Publications
Generation of Induced Pluripotent Stem Cell Lines (RFSCi003-a, RFSCi004-A) From Monozygotic Twins Discordant for Age-Related Macular Degeneration. Rajendran N, Runyon W, Hu S, Singh A, Ratnapriya R, Kumar R, Csaky K, Sripathi SR. Stem Cell Res. 2025 Jul 5;87:103768. doi: 10.1016/j.scr.2025.103768. PMID: 40627958.
Optimized, Efficient Measurement of the Expression of Undifferentiated Stem Cell Markers in Human Induced Pluripotent Stem Cells (iPSCs) by Flow Cytometry. Saware V, Runyon W, Hu S, van Soldt B, Kumar R, Srivastava J. Curr Protoc. 2025 Mar;5(3):e70105. doi: 10.1002/cpz1.70105. PMID: 40028708.
Functional Analysis of a Common BAG3 Allele Associated With Protection From Heart Failure. Perez-Bermejo JA, Judge LM, Jensen CL, Wu K, Watry HL, Truong A, Ho JJ, Carter M, Runyon WV, Kaake RM, Pulido EH, Mandegar MA, Swaney DL, So PL, Krogan NJ, Conklin BR. Nat Cardiovasc Res. 2023 Jul;2(7):615-628. doi: 10.1038/s44161-023-00288-w. Epub 2023 Jun 26. PMID: 39195919.
Transcription Factor Protein Interactomes Reveal Genetic Determinants in Heart Disease. Barbara Gonzalez-Teran, Maureen Pittman, Franco Felix, Reuben Thomas, Desmond Richmond-Buccola, Ruth Hüttenhain, Krishna Choudhary, Elisabetta Moroni, Mauro W Costa, Yu Huang, Arun Padmanabhan, Michael Alexanian, Clara Youngna Lee, Bonnie E J Maven, Kaitlen Samse-Knapp, Sarah U Morton, Michael McGregor, Casey A Gifford, J G Seidman, Christine E Seidman, Bruce D Gelb, Giorgio Colombo, Bruce R Conklin, Brian L Black, Benoit G Bruneau, Nevan J Krogan, Katherine S Pollard, Deepak Srivastava. Cell 2022 Mar 3;185(5):794-814.
Brahma Safeguards Canalization of Cardiac Mesoderm Differentiation. Swetansu K Hota , Kavitha S Rao , Andrew P Blair , Ali Khalilimeybodi , Kevin M Hu , Reuben Thomas , Kevin So , Vasumathi Kameswaran , Jiewei Xu , Benjamin J Polacco , Ravi V Desai , Nilanjana Chatterjee , Austin Hsu , Jonathon M Muncie , Aaron M Blotnick , Sarah A B Winchester , Leor S Weinberger , Ruth Hüttenhain , Irfan S Kathiriya , Nevan J Krogan , Jeffrey J Saucerman , Benoit G Bruneau. Nature 2022 Feb;602(7895):129-134.
Transcription Factor GATA4 Regulates Cell Type-Specific Splicing Through Direct Interaction With RNA in Human Induced Pluripotent Stem Cell-Derived Cardiac Progenitors. Lili Zhu, Krishna Choudhary, Barbara Gonzalez-Teran, Yen-Sin Ang, Reuben Thomas, Nicole R Stone, Lei Liu, Ping Zhou, Chenchen Zhu, Hongmei Ruan, Yu Huang, Shibo Jin, Angelo Pelonero, Frances Koback, Arun Padmanabhan, Nandhini Sadagopan, Austin Hsu, Mauro W Costa, Casey A Gifford, Joke G van Bemmel, Ruth Hüttenhain, Vasanth Vedantham, Bruce R Conklin, Brian L Black, Benoit G Bruneau, Lars Steinmetz, Nevan J Krogan, Katherine S Pollard, Deepak Srivastava. Circulation 2022 Sep 6;146(10):770-787.
Sars-Cov-2 Infection Of Human Ipsc-Derived Cardiac Cells Reflects Cytopathic Features in Hearts of Patients with Covid-19. Perez-Bermejo JA, Kang S, Rockwood SJ, Simoneau CR, Joy DA, Silva AC, Ramadoss GN, Flanigan WR, Fozouni P, Li H, Chen PY, Nakamura K, Whitman JD, Hanson PJ, McManus BM, Ott M, Conklin BR, McDevitt TC. Sci Transl Med 2021 Apr 21;13(590).
Allele-Specific Gene Editing Rescues Pathology in a Human Model of Charcot-Marie-Tooth Disease Type 2E. Feliciano CM, Wu K, Watry HL, Marley CBE, Ramadoss GN, Ghanim HY, Liu AZ, Zholudeva LV, McDevitt TC, Saporta MA, Conklin BR, Judge LM. Front Cell Dev Biol 2021 Aug 16;9:723023.
Transcription Factor Overexpression Drives Reliable Differentiation of Retinal Pigment Epithelium From Human Induced Pluripotent Stem Cells. Dewell TE, Gjoni K, Liu AZ, Libby ARG, Moore AT, So PL, Conklin BR. Stem Cell Res 2021 May;53:102368.
Sox2 and Klf4 as the Functional Core in Pluripotency Induction without Exogenous Oct4. An, Z., Liu, P., Zheng, J., et al. 2019. Cell Reports 29(7), p. 1986–2000.e8.
Differentiation of V2a interneurons from human pluripotent stem cells. Butts, J.C., McCreedy, D.A., Martinez-Vargas, J.A., et al. 2017. Proceedings of the National Academy of Sciences of the United States of America 114(19), pp. 4969–4974.
Oligogenic inheritance of a human heart disease involving a genetic modifier. Gifford, C.A., Ranade, S.S., Samarakoon, R., et al. 2019. Science 364(6443), pp. 865–870.
BMP-SMAD-ID promotes reprogramming to pluripotency by inhibiting p16/INK4A-dependent senescence. Hayashi, Y., Hsiao, E.C., Sami, S., et al. 2016. Proceedings of the National Academy of Sciences of the United States of America 113(46), pp. 13057–13062.
Miniaturized iPS-Cell-Derived Cardiac Muscles for Physiologically Relevant Drug Response Analyses. Huebsch, N., Loskill, P., Deveshwar, N., et al. 2016. Scientific Reports 6, p. 24726.
Automated Video-Based Analysis of Contractility and Calcium Flux in Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Cultured over Different Spatial Scales. Huebsch, N., Loskill, P., Mandegar, M.A., et al. 2015. Tissue Engineering. Part C, Methods 21(5), pp. 467–479.
A BAG3 chaperone complex maintains cardiomyocyte function during proteotoxic stress. Judge, L.M., Perez-Bermejo, J.A., Truong, A., et al. 2017. Journal of Clinical Investigation Insight 2(14). PMC5518554
Spatiotemporal mosaic self-patterning of pluripotent stem cells using CRISPR interference. Libby, A.R., Joy, D.A., So, P.-L., et al. 2018. eLife 7.
CRISPR Interference Efficiently Induces Specific and Reversible Gene Silencing in Human iPSCs. Mandegar, M.A., Huebsch, N., Frolov, E.B., et al. 2016. Cell Stem Cell 18(4), pp. 541–553.
Isolation of single-base genome-edited human iPS cells without antibiotic selection. Miyaoka, Y., Chan, A.H., Judge, L.M., et al. 2014. Nature Methods 11(3), pp. 291–293.
Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Wienert, B., Wyman, S.K., Richardson, C.D., et al. 2019. Science 364(6437), pp. 286–289.
The Cellular NMD Pathway Restricts Zika Virus Infection and Is Targeted by the Viral Capsid Protein. Fontaine, K.A., Leon, K.E., Khalid, M.M, Tomar, S., Jimenez-Morales, D., Dunlap, M., Kaye, J.A., Shah, P.S., Finkbeiner, S., Krogan, N.J., Ott. M. 2018. mBio. Nov-Dec; 9(6) PMCID: PMC6222128
Efficient CRISPR/Cas9-Based Genome Engineering in Human Pluripotent Stem Cells. Kime, C., Mandegar, M. A., Srivastava, D., Yamanaka, S., Conklin, B. R., & Rand, T. A. (2016). Current Protocols in Human Genetics, 88, 21.4.1–21.4.23.
Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency. Theodoris, C. V., Li, M., White, M. P., Liu, L., He, D., Pollard, K. S., Bruneau, B. G., & Srivastava, D. (2015). Cell, 160(6), 1072–1086.
More Publications
