Publications
Publications
2023
High-Resolution Genomic Profiling of Liver Cancer Links Etiology With Mutation and Epigenetic Signatures.
Perez S, Lavi-Itzkovitz A, Gidoni M, Domovitz T, Dabour R, Khurana I, Davidovich A, Tobar A, Livoff A, Solomonov E, Maman Y, El-Osta A, Tsai Y, Yu ML, Stemmer SM, Haviv I, Yaari G, Gal-Tanamy M. (2023) Cell Mol Gastroenterol Hepatol. 16(1):63-81. doi: 10.1016/j.jcmgh.2023.03.004.
2022
Ig Enhancers Increase RNA Polymerase II Stalling at Somatic Hypermutation Target Sequences
Tarsalainen A*, Maman Y*, Meng FL, Kyläniemi MK, Soikkeli A, Budzyńska P, McDonald JJ, Šenigl F, Alt FW, Schatz DG, Alinikula J. (2022). J Immunol. 208(1):143-154. doi: 10.4049/jimmunol.2100923.
*Co-first authors
HCV Infection Increases the Expression of ACE2 Receptor, Leading to Enhanced Entry of Both HCV and SARS-CoV-2 into Hepatocytes and a Coinfection State.
Domovitz, T., Ayoub, S., Werbner, M., Alter, J., Izhaki Tavor, L., Yahalom-Ronen, Y., Tikhonov, E., Meirson, T., Maman, Y., Paran, N. and Israely, T., Dessau, M, Gal-Tanamy, M. (2022). Microbiology Spectrum,e01150-22.
2021
Image-based pooled whole genome CRISPR screening for Parkin and TFEB subcellular localization
Kanfer G, Sarraf SA, Maman Y, Baldwin H, Johnson KR, Ward ME, Kampmann M, Lippincott-Schwartz J & Youle RJ. 2021), JCB.220(2):e202006180. doi: 10.1083
2020
ATM and PRDM9 regulate SPO11-bound recombination intermediates during meiosis
Paiano J, Wu W, Yamada S, Sciascia N, Callen E, Paola Cotrim A, Deshpande RA, Maman Y, Day A, Paull TT, Nussenzweig A.(2020), Nature Communications.11(1):857.
2019
Topologically Associated Domains Delineate Susceptibility to Somatic Hypermutation
Senigl F, Maman Y, Dinesh RK, Alinikula J, Seth RB, Pecnova L, Omer AD, Rao SP, Weisz D, Buerstedde JM, Lieberman-Aiden E, Casellas R, Jiri Hejnar J, Schatz DG (2019), Cell Reports. In press
Intra-Vk Cluster Recombination Shapes the Ig Kappa Locus Repertoire
Shinoda K*, Maman Y*, Canela A, Schatz DG, Livak F, Nussenzweig A (2019), Cell Reports. In press
*Co-first authors
53BP1 Enforces Distinct Pre- and Post-resection Blocks on Homologous Recombination
Callen E, Zong D, Wu W, Wong N, Stanlie A, Ishikawa M, Pavani R, Dumitrache LC, Byrum AK, Mendez-Dorantes C, Martinez P, Canela A, Maman Y, Day A, Kruhlak MJ, Blasco MA, Stark JM, Mosammaparast N, McKinnon PJ, Nussenzweig A. (2019). Molecular Cell. 77, 1–13
Topoisomerase II-induced Chromosome Breakage and Translocation Is Determined by Chromosome Architecture and Transcriptional Activity
Canela A*, Maman Y*, Huang, SH, Wutz G, Tang W, Zagnoli-Vieira G, Callen E, Wong N, Day A, Peters JM, Caldecott KW, Pommier Y, Nussenzweig A. (2019), Molecular Cell. 75: 252–266
*Co-first authors
2018
Dual Roles of Poly(dA:dT) Tracts in Replication Initiation and Fork Collapse
Tubbs A, Sridharan S, van Wietmarschen N, Maman Y, Callen E, Stanlie A, Wu W, Wu X, Day A, Wong W, Yin M, Canela A, Fu H, Redon C, C. Pruitt S, Jaszczyszyn Y, Aladjem MI, Aplan PD, Hyrien O, Nussenzweig A.(2018), Cell. 174(5):1127-1142.e19.
The Energetics and Physiological Impact of Cohesin Extrusion
Vian L, Pękowska A, Rao SSP, Kieffer-Kwon KR, Jung S, Baranello L, Huang SC, El Khattabi L, Dose M, Pruett N, Sanborn AL, Canela A, Maman Y, Oksanen A, Resch W, Li X, Lee B, Kovalchuk AL, Tang Z, Nelson S, Di Pierro M, Cheng RR, Machol I, St Hilaire BG, Durand NC, Shamim MS, Stamenova EK, Onuchic JN, Ruan Y, Nussenzweig A, Levens D, Aiden EL, Casellas R. (2018), Cell. 173(5):1165-1178.e20
2017
Genome Organization Drives Chromosome Fragility
Canela A*, Maman Y*, Jung S, Wong N, Callen E, Day A, Kieffer-Kwon KR, Pekowska A, Zhang H, Rao SSP, Huang SC, Mckinnon PJ, Aplan PD, Pommier Y, Lieberman Aiden E, Casellas R, Nussenzweig A. (2017), Cell. 170,507-521.
*Co-first authors
2016
RAG1 targeting in the genome is dominated by chromatin interactions mediated by the non-core regions of RAG1 and RAG2
Maman Y, Teng G, Seth R, Kleinstein SH, Schatz DG. (2016), Nucleic Acid Research, 44(20):9624-963
Bcl6 Is Required for Somatic Hypermutation and Gene Conversion in Chicken DT40 Cells
Williams AM, Maman Y, Alinikula J, Schatz DG. (2016), PLoS ONE, 11(2): e0149146;
2009-2015
Estimate of Within Population Incremental Selection Through Branch Imbalance in Lineage Trees
Liberman, G., Benichou, J., Maman, Y., Glanville, J., Alter, I., Louzoun, Y. (2015), Nucleic Acid Research, 44(5):e46
RAG Represents a Widespread Threat to the Lymphocyte Genome
Teng, G., Maman, Y., Resch W., Kim, M, Yamane, A., Qian J., Kieffer-Kwon KR, Manda, M., Meffre,E., Clark M., Cowell, LG., Casellas, R., and Schatz, DG.(2015), Cell, 162, 751–765.
Genomic landscape of cutaneous T cell lymphoma
Choi, J. ,Goh, G. ,Chen, K. ,Wang,T. ,Walradt, T. ,Tordoff, J.,Overton J. , Liu K. ,Lewis, J. , Devine, L. , Barbarotta, L. , Foss, F. , Vonderheid, E. , Edelson, R. ,Boggon, T. ,Girardi, M. , Bjornson, R. , Maman, Y. ,Subtil, A., Hong, B. , Schatz, DG. , Bunick, C. , Carlson, K., Lifton, RP. (2015), Nature Genetics, 47, 1011–1019.
Viral CD8 T cell epitope nucleotide composition shows evidence of short- and long-term evolutionary strategies
Maman Y, Hershberg U, Louzoun Y. (2015), Immunogenetics.;67(1):15-24
Viral proteome size and CD8+ T cell epitope density are correlated: the effect of complexity on selection
Agranovich A*, Maman Y*, Louzoun Y. (2013), Infect Genet Evol.;20:71-7.
*Co-first authors
Predictor for the effect of amino acid composition on CD4+ T cell epitopes preprocessing
Hoze E, Tsaban, L, Maman, Y., Louzoun, Y. (2013), J Immunol Methods;391(1-2):163-73.
Bacteria modulate the CD8+ T cell epitope repertoire of host cytosol-exposed proteins to manipulate the host immune response.
Maman, Y., R. Nir-Paz, et al. (2011), PLoS Comput Biol 7(10): e1002220
Immune-induced evolutionary selection focused on a single reading frame in overlapping hepatitis B virus proteins
Maman, Y., A. Blancher, et al. (2011), J Virol 85(9): 4558-4566.
Universal peptide vaccines – optimal peptide vaccine design based on viral sequence conservation
Toussaint, N. C., Maman, Y. et al. (2011), Vaccine 29(47): 8745-8753.
Viruses selectively mutate their CD8+ T-cell epitopes–a large-scale immunomic analysis
Vider-Shalit, T., R. Sarid, et al. (2009), Bioinformatics 25(12): i39-44.
Book Chapter
Evolutionary Principles In Viral Epitopes
Maman, Y., Agranovich, A., Vider-Shalit, T. and Louzoun, Y. (2013), Mathematical Models and Methods in Biomedicine. ISBN 978-1-4614-4178-