Publications

FANCJ promotes PARP1 activity during DNA replication that is essential in BRCA1 deficient cells. Cong K, MacGilvary N, Lee S, MacLeod SG, Calvo J, Peng M, Nedergaard Kousholt A, Day TA, Cantor SB. Nat Commun. 2024 Mar 23;15(1):2599. doi:10.1038/s41467-024-46824-5. PMID: 38521768; PMCID: PMC10960859.

Chromosome evolution screens recapitulate tissue-specific tumor aneuploidy patterns. Watson EV, Lee JJ, Gulhan DC, Melloni GEM, Venev SV, Magesh RY, Frederick A, Chiba K, Wooten EC, Naxerova K, Dekker J, Park PJ, Elledge SJ. Nat Genet. 2024 Feb 22. doi: 10.1038/s41588-024-01665-2. Epub ahead of print. PMID: 38388848.

Single-cell transcriptomic and genomic changes in the aging human brain. Jeffries AM, Yu T, Ziegenfuss JS, Tolles AK, Kim Y, Weng Z, Lodato MA. bioRxiv [Preprint]. 2023 Nov 7:2023.11.07.566050. doi: 10.1101/2023.11.07.566050. PMID: 37986960; PMCID: PMC10659272.

Consequences of gaining an extra chromosome. Torres EM. Chromosome Res. 2023 Aug 25;31(3):24. doi: 10.1007/s10577-023-09732-w. PMID: 37620607; PMCID: PMC10449985.

ERα-associated translocations underlie oncogene amplifications in breast cancer. Lee JJ, Jung YL, Cheong TC, Espejo Valle-Inclan J, Chu C, Gulhan DC, Ljungström V, Jin H, Viswanadham VV, Watson EV, Cortés-Ciriano I, Elledge SJ, Chiarle R, Pellman D, Park PJ. Nature. 2023 Jun;618(7967):1024-1032. doi:10.1038/s41586-023-06057-w. Epub 2023 May 17. PMID: 37198482; PMCID: PMC10307628.

Genome-wide profiling of prime editor off-target sites in vitro and in vivo using PE-tag. Liang SQ, Liu P, Ponnienselvan K, Suresh S, Chen Z, Kramme C, Chatterjee P, Zhu LJ, Sontheimer EJ, Xue W, Wolfe SA. Nat Methods. 2023 Jun;20(6):898-907. doi: 10.1038/s41592-023-01859-2. Epub 2023 May 8. PMID: 37156841.

Non-metabolic functions of phosphofructokinase-1 orchestrate tumor cellular invasion and genome maintenance under bevacizumab therapy. Lim YC, Jensen KE, Aguilar-Morante D, Vardouli L, Vitting-Seerup K, Gimple RC, Wu Q, Pedersen H, Elbaek KJ, Gromova I, Ihnatko R, Kristensen BW, Petersen JK, Skjoth-Rasmussen J, Flavahan W, Rich JN, Hamerlik P. Neuro Oncol. 2023 Feb 14;25(2):248-260. doi: 10.1093/neuonc/noac135. PMID: 35608632; PMCID: PMC9925708.

Phosphosite Scanning reveals a complex phosphorylation code underlying CDK-dependent activation of Hcm1. Conti MM, Li R, Narváez Ramos MA, Zhu LJ, Fazzio TG, Benanti JA. Nat Commun. 2023 Jan 19;14(1):310. doi:10.1038/s41467-023-36035-9. PMID: 36658165; PMCID: PMC9852432.

Repression of essential cell cycle genes increases cellular fitness. Conti MM, Ghizzoni JM, Gil-Bona A, Wang W, Costanzo M, Li R, Flynn MJ, Zhu LJ, Myers CL, Boone C, Andrews BJ, Benanti JA. PLoS Genet. 2022 Aug 29;18(8):e1010349. doi:10.1371/journal.pgen.1010349. PMID: 36037231; PMCID: PMC9462756.

Somatic genomic changes in single Alzheimer's disease neurons. Miller MB, Huang AY, Kim J, Zhou Z, Kirkham SL, Maury EA, Ziegenfuss JS, Reed HC, Neil JE, Rento L, Ryu SC, Ma CC, Luquette LJ, Ames HM, Oakley DH, Frosch MP, Hyman BT, Lodato MA, Lee EA, Walsh CA. Nature. 2022 Apr;604(7907):714-722. doi:10.1038/s41586-022-04640-1. Epub 2022 Apr 20. PMID: 35444284; PMCID: PMC9357465.

Genome-wide detection of CRISPR editing in vivo using GUIDE-tag. Liang SQ, Liu P, Smith JL, Mintzer E, Maitland S, Dong X, Yang Q, Lee J, Haynes CM, Zhu LJ, Watts JK, Sontheimer EJ, Wolfe SA, Xue W. Nat Commun. 2022 Jan 21;13(1):437. doi: 10.1038/s41467-022-28135-9. PMID: 35064134; PMCID: PMC8782884.

Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis. Bryll AR, Peterson CL. Genes Dev. 2022 Jan 1;36(1-2):17-22. doi: 10.1101/gad.348923.121. Epub 2021 Dec 16. PMID: 34916303; PMCID: PMC8763048.

EpoR stimulates rapid cycling and larger red cells during mouse and human erythropoiesis. Hidalgo D, Bejder J, Pop R, Gellatly K, Hwang Y, Maxwell Scalf S, Eastman AE, Chen JJ, Zhu LJ, Heuberger JAAC, Guo S, Koury MJ, Nordsborg NB, Socolovsky M. Nat Commun. 2021 Dec 17;12(1):7334. doi:10.1038/s41467-021-27562-4. PMID: 34921133; PMCID: PMC8683474.

The chromatin-binding domain of Ki-67 together with p53 protects human chromosomes from mitotic damage. Garwain O, Sun X, Iyer DR, Li R, Zhu LJ, Kaufman PD. Proc Natl Acad Sci U S A. 2021 Aug 10;118(32):e2021998118. doi:10.1073/pnas.2021998118. PMID: 34353903; PMCID: PMC8364191.

Genome-wide mapping of human DNA replication by optical replication mapping supports a stochastic model of eukaryotic replication. Wang W, Klein KN, Proesmans K, Yang H, Marchal C, Zhu X, Borrman T, Hastie A, Weng Z, Bechhoefer J, Chen CL, Gilbert DM, Rhind N. Mol Cell. 2021 Jul 15;81(14):2975-2988.e6. doi:10.1016/j.molcel.2021.05.024. Epub 2021 Jun 21. PMID: 34157308; PMCID: PMC8286344.

The capacity of origins to load MCM establishes replication timing patterns. Dukaj L, Rhind N. PLoS Genet. 2021 Mar 25;17(3):e1009467. doi:10.1371/journal.pgen.1009467. PMID: 33764973; PMCID: PMC8023499.

The shifting shape and functional specializations of the cell cycle during lineage development. Hwang Y, Hidalgo D, Socolovsky M.  WIREs Mech Dis. 2021 Mar;13(2):e1504. doi: 10.1002/wsbm.1504. Epub 2020 Sep 11. PMID: 32916032; PMCID: PMC9004340.

Consequences of aneuploidy in human fibroblasts with trisomy 21. Hwang S, Cavaliere P, Li R, Zhu LJ, Dephoure N, Torres EM.  Proc Natl Acad Sci U S A. 2021 Feb 9;118(6):e2014723118. doi: 10.1073/pnas.2014723118. PMID: 33526671; PMCID: PMC8017964.

INO80C Remodeler Maintains Genomic Stability by Preventing Promiscuous Transcription at Replication Origins. Topal S, Van C, Xue Y, Carey MF, Peterson CL.Cell Rep. 2020 Sep 8;32(10):108106. doi: 10.1016/j.celrep.2020.108106. PMID: 32905765; PMCID: PMC7540730.

Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE.Nature. 2019 Nov;575(7781):229-233. doi:10.1038/s41586-019-1668-3. Epub 2019 Oct 16. PMID: 31666694; PMCID: PMC6913936.

Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability. Feldman JL, Peterson CL. Cell Rep. 2019 Jun 4;27(10):2978-2989.e5. doi: 10.1016/j.celrep.2019.05.009. PMID: 31167142; PMCID:PMC6640630.

Ki-67: more than a proliferation marker. Sun X, Kaufman PD. Chromosoma. 2018 Jun;127(2):175-186. doi: 10.1007/s00412-018-0659-8. Epub 2018 Jan 10. PMID:29322240; PMCID: PMC5945335.

Population snapshots predict early haematopoietic and erythroid hierarchies. Tusi BK, Wolock SL, Weinreb C, Hwang Y, Hidalgo D, Zilionis R, Waisman A, Huh JR, Klein AM, Socolovsky M.Nature. 2018 Mar 1;555(7694):54-60. doi: 10.1038/nature25741. Epub 2018 Feb 21. PMID: 29466336; PMCID: PMC5899604.

Aging and neurodegeneration are associated with increased mutations in single human neurons. Lodato MA, Rodin RE, Bohrson CL, Coulter ME, Barton AR, Kwon M, Sherman MA, Vitzthum CM, Luquette LJ, Yandava CN, Yang P, Chittenden TW, Hatem NE, Ryu SC, Woodworth MB, Park PJ, Walsh CA. Science. 2018 Feb 2;359(6375):555-559. doi: 10.1126/science.aao4426. Epub 2017 Dec 7. Erratum in: Science. 2018 Jul 6;361(6397): PMID: 29217584; PMCID: PMC5831169.

Ki-67 Contributes to Normal Cell Cycle Progression and Inactive X Heterochromatin in p21 Checkpoint-Proficient Human Cells. Sun X, Bizhanova A, Matheson TD, Yu J, Zhu LJ, Kaufman PD. Mol Cell Biol. 2017 Aug 11;37(17):e00569-16. doi:10.1128/MCB.00569-16. PMID: 28630280; PMCID: PMC5559680.