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Amnon Koren, Ph.D. - Publications

Affiliations: 
2009 MGV Molecular Genetics Weizmann Institute of Science, Rehovot, Israel 
Area:
Genetics
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54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Edwards MM, Wang N, Massey DJ, Bhatele S, Egli D, Koren A. Incomplete reprogramming of DNA replication timing in induced pluripotent stem cells. Cell Reports. 43: 113664. PMID 38194345 DOI: 10.1016/j.celrep.2023.113664  0.405
2023 Xu S, Wang N, Zuccaro MV, Gerhardt J, Baslan T, Koren A, Egli D. DNA replication in early mammalian embryos is patterned, predisposing lamina-associated regions to fragility. Biorxiv : the Preprint Server For Biology. PMID 38234839 DOI: 10.1101/2023.12.25.573304  0.379
2023 Edwards MM, Wang N, Massey DJ, Egli D, Koren A. Incomplete Reprogramming of DNA Replication Timing in Induced Pluripotent Stem Cells. Biorxiv : the Preprint Server For Biology. PMID 37398435 DOI: 10.1101/2023.06.12.544654  0.413
2023 Caballero M, Boos D, Koren A. Cell-type specificity of the human mutation landscape with respect to DNA replication dynamics. Cell Genomics. 3: 100315. PMID 37388911 DOI: 10.1016/j.xgen.2023.100315  0.365
2023 Caballero M, Koren A. The landscape of somatic mutations in lymphoblastoid cell lines. Cell Genomics. 3: 100305. PMID 37388907 DOI: 10.1016/j.xgen.2023.100305  0.311
2023 Bracci AN, Dallmann A, Ding Q, Hubisz MJ, Caballero M, Koren A. The evolution of the human DNA replication timing program. Proceedings of the National Academy of Sciences of the United States of America. 120: e2213896120. PMID 36848554 DOI: 10.1073/pnas.2213896120  0.435
2022 Webster ALH, Sanders MA, Patel K, Dietrich R, Noonan RJ, Lach FP, White RR, Goldfarb A, Hadi K, Edwards MM, Donovan FX, Hoogenboezem RM, Jung M, Sridhar S, Wiley TF, ... ... Koren A, et al. Genomic signature of Fanconi anaemia DNA repair pathway deficiency in cancer. Nature. PMID 36450981 DOI: 10.1038/s41586-022-05253-4  0.301
2022 Deshpande M, Paniza T, Jalloul N, Nanjangud G, Twarowski J, Koren A, Zaninovic N, Zhan Q, Chadalavada K, Malkova A, Khiabanian H, Madireddy A, Rosenwaks Z, Gerhardt J. Error-prone repair of stalled replication forks drives mutagenesis and loss of heterozygosity in haploinsufficient BRCA1 cells. Molecular Cell. PMID 36099913 DOI: 10.1016/j.molcel.2022.08.017  0.338
2022 Palmerola KL, Amrane S, De Los Angeles A, Xu S, Wang N, de Pinho J, Zuccaro MV, Taglialatela A, Massey DJ, Turocy J, Robles A, Subbiah A, Prosser B, Lobo R, Ciccia A, ... Koren A, et al. Replication stress impairs chromosome segregation and preimplantation development in human embryos. Cell. PMID 35858625 DOI: 10.1016/j.cell.2022.06.028  0.338
2022 Massey DJ, Koren A. Telomere-to-telomere human DNA replication timing profiles. Scientific Reports. 12: 9560. PMID 35688856 DOI: 10.1038/s41598-022-13638-8  0.457
2022 Massey DJ, Koren A. High-throughput analysis of single human cells reveals the complex nature of DNA replication timing control. Nature Communications. 13: 2402. PMID 35504890 DOI: 10.1038/s41467-022-30212-y  0.44
2022 Caballero M, Ge T, Rebelo AR, Seo S, Kim S, Brooks K, Zuccaro M, Kanagaraj R, Vershkov D, Kim D, Smogorzewska A, Smolka M, Benvenisty N, West SC, Egli D, ... ... Koren A, et al. Comprehensive analysis of DNA replication timing across 184 cell lines suggests a role for MCM10 in replication timing regulation. Human Molecular Genetics. PMID 35394024 DOI: 10.1093/hmg/ddac082  0.484
2022 Kanagaraj R, Mitter R, Kantidakis T, Edwards MM, Benitez A, Chakravarty P, Fu B, Becherel O, Yang F, Lavin MF, Koren A, Stewart A, West SC. Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2. Proceedings of the National Academy of Sciences of the United States of America. 119. PMID 35042798 DOI: 10.1073/pnas.2114314119  0.312
2021 Edwards MM, Zuccaro MV, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A. Delayed DNA replication in haploid human embryonic stem cells. Genome Research. PMID 34810218 DOI: 10.1101/gr.275953.121  0.392
2021 Ding Q, Edwards MM, Wang N, Zhu X, Bracci AN, Hulke ML, Hu Y, Tong Y, Hsiao J, Charvet CJ, Ghosh S, Handsaker RE, Eggan K, Merkle FT, Gerhardt J, ... ... Koren A, et al. The genetic architecture of DNA replication timing in human pluripotent stem cells. Nature Communications. 12: 6746. PMID 34799581 DOI: 10.1038/s41467-021-27115-9  0.383
2021 Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J. Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila. Genetics. 219. PMID 34740250 DOI: 10.1093/genetics/iyab147  0.386
2021 Yaacov A, Vardi O, Blumenfeld B, Greenberg A, Massey DJ, Koren A, Adar S, Simon I, Rosenberg S. Cancer mutational processes vary in their association with replication timing and chromatin accessibility. Cancer Research. PMID 34702725 DOI: 10.1158/0008-5472.CAN-21-2039  0.318
2021 Koren A, Massey DJ, Bracci AN. TIGER: inferring DNA replication timing from whole-genome sequence data. Bioinformatics (Oxford, England). PMID 33704387 DOI: 10.1093/bioinformatics/btab166  0.486
2021 Jones MJK, Gelot C, Munk S, Koren A, Kawasoe Y, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini MG, Takahashi TS, Jallepalli PV. Human DDK rescues stalled forks and counteracts checkpoint inhibition at unfired origins to complete DNA replication. Molecular Cell. 81: 426-441.e8. PMID 33545059 DOI: 10.1016/j.molcel.2021.01.004  0.371
2020 Ding Q, Koren A. Positive and Negative Regulation of DNA Replication Initiation. Trends in Genetics : Tig. PMID 32739030 DOI: 10.1016/J.Tig.2020.06.020  0.51
2020 Kaya A, Mariotti M, Tyshkovskiy A, Zhou X, Hulke ML, Ma S, Gerashchenko MV, Koren A, Gladyshev VN. Molecular signatures of aneuploidy-driven adaptive evolution. Nature Communications. 11: 588. PMID 32001709 DOI: 10.1038/S41467-019-13669-2  0.402
2019 Hulke ML, Massey DJ, Koren A. Genomic methods for measuring DNA replication dynamics. Chromosome Research : An International Journal On the Molecular, Supramolecular and Evolutionary Aspects of Chromosome Biology. PMID 31848781 DOI: 10.1007/S10577-019-09624-Y  0.536
2019 Rivera-Mulia JC, Sasaki T, Trevilla-Garcia C, Nakamichi N, Knapp DJHF, Hammond CA, Chang BH, Tyner JW, Devidas M, Zimmerman J, Klein KN, Somasundaram V, Druker BJ, Gruber TA, Koren A, et al. Replication timing alterations in leukemia affect clinically relevant chromosome domains. Blood Advances. 3: 3201-3213. PMID 31698451 DOI: 10.1182/Bloodadvances.2019000641  0.384
2019 Hulke ML, Siefert JC, Sansam CL, Koren A. Germline Structural Variations Are Preferential Sites of DNA Replication Timing Plasticity during Development. Genome Biology and Evolution. PMID 31076752 DOI: 10.1093/Gbe/Evz098  0.479
2019 Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A. Next-Generation Sequencing Enables Spatiotemporal Resolution of Human Centromere Replication Timing. Genes. 10. PMID 30987063 DOI: 10.3390/Genes10040269  0.502
2019 Kubler K, Karlic R, Haradhvala NJ, Ha K, Kim J, Kuzman M, Jiao W, Gakkhar S, Mouw KW, Braunstein LZ, Elemento O, Biankin AV, Rooman I, Miller M, Nogiec CD, ... ... Koren A, et al. Abstract 2727: The premalignant state captured in the landscape of somatic mutations can reveal the cancer cell-of-origin Cancer Research. 79: 2727-2727. DOI: 10.1158/1538-7445.Am2019-2727  0.402
2018 Brody Y, Kimmerling RJ, Maruvka YE, Benjamin D, Elacqua JJ, Haradhvala NJ, Kim J, Mouw KW, Frangaj K, Koren A, Getz G, Manalis SR, Blainey PC. Quantification of somatic mutation flow across individual cell division events by lineage sequencing. Genome Research. PMID 30459213 DOI: 10.1101/Gr.238543.118  0.417
2018 Yehuda Y, Blumenfeld B, Mayorek N, Makedonski K, Vardi O, Cohen-Daniel L, Mansour Y, Baror-Sebban S, Masika H, Farago M, Berger M, Carmi S, Buganim Y, Koren A, Simon I. Germline DNA replication timing shapes mammalian genome composition. Nucleic Acids Research. PMID 29986092 DOI: 10.1093/Nar/Gky610  0.495
2018 Siefert JC, Clowdus EA, Goins D, Koren A, Sansam CL. Profiling DNA Replication Timing Using Zebrafish as an In Vivo Model System. Journal of Visualized Experiments : Jove. PMID 29757277 DOI: 10.3791/57146  0.523
2017 Massey DJ, Koren A. Mismatch repair prefers exons. Nature Genetics. 49: 1673-1674. PMID 29186127 DOI: 10.1038/Ng.3993  0.45
2017 Siefert JC, Georgescu C, Wren JD, Koren A, Sansam CL. DNA replication timing during development anticipates transcriptional programs and parallels enhancer activation. Genome Research. PMID 28512193 DOI: 10.1101/Gr.218602.116  0.495
2016 Haradhvala NJ, Polak P, Stojanov P, Covington KR, Shinbrot E, Hess JM, Rheinbay E, Kim J, Maruvka YE, Braunstein LZ, Kamburov A, Hanawalt PC, Wheeler DA, Koren A, Lawrence MS, et al. Mutational Strand Asymmetries in Cancer Genomes Reveal Mechanisms of DNA Damage and Repair. Cell. PMID 26806129 DOI: 10.1016/J.Cell.2015.12.050  0.477
2015 Gitlin AD, Mayer CT, Oliveira TY, Shulman Z, Jones MJ, Koren A, Nussenzweig MC. T cell help controls the speed of the cell cycle in germinal center B cells. Science (New York, N.Y.). PMID 26184917 DOI: 10.1126/Science.Aac4919  0.368
2015 Francioli LC, Polak PP, Koren A, Menelaou A, Chun S, Renkens I, van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboom PE, Boomsma DI, Ye K, Guryev V, et al. Genome-wide patterns and properties of de novo mutations in humans. Nature Genetics. PMID 25985141 DOI: 10.1038/Ng.3292  0.358
2015 Polak P, Karli? R, Koren A, Thurman R, Sandstrom R, Lawrence MS, Reynolds A, Rynes E, Vlahovi?ek K, Stamatoyannopoulos JA, Sunyaev SR. Cell-of-origin chromatin organization shapes the mutational landscape of cancer. Nature. 518: 360-4. PMID 25693567 DOI: 10.1038/Nature14221  0.398
2014 Koren A, Handsaker RE, Kamitaki N, Karli? R, Ghosh S, Polak P, Eggan K, McCarroll SA. Genetic variation in human DNA replication timing. Cell. 159: 1015-26. PMID 25416942 DOI: 10.1016/J.Cell.2014.10.025  0.521
2014 McCole RB, Fonseka CY, Koren A, Wu CT. Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells. Plos Genetics. 10: e1004646. PMID 25340765 DOI: 10.1371/Journal.Pgen.1004646  0.352
2014 Tsai HJ, Baller JA, Liachko I, Koren A, Burrack LS, Hickman MA, Thevandavakkam MA, Rusche LN, Berman J. Origin replication complex binding, nucleosome depletion patterns, and a primary sequence motif can predict origins of replication in a genome with epigenetic centromeres. Mbio. 5: e01703-14. PMID 25182328 DOI: 10.1128/Mbio.01703-14  0.468
2014 Kaya A, Lobanov AV, Gerashchenko MV, Koren A, Fomenko DE, Koc A, Gladyshev VN. Thiol peroxidase deficiency leads to increased mutational load and decreased fitness in Saccharomyces cerevisiae. Genetics. 198: 905-17. PMID 25173844 DOI: 10.1534/Genetics.114.169243  0.392
2014 Koren A. DNA replication timing: Coordinating genome stability with genome regulation on the X chromosome and beyond. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 36: 997-1004. PMID 25138663 DOI: 10.1002/Bies.201400077  0.531
2014 Koren A, McCarroll SA. Random replication of the inactive X chromosome. Genome Research. 24: 64-9. PMID 24065775 DOI: 10.1101/Gr.161828.113  0.501
2013 Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, Carter SL, Stewart C, Mermel CH, Roberts SA, Kiezun A, Hammerman PS, McKenna A, Drier Y, Zou L, ... ... Koren A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 499: 214-8. PMID 23770567 DOI: 10.1038/Nature12213  0.399
2012 Michaelson JJ, Shi Y, Gujral M, Zheng H, Malhotra D, Jin X, Jian M, Liu G, Greer D, Bhandari A, Wu W, Corominas R, Peoples A, Koren A, Gore A, et al. Whole-genome sequencing in autism identifies hot spots for de novo germline mutation. Cell. 151: 1431-42. PMID 23260136 DOI: 10.1016/J.Cell.2012.11.019  0.397
2012 Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev SR, McCarroll SA. Differential relationship of DNA replication timing to different forms of human mutation and variation. American Journal of Human Genetics. 91: 1033-40. PMID 23176822 DOI: 10.1016/J.Ajhg.2012.10.018  0.522
2011 Koren A, Tsai H, Tirosh I, Burrack LS, Barkai N, Berman J. Correction: Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase Plos Genetics. 7. DOI: 10.1371/annotation/2aba8d24-7a24-4bbc-91f7-9b9e228cc84d  0.626
2011 Koren A, Tsai H, Tirosh I, Burrack LS, Barkai N, Berman J. Correction: Epigenetically-Inherited Centromere and Neocentromere DNA Replicates Earliest in S-Phase Plos Genetics. 7. DOI: 10.1371/Annotation/2Aba8D24-7A24-4Bbc-91F7-9B9E228Cc84D  0.609
2010 Koren A, Tsai HJ, Tirosh I, Burrack LS, Barkai N, Berman J. Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase. Plos Genetics. 6: e1001068. PMID 20808889 DOI: 10.1371/Journal.Pgen.1001068  0.669
2010 Koren A, Soifer I, Barkai N. MRC1-dependent scaling of the budding yeast DNA replication timing program. Genome Research. 20: 781-90. PMID 20219942 DOI: 10.1101/Gr.102764.109  0.674
2007 Koren A, Tirosh I, Barkai N. Autocorrelation analysis reveals widespread spatial biases in microarray experiments. Bmc Genomics. 8: 164. PMID 17565680 DOI: 10.1186/1471-2164-8-164  0.566
2007 Koren A. The role of the DNA damage checkpoint in regulation of translesion DNA synthesis. Mutagenesis. 22: 155-60. PMID 17290049 DOI: 10.1093/Mutage/Gem003  0.448
2006 Koren A. Is Saccharomyces cerevisiae apoptotic cell death associated with gene transfer? Iubmb Life. 58: 203-7. PMID 16754298 DOI: 10.1080/15216540600719606  0.326
2003 Ben-Aroya S, Koren A, Liefshitz B, Steinlauf R, Kupiec M. ELG1, a yeast gene required for genome stability, forms a complex related to replication factor C. Proceedings of the National Academy of Sciences of the United States of America. 100: 9906-11. PMID 12909721 DOI: 10.1073/Pnas.1633757100  0.429
2003 Koren A, Ben-Aroya S, Steinlauf R, Kupiec M. Pitfalls of the synthetic lethality screen in Saccharomyces cerevisiae: an improved design. Current Genetics. 43: 62-9. PMID 12684846 DOI: 10.1007/S00294-003-0373-8  0.347
2002 Koren A, Ben-Aroya S, Kupiec M. Control of meiotic recombination initiation: a role for the environment? Current Genetics. 42: 129-39. PMID 12491006 DOI: 10.1007/S00294-002-0340-9  0.37
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