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Publications

*co-first authors; #corresponding authors

Preprint

Sun X#, Dadon S, Ennis D, Fan W, Awawdy M, Reuveni E, Alajem A, Ram O#. Expanding single-cell toolbox with a cost-effective full-length total RNA droplet-based sequencing technology. bioRxiv 2025. [bioRxiv]

2024

Moses E*, Atlan T*, Sun X, FranÄ›k R, Siddiqui A, Marinov G K, Shifman S, Zucker D M, Oron-Gottesman A, Greenleaf W J, Cohen E, Ram O, Harel I#. The Killifish Germline Regulates Longevity and Somatic Repair in a Sex-Specific Manner. Nature Aging 2024, 4 (6), 791–813. [Full Text]

2022

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 Pluripotency and XEN Differentiation. Stem Cell Reports 2022, 17 (6), 1334–1350. [Full Text]

Mellul M*, Lahav S*, Imashimizu M, Tokunaga Y, Lukatsky D. B#, Ram O#. Repetitive DNA Symmetry Elements Negatively Regulate Gene Expression in Embryonic Stem Cells. Biophysical Journal 2022, 121 (16), 3126–3135. [Full Text]

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2021

Sun X*#, Bavli D*#, Kozulin C*, Motzik A, Buxboim A, Ram, O#. CloneSeq - Single-Cell Clonal 3D Culture and Analysis Protocol. STAR Protocols 2021, 2 (4). [Full Text] 

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. Developmental Cell 2021, 56 (12), P1804-1817. [Full Text] (Cover paper)

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. PLOS Genetics 2021, 17 (4), e1009498. [Full Text]

Brielle S, Bavli D, Motzik A, Kan-Tor Y, Sun X, Kozulin C, Avni B, Ram O#, Buxboim A#. Delineating the Heterogeneity of Matrix-Directed Differentiation toward Soft and Stiff Tissue Lineages via Single-Cell Profiling. Proceedings of the National Academy of Sciences 2021, 118 (19), e2016322118. [Full Text]

Rappaport Y*, Achache H*, Falk R, Murik O, Ram O, Tzur, Y. B#. Bisection of the X Chromosome Disrupts the Initiation of Chromosome Silencing during Meiosis in Caenorhabditis Elegans. Nature Communication 2021, 12 (1), 4802. [Full Text]

Masalha M, Ben-Dov I. Z, Ram O, Meningher T, Jacob-Hirsch J, Kassem R, Sidi Y, Avni D#. H3K27Ac Modification and Gene Expression in Psoriasis. Journal of Dermatological Science 2021, 103 (2), 93–100. [Full Text]

2020

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. Biophysical Journal 2020, 118 (8), 2015–2026. [Full Text]

​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. Nature Communications 2020, 11 (1), 1–9. [Full Text]

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, 11. [Full Text]

2019 and before
Selected publications:​​

  1. 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. Nature Biotechnology 2015, 33 (11), 1165–1172. [Full Text]

  2. 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, 147 (7), 1628–1639. [Full Text]

  3. Rotem A*, Ram O*, Sperling, R. A., Schnall-Levin M, Shoresh N, Zhang H, Basu A, Bernstein E B# and Weitz A D#. High-Throughput Single Cell Labeling (Hi-SCL) for RNA-Seq using drop-based microfluidics. PLoS One 2015, 10 (5), e0116328. [Full Text]

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Full publications:​

  1. 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.

  2. 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.

  3. Gutin J, Sadeh R, Bodenheimer N, Joseph-Strauss D, Brill AK, Alajem A, Ram O, Friedman N. Fine-Resolution Mapping of TF Binding and Chromatin Interactions. Cell Reports. 2018.

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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

  11. 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.

  12. 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.

  13. 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.

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

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

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

  17. 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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© 2014 by Oren Ram. 

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