2023
RNA-seq
Shaiken, T. E., Grimm, S. L., Siam, M., Williams, A., Rezaeian, A. H., Kraushaar, D., Ricco, E., Robertson, M. J., Coarfa, C., Jain, A., Malovannaya, A., Stossi, F., Opekun, A. R., Price, A. P., & Dubrulle, J. (2023). Transcriptome, proteome, and protein synthesis within the intracellular cytomatrix. iScience, 26(2), 105965. https://doi.org/10.1016/j.isci.2023.105965. PMID: 36824274
Szwarc, M. M., Hai, L., Maurya, V. K., Rajapakshe, K., Perera, D., Ittmann, M. M., Mo, Q., Lin, Y., Bettini, M. L., Coarfa, C., & Lydon, J. P. (2022). Histopathologic and transcriptomic phenotypes of a conditional RANKL transgenic mouse thymus. Cytokine, 160, 156022. https://doi.org/10.1016/j.cyto.2022.156022. PMID: 36099756.
Watanabe, N., Mo, F., Zheng, R., Ma, R., Bray, V. C., van Leeuwen, D. G., Sritabal-Ramirez, J., Hu, H., Wang, S., Mehta, B., Srinivasan, M., Scherer, L. D., Zhang, H., Thakkar, S. G., Hill, L. C., Heslop, H. E., Cheng, C., Brenner, M. K., & Mamonkin, M. (2023). Feasibility and preclinical efficacy of CD7-unedited CD7 CAR T cells for T cell malignancies. Molecular therapy: the journal of the American Society of Gene Therapy, 31(1), 24–34. https://doi.org/10.1016/j.ymthe.2022.09.003 PMID: 36086817.
Chambers, C., Cermakova, K., Chan, Y. S., Kurtz, K., Wohlan, K., Lewis, A. H., Wang, C., Pham, A., Dejmek, M., Sala, M., Loeza Cabrera, M., Aguilar, R., Nencka, R., Lacorazza, H. D., Rau, R. E., & Hodges, H. C. (2023). SWI/SNF Blockade Disrupts PU.1-Directed Enhancer Programs in Normal Hematopoietic Cells and Acute Myeloid Leukemia. Cancer research, 83(7), 983–996. https://doi.org/10.1158/0008-5472.CAN-22-2129 PMID: 36662812.
Gou, X., Kim, B. J., Anurag, M., Lei, J. T., Young, M. N., Holt, M. V., Fandino, D., Vollert, C. T., Singh, P., Alzubi, M. A., Malovannaya, A., Dobrolecki, L. E., Lewis, M. T., Li, S., Foulds, C. E., & Ellis, M. J. (2023). Kinome reprogramming is a targetable vulnerability in ESR1 fusion-driven breast cancer. Cancer research, CAN-22-3484. Advance online publication. https://doi.org/10.1158/0008-5472.CAN-22-3484. PMID: 37071495
Fu X, Pereira R, Liu CC, De Angelis C, Shea MJ, Nanda S, Qin L, Mitchell T, Cataldo ML, Veeraraghavan J, Sethunath V, Giuliano M, Gutierrez C, Győrffy B, Trivedi MV, Cohen O, Wagle N, Nardone A, Jeselsohn R, Rimawi MF, Osborne CK, Schiff R. High FOXA1 levels induce ER transcriptional reprogramming, a pro-metastatic secretome, and metastasis in endocrine-resistant breast cancer. Cell Rep. 2023 Aug 29;42(8):112821. doi: 10.1016/j.celrep.2023.112821. Epub 2023 Jul 18. PMID: 37467106.
Cobos FA, Panah MJN, Epps J, Long X, Man TK, Chiu HS, Chomsky E, Kiner E, Krueger MJ, di Bernardo D, Voloch L, Molenaar J, van Hooff SR, Westermann F, Jansky S, Redell ML, Mestdagh P, Sumazin P. Effective methods for bulk RNA-seq deconvolution using scnRNA-seq transcriptomes. Genome Biol. 2023 Aug 1;24(1):177. doi: 10.1186/s13059-023-03016-6. PMID: 37528411; PMCID: PMC10394903
Whole genome bisulfite sequencing
Li Z, Chang TC, Junco JJ, Devidas M, Li Y, Yang W, Huang X, Hedges DJ, Cheng Z, Shago M, Carroll AJ, Heerema NA, Gastier-Foster J, Wood BL, Borowitz MJ, Sanclemente L, Raetz EA, Hunger SP, Feingold E, Rosser TC, Sherman SL, Loh ML, Mullighan CG, Yu J, Wu G, Lupo PJ, Rabin KR, Yang JJ. Genomic landscape of Down syndrome-associated acute lymphoblastic leukemia. Blood. 2023 Jul 13;142(2):172-184. doi: 10.1182/blood.2023019765. PMID: 37001051; PMCID: PMC10352600.
2022
10x VISIUM
Stur, E., Corvigno, S., Xu, M., Chen, K., Tan, Y., Lee, S., Liu, J., Ricco, E., Kraushaar, D., Castro, P., Zhang, J., and Sood, A. K. (2022). Spatially resolved transcriptomics of high-grade serous ovarian carcinoma. iScience 25, 103923. PMID: 35252817.
Nanostring
Sumazin P, Peters TL, Sarabia, SF, Kim HR, Hollingsworth EF, Alvarez KR, Perez C, Sayeed H, Pozza A, Ranganathan S, Rangaswami AA, Goss JA, Vasudevan SA, Heczey A, Roy A, Alaggio R, Finegold MJ, López-Terrada DH, (2022). Hepatoblastomas with carcinoma features represent a biological spectrum of aggressive hepatocellular neoplasms in children and adolescents. Journal of Hepatology, https://doi.org/10.1101/2021.07.15.445600.
De Paiva, C. S., Trujillo-Vargas, C. M., Schaefer, L., Yu, Z., Britton, R. A., and Pflugfelder, S. C. (2021). Differentially Expressed Gene Pathways in the Conjunctiva of Sjogren Syndrome Keratoconjunctivitis Sicca. Front Immunol 12, 702755. PMID: 34349764
Trujillo-Vargas, C. M., Mauk, K. E., Hernandez, H., de Souza, R. G., Yu, Z., Galletti, J. G., Dietrich, J., Paulsen, F., and de Paiva, C. S. (2022). Immune phenotype of the CD4(+) T cells in the aged lymphoid organs and lacrimal glands. Geroscience. PMID: 35279788.
Alam, J., Yazdanpanah, G., Ratnapriya, R., Borcherding, N., de Paiva, C. S., Li, D., Guimaraes de Souza, R., Yu, Z., and Pflugfelder, S. C. (2022). IL-17 Producing Lymphocytes Cause Dry Eye and Corneal Disease with Aging in RXRalpha Mutant Mouse. Front Med (Lausanne) 9, 849990. PMID: 3540243.
RNA-seq
Piyarathna,B., Coarfa, C., and Weigel, N. L. (2022). Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR-V7 splice variant chromatin binding and transcriptional activities. Scientific Report 12, 5351. PMID: 35354884.
Karolak, J. A., Deutsch G, Gambin T., Szafranski P., Popek E., and Stankiewicz, P. (2022). Transcriptome and Immunohistochemical Analyses in TBX4- and FGF10-Deficient Lungs Imply TMEM100 as a Mediator of Human Lung Development. Amer Jour of Respiratory Cell & Molec Biol, V66-6. PMID: 35648090.
Zhou, J., Hamdan, H., Yalamanchili, H. K., Pang, K., Pohodich, A. E., Lopez, J., Shao, Y., Oses-Prieto, J. A., Li, L., Kim, W., Durham, M. A., Bajikar, S. S., Palmer, D. J., Ng, P., Thompson, M. L., Bebin, E. M., Muller, A. J., Kuechler, A., Kampmeier, A., Haack, T. B., Burlingame, A. L., Liu, Z., Rasband, M. N., and Zoghbi, H. Y. (2022). Disruption of MeCP2-TCF20 complex underlies distinct neurodevelopmental disorders. Proc Natl Acad Sci U S A 119. PMID: 35074918, PMCID: PMC8794850.
Steimle, J. D., Grisanti Canozo, F. J., Park, M., Kadow, Z. A., Samee, M. A. H., and Martin, J. F. (2022). Decoding the PITX2 controlled genetic network in atrial fibrillation. JCI Insight. PMID: 35471998.
Singh, S, Lee, N, Pedroza, D, Bado, I, Zhang, L, Aguirre, S, Hamor, C, Shen, Y, Xu, Y, Hu, J, Gao, Y, , Zhao, N, Chen, S-H, Wan, Y-W, Liu, Z, Chang, JT, Hollern, D, Perou, CM, Zhang, X. H-F, and Rosen, JM. Chemotherapy coupled to macrophage inhibition induces T-cell and B-cell infiltration and durable regression in triple-negative breast cancer, Cancer Res, (2022) Apr 20:canres.3714. doi: 10.1158/0008-5472.CAN-21-3714. Online ahead of print. PMID: 35442423.
Alam, J., Yazdanpanah, G., Ratnapriya, R., Borcherding, N., de Paiva, C. S., Li, D., and Pflugfelder, S. C. (2022). Single-cell transcriptional profiling of murine conjunctival immune cells reveals distinct populations expressing homeostatic and regulatory genes. Mucosal Immunol. PMID: 35361907.
Alam, J., Yazdanpanah, G., Ratnapriya, R., Borcherding, N., de Paiva, C. S., Li, D., Guimaraes de Souza, R., Yu, Z., and Pflugfelder, S. C. (2022). IL-17 Producing Lymphocytes Cause Dry Eye and Corneal Disease with Aging in RXRalpha Mutant Mouse. Front Med (Lausanne) 9, 849990. PMID: 3540243.
2021
RNA-seq
Karolak, J. A., Gambin, T., Szafranski, P., Maywald, R. L., Popek, E., Heaney, J. D., and Stankiewicz, P. (2021) Perturbation of semaphorin and VEGF signaling in ACDMPV lungs due to FOXF1 deficiency. Respir Res 22, 212. PMID: 34315444.
Gou, X., Anurag, M., Lei, J. T., Kim, B. J., Singh, P., Seker, S., Fandino, D., Han, A., Rehman, S., Hu, J., Korchina, V., Doddapaneni, H., Dobrolecki, L. E., Mitsiades, N., Lewis, M. T., Welm, A. L., Li, S., Lee, A. V., Robinson, D. R., Foulds, C. E., and Ellis, M. J. (2021) Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer. Cancer Res 81, 6259-6272. PMID: 34711608.
Nanostring
McCullough LD, Roy-O’Reilly M, Lai YJ, Patrizz A, Xu Y, Lee J, Holmes A, Kraushaar DC, Chauhan A, Sansing LH, Stonestreet BS, Zhu L, Kofler J, Lim Y, Venna VR.. Exogenous inter-α inhibitor proteins prevent cell death and improve ischemic stroke outcomes in mice. The Journal of Clinical investigation. 2021 Sep 1;131(17). PMID: 34580244, PMCID: PMC8409590.
Alam, J., de Paiva, C. S., and Pflugfelder, S. C. (2021) Desiccation Induced Conjunctival Monocyte Recruitment and Activation - Implications for Keratoconjunctivitis. Front Immunol 12, 701415. PMID: 34305940.
de Paiva, C. S., Trujillo-Vargas, C. M., Schaefer, L., Yu, Z., Britton, R. A., and Pflugfelder, S. C. (2021) Differentially Expressed Gene Pathways in the Conjunctiva of Sjogren Syndrome Keratoconjunctivitis Sicca. Front Immunol 12, 702755. PMID: 34349764.
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
McCullough LD, Roy-O’Reilly M, Lai YJ, Patrizz A, Xu Y, Lee J, Holmes A, Kraushaar DC, Chauhan A, Sansing LH, Stonestreet BS, Zhu L, Kofler J, Lim Y, Venna VR.. Exogenous inter-α inhibitor proteins prevent cell death and improve ischemic stroke outcomes in mice. The Journal of Clinical investigation. 2021 Sep 1;131(17). PMID: 34580244, PMCID: PMC8409590.
Alam, J., de Paiva, C. S., and Pflugfelder, S. C. (2021) Desiccation Induced Conjunctival Monocyte Recruitment and Activation - Implications for Keratoconjunctivitis. Front Immunol 12, 701415. PMID: 34305940.
de Paiva, C. S., Trujillo-Vargas, C. M., Schaefer, L., Yu, Z., Britton, R. A., and Pflugfelder, S. C. (2021) Differentially Expressed Gene Pathways in the Conjunctiva of Sjogren Syndrome Keratoconjunctivitis Sicca. Front Immunol 12, 702755. PMID: 34349764.
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
Karolak, J. A., Gambin, T., Szafranski, P., Maywald, R. L., Popek, E., Heaney, J. D., and Stankiewicz, P. (2021) Perturbation of semaphorin and VEGF signaling in ACDMPV lungs due to FOXF1 deficiency. Respir Res 22, 212. PMID: 34315444.
Gou, X., Anurag, M., Lei, J. T., Kim, B. J., Singh, P., Seker, S., Fandino, D., Han, A., Rehman, S., Hu, J., Korchina, V., Doddapaneni, H., Dobrolecki, L. E., Mitsiades, N., Lewis, M. T., Welm, A. L., Li, S., Lee, A. V., Robinson, D. R., Foulds, C. E., and Ellis, M. J. (2021) Transcriptional Reprogramming Differentiates Active from Inactive ESR1 Fusions in Endocrine Therapy-Refractory Metastatic Breast Cancer. Cancer Res 81, 6259-6272. PMID: 34711608.
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.
