Publications

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Hanson RL, Batchelor ECoordination of MAPK and p53 dynamics in the cellular responses to DNA damage and oxidative stress. Mol Syst Biol2022 Dec;18(12):e11401doi: 10.15252/msb.202211401. PubMed PMID: 36472304; PubMed Central PMCID: PMC9724178.

Larson A, Shams A, McMillin S, Sullivan B, Vue C, Roloff Z, Batchelor E, Kyba M, and Lowe D. Estradiol deficiency reduces the satellite cell pool by impairing cell cycle progression. Am J Physiol Cell Physiol. 2022 Apr 20. doi: 10.1152/ajpcell.00429.2021 PMID: 35442828.

Yang Z*, Hanson RL*, and Batchelor E. Progress and challenges in understanding the regulation and function of p53 dynamics. Biochem Soc Trans. 2021 Sep 8; doi: 10.1042/BST20210148. PMID:34495325. (*authors contributed equally)

Hanson RL and Batchelor E. Rucaparib alters p53 oscillations in single cells to enhance DNA-double-strand-break-induced cell cycle arrest. Cell Rep 2020 Oct 13; 33(2): 108240. PMID: 33053351.

molecular systems bio

Zheng Y, Dubois W, Benham C, Batchelor E, and Levens D. Two-Stage Regulation of MYC Expression in Primary Single Cells. Commun Biol 2020 Oct 1; 3(1): 454. PMID: 33005010.

Nie Z, Guo C, Das SK, Chow C, Batchelor E*, Simons Jr SS*, and Levens D*. Dissecting transcriptional amplification by MYC. eLife 2020; 9: e52483. PMID: 32715994 (*co-corresponding authors)

Harton MD, Koh WS, Bunker AD, Singh A, and Batchelor E. p53 pulse modulation differentially regulates target gene promoters to regulate cell fate decisions. Mol Syst Biol 2019 Sep; 15(9):e8685. PMID: 31556489.

Koh WS, Porter J, and Batchelor E. Tuning mRNA stability through altering 3’-UTR sequences generates distinct output expression dynamics in a synthetic oscillatory circuit. Sci Rep 2019 Apr 12; 9(1):5976. PMID: 30979970. PMCID: PMC6461691.

Hanson, RL, Porter JR, and Batchelor E. Protein stability of p53 targets determines their temporal expression patterns in response to p53 pulsing. J Cell Biol 2019 Apr 1; 218(4):1282-1297. PMID:30745421

House CD, Jordan E, Hernandez L, Ozaki M, James J, Kim M, Kruhlak MJ, Batchelor E, Elloumi F, Cam M, and Annunziata CM. The alternative NF-kB signaling transcription factor RelB supports ovarian cancer tumorigenesis via regulation of CD133+ ALDH+ tumor-initiating cells. Cancer Res 2017 Dec 15;77(24):6927-6940. PMID: 29074539.

Yuen G, Khan FJ, Gao S, Stommel JM, Batchelor E, Wu X, and Luo J. CRISPR/Cas9-mediated gene knockout is insensitive to target copy number but is dependent on guide RNA potency and Cas9/sgRNA threshold expression level. Nucl Acids Res 2017 Nov 16;45(20):12039-12053. PMID: 29036671.

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Porter JR, Fisher BE, Baranello L, Liu JC, Kambach DM, Nie Z, Koh WS, Luo J, Stommel JM, Levens D, and Batchelor E. Global inhibition with specific activation: how p53 and MYC redistribute the transcriptome in the DNA double-strand break response. Mol Cell 2017 Sep 21;67(6):1013-1025. PMID: 28867293.

Kieffer-Kwon KR, Nimura K, Rao SSP, Xu J, Jung S, Pekowska A, Dose M, Stevens E, Mathe E, Dong P, Huang SC, Ricci MA, Baranello L, Zheng Y, Ardori FT, Resch W, Stavreva D, Nelson S, McAndrew M, Casellas A, Finn E, Gregory C, St Hilaire BG, Johnson SM, Dubois W, Cosma MP, Batchelor E, Levens D, Phair RD, Misteli T, Tessarollo L, Hager G, Lakadamyali M, Liu Z, Floer M, Shroff H, Aiden EL, Casellas R. Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 2017 Aug 17;67(4):566-578. PMID: 28803781.

Batchelor E and Loewer A. Recent progress and open challenges in modeling p53 dynamics in single cells. Curr. Opin. Syst. Biol. 2017 Jun; 3:54-59. PMID: 29062976.

Read A, Gao S, Batchelor E, and Luo J. Flexible CRISPR library construction using parallel oligonucleotide retrieval. Nucleic Acids Res. 2017 Jun 20;45(11):e101. PMID: 28334828 PMCID: PMC5499874.

Harton M and Batchelor E. Determining the limitations and benefits of noise in gene regulation and signal transduction through single cell, microscopy-based analysis. J. Mol Biol. 2017 429:1143-1154.

Kambach D, Cauer AG, Tristan CA, Brown MF, Celiku O, Kesarwala AH, Shankavaram U, Batchelor E, Stommel JM. Disabled cell density sensing leads to dysregulated cholesterol synthesis in glioblastoma. Oncotarget. 2017 Feb 28;8(9):14860-14875. PMID: 28118603.

Porter JR, Telford WG, and Batchelor E. Single-cell gene expression profiling using FACS and qPCR with internal standards. J. Vis. Exp. 2017 (120), e55219, doi:10.3791/55219.

Porter JR, Fisher BE, and Batchelor E. p53 pulses diversify target gene expression in an mRNA half-life-dependent manner and delineate co-regulated target gene subnetworks. Cell Systems. 2016; 2(4):272-82. PMID: 27135539.

Zhou W, Chung YJ, Parrilla Castellar ER, Zheng Y, Chung HJ, Bandle R, Liu J, Tessarollo L, Batchelor E, Aplan PD, Levens D. Far Upstream Element Binding Protein plays a crucial role in embryonic development, hematopoiesis, and stabilizing Myc expression levels. Am J Pathol. 2016; 186(3): 701-15. PMID: 26774856.

Porter JR and Batchelor E. Using computational modeling and experimental synthetic perturbations to probe biological circuits. Methods Mol Biol. 2015; 1244:259-76. PMID 25487101.

Moody AD and Batchelor E. Promoter decoding of transcription factor dynamics. Mol Syst Biol. 2013 Nov 5;9:703. PMID: 24189398.

Batchelor E, Kann MG, Przytycka TM, Raphael BJ, and Wojtowicz D. Modeling cell heterogeneity: from single-cell variations to mixed cells. Pac Symp Biocomput. (2013) 2013: 445-450. PMID: 23424148.

Purvis JE, Karhohs KW, Mock C, Batchelor E, Loewer A, and Lahav G.  p53 dynamics control cell fate. Science 15 June 2012; 336: 1440-1444. PMID22700930.

Batchelor E and Lahav G. Suppressing variation in synthetic circuits. Mol Syst Biol. 2 August 2011; 7:520. PMC3202793, PMID21811231.

Batchelor E, Loewer A, Mock CS, and Lahav G. Stimulus-dependent dynamics of p53 in single cells. Mol Syst Biol. 10 May 2011; 7: 488. PMID21556066.

Toettcher J, Mock CS, Batchelor E, Loewer A, and Lahav G. A synthetic-natural hybrid oscillator in human cells. Proc Natl Acad Sci USA. 2010, 107(39) 17047-52. PMC2947868, PMID20837528.

Geva-Zatorsky N, Dekel E, Batchelor E, Lahav G, Alon U. Fourier analysis and systems identification of the p53 feedback loop. Proc Natl Acad Sci USA 2010, 107(30) 13550-5. PMC2922141, PMID20622152.

Loewer A, Batchelor E, Gaglia G and Lahav G. Basal dynamics of p53 reveal transcriptionally attenuated pulses in cycling cells. Cell 2010, 142(1) 89-100. NIHMS220847, PMC3003696, PMID20598361.

Batchelor E, Loewer A, and Lahav G. The ups and downs of p53: understanding protein dynamics in single cells. Nat Rev Cancer 2009, 9(5) 371-7. NIHMS193653, PMC2892289, PMID19360021. 

Batchelor E, Mock CS, Bhan I, Loewer A, and Lahav G. Recurrent initiation: a mechanism for triggering p53 pulses in response to DNA damage. Mol Cell 2008, 30(3) 277-289. NIHMS51304, PMC2579769, PMID18471974. 

Batchelor E and Goulian M. Imaging OmpR localization in Escherichia coli. Mol Microbiol 2006, 59(6) 1767-1778. PMID: 16553882.

Batchelor E, Walthers D, Kenney LJ, and Goulian M. The ompC and ompF porin genes are regulated by the CpxA-CpxR envelope stress system in Escherichia coli. J Bacteriol 2005, 187(16), 5723-31. PMC1196077, PMID16077119.

Besson M and Batchelor EP. AM1 study of N-2-acetylaminofluorene bonded to deoxyguanosine at the minor adduct site. J Biol Phys 2004, 30, 161-170. PMC3456492, PMID23345866.

Batchelor E, Silhavy TJ, and Goulian M. Continuous control in bacterial regulatory circuits. J Bacteriol 2004, 186(22), 7618-7625. PMC524909, PMID15516575.

Batchelor E and Goulian M. Robustness and the cycle of phosphorylation and dephosphorylation  in a two-component regulatory system. Proc Natl Acad Sci USA 2003, 100, 691-696. PMC141058, PMID12522261.