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Publications

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  1. Herchcovici LS*, Feldman S*, Arnon L*, Alajem A, Bavli D, Sun X, Buganim Y, Ram O. Esrrb is a cell cycle dependent associated factor balancing between pluripotency and XEN differentiation. Stem Cell Rep. 2021. 

  2. Meir M*, Shlomtzion L*, David B. L, Oren R. DNA repeats apply negative design on gene expression in embryonic stem cells. Biophys J. 2022. 

  3. Sun X, Bavli D, Kozulin C, Motzik A, Buxboim A, Ram O. CloneSeq - single-cell clonal 3D culture and analysis protocol. STAR Protocols. 2021.

  4. Rappaport Y, Achache H, Falk R, Murik O, Ram O, Tzur B.Y. Chromosome Integrity is Required for the Initiation of Meiotic Sex Chromosome Inactivation in Caenorhabditis elegans. BioRxiv: doi: https://doi.org/10.1101/2020.11.05.369132. Accepted. Nat Communications. 2021.

  5. Masalha M, Ben-Dov I,  Ram O, Meningher T, Jacob-Hirsch J, Kassem R,  Sidi Y, Avni D.  H3K27Ac modification and gene expression in psoriasis with dror avni. Under revision in British Journal of Dermatology. 2020.

  6. Brielle S, Bavli D, Sun X, Kozulin C, Motzik A, Kan-Tor Y, Avni B, Ram O*, Buxboim A*. Tropomyosin mediates matrix-directed differentiation of distinctive subpopulations of primary mesenchymal stem cells. BioRxiv: doi: https://doi.org/10.1101/2020.11.23.394460. PNAS. 2021.

  7. Bavli D, Sun X, Kozulin C, Ennis D, Motzik A, Biran A, Brielle S, Alajem A, Meshorer E, Buxboim A, Ram O. CloneSeq: A Highly Sensitive Single-cell Analysis Platform for Comprehensive Characterization of Cells from 3D Culture. BioRxiv: doi: https://doi.org/10.1101/2020.11.24.395541. Developmental Cell. 2021.

  8. Alajem A, Roth H, Ratgauzer S, Bavli D, Motzik A, Lahav S, Peled I, Ram O. DNA Methylation Patterns Expose Variations in Enhancer-Chromatin Modifications during Embryonic Stem Cell Differentiation. BioRxiv: doi: https://doi.org/10.1101/2020.11.25.39728. PLoS Genet. 2021.

  9. Aramin S, Fassler R, Chikne A,  Goldenberg M, Arian T, Eliaz K.L, Rimon O, Ram O, Michaeli S, Reichmann D. TrypOx, a Novel Eukaryotic Homolog of the Redox-Regulated Chaperone Hsp33 in Trypanosoma brucei. Frontiers in Microbiology. 2020.

  10. Tayri-Wilk T, Slavin M, Zamel J, Blass A, Cohen S, Motzik A, Sun X, E Shalev D, Ram O, Kalisman N. Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins. Nat Communications. 2020.

  11. Goldshtein M, Mellul M, Deutch G, Imashimizu M, Takeuchi K, Meshorer E, Ram O*, Lukatsky DB*. Transcription Factor Binding in Embryonic Stem Cells Is Constrained by DNA Sequence Repeat Symmetry. Biophys J. 2020.​

  12. Benchetrit H, Jaber M, Zayat V, Sebban S, Pushett A, Makedonski K, Zakheim Z, Radwan A, Maoz N, Lasry R, Renous N, Inbar M, Ram O, Kaplan T, Buganim Y. Direct Induction of the Three Pre-implantation Blastocyst Cell Types from Fibroblasts. Cell Stem Cell. 2019.

  13. Diab A. M, Mor-Shaked H, Cohen E, Cohen-Hadad Y, Ram O, Epsztejn-Litman S and Eiges R. The G-rich Repeats in FMR1 and C9orf72 Loci Are Hotspots for Local Unpairing of DNA. GENETICS.  2018.

  14. Gutin J, Sadeh R, Bodenheimer N,..., Alajem A, Ram O, Friedman N. Fine-Resolution Mapping of TF Binding and Chromatin Interactions. Cell Reports. 2018.

  15. Yaacoby E S, Jones D, Shoresh N, Donohue Laura, Ram O, Bernstein E B. Single-Molecule Decoding of Combinatorially Modified Nucleosomes. Science. 2016

  16. Galen V P, Aaron D. Viny, Ram O, Ryan J H R, Cotton J M, Donohue L, Sievers C, Drier Y, Brian B. Liau, Gillespie M S, Kaitlin M. Carroll, Michael B. Cross, Ross L. Levine​, Bernstein E B. A multiplexed system for quantitative comparisons of chromatin landscapes. Mol Cell. 2015

  17. Rotem A*, Ram O*, Shoresh N*, Sperling R, A Goren, Weitz A D and Bernstein E, B. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnology. 2015.

  18. Rotem A*, Ram O*, Sperling, R. A., Schnall-Levin Michael, Shoresh, N., Zhang, H., Basu, A., Bernstein, B.E., and Weitz, D.A. High-Throughput Single Cell Labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics. PLoS One. 2015.

  19. Mendenhall EM, W.K., Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE, Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnology, 2013.

  20. Sebastián C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, MacDonald AI, McGlynn L, Maxwell F, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012.

  21. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, Gunter C, Snyder M. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012.

  22. Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell. 2012.

  23. Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein C.B, Regev A and Bernstein BE. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011.

  24. Schwartz S*, Ram O* and Ast G. Detection and removal of biases in the analysis of next-generation sequencing reads. PLoS One. 2011.

  25. Goren A, Kim E, Amit M, Vaknin K, Kfir N, Ram O and Ast G. Overlapping splicing regulatory motifs-combinatorial effects on splicing. Nucleic Acids Res. 38(10):3318-27. 2010.

  26. Gal-Mark N, Schwartz S, Ram O, Eyras E, Ast G. The pivotal roles of TIA proteins in 5' splice site selection of Alu exons and across evolution. PLoS Genet. 5(11). 2009.

  27. Schwartz S, Gal-Mark N, Kfir N, Ram O, and Ast G. Alu exonization events illuminate the features required for exon selection. PLoS Comput Biol. 2009.

  28. Lev-Maor G*, Ram O*, Kim E, Sela N, Goren A and Ast G. Intronic Alus influence alternative splicing. PLoS Genet. 2008.

  29. Ram O, Schwartz S and Ast G. Multifactorial interplay controls the plicing profile of Alu derived exons. Mol Cell Biol. 2008.

  30. Ram O and Ast G. SR proteins: a foot on the exon before the transition from intron to exon definition. Trends Genet. 2007.​

  31. Goren A*, Ram O*, Amit M, Keren H, Lev-Maor G, Vig I, Pupko T and Ast G. Comparative analysis identifies exonic splicing regulatory sequences—The complex definition of enhancers and silencers. Mol Cell.

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