• Chakraborty S, Wenzlitschke N, Anderson MJ, Eraso A, Baudic M, Thompson JT, Evans AA, Shatford-Adams LM, Chari R, Awasthi P, Dale RK, Lewandoski M, Petros TJ, Rocha PP Structural perturbation of chromatin domains with multiple developmental regulators can severely impact gene regulation and development BioRxiv 2024
• Chakraborty S, Kopitchinski N, Zuo Z, Eraso A, Awasthi P, Chari R, Mitra A, Tobias IC, Moorthy SD, Dale RK, Petros TJ, Rocha PP. Enhancer-promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness. Nature Genetics 2023
• Thompson JJ, Lee DJ, Mitra A, Frail S, Dale RK, Rocha PP. Extensive co-binding and rapid redistribution of NANOG and GATA6 during emergence of divergent lineages. Nature Communications 2022
• Kurotaki D, Kikuchi K, Cui K, Kawase W, Saeki K, Fukumoto J, Nishiyama A, Nagamune K, Zhao K, Ozato K, Rocha PP*, Tamura T. Chromatin structure undergoes global and local reorganization during murine dendritic cell development and activation. PNAS 2022 *co-corresponding author
• Zuo Z & Rocha PP. Repetitive Elements: Different Subtypes Hint at Distinct Functions. Trends in Genetics 2020

Collaborative publications:

• Brown JL, Zhang L, Rocha PP, Kassis JA, Sun MA  Polycomb protein binding and looping in the ON transcriptional state. Polycomb protein binding and looping in the ON transcriptional state. Science Advances 2024
• Rhodes CT, Asokumar D, Sohn M, Naskar S, Elisha L, Stevenson P, Lee DR, Zhang Y, Rocha PP, Dale RK, Lee S, Petros TJ. Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles. Frontiers in Cellular Neuroscience 2024
• Xie G, Lee J, Senft AD, Park Y, Chakraborty S, Thompson JJ, Liu,C, Macfarlan TS, Rocha PP, Peng W, Ge K. MLL3/MLL4 methyltransferase activities control early embryonic development and embryonic stem cell differentiation in a lineage-selective manner. Nature Genetics 2023
• Rhodes CT, Thompson JJ, Mitra A, Asokumar D, Lee DR, Lee DJ, Zhang Y, Jason E, Dale RK, Rocha PP, Petros TJ. An epigenome atlas of neural progenitors within the embryonic mouse forebrain. Nat Communications 2022
• Lancho O, Singh A, Silva-Diz V, Tottone L, Nunes PR, Khatun J, Luo S, Chules E, Zuo Z, Rocha PP, Su X, Hossein K, Herranz D. A therapeutically targetable NOTCH1-SIRT1-KAT7 axis in T-cell Leukemia. Blood Cancer Discovery 2022
• Erdogmus S, Concepcion AR, Yamashita M, Sidhu I, Tao AY, Li W, Rocha PP, Huang B, Garippa R, Lee B, Lee A, Hell JW, Lewis RS, Prakriya M, Feske S. Cavβ1 regulates T cell expansion and apoptosis independently of voltage-gated Ca²⁺ channel function. Nature Communications 2022
• Payer LM, Steranka JP, Kryatova MS, Grillo G, Lupien M, Rocha PP, Burns KH. Alu insertion variants alter gene transcript levels. Genome Research 2021
• Tottone L, Lancho O, Loh JW, Singh A, Kimura S, Roels J, Kuchmiy A, Strubbe S, Lawlor MA, da Silva-Diz V, Luo S, Gachet S, García-Prieto CA, Hagelaar R, Esteller M, Meijerink JPP, Soulier J, Taghon T, Van Vlierberghe P, Mullighan CG, Khiabanian H, Rocha PP, Herranz D.
  A Tumor Suppressor Enhancer of PTEN in T-cell development and leukemia. Blood Cancer Discovery 2021
• Beck DB, Basar MA, Asmar AJ, Thompson JJ, Oda H, Uehara DT, Saida K, Pajusalu S, Talvik I, D'Souza P, Bodurtha J, Barañano KW, Miyake N, Wang R, Kempers M, Tamada T, Nishimura Y, Kosho T, Dale R, Mitra A, Macnamara E, Matsumoto N, Tifft CJ, Aksentijevich I, Kastner DL, Rocha PP, Werner A. Linkage-specific deubiquitylation by OTUD5 defines an embryonic pathway intolerant to genomic variation. Science Advances 2021
• Belver L, Yang AY, Albero R, Herranz D, Brundu FG, Quinn SA, Pérez-Durán P, Álvarez S, Gianni F, Rashkovan M, Gurung D, Rocha PP, Raviram R, Reglero C, Cortés JR, Cooke AJ, Wendorff AA, Cordó V, Meijerink JP, Rabadan R, Ferrando AA. GATA3-Controlled Nucleosome Eviction Drives MYC Enhancer Activity in T-cell Development and Leukemia. Cancer Discovery 2019