PREPRINTS

Sequencing micronuclei reveals the landscape of chromosomal instability

Pereira C, Rebelo AR, Massey D, Schimenti JC, Weiss RS, Koren A  

BioRxiv doi.org/10.1101/2021.10.28.466311

Comprehensive analysis of DNA replication timing in genetic diseases and gene knockouts identifies MCM10 as a novel regulator of the replication program

Caballero M, Ge T, Rebelo AR, Seo S, Zuccaro MV, Kim S, Brooks K, Radhakrishnan K, Vershkov D, Kim D, Smogorzewska A, Smolka M, West S, Benvenisty N, Egli D, Mace E, Koren A

BioRxiv doi.org/10.1101/2021.09.08.459433

 

High-throughput analysis of DNA replication in single human cells reveals the complex nature of replication timing control

Massey DJ, Koren A

BioRxiv doi.org/10.1101/2021.05.14.443897

Fanconi Anemia pathway deficiency drives copy number variation in squamous cell carcinomas

Webster ALH, Sanders MA, Patel K, Dietrich R, Noonan RJ, Lach FP, White RR, Goldbfarb A, Hadi K, Edwards MM, Donavan FX, Jung M, Sridhar S, Fedrigo O, Tian H, Rosiene J, Heineman T, Kenedy JA, Bean L, Rosti O, Tryon R, Gonzalez A-M, Rosenberg A, Luo J-D, Carrol T, Velleuer E, Rastatter JC, Wells SI, Surralles J, Bagby G, MacMillan ML, Wagner JE, Cancio M, Boulad F, Scognamiglio T, Vaughan R, Koren A, Imielinski M, Chandrasekharappa S, Auerbach AD, Singh B, Kutler DI, Campbell PJ, Smogorzewska A

BioRxiv doi.org/10.1101/2021.08.14.456365

Integrated genome and transcriptome analyses reveal the mechanism of genome instability in Ataxia with Oculomotor Apraxia 2

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

BioRxiv doi.org/10.1101/2021.05.07.443085

DNA breaks due to replication stress limit the developmental potential of human preimplantation embryos

Palmerola KL, Amrane S, De Los Angeles A, Xu S, Zuccaro MV, Massey DJ, de Pinho J, Subbiah A, Prosser B, Lobo R, Koren A, Baslan T, Egli D

dx.doi.org/10.2139/ssrn.3825160

Tumor mutational landscape is a record of the pre-malignant state

Kübler K, Karlic R, Haradhvala N, Ha K, Jiao W, Mouw K, Louis D, Biankin A, Rooman I, Nogiec C, Mino-Kenudson M, Ellisen LW, Tomasetti C, Kim H-G, Lee H, Koren A, Arndt PF, Louis DN, Stein L, Foulkes W, Polak P, Getz G, for the PCAWG-13 working group

BioRxiv doi.org/10.1101/517565

Robust foreground detection in somatic copy number data

Deshpande A, Walradt T, Hu Y, Koren A, Imielinski, M

BioRxiv doi.org/10.1101/847681

PUBLICATIONS

The genetic architecture of DNA replication timing in human pluripotent stem cells

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, Egli D, Clark AG, Koren A

Nature Communications 12:6746 (2021)

Delayed DNA replication in human haploid embryonic stem cells

Edwards MM, Zuccaro M, Sagi I, Ding Q, Vershkov D, Benvenisty N, Egli D, Koren A

Genome Research doi:10.1101/gr.275953.121 (2021)

Replication timing analysis in polyploid cells reveals Rif1 uses multiple mechanisms to promote underreplication in Drosophila

Das S, Caballero M, Kolesnikova T, Zhimulev I, Koren A, Nordman J

Genetics 219(3):iyab147 (2021)

Cancer mutational processes vary in their association with replication timing and chromatin accessibility

Yaacov A, Vardi O, Blumenfeld B, Greenberg A, Massey DJ, Koren A, Adar S, Simon I, Rosenberg S

Cancer Research doi: 10.1158/0008-5472.CAN-21-2039 (2021)

Cohesin core complex gene dosage contributes to germinal center derived lymphoma phenotypes and outcomes. 

Rivas M, Durmaz C, Klötgen A, Chin C, Chen Z, Bhinder B, Koren A, Viny AD, Scharer C, Boss J, Elemento E, Mason CE, Melnick AM 

Frontiers in Immunology 12:688493 (2021)

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

Koren A, Massey DJ, Bracci AN

Bioinformatics btab166 (2021)

Mutation rate variability across human Y-chromosome haplogroups

Ding Q, Hu Y, Koren A, Clark AG 

Molecular Biology and Evolution 38(3):1000-1005 (2021)

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

Jones M, Gelot C, Munk S, Koren A, George KA, Santos RE, Olsen JV, McCarroll SA, Frattini, MG, Takahashi TS, Jallepalli P

Molecular Cell 81(3):P426-441 (2020) 

Positive and negative regulation of DNA replication initiation (Review)

Ding Q, Koren A

Trends in Genetics doi: 10.1016/j.tig.2020.06.020 (2020)

Molecular signatures of aneuploidy-driven adaptive evolution

Kaya A, Mariotti M, Tyshkovskiy A, Zhou X, Hulke ML, Ma S, Gerashchenko MV, Koren A, Gladyshev VN

Nature Communications 11(1):588 (2020)

Genomic methods for measuring DNA replication dynamics (Review)

Hulke ML, Massey DJ, Koren A

Chromosome Research doi: 10.1007/s10577-019-09624-y (2019) 

Replication timing alterations in leukemia affect clinically relevant chromosome domains

Rivera-Mulia JC, Sasaki T, Trevilla-Garcia C, Nakamichi N, Knapp D, Hammond C, Chang B, Tyner T, Devidas M, Zimmerman J, Klein K, Somasundaram V, Druker B, Gruber T, Koren A, Eaves C, Gilbert D

Blood Advances 3 (21): 3201-3213 (2019)

Germline structural variations are preferential sites of DNA replication timing plasticity during development

Hulke ML, Siefert JC, Sansam CL, Koren A

Genome Biology and Evolution 11(6):1663-1678 (2019)

Next-generation sequencing enables spatiotemporal resolution of human centromere replication timing

Massey DJ, Kim D, Brooks KE, Smolka MB, Koren A

Genes 10(4):269 (2019)

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

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

Genome Research 28(12):1901-1918 (2018)

Germline DNA replication timing shapes mammalian genome composition  

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

Nucleic Acids Research 46(16):8299-8310 (2018)

Analysis of somatic microsatellite indels identifies driver events in human tumors

Maruvka YE, Mouw KW, Karlic R, Parasuraman P, Kamburov A, Polak P, Haradhvala NJ, Hess JM, Rheinbay E, Brody Y, Koren A, Braunstein LZ, D’Andrea A, Lawrence MS, Bass A, Bernards A, Michor F, Getz G

Nature Biotechnology 35(10):951-959 (2017)

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

Siefert JC, Georgescu C, Wren JD, Koren A, Sansam CL

Genome Research 27:1406-1416 (2017)

Mutational strand asymmetries in cancer genomes reveal mechanisms of DNA damage and repair

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, Getz G

Cell 164(3):538-549 (2016)

[Cover article]

OTHER PUBLICATIONS

 

Mismatch repair prefers exons (News and Views)

Massey DJ, Koren A

Nature Genetics 49:1673-1674 (2017)

PUBLICATIONS BEFORE CORNELL

 

T cell help controls the speed of the cell cycle in germinal center B cells

Gitlin AD, Mayer CT, Oliveira TY, Shulman Z, Jones MJK, Koren A, Nussenzweig MC

Science 349(6248):643-646 (2015)

 

Genome-wide patterns and properties of de novo mutations in humans

Francioli LC, Polak P, Koren A, Menelaou A, Chun S, Renkens I, Genome of the Netherlands Consortium , van Duijn CM, Swertz M, Wijmenga C, van Ommen G, Slagboo PE, Boomsma DI, Ye K, Guryev V, Arndt PF, Kloosterman WP, de Bakker PIW, Sunyaev S

Nature Genetics 47(7):822-826 (2015)

 

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

Polak P, Karlic R, Koren A, Thurman B, Sandstrom R, Reynolds A, Rynes E,  Vlahovicek K, Stamatoyannopoulos J, Sunyaev S 

Nature 518(7539):360-364 (2015)

[Perspective by M. Teresa Villanueva]

 

Genetic variation in human DNA replication timing

Koren A, Handsaker R, Kamitaki N, Karlic R, Ghosh S, Polak P, Eggan K, McCarroll SA

Cell 159(5):1015-1026 (2014)

[Perspective by Ronald Hause and Jay Shendure]

[Research highlights by Kyle Vogan]

 

Abnormal dosage of ultraconserved elements is highly disfavored in healthy cells but not cancer cells

McCole RB, Fonseka CY, Koren A, Wu C-T

PLoS Genetics 10(10):e1004646 (2014)

 

DNA replication timing: coordinating genome stability with genome regulation on the X chromosome and beyond (Review)

Koren A 

BioEssays 36(10):997-1004 (2014)

 

Thiol Peroxidase deficiency leads to increased mutational load and decreased fitness in Saccharomyces cerevisiae

Kaya A, Lobanov AV, Gerashchenko MV, Koren A, Fomenko DE, Koc A, Gladyshev VN 

Genetics 198(3):905-917 (2014)

 

Origin replication complex binding, nucleosome depletion patterns, and a primary sequence motif can predict origins of replication in a genome with epigenetic centromeres

Tsai H-J, Baller JA, Liachko I, Koren A, Burrack LS, Hickman MA, Thevandavakkam MA, Rusche LN, Berman J 

mBio 5(5):e01703-14 (2014)

 

Random replication of the inactive X chromosome

Koren A, McCarroll SA

Genome Research 24:64-69 (2014)

 

Mutational heterogeneity in cancer and the search for new cancer-associated genes

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, Ramos AH, Pugh TJ, Stransky N, Helman E, Kim J, Sougnez C, Ambrogio L, Nickerson E, Shefler E, Cortés ML, Auclair D, Saksena G, Voet D, Noble M, DiCara, D, Lin P, Lichtenstein L, Heiman DI, Fennell T, Imielinski M, Hernandez B, Hodis E, Baca S, Dulak AM, Lohr J, Landau DA, Wu CJ, Melendez-Zajgla J, Hidalgo-Miranda A, Koren A, McCarroll SA, Mora J, Lee RS, Crompton B, Onofrio R, Parkin M, Winckler W, Ardlie K, Gabriel SB, Roberts CW, Biegel JA, Stegmaier K, Bass AJ, Garraway LA, Meyerson M, Golub TR, Gordenin DA, Sunyaev S, Lander ES, Getz G

Nature 499(7457):214-218 (2013)

[Perspective by Li Ding and Michael Wendl]

 

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

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, Kang S, Ning Lin G, Estabillo J, Gadomski T, Singh B, Zhang K, Akshoomoff N, Corsello C, McCarroll SA, Lakoucheva LM, Li Y, Wang J, Sebat J 

Cell 151(7):1431-1442 (2012)

[Perspective by Chris Ponting]

[Cover article]

 

Differential relationship of DNA replication timing to different forms of human mutation and variation

Koren A, Polak P, Nemesh J, Michaelson JJ, Sebat J, Sunyaev S, McCarroll SA

American Journal of Human Genetics 91(6):1033-1040 (2012)

 

Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase

Koren A, Tsai H-J, Tirosh I, Burrack LS, Barkai N, Berman J

PLoS Genetics 6(8): e1001068 (2010)

 

MRC1-dependent scaling of the budding yeast DNA replication timing program

Koren A, Soifer I, Barkai N

Genome Research 20(6):781-790 (2010)

 

Autocorrelation analysis reveals widespread spatial biases in microarray experiments

Koren A, Tirosh I, Barkai N

BMC Genomics 8:164 (2007)

 

The role of the DNA damage checkpoint in regulation of translesion DNA synthesis (Review)

Koren A

Mutagenesis 22(3):155-160 (2007)

 

Is Saccharomyces cerevisiae apoptotic cell death associated with gene transfer? (Hypothesis)

Koren A

IUBMB Life 58(4):203-207 (2006)

[Cover article]

 

ELG1, a yeast gene required for genome stability, forms a complex related to replication factor C

Ben-Aroya S, Koren A, Liefshitz B, Steinlauf R, Kupiec M

Proceedings of the National Academy of Sciences USA 100:9906-9911 (2003)

 

Pitfalls of the synthetic lethality screen in Saccharomyces cerevisiae: an improved design

Koren A, Ben-Aroya S, Steinlauf R, Kupiec M

Current Genetics 43:62-69 (2003)

 

Control of meiotic recombination initiation: a role for the environment? (Review)

Koren A, Ben-Aroya S, Kupiec M

Current Genetics 42:129-139 (2002)