Publications

 

    • Geng R, Kidder BL. ColonyQuant: automated quantification and morphometric analysis of pluripotent stem cell colonies. BMC Bioinformatics. 2026. doi: 10.1186/s12859-026-06403-5. PMID: 41714932.
    • Kidder BL. Decoding the universal human chromatin landscape through teratoma-based profiling. Nucleic Acids Res. 2024 Apr 24;52(7):3589-3606. doi: 10.1093/nar/gkae021. PMID: 3828124.
    • Kidder BL. Advanced image generation for cancer using diffusion models. Biol Methods Protoc. 2024 Aug 23;9(1):bpae062. doi: 10.1093/biomethods/bpae062. eCollection 2024. PubMed PMID: 39258159; PMCID: PMC10453000.
    • Kidder BL, Ruden X, Singh A, Marben TA, Rass L, Chakravarty A, Xie Y, Puscheck EE, Awonuga AO, Harris S, Ruden DM, Rappolee DA. Placenta. 2024 Jul;152:72-85. doi: 10.1016/j.placenta.2023.12.020. Epub 2024 Jan 19. PMID: 3824540.
    • Kurup JT, Kim S, Kidder BL. Identifying Cancer Type-Specific Transcriptional Programs through Network Analysis. Cancers (Basel). 2023;15(16). doi: 10.3390/cancers15164167. PubMed PMID: 37627195; PMCID: PMC10453000.
    • Mitchell AV, Wu L , Block CJ, Zhang M, Hackett J, Craig DB, Chen W, Zhao Y, Zhang B, Dang Y, Zhang X, Zhang S, Wang C, Gibson H, Pile LA, Kidder B, Matherly L, Yang Z, Dou Y, Wu G. FOXQ1 recruits the MLL complex to activate transcription of EMT and promote breast cancer metastasis. Nature Communications. 2022 Nov 1;13(1):6548. doi: 10.1038/s41467-022-34239-z. PMID: 36319643
    • He R, Xhabija B, Gopi LK, Kurup JT, Xu Z, Liu Z, Kidder BL. H3K4 demethylase KDM5B regulates cancer cell identity and epigenetic plasticity. Oncogene. 2022 Apr 19. doi: 10.1038/s41388-022-02311-z. Online ahead of print. PMID: 35440714
    • Gopi LK, Kidder BL. Integrative pan cancer analysis reveals epigenomic variation in cancer type and cell specific chromatin domains. Nature Communications. 2021;12(1):1419. doi: 10.1038/s41467-021-21707-1.
    • Kurup JT, Kidder BL. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells. Development. 2020 Dec 4;147(23):dev188516. doi: 10.1242/dev.188516. PMID: 33144397
    • Zhang Q, Thakur C, Fu Y, Bi Z, Wadgaonkar P, Xu L, Liu Z, Liu W, Wang J, Kidder BL, Chen F. Mdig promotes oncogenic gene expression through antagonizing repressive histone methylation markers. Theranostics. 2020 Jan 1;10(2):602-614. doi: 10.7150/thno.36220. eCollection 2020. PMID: 31903140
    • Xhabija B, Kidder BL. KDM5B is a master regulator of the H3K4-methylome in stem cells, development and cancer. Semin Cancer Biol. 2019 Aug;57:79-85. doi: 10.1016/j.semcancer.2018.11.001. Epub 2018 Nov 16. Review. PMID: 30448242
    • Kurup JT, Campeanu IJ, Kidder BL. Contribution of H3K4 demethylase KDM5B to nucleosome organization in embryonic stem cells revealed by micrococcal nuclease sequencing. Epigenetics Chromatin. 2019 Apr 2;12(1):20. doi: 10.1186/s13072-019-0266-9. PMID: 30940185
    • Rosati R, Polin L, Ducker C, Li J, Bao X, Selvakumar D, Kim S, Xhabija B, Larsen M, McFall T, Huang Y, Kidder BL, Fribley A, Saxton J, Kakuta H, Shaw P, Ratnam M. Strategy for Tumor-Selective Disruption of Androgen Receptor Function in the Spectrum of Prostate Cancer. Clin Cancer Res. 2018 Sep 5. doi: 10.1158/1078-0432.CCR-18-0982. [Epub ahead of print]. PMID: 30185422
    • Kurup JT, Kidder BL. Identification of H4K20me3- and H3K4me3-associated RNAs using CARIP-Seq expands the transcriptional and epigenetic networks of embryonic stem cells. J Biol Chem. 2018 Sep 28;293(39):15120-15135. doi: 10.1074/jbc.RA118.004974. Epub 2018 Aug 16. PMID: 30115682
    • He R, Kidder BL. Culture of haploid blastocysts in FGF4 favors the derivation of epiblast stem cells with a primed epigenetic and transcriptional landscape. Sci Rep. 2018 Jul 17;8(1):10775. doi: 10.1038/s41598-018-29074-6. PMID: 30018329
    • Xu J, Kidder BL. H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells. BMC Genomics. 2018 Jul 3;19(1):514. doi: 10.1186/s12864-018-4886-4. PMID: 29969988
    • Kidder BL. CARIP-Seq and ChIP-Seq: Methods to Identify Chromatin-Associated RNAs and Protein-DNA Interactions in Embryonic Stem Cells. J Vis Exp. 2018 May 25;(135). doi: 10.3791/57481. PMID: 29748167
    • Xu J, Kidder BL. KDM5B decommissions the H3K4 methylation landscape of self-renewal genes during trophoblast stem cell differentiation. Biol Open. 2018 May 10;7(5). pii: bio031245. doi: 10.1242/bio.031245. PMID: 29748167
    • Vizcardo R, Klemen ND, Islam SMR, Gurusamy D, Tamaoki N, Yamada D, Koseki H, Kidder BL, Yu Z, Jia L, Henning AN, Good ML, Bosch-Marce M, Maeda T, Liu C, Abdullaev Z, Pack S, Palmer DC, Stroncek DF, Ito F, Flomerfelt FA, Kruhlak MJ, Restifo NP. Generation of Tumor Antigen-Specific iPSC-Derived Thymic Emigrants Using a 3D Thymic Culture System. CELL REPORTS. 2018 Mar 20;22(12):3175-3190. doi: 10.1016/j.celrep.2018.02.087. PMID: 29562175
    • He R, Xhabija B, Al-Qanber B, Kidder BL. OCT4 supports extended LIF-independent self-renewal and maintenance of transcriptional and epigenetic networks in embryonic stem cells. SCIENTIFIC REPORTS 2017 Nov 27;7(1):16360. doi: 10.1038/s41598-017-16611-y. PMID: 29180818
    • Kidder BL*, He R, Wangsa D, Padilla-Nash HM, Bernardo MM, Sheng S, Ried T, Zhao K*. SMYD5 controls heterochromatin and chromosome integrity during embryonic stem cell differentiation. CANCER RESEARCH 2017 Sep 26. pii: canres.0828.2017. doi: 10.1158/0008-5472.CAN-17-0828. [Epub ahead of print]. PMID: 28951459. *Corresponding author

Book Editorships

Book Chapters

    • Kidder BL. Direct Reprogramming of Mouse Embryonic Fibroblasts to Induced Trophoblast Stem Cells. METHODS IN MOLECULAR BIOLOGY. 2020;2117:285-292. doi: 10.1007/978-1-0716-0301-7_18. PMID: 31960387
    • Kidder BL. Derivation of Maternal Epiblast Stem Cells from Haploid Embryos. METHODS IN MOLECULAR BIOLOGY. 2020;2117:219-227. doi: 10.1007/978-1-0716-0301-7_12. PMID: 31960381
    • Kidder BL. Simultaneous Derivation of Embryonic and Trophoblast Stem Cells from Mouse Blastocysts. METHODS IN MOLECULAR BIOLOGY. 2020;2117:235-241. doi: 10.1007/978-1-0716-0301-7_14. PMID: 31960383
    • Kidder BL. Derivation of LIF-Independent Embryonic Stem Cells Using Inducible OCT4 Expression. METHODS IN MOLECULAR BIOLOGY. 2020;2117:229-234.doi: 10.1007/978-1-0716-0301-7_13. PMID: 31960382
    • Kidder BL*, Zhao K. Efficient library preparation for next-generation sequencing analysis of genome-wide epigenetic and transcriptional landscapes in embryonic stem cells. METHODS IN MOLECULAR BIOLOGY. 2014;1150:3-20. doi:10.1007/978-1-4939-0512-6_1.PMID: 24743988 *Corresponding author
    • Kidder BL. Generation of induced pluripotent stem cells using chemical inhibition and three transcription factors. METHODS IN MOLECULAR BIOLOGY. 2014;1150:227-36. doi: 10.1007/978-1-4939-0512-6_15. PMID: 24744002
    • Kidder BL. Derivation and manipulation of trophoblast stem cells from mouse blastocysts. METHODS IN MOLECULAR BIOLOGY, 2014;1150:201-12. doi: 10.1007/978-1-4939-0512-6_13. PMID: 24744000
    • Kidder BL. In vitro maturation and in vitro fertilization of mouse oocytes and preimplantation embryo culture. METHODS IN MOLECULAR BIOLOGY, 2014;1150:191-9. doi: 10.1007/978-1-4939-0512-6_12. PMID: 24743999