2024
Chen Z, Seman M, Fyodorova Y, Farhat A, Ames A, Levashkevich A, Biswas S, Huang F, Freddolino L*, Biteen JS*, Ragunathan K.* : "Tracking live-cell single-molecule dynamics enables measurements of heterochromatin-associated protein-protein interactions." Nucleic Acids Res. doi: 10.1093/nar/gkae692 (2024). PMID: 39142658
Breakthrough Article: represents the top 2-3% of NAR papers in terms of originality, significance and scientific excellence. 

Larkin A, Kunze C, Seman M, Levashkevich A, Curran J, Morris-Evans D, Lemieux S, Khalil AS*, Ragunathan K.*:"Mapping the dynamics of epigenetic adaptation in S. pombe during heterochromatin misregulation." Developmental Cell. 59(16):2222-2238.e4. doi: 10.1016/j.devcel.2024.07.006 (2024). PMID: 39094565.

Ames A, Seman M, Larkin A, Raiymbek G, Chen Z, Levashkevich A, Kim B, Biteen JS, Ragunathan K.*: "Epigenetic memory is governed by an effector recruitment specificity toggle in Heterochromatin Protein 1." Nature Communications. 15(1):6276. doi: 10.1038/s41467-024-50538-z (2024). PMCID: PMC11272775.

Williams JF, Surovtsev IV, Schreiner SM, Chen Z, Raiymbek G, Nguyen H, Hu Y, Biteen JS, Mochrie SGJ, Ragunathan K.*, King MC*. The condensation of HP1α/Swi6 imparts nuclear stiffness. Cell Reports. 43(7):114373. doi: 10.1016/j.celrep.2024.114373 (2024). PMID: 38900638.

Moochickal Assainar, B., Ragunathan, K.* & Baldridge, R.D.* "Direct observation of autoubiquitination for an integral membrane ubiquitin ligase in ERAD." Nature Communications 15, 1340 doi: 10.1038/s41467-024-45541-3 (2024). PMCID: PMC10864399

 2023
Seman M, Levashkevich A, Larkin A, Huang F, Ragunathan K.*, "Uncoupling the distinct functions of HP1 proteins during heterochromatin establishment and maintenance." Cell Reports. 42(11):113428. doi: 10.1016/j.celrep.2023.113428 (2023) PMCID: PMC10749556.

Moritz L, Schon SB, Rabbani M, Sheng Y, Agrawal R, Glass-Klaiber J, Sultan C, Camarillo JM, Clements J, Baldwin MR, Diehl AG, Boyle AP, O'Brien PJ, Ragunathan K, Hu YC, Kelleher NL, Nandakumar J, Li JZ, Orwig KE, Redding S, Hammoud SS. "Sperm chromatin structure and reproductive fitness are altered by substitution of a single amino acid in mouse protamine 1." Nat Struct Mol Biol doi: 10.1038/s41594-023-01033-4 (2023). PMCID: PMC10833441.

2022
Biswas S, Chen Z, Karslake JD, Farhat A, Ames A, Raiymbek G, Freddolino PL*, Biteen JS*, Ragunathan K.*: "HP1 oligomerization compensates for low-affinity H3K9me recognition and provides a tunable mechanism for heterochromatin-specific localization." Science Advances 8(27): p. eabk0793 doi: 10.1126/sciadv.abk0793 (2022).PMCID: PMC9269880.

Bao K, Shan CM, Chen X, Raiymbek G, Monroe JG, Fang Y, Toda T, Koutmou KS, Ragunathan K, Lu C, Berchowitz LE, Jia S: The cAMP signaling pathway regulates Epe1 protein levels and heterochromatin assembly: PLoS Genetics. doi: 10.1371/journal.pgen.1010049 (2022). PMCID: PMC8887748.

2020
Raiymbek G, An S, Khurana N, Gopinath S, Larkin A, Biswas S, Trievel RC, Cho US, Ragunathan K: An H3K9 methylation-dependent protein interaction regulates the non-enzymatic functions of a putative histone demethylase. eLife 9: PM32195666 (2020). PMCID: PMC7192584.

Abeysirigunawardena SC, Kim H, Lai J, Ragunathan K, Rappé MC, Luthey-Schulten Z, Ha T, Woodson SA: “Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes” Nature Communications 8(1): PM28887451 (2017)

Ragunathan K, Jih G, Moazed D: “Epigenetic inheritance uncoupled from sequence-specific recruitment” Science 348 (6230): PM25831549 (2015) Cited as part of “A timeline of major discoveries and advances in epigenetic research between 1996 and 2016”(Allis,D.C. and Jenuwein,T. Nature Reviews Genetics, 2016); Highlighted in Nat. Rev. Genetics.

Kim SH, Ragunathan K, Park J, Joo C, Kim D, Ha T: “Cooperative conformational transitions keep reca filament active during ATPase cycle” Journal of the American Chemical Society 136(42): 14796-14800, PM25252114 (2014)

Kim H, Abeysirigunawardena SC, Chen K, Mayerle M, Ragunathan K, Luthey-Schulten Z, Ha T, Woodson SA: “Protein-guided RNA dynamics during early ribosome assembly" Nature 506(7488): 334-338, PM24522531 (2014)

Koh HR, Kidwell MA, Ragunathan K, Doudna JA, Myong S: ATP-independent diffusion of doublestranded RNA binding proteins Proceedings of the National Academy of Sciences 110(1): 151-156, PM23251028 (2013).

Ragunathan K, Liu C, Ha T: RecA filament sliding on DNA facilitates homology search eLife 1:e00067. PM23240082 (2012). 

Ragunathan K, Joo C, Ha T: Real-time observation of strand exchange reaction with high spatiotemporal resolution Structure 19(8): 1064-1073, PM21827943 (2011).

Lee J, Lee S, Ragunathan K, Joo C, Ha T, Hohng S: Single-molecule four-color FRET Angewandte Chemie - International Edition 49(51): 9922-9925, PM21104966 (2010).

Book Chapters

Larkin A, Ames A, Seman M, Ragunathan K.*: "Investigating Mitotic Inheritance of Histone Modifications Using Tethering Strategies." Methods Mol Biol (Springer-Nature series) 2529:419-440. doi: 10.1007/978-1-0716-2481-4_18 (2022). PMCID: PMC10325796.