21):14785-14795.
- Dai Z, Mentch SJ, Gao X, Nichenametla SN, Locasale JW. Methionine
metabolism influences genomic
architecture and gene expression through H3K4me3 peak width. Nat Commun. 2018 May 16;9(1):1955.
- Reid MA, Dai Z, Locasale JW. The impact of cellular metabolism on
chromatin dynamics and
epigenetics.
Nat Cell Biol. 2017 Nov;19(11):1298-1306.
2017
- Liberti MV, Dai Z, Wardell SE, Baccile JA, Liu X, Gao X, Baldi R, Mehrmohamadi M, Johnson MO,
Madhukar
NS, Shestov AA, Chio IIC, Elemento O, Rathmell JC, Schroeder FC, McDonnell DP, Locasale JW. A Predictive
Model for Selective Targeting of the Warburg Effect through GAPDH Inhibition with a Natural
Product.
Cell Metab.
2017 Oct 3;26(4):648-659.e8.
- Dai Z, Locasale JW. Metabolic pattern formation in the
tumor microenvironment. Mol Syst Biol.
2017 Feb
9;13(2):915.
- Guinney J, Wang T, Laajala TD, Winner KK, Bare JC, Neto EC, Khan SA, Peddinti G, Airola A, Pahikkala T,
Mirtti T, Yu T, Bot BM, Shen L, Abdallah K, Norman T, Friend S, Stolovitzky G, Soule H, Sweeney CJ, Ryan
CJ, Scher HI, Sartor O, Xie Y, Aittokallio T, Zhou FL, Costello JC; Prostate Cancer Challenge DREAM
Community. Prediction of overall survival for patients with metastatic
castration-resistant prostate
cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial
data. Lancet Oncol. 2017 Jan;18(1):132-142.
- Dai Z, Locasale JW. Understanding metabolism with flux analysis: From
theory to application.
Metab Eng. 2017 Sep;43(Pt B):94-102.
2016
- Dai Z, Shestov AA, Lai L, Locasale JW. A Flux Balance of Glucose
Metabolism Clarifies the
Requirements
of the Warburg Effect. Biophys J. 2016 Sep 6;111(5):1088-100.
- Xu Y, Dai Z, Chen F, Gao S, Pei J, Lai L. Deep Learning for
Drug-Induced Liver Injury. J Chem Inf
Model.
2015 Oct 26;55(10):2085-93.
- Meng H, McClendon CL, Dai Z, Li K, Zhang X, He S, Shang E, Liu Y, Lai L. Discovery of Novel
15-Lipoxygenase Activators To Shift the Human Arachidonic Acid Metabolic Network toward Inflammation
Resolution. J Med Chem. 2016 May 12;59(9):4202-9.
2015
- Eduati F, Mangravite LM, Wang T, Tang H, Bare JC, Huang R, Norman T, Kellen M, Menden MP, Yang J, Zhan
X, Zhong R, Xiao G, Xia M, Abdo N, Kosyk O; NIEHS-NCATS-UNC DREAM Toxicogenetics Collaboration,
Friend
S, Dearry A, Simeonov A, Tice RR, Rusyn I, Wright FA, Stolovitzky G, Xie Y, Saez-Rodriguez J. Prediction
of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol.
2015
Sep;33(9):933-40.
- Wu Y, Zhuo X, Dai Z, Guo X, Wang Y, Zhang C, Lai L. Modeling the mitotic
regulatory network
identifies highly efficient anti-cancer drug combinations. Mol Biosyst. 2015 Feb;11(2):497-505.
2014
2013