Research

Publications

Master
Content

2020

Whole-Genome Bisulfite Sequencing

Tovy A, Reyes J, Gundry M, Brunetti L, Lee-Six H, Petljak M, Jung Park H, Guzman A, Rosas C, Jeffries A, Baple E, Mill J, Crosby A, Sency V, Xin B, Machado H, Castillo D, Weitzel J, Li W, Stratton M, Campbell P, Wang H, Sanders M, Goodell M. Tissue-Biased Expansion of DNMT3A-Mutant Clones in a Mosaic Individual Is Associated with Conserved Epigenetic Erosion. Cell Stem Cell 2020 Aug 6;27(2):326-335.e4. doi: 10.1016/j.stem.2020.06.018. PMID: 32673568; PMCID: PMC7494054.

Nanostring

Ghosh, A., Comerota, M.E., Wan, D., Chen, F., Propson, N.E., Hwang, S.H., Hammock, B.D., and Zheng, H. An epoxide hydrolase inhibitor reduces neuroinflammation in a mouse model of Alzheimer’s disease. Sci. Trans. Med. 2020; 12, eabb1206. PMID: 33298560.

RNA-seq

Zheng Z, Anurag M, Cao J, Lei JT, Du X-h, Li J, Lavere P, Singh P, Seker S, Song W, Peng J-h, Kim B-j, Nguyen T, Cakar B, Chan D, Chen X, Banks KC, Lanman RB, Nemati-Shafaee M, Zhang X, Vasakair S, Zhang B, Hilsenbeck S, Foulds CE, Ellis MJ*, Chang EC. Neurofibromin is an estrogen receptor alpha transcriptional corepressor in breast cancer. Cancer Cell, 16: 387-402. 2020. PMID: 32142667, PMCID:7286719.

Da Silva TS, Harrison K, Uzodike M, Rajapakshe K, Coarfa C, He Y, Xu Y, Sisley S.J. Steroid Vitamin D actions in neurons require the PI3K pathway for both enhancing insulin signaling and rapid depolarizing effects. Steroid Biochem Mol Biol. 2020 Jun;200:105690. doi: 10.1016/j.jsbmb.2020.105690. Epub 2020 May 11.PMID: 32408067

Lavery LA, Ure K, Wan YW, Luo C, Trostle AJ, Wang W, Jin H, Lopez J, Lucero J, Durham MA, Castanon R, Nery JR, Liu Z, Goodell MA, Ecker JR, Behrens MM,. Zoghbi HY. “Losing Dnmt3a dependent methylation in inhibitory neurons impairs neural function by a mechanism impacting Rett syndrome.” Elife. 2020 Mar 11;9. pii: e52981. doi: 10.7554/eLife.52981. PMID: 32159514; PMCID: PMC7065908.

ChIP-seq

Liping Liu, Zhenxin Yan, Beth A. Osia, Jerzy Twarowski, Luyang Sun, Juraj Kramara, Rosemary S. Lee, Sandeep Kumar, Rajula Elango, Hanzeng Li, Weiwei Dang, Grzegorz Ira & Anna Malkova. Tracking break-induced replication shows that it stalls at roadblocks. Nature 2021 Jan 20. doi: 10.1038/s41586-020-03172-w. PMID: 33473214

2019

RNA-seq

Hai L, Szwarc MM, Lonard DM, Rajapakshe K, Perera D, Coarfa C, Ittmann M3, Fernandez-Valdivia R, Lydon JP. Short-term RANKL exposure initiates a neoplastic transcriptional program in the basal epithelium of the murine salivary gland. Cytokine. 2019 Nov;123:154745. doi: 10.1016/j.cyto.2019.154745. PMID: 31226438.

Rodriguez A, Briley SM, Patton BK, Tripurani SK, Rajapakshe K, Coarfa C, Rajkovic A, Andrieux A, Dejean A, Pangas SA. Loss of the E2 SUMO-conjugating enzyme Ube2i in oocytes during ovarian folliculogenesis causes infertility in mice. Development. 2019 Dec 2;146(23):dev176701. doi: 10.1242/dev.176701. PMID: 31704792.

Szwarc MM, Hai L, Gibbons WE, Mo Q, Lanz RB, DeMayo FJ, Lydon JP. Early growth response 1 transcriptionally primes the human endometrial stromal cell for decidualization. J Steroid Biochem Mol Biol. 2019 May;189:283-290. doi: 10.1016/j.jsbmb.2019.01.021. Epub 2019 Jan 31. PMID: 30711473.

NanoString

Haines K, Sarabia SF, Alvarez KR, Tomlinson G, Vasudevan SA, Heczey AA, Roy A, Finegold MJ, Parsons DW, Plon SE, López-Terrada D. Characterization of pediatric hepatocellular carcinoma reveals genomic heterogeneity and diverse signaling pathway activation. Pediatr Blood Cancer. 2019 Jul;66(7):e27745. doi: 10.1002/pbc.27745. Epub 2019 Apr 11. PMID: 30977242.

ChIP-seq

Likhite N, Yadav V, Milliman EJ, Sopariwala DH, Lorca S, Narayana NP, Sheth M, Reineke EL, Giguère V, Narkar V. Mol. Cell Biol. 2019 Feb 15;39(5). pii: e00411-18. doi: 10.1128/MCB.00411-18. Loss of Estrogen-Related Receptor Alpha Facilitates Angiogenesis in Endothelial Cells.

Zhou W, He Y, Rehman AU, Kong Y, Hong S, Ding G, Yalamanchili HK, Wan YW, Paul B, Wang C, Gong Y, Zhou W, Liu H, Dean J, Scalais E, O'Driscoll M, Morton JEV; DDD study, Hou X, Wu Q, Tong Q, Liu Z, Liu P, Xu Y, Sun Z. Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus-CA3 projection. Nat Neurosci. 2019 Feb;22(2):205-217. doi: 10.1038/s41593-018-0311-1. PMID: 30664766.

2018

Nanostring

DiNardo AR, Nishiguchi T, Mace EM, Rajapakshe K, Mtetwa G, Kay A, Maphalala G, Secor WE, Mejia R, Orange JS, et al. Schistosomiasis Induces Persistent DNA Methylation and Tuberculosis-Specific Immune Changes. J Immunol 2018. PMID 29752313.

RNA-seq

De Maio A, Yalamanchili HK, Adamski CJ, Gennarino VA, Liu Z, Qin J, Jung SY, Richman R, Orr H, Zoghbi HY. RBM17 Interacts with U2SURP and CHERP to Regulate Expression and Splicing of RNA-Processing Proteins. Cell Rep. 2018 Oct 16;25(3):726-736.e7. doi: 10.1016/j.celrep.2018.09.041. PMID:30332651.

ChIP-seq

Ito-Ishida A, Yamalanchili HK, Shao Y, Baker SA, Heckman LD, Lavery LA, Kim JY, Lombardi LM, Sun Y, Liu Z, Zoghbi HY. Genome-wide distribution of linker histone H1.0 is independent of MeCP2. Nat Neurosci. 2018 Jun;21(6):794-798. doi: 10.1038/s41593-018-0155-8. Epub 2018 May 25. PMID:29802390.

2017

RNA-seq

Brinegar, A.E., Zheng, X., Loehr J.A., Li, W., Rodney G.G., and Cooper T.A. (2017) Extensive alternative splicing transitions during postnatal skeletal muscle development are required for calcium handling functions. eLife 6:e27192. PMID: 28826478.

John Lin CC, Yu K, Hatcher A, Huang TW, Lee HK, Carlson J, Weston MC, Chen F, Zhang Y, Zhu W, Mohila CA, Ahmed N, Patel AJ, Arenkiel BR, Noebels JL, Creighton CJ, Deneen B. Identification of diverse astrocyte populations and their malignant analogs. Nat Neurosci. 2017 Mar;20(3):396-405. doi: 10.1038/nn.4493. Epub 2017 Feb 6. PMID: 28166219.

Sreekumar A, Toneff MJ, Toh E, Roarty K, Creighton CJ, Belka GK, Lee DK, Xu J, Chodosh LA, Richards JS, Rosen JM. WNT-Mediated Regulation of FOXO1 Constitutes a Critical Axis Maintaining Pubertal Mammary Stem Cell Homeostasis. Dev Cell. 2017 Nov 20;43(4):436-448.e6. doi: 10.1016/j.devcel.2017.10.007. Epub 2017 Nov 2. PMID: 29103953.

Neelakantan D, Zhou H, Oliphant MUJ, Zhang X, Simon LM, Henke DM, Shaw CA, Wu MF, Hilsenbeck SG, White LD, Lewis MT, Ford HL. EMT cells increase breast cancer metastasis via paracrine GLI activation in neighbouring tumour cells. Nat Commun. 2017;8:15773. doi: 10.1038/ncomms15773. PMID: 28604738.