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Hislop J, Song Q, Keshavarz F K, Alavi A, Schoenberger R, LeGraw R, Velazquez JJ, Mokhtari T, Taheri MN, Rytel M, Chuva de Sousa Lopes SM, Watkins S, Stolz D, Kiani S, Sozen B, Bar-Joseph Z, Ebrahimkhani MR. Modelling post-implantation human development to yolk sac blood emergence. Nature 2024;626:367-376. [PMID: 38092041 PMCID: PMC10849971 DOI: 10.1038/s41586-023-06914-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 11/29/2023] [Indexed: 01/16/2024]
2
Glessner JT, Ningappa MB, Ngo KA, Zahid M, So J, Higgs BW, Sleiman PMA, Narayanan T, Ranganathan S, March M, Prasadan K, Vaccaro C, Reyes-Mugica M, Velazquez J, Salgado CM, Ebrahimkhani MR, Schmitt L, Rajasundaram D, Paul M, Pellegrino R, Gittes GK, Li D, Wang X, Billings J, Squires R, Ashokkumar C, Sharif K, Kelly D, Dhawan A, Horslen S, Lo CW, Shin D, Subramaniam S, Hakonarson H, Sindhi R. Biliary atresia is associated with polygenic susceptibility in ciliogenesis and planar polarity effector genes. J Hepatol 2023;79:1385-1395. [PMID: 37572794 PMCID: PMC10729795 DOI: 10.1016/j.jhep.2023.07.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/14/2023]
3
Lo EKW, Velazquez JJ, Peng D, Kwon C, Ebrahimkhani MR, Cahan P. Platform-agnostic CellNet enables cross-study analysis of cell fate engineering protocols. Stem Cell Reports 2023;18:1721-1742. [PMID: 37478860 PMCID: PMC10444577 DOI: 10.1016/j.stemcr.2023.06.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 06/16/2023] [Accepted: 06/17/2023] [Indexed: 07/23/2023]  Open
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Hislop J, Alavi A, Song Q, Schoenberger R, Kamyar KF, LeGraw R, Velazquez J, Mokhtari T, Taheri MN, Rytel M, de Sousa Lopes SMC, Watkins S, Stolz D, Kiani S, Sozen B, Bar-Joseph Z, Ebrahimkhani MR. Modelling Human Post-Implantation Development via Extra-Embryonic Niche Engineering. bioRxiv 2023:2023.06.15.545118. [PMID: 37398391 PMCID: PMC10312773 DOI: 10.1101/2023.06.15.545118] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
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Chao Y, Xiang Y, Xiao J, Zheng W, Ebrahimkhani MR, Yang C, Wu AR, Liu P, Huang Y, Sugimura R. Organoid-based single-cell spatiotemporal gene expression landscape of human embryonic development and hematopoiesis. Signal Transduct Target Ther 2023;8:230. [PMID: 37264003 PMCID: PMC10235070 DOI: 10.1038/s41392-023-01455-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 04/04/2023] [Accepted: 04/27/2023] [Indexed: 06/03/2023]  Open
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Maggiore JC, LeGraw R, Przepiorski A, Velazquez J, Chaney C, Streeter E, Silva-Barbosa A, Franks J, Hislop J, Hill A, Wu H, Pfister K, Howden SE, Watkins SC, Little M, Humphreys BD, Watson A, Stolz DB, Kiani S, Davidson AJ, Carroll TJ, Cleaver O, Sims-Lucas S, Ebrahimkhani MR, Hukriede NA. Genetically engineering endothelial niche in human kidney organoids enables multilineage maturation, vascularization and de novo cell types. bioRxiv 2023:2023.05.30.542848. [PMID: 37333155 PMCID: PMC10274893 DOI: 10.1101/2023.05.30.542848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
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Shafritz DA, Ebrahimkhani MR, Oertel M. Therapeutic Cell Repopulation of the Liver: From Fetal Rat Cells to Synthetic Human Tissues. Cells 2023;12:529. [PMID: 36831196 PMCID: PMC9954009 DOI: 10.3390/cells12040529] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023]  Open
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Li D, Velazquez JJ, Ding J, Hislop J, Ebrahimkhani MR, Bar-Joseph Z. TraSig: inferring cell-cell interactions from pseudotime ordering of scRNA-Seq data. Genome Biol 2022;23:73. [PMID: 35255944 PMCID: PMC8900372 DOI: 10.1186/s13059-022-02629-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 02/09/2022] [Indexed: 02/08/2023]  Open
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Ding J, Alavi A, Ebrahimkhani MR, Bar-Joseph Z. Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. Cell Rep Methods 2021;1:100087. [PMID: 35474899 PMCID: PMC9017169 DOI: 10.1016/j.crmeth.2021.100087] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
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Boulter L, Ebrahimkhani MR. Build to understand biliary oncogenesis via organoids and FGFR2 fusion proteins. J Hepatol 2021;75:262-264. [PMID: 34029636 PMCID: PMC8887813 DOI: 10.1016/j.jhep.2021.05.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/30/2022]
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Velazquez JJ, Ebrahimkhani MR. Cholangiocyte organoids as a cell source for biliary repair. Transpl Int 2021;34:999-1001. [PMID: 33977592 DOI: 10.1111/tri.13902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Indexed: 11/30/2022]
12
Pandelakis M, Delgado E, Ebrahimkhani MR. CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming. Cell Syst 2021;10:1-14. [PMID: 31972154 DOI: 10.1016/j.cels.2019.10.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 08/14/2019] [Accepted: 10/09/2019] [Indexed: 01/04/2023]
13
Ebrahimkhani MR, Levin M. Synthetic living machines: A new window on life. iScience 2021;24:102505. [PMID: 34041452 PMCID: PMC8141884 DOI: 10.1016/j.isci.2021.102505] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
14
Gough A, Soto-Gutierrez A, Vernetti L, Ebrahimkhani MR, Stern AM, Taylor DL. Human biomimetic liver microphysiology systems in drug development and precision medicine. Nat Rev Gastroenterol Hepatol 2021;18:252-268. [PMID: 33335282 PMCID: PMC9106093 DOI: 10.1038/s41575-020-00386-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/02/2020] [Indexed: 02/07/2023]
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Velazquez JJ, LeGraw R, Moghadam F, Tan Y, Kilbourne J, Maggiore JC, Hislop J, Liu S, Cats D, Chuva de Sousa Lopes SM, Plaisier C, Cahan P, Kiani S, Ebrahimkhani MR. Gene Regulatory Network Analysis and Engineering Directs Development and Vascularization of Multilineage Human Liver Organoids. Cell Syst 2020;12:41-55.e11. [PMID: 33290741 PMCID: PMC8164844 DOI: 10.1016/j.cels.2020.11.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/13/2020] [Accepted: 11/09/2020] [Indexed: 12/19/2022]
16
Hernandez-Gordillo V, Casolaro TC, Ebrahimkhani MR, Kiani S. Multicellular Systems to Translate Somatic Cell Genome Editors to Humans. Curr Opin Biomed Eng 2020;16:72-81. [PMID: 33718690 DOI: 10.1016/j.cobme.2020.100249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
17
Moghadam F, LeGraw R, Velazquez JJ, Yeo NC, Xu C, Park J, Chavez A, Ebrahimkhani MR, Kiani S. Synthetic immunomodulation with a CRISPR super-repressor in vivo. Nat Cell Biol 2020;22:1143-1154. [PMID: 32884147 PMCID: PMC7480217 DOI: 10.1038/s41556-020-0563-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 07/24/2020] [Indexed: 12/19/2022]
18
Ebrahimkhani MR, Ebisuya M. Synthetic developmental biology: build and control multicellular systems. Curr Opin Chem Biol 2019;52:9-15. [PMID: 31102790 DOI: 10.1016/j.cbpa.2019.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 04/03/2019] [Accepted: 04/09/2019] [Indexed: 02/08/2023]
19
Yeo NC, Chavez A, Lance-Byrne A, Chan Y, Menn D, Milanova D, Kuo CC, Guo X, Sharma S, Tung A, Cecchi RJ, Tuttle M, Pradhan S, Lim ET, Davidsohn N, Ebrahimkhani MR, Collins JJ, Lewis NE, Kiani S, Church GM. An enhanced CRISPR repressor for targeted mammalian gene regulation. Nat Methods 2018;15:611-616. [PMID: 30013045 PMCID: PMC6129399 DOI: 10.1038/s41592-018-0048-5] [Citation(s) in RCA: 273] [Impact Index Per Article: 45.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 05/03/2018] [Indexed: 01/12/2023]
20
Velazquez JJ, Su E, Cahan P, Ebrahimkhani MR. Programming Morphogenesis through Systems and Synthetic Biology. Trends Biotechnol 2017;36:415-429. [PMID: 29229492 DOI: 10.1016/j.tibtech.2017.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/15/2017] [Accepted: 11/16/2017] [Indexed: 01/07/2023]
21
Pineda M, Moghadam F, Ebrahimkhani MR, Kiani S. Engineered CRISPR Systems for Next Generation Gene Therapies. ACS Synth Biol 2017;6:1614-1626. [PMID: 28558198 DOI: 10.1021/acssynbio.7b00011] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
22
Ebrahimkhani MR. A New Positive Feedback Circuit in the Fibrosis-Cancer Axis for Male Livers. Cell Mol Gastroenterol Hepatol 2017;3:301-302. [PMID: 28462371 PMCID: PMC5404096 DOI: 10.1016/j.jcmgh.2017.02.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
23
Wheeler SE, Taylor DP, Clark AM, Borenstein JT, Ebrahimkhani MR, Inman W, Nguyen T, Pillai VC, Prantil-Baun R, Ulrich TA, Venkataramanan R, Lauffenburger DA, Griffith L, Stolz DB, Wells A. Abstract P5-04-08: Modeling breast cancer dormancy. Cancer Res 2013. [DOI: 10.1158/0008-5472.sabcs13-p5-04-08] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
24
Ebrahimkhani MR, Kiani S, Oakley F, Kendall T, Shariftabrizi A, Tavangar SM, Moezi L, Payabvash S, Karoon A, Hoseininik H, Mann DA, Moore KP, Mani AR, Dehpour AR. Naltrexone, an opioid receptor antagonist, attenuates liver fibrosis in bile duct ligated rats. Gut 2006;55:1606-16. [PMID: 16543289 PMCID: PMC1860108 DOI: 10.1136/gut.2005.076778] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
25
Ebrahimkhani MR, Mani AR, Moore K. Hydrogen sulphide and the hyperdynamic circulation in cirrhosis: a hypothesis. Gut 2005;54:1668-71. [PMID: 16174660 PMCID: PMC1774792 DOI: 10.1136/gut.2004.056556] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
26
Honar H, Riazi K, Homayoun H, Sadeghipour H, Rashidi N, Ebrahimkhani MR, Mirazi N, Dehpour AR. Ultra-low dose naltrexone potentiates the anticonvulsant effect of low dose morphine on clonic seizures. Neuroscience 2005;129:733-42. [PMID: 15541894 DOI: 10.1016/j.neuroscience.2004.08.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2004] [Indexed: 11/26/2022]
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