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1.

Replication stress impairs chromosome segregation and preimplantation development in human embryos.

Palmerola, Katherine L; Amrane, Selma; De Los Angeles, Alejandro; Xu, Shuangyi; Wang, Ning; de Pinho, Joao; Zuccaro, Michael V; Taglialatela, Angelo; Massey, Dashiell J; Turocy, Jenna; Robles, Alex; Subbiah, Anisa; Prosser, Bob; Lobo, Rogerio; Ciccia, Alberto; Koren, Amnon; Baslan, Timour; Egli, Dieter.

Cell ; 185(16): 2988-3007.e20, 2022 08 04.

Article in English | MEDLINE | ID: mdl-35858625

2.

Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair.

Haradhvala, Nicholas J; Polak, Paz; Stojanov, Petar; Covington, Kyle R; Shinbrot, Eve; Hess, Julian M; Rheinbay, Esther; Kim, Jaegil; Maruvka, Yosef E; Braunstein, Lior Z; Kamburov, Atanas; Hanawalt, Philip C; Wheeler, David A; Koren, Amnon; Lawrence, Michael S; Getz, Gad.

Cell ; 164(3): 538-49, 2016 Jan 28.

Article in English | MEDLINE | ID: mdl-26806129

3.

Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells.

Deshpande, Madhura; Paniza, Theodore; Jalloul, Nahed; Nanjangud, Gouri; Twarowski, Jerzy; Koren, Amnon; Zaninovic, Nikica; Zhan, Qiansheng; Chadalavada, Kalyani; Malkova, Anna; Khiabanian, Hossein; Madireddy, Advaitha; Rosenwaks, Zev; Gerhardt, Jeannine.

Mol Cell ; 82(20): 3781-3793.e7, 2022 10 20.

Article in English | MEDLINE | ID: mdl-36099913

4.

Genetic variation in human DNA replication timing.

Koren, Amnon; Handsaker, Robert E; Kamitaki, Nolan; Karlic, Rosa; Ghosh, Sulagna; Polak, Paz; Eggan, Kevin; McCarroll, Steven A.

Cell ; 159(5): 1015-1026, 2014 Nov 20.

Article in English | MEDLINE | ID: mdl-25416942

5.

Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication.

Jones, Mathew J K; Gelot, Camille; Munk, Stephanie; Koren, Amnon; Kawasoe, Yoshitaka; George, Kelly A; Santos, Ruth E; Olsen, Jesper V; McCarroll, Steven A; Frattini, Mark G; Takahashi, Tatsuro S; Jallepalli, Prasad V.

Mol Cell ; 81(3): 426-441.e8, 2021 02 04.

Article in English | MEDLINE | ID: mdl-33545059

6.

Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer.

Webster, Andrew L H; Sanders, Mathijs A; Patel, Krupa; Dietrich, Ralf; Noonan, Raymond J; Lach, Francis P; White, Ryan R; Goldfarb, Audrey; Hadi, Kevin; Edwards, Matthew M; Donovan, Frank X; Hoogenboezem, Remco M; Jung, Moonjung; Sridhar, Sunandini; Wiley, Tom F; Fedrigo, Olivier; Tian, Huasong; Rosiene, Joel; Heineman, Thomas; Kennedy, Jennifer A; Bean, Lorenzo; Rosti, Rasim O; Tryon, Rebecca; Gonzalez, Ashlyn-Maree; Rosenberg, Allana; Luo, Ji-Dung; Carroll, Thomas S; Shroff, Sanjana; Beaumont, Michael; Velleuer, Eunike; Rastatter, Jeff C; Wells, Susanne I; Surrallés, Jordi; Bagby, Grover; MacMillan, Margaret L; Wagner, John E; Cancio, Maria; Boulad, Farid; Scognamiglio, Theresa; Vaughan, Roger; Beaumont, Kristin G; Koren, Amnon; Imielinski, Marcin; Chandrasekharappa, Settara C; Auerbach, Arleen D; Singh, Bhuvanesh; Kutler, David I; Campbell, Peter J; Smogorzewska, Agata.

Nature ; 612(7940): 495-502, 2022 12.

Article in English | MEDLINE | ID: mdl-36450981

7.

Whole-genome sequencing in autism identifies hot spots for de novo germline mutation.

Michaelson, Jacob J; Shi, Yujian; Gujral, Madhusudan; Zheng, Hancheng; Malhotra, Dheeraj; Jin, Xin; Jian, Minghan; Liu, Guangming; Greer, Douglas; Bhandari, Abhishek; Wu, Wenting; Corominas, Roser; Peoples, Aine; Koren, Amnon; Gore, Athurva; Kang, Shuli; Lin, Guan Ning; Estabillo, Jasper; Gadomski, Therese; Singh, Balvindar; Zhang, Kun; Akshoomoff, Natacha; Corsello, Christina; McCarroll, Steven; Iakoucheva, Lilia M; Li, Yingrui; Wang, Jun; Sebat, Jonathan.

Cell ; 151(7): 1431-42, 2012 Dec 21.

Article in English | MEDLINE | ID: mdl-23260136

8.

The evolution of the human DNA replication timing program.

Bracci, Alexa N; Dallmann, Anissa; Ding, Qiliang; Hubisz, Melissa J; Caballero, Madison; Koren, Amnon.

Proc Natl Acad Sci U S A ; 120(10): e2213896120, 2023 03 07.

Article in English | MEDLINE | ID: mdl-36848554

9.

Genome replication in space and time.

Koren, Amnon.

Nat Rev Genet ; 25(5): 308, 2024 May.

Article in English | MEDLINE | ID: mdl-38337019

10.

Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2.

Kanagaraj, Radhakrishnan; Mitter, Richard; Kantidakis, Theodoros; Edwards, Matthew M; Benitez, Anaid; Chakravarty, Probir; Fu, Beiyuan; Becherel, Olivier; Yang, Fengtang; Lavin, Martin F; Koren, Amnon; Stewart, Aengus; West, Stephen C.

Proc Natl Acad Sci U S A ; 119(4)2022 01 25.

Article in English | MEDLINE | ID: mdl-35042798

11.

Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation.

Caballero, Madison; Ge, Tiffany; Rebelo, Ana Rita; Seo, Seungmae; Kim, Sean; Brooks, Kayla; Zuccaro, Michael; Kanagaraj, Radhakrishnan; Vershkov, Dan; Kim, Dongsung; Smogorzewska, Agata; Smolka, Marcus; Benvenisty, Nissim; West, Stephen C; Egli, Dieter; Mace, Emily M; Koren, Amnon.

Hum Mol Genet ; 31(17): 2899-2917, 2022 08 25.

Article in English | MEDLINE | ID: mdl-35394024

12.

Delayed DNA replication in haploid human embryonic stem cells.

Edwards, Matthew M; Zuccaro, Michael V; Sagi, Ido; Ding, Qiliang; Vershkov, Dan; Benvenisty, Nissim; Egli, Dieter; Koren, Amnon.

Genome Res ; 31(12): 2155-2169, 2021 Dec.

Article in English | MEDLINE | ID: mdl-34810218

13.

Positive and Negative Regulation of DNA Replication Initiation.

Ding, Qiliang; Koren, Amnon.

Trends Genet ; 36(11): 868-879, 2020 11.

Article in English | MEDLINE | ID: mdl-32739030

14.

Mutation Rate Variability across Human Y-Chromosome Haplogroups.

Ding, Qiliang; Hu, Ya; Koren, Amnon; Clark, Andrew G.

Mol Biol Evol ; 38(3): 1000-1005, 2021 03 09.

Article in English | MEDLINE | ID: mdl-33049047

15.

TIGER: inferring DNA replication timing from whole-genome sequence data.

Koren, Amnon; Massey, Dashiell J; Bracci, Alexa N.

Bioinformatics ; 37(22): 4001-4005, 2021 11 18.

Article in English | MEDLINE | ID: mdl-33704387

16.

Quantification of somatic mutation flow across individual cell division events by lineage sequencing.

Brody, Yehuda; Kimmerling, Robert J; Maruvka, Yosef E; Benjamin, David; Elacqua, Joshua J; Haradhvala, Nicholas J; Kim, Jaegil; Mouw, Kent W; Frangaj, Kristjana; Koren, Amnon; Getz, Gad; Manalis, Scott R; Blainey, Paul C.

Genome Res ; 28(12): 1901-1918, 2018 12.

Article in English | MEDLINE | ID: mdl-30459213

17.

Genomic methods for measuring DNA replication dynamics.

Hulke, Michelle L; Massey, Dashiell J; Koren, Amnon.

Chromosome Res ; 28(1): 49-67, 2020 03.

Article in English | MEDLINE | ID: mdl-31848781

18.

Cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Polak, Paz; Karlic, Rosa; Koren, Amnon; Thurman, Robert; Sandstrom, Richard; Lawrence, Michael; Reynolds, Alex; Rynes, Eric; Vlahovicek, Kristian; Stamatoyannopoulos, John A; Sunyaev, Shamil R.

Nature ; 518(7539): 360-364, 2015 Feb 19.

Article in English | MEDLINE | ID: mdl-25693567

19.

DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation.

Siefert, Joseph C; Georgescu, Constantin; Wren, Jonathan D; Koren, Amnon; Sansam, Christopher L.

Genome Res ; 27(8): 1406-1416, 2017 08.

Article in English | MEDLINE | ID: mdl-28512193

20.

Germline DNA replication timing shapes mammalian genome composition.

Yehuda, Yishai; Blumenfeld, Britny; Mayorek, Nina; Makedonski, Kirill; Vardi, Oriya; Cohen-Daniel, Leonor; Mansour, Yousef; Baror-Sebban, Shulamit; Masika, Hagit; Farago, Marganit; Berger, Michael; Carmi, Shai; Buganim, Yosef; Koren, Amnon; Simon, Itamar.

Nucleic Acids Res ; 46(16): 8299-8310, 2018 09 19.

Article in English | MEDLINE | ID: mdl-29986092

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