1. Moon KR, van Dijk D, Wang Z, Gigante S, Burkhardt DB, Chen WS, Yim K, Elzen AVD, Hirn MJ, Coifman RR, Ivanova NB§#, Wolf G§, Krishnaswamy S§. Visualizing structure and transitions in high-dimensional biological data. Nat Biotechnol. 2019;37(12):1482-92. §Equal senior contributors, #Corresponding author for experiments.  *Paper is highlighted in News & Views and on the Cover.

2. Wang Z, Zhang Y, Lee YW, Ivanova NB. Combining CRISPR/Cas9-mediated knockout with genetic complementation for in-depth mechanistic studies in human ES cells. Biotechniques. 2019; vol. 66, no. 1;

3. Hernandez C, Wang Z, Ramazanov B, Tang Y, Mehta S, Dambrot C, Lee YW, Tessema K, Kumar I, Astudillo M, Neubert T, Guo S and Ivanova NB. Chromatin-associated factors Dppa2 and Dppa4 guide epigenetic remodeling during reprogramming to pluripotency. Cell Stem Cell. 2018; 23 (3), 396–411.

4. Wang Z., Gearhart MD, Lee YW, Kumar I, Ramazanov B, Zhang Y, Hernandez C, Lu AY, Neuenkirchen N, Deng J, Jin J, Kluger Y, Neubert TA, Bardwell VJ, Ivanova NB. BCOR, a component of the non-canonical Polycomb Repressive Complex PRC1.1, is required to repress critical developmental genes in human ESCs. Cell Stem Cell, 2018;22(2):235-51.

5. Kumar I, Ivanova N. Moving Toward the Ground State. Cell Stem Cell. 2015 Oct 1; 17(4): 375-6.

6. Stem cell epigenetics: looking forward. SA Benitah, A Bracken, Y Dou, D Huangfu, N Ivanova, H Koseki, et al. Cell Stem Cell. 2014; 14 (6), 706-709.

7. Zhang Y, Schulz V, Reed B, Wang Z, Pan X, Mariani J, Euskirchen G, Snyder M, Vaccarino F, Ivanova N, Weissman S, Szekely A. Functional genomic screen of human stem cell differentiation reveals pathways involved in neurodevelopment and neurodegeneration. PNAS. 2013; 110(30):12361-6.

8. Oron E, Ivanova N. Cell fate regulation in early mammalian development. Physical Biology. 2012 Aug; 9(4):045002. * This paper was highlighted among the 10 best articles in Physical Biology of 2012.

9. Kloc A, Ivanova N. Chromatin and Pluripotency: the MYSTerious Connection. Cell Stem Cell. 2012 Aug 3; 11(2):139-40.

10. Wang Z., Oron E., Nelson B., Razis S., Ivanova N. Distinct lineage specification roles for NANOG, OCT4 and SOX2 in human embryonic stem cells. Cell Stem Cells 2012 10: 440-454. * This paper was highlighted among the 10 best Cell Stem Cell articles of 2012.

11. Ivanova N, Dobrin R, Lu R, Kotenko I, Levorse J, DeCoste C, Schafer X, Lun Y, Lemischka IR. Dissecting self-renewal in stem cells with RNA interference. Nature 2006 Aug 3; 442: 533-8.

12. De Haan G, Bystrykh L, Weersing E, Dontje B, Geiger H, Ivanova N, Lemischka I, Vellenga E, Van Zant G. A genetic and genomic analysis identifies a cluster of genes associated with hematopoietic turnover. Blood 2002, 100(6): 2056-2062

13. Ivanova N, Dimos J, Schaniel C, Hackney J, Moore K, Lemischka I. A Stem Cell Molecular Signature. Science 2002 298: 601-604

14. Phillips R, Ernst R, Brunk B, Ivanova N, Moore K, Overton G and Lemischka I. The Genetic Program of Hematopoietic Stem Cells. Science. 2000 Jun 2;288(5471):1635-40.