​​​​​​​​

• Majumdar, S., Bammidi, L.S., Naik, H.C., Manhas, A., Baro, R., Kalita, A., Naskar, A.J., Nidharshan, S., Bariha, G.S., Notani, D. and Gayen, S., 2025. Xist upstream deletion leads to dysregulation of Xist and autosomal gene expression. Genome Research. Article_link

​

• Rana, P., Edathil Kadangodan, A., Koley, P., Ghosh, R., Pullagurla, N.J., Naik, H.C., Mondal, P., Gayen, S. and Laha, D., 2025. GA-independent DELLA regulation by inositol pyrophosphate in a nonvascular land plant. Nature Chemical Biology, pp.1-12. Article_link

​

• Naik, H.C., Chandel, D., Majumdar, S., Arava, M., Baro, R., Bv, H., Hari, K., Ayyamperumal, P., Manhas, A., Jolly, M.K. and Gayen, S., 2024. Lineage-specific dynamics of loss of X upregulation during inactive-X reactivation. Stem Cell Reports, 19(11), pp.1564-1582.​ Article_link

​

• Bammidi, L.S., Gayen, S. Multifaceted role of CTCF in X-chromosome inactivation. Chromosoma (2024). Article_link

​

• Ayyamperumal, P., Naik, H. C., Naskar, A. J., & Gayen, S. (2024). Single-cell allelic transcriptomic analysis unravels intratumoral gene expression heterogeneity linked to TNBC pathogenesis. bioRxiv, 2024-04. Article_link​

​

• Manhas, A., Sarkar, A., & Gayen, S. (2024). Gestational exposure to high heat-humidity conditions impairs mouse embryonic development. bioRxiv, 2024-04. Article_link

​

• Naik, H. C., Baro, R., Sarkar, A., Sunagar, K., & GAYEN, S. (2024). Role of m6A RNA methylation in dosage compensation. bioRxiv, 2024-04. Article_link

​

• Ayyamperumal, P., Naik, H.C., Naskar, A.J., Bammidi, L.S. and Gayen, S., 2024. Epigenomic states contribute to coordinated allelic transcriptional bursting in iPSC reprogramming. Life Science Alliance, 7(4). Article_link​​

​

• Arava, M., Majumdar, S., Bammidi, L.S., Naik, H., Baro, R. and GAYEN, S., 2023. Gene-specific reactivation of X-linked genes upon Xist loss is linked to the chromatin states in extraembryonic endoderm and epiblast stem cells. bioRxiv, pp.2023-10. Article_link​​

​

• Naik, H.C., Hari, K., Chandel, D., Jolly, M.K. and Gayen, S., 2022. Single-cell analysis reveals X upregulation is not global in pre-gastrulation embryos. Iscience, 25(6). Article_link​

​​

• Samanta, M.K*., Gayen, S*., Harris, C., Maclary, E., Murata-Nakamura, Y., Malcore, R.M., Porter, R.S., Garay, P.M., Vallianatos, C.N., Samollow, P.B. and Iwase, S., 2022. Activation of Xist by an evolutionarily conserved function of KDM5C demethylase. Nature communications, 13(1), pp.1-1 Article_link

​

• Vinithra Iyer; Sheetal Tushir; Shreekant Verma; Sudeshna Majumdar; Srimonta Gayen; Rakesh Mishra; Utpal Tatu (2021) The role of nuclear organization in trans-splicing based expression of Heat shock protein 90 in Giardia lamblia. PLOS Neglected Tropical Diseases 15(9), p.e0009810. Article_link

​

• Naik, H.C., Hari, K., Chandel, D., Mandal, S., Jolly, M.K. and Gayen, S., 2021. Semicoordinated allelic-bursting shape dynamic random monoallelic expression in pregastrulation embryos. IScience, 24(9). Article_link

​

• RV P, Sundaresh A, Karunyaa M, Arun A, Gayen S (2020) Autosomal Random Monoallelic Expression: Natural or Artifactual? Trends in Genetics Article_link

 

• Mandal, S., Chandel, D., Kaur, H., Majumdar, S., Arava, M. and Gayen, S., 2020. Single-cell analysis reveals partial reactivation of X chromosome instead of chromosome-wide dampening in naive human pluripotent stem cells. Stem Cell Reports, 14(5), pp.745-754. Article_link

​

• Y Xiang, Y Zhang, Q Xu, C Zhou, B Liu, Z Du, K Zhang, Zhang B, Wang  X, Gayen  S, Liu L, Wang Y,  Li Y, Wang Q, Kalantry S, Li L, Wei Xie (2019) Epigenomic analysis of gastrulation identifies a unique chromatin state for primed pluripotency  Nature Genetics, 1-11. Article_link

​

• Saravanan B, Soota D, Islam Z, Jayani RS, Mann R, Farooq U, Meel S, Walavalkar K, Gayen S, Singh AK, Sridhar H, Dimple Notani (2019) Ligand dependent gene regulation by transient ERα clustered enhancers. PLOS  Genetics.​ Article_link​

​

• Kaur H, RV P, Gayen S (2019) Dampened X-chromosomes in human pluripotent stem cells: dampening or erasure of X-upregulation?  Chromosoma ; 1-3 Article_link

​

• Harris C, Cloutier M, Trotter M,  Hinten M, Gayen S,  Du Z, Xie W and Kalantry S (2019) Conversion of random X-inactivation to imprinted X-inactivation by maternal PRC2 Elife  ;8:e44258 DOI: 10.7554/eLife.44258​ Article_link

​​

• Muthusamy B, Nguyen TT , Bandari AK, Basheer S ,  Chandel D, Manoj J, Gayen S, Seshagiri S, Girimaji SC, and Akhilesh Pandey (2019) Exome sequencing reveals a novel splice site variant in HUWE1 gene in patients with suspected Say-Meyer Syndrome. European Journal of Medical Genetics. Article_link​

​

• Roni Saiba, Maniteja Arava and Gayen S* (2018) Dosage Compensation in Human Pre-Implantation Embryos: X-chromosome Inactivation or Dampening?  EMBO Reports 19 (8), e46294 Article_link​

​

• Gayen S*, and Kalantry S* (2017) Chromatin-Enriched lncRNAs: A novel class of enhancer RNAs. Nature Structural and Molecular Biology 24 (7), 556 Article_link

​

• Maclary E, Hinten M, Harris C, Sethuraman S, Gayen S, and Kalantry S (2017) PRC2 represses transcriptionally active genes on the inactive X-Chromosome. Genome Biology 18(1) 82 Article_link

​

• Zhang H, Gayen S, Xiong J, Zhou B, Shanmugam AK, Sun Y, Karatas H, Liu L, Rao RC, Wang S, Nesvizhskii AI, Kalantry S, and Dou Y (2016) MLL1 Inhibition Reprograms Epiblast Stem cells to Naive Pluripotency. Cell Stem Cell 18(4), 481-494. Article_link

​

• Gayen S, Maclary E, Hinten M, and Kalantry S (2016) Sex-specific Silencing of X-linked Genes by Xist RNA. PNAS 113(3), E309-318. Article_link

​

• Sarkar MK*, Gayen S*, Kumar S*, Maclary E, Buttigieg E, Hinten M, Sado T, and Kalantry S (2015) An Xist Activating Antisense RNA Required for X-chromosome Inactivation. Nature Communications 6, 8564. Article_link

​

• Gayen S, Maclary E, Buttigieg E, Hinten M, and Kalantry S (2015) A Primary Role for the Tsix lncRNA in Maintaining Random X-Chromosome Inactivation. Cell Reports 11(8), 1251-65 Article_link

​

• Maclary E, Buttigieg E, Hinten M, Gayen S, Harris C, Sarkar MK, Purushothaman S, and Kalantry S (2014) Differentiation-dependent requirement of Tsix long non-coding RNA in imprinted X- chromosome inactivation. Nature Communications 5, 4209. Article_link

​​

• Taniguchi K, Townshend RF, Freddo AM, Prakash A, Gayen S, Harris CE, Tsai Y-H, DeLong CJ, Chue DJ, Lopez SA, Spence JR, O’Shea KS, Margolis B, Kalantry S, and Gumucio DL (2015) Pluripotent Stem Cells: An Improved Model of Lumen Formation. Stem Cell Reports 5, 954-962. Article_link 

​