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Selected Publications

  • Hislop J, Song Q, Keshavarz F K, Alavi A, Schoenberger R, LeGraw R, Velazquez J,
    Mokhtari T, Taheri MN, Rytel M, Chuva de Sousa Lopes SM, Watkins S, Stolz D, Kiani S,
    Sozen B, Bar-Joseph Z, Ebrahimkhani MR # . Modeling post-implantation human
    development to yolk sac blood emergence.     Nature. 2023 Dec 13. doi: 10.1038/s41586-023-
    06914-8. Epub ahead of print. PMID: 38092041. ( # corresponding author): Highlighted in
    New York Times, Stat News, Eurek Alert, ScienMag, Mirage news, Phys- org, MSN,
    Technology Network, Technology Network, among others.
  • Chao Y, Xiang Y, Xiao J, Zhang S, Zheng W, Wan X, Li Z, Gao M, Wang G, Chen Z,
    Ebrahimkhani MR, Yang C, Ruohao Wu A, Liu P, Huang Y, Sugimura R. Organoid-based
    singlecell spatiotemporal gene expression landscape of human embryonic development
    and hematopoiesis    . Signal Transduction and Targeted Therapy (accepted).
  • 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
    Aug 10:S0168-8278(23)05040-7. doi: 10.1016/j.jhep.2023.07.039. Epub ahead of print.
    PMID: 37572794.
  • Lo E.K.W, Velazquez J, Peng D, Kwon C, Ebrahimkhani MR, Cahan P. Platform-AgnosticCellNet (PACNet) enables cross-study meta-analysis of cell fate engineering protocols. Stem CellReport (revision) 2022.09.07.506886; doi: https://doi.org/10.1101/2022.09.07.506886
  • 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 [Preprint]. 2023 May 30:2023.05.30.542848. doi: 10.1101/2023.05.30.542848.
    PMID: 37333155; PMCID: PMC10274893. (co-corresponding role)
  • Shafritz DA, Ebrahimkhani MR, Oertel M. Therapeutic Cell Repopulation of the Liver: FromFetal Rat Cells to Synthetic Human Tissues. Cells. 2023 Feb 6;12(4):529. doi:10.3390/cells12040529
  • 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 Biology. 2022 Mar 7;23(1):73.doi: 10.1186/s13059-022-0.2629-
  • Ding J, Alavi A, Ebrahimkhani MR, Bar-Joseph Z. Computational tools for analyzing single-cell data in pluripotent cell differentiation studies. Cell Reports Methods. 2021 Oct 4;1(6):100087. doi: 10.1016/j.crmeth.2021.100087.7.
  • Ebrahimkhani MR, Levin M. Synthetic living machines: A new window on life. iScience. 2021 May 4;24(5):102505. doi: 10.1016/j.isci.2021.102505. PMID: 34041452; PMCID: PMC8141884.
  • Boulter L, Ebrahimkhani MR. Build to understand biliary oncogenesis via organoids and FGFR2 fusion proteins. J Hepatol. 2021 Aug;75(2):262-264. doi: 10.1016/j.jhep.2021.05.006. Epub 2021 May 21. PMID: 34029636.
  • Velazquez JJ, Ebrahimkhani MR. Cholangiocyte organoids as a cell source for biliary repair. Transpl Int. 2021 Jun;34(6):999-1001. doi: 10.1111/tri.13902. Epub 2021 Jun 10. PMID: 33977592.
  • Ebrahimkhani MR, Hislop J, editors. Programmed Morphogenesis. Methods in Molecular Biology, vol 2258. New York: Humana; 2021.
  • ​Carter SR, Hislop J, Hsu J, Velazquez JJ, Ebrahimkhani MR. Neighborhood Impact Factor to Study Cell-Fate Decision-Making in Cellular Communities. In: Ebrahimkhani MR, Hislop J (eds). Programmed Morphogenesis. Methods in Molecular Biology, vol 2258. New York: Humana; 2021.
  • 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 Apr;18(4):252-268. doi: 10.1038/s41575-020-00386-1. Epub 2020 Dec 17. PMID: 33335282.
  • 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 Systems. 2021 Jan 20.
  • Hernandez-Gordillo V*, Casolaro TC*, Ebrahimkhani MR, Kiani S. Multicellular Systems to Translate Somatic Cell Genome Editors to Humans. Current Opinion in Biomedical Engineering 2020. (*co-first authors)​
  • 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 Sep 3;22:1143–1154. 
  • Pandelakis M, Delgado E, Ebrahimkhani MR. CRISPR-Based Synthetic Transcription Factors In Vivo: The Future of Therapeutic Cellular Programming. Cell Systems. 2020 Jan 22;10(1):1-4.
  • Ebrahimkhani MR, Ebisuya M. Synthetic developmental biology: build and control multicellular systems. Current opinion in chemical biology. 2019 Oct 1;52:9-15.
  • Ferdosi SR, Ewaisha R, Moghadam F, Krishna S, Park JG, Ebrahimkhani MR, Kiani S, Anderson KS. Multifunctional CRISPR-Cas9 with engineered immunosilenced human T cell epitopes. Nature communications. 2019 Apr 23;10(1):1-0.
  • 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 Jul 16.
  • Velazquez JJ*, Su E*, Cahan P#, Ebrahimkhani MR#. Programming Morphogenesis through Systems and Synthetic Biology. Trends in Biotechnology. 2018 Apr;36(4):415-429. (*co-first authors, #corresponding authors).
  • Pineda M, Moghadam F, Ebrahimkhani MR, Kiani S. Engineered CRISPR Systems for Next Generation Gene Therapies. ACS Synth Biol. 2017 Sep 15;6(9):1614-1626.
  • Ebrahimkhani MR. A New Positive Feedback Circuit in the Fibrosis-Cancer Axis for Male Livers. Cell Mol Gastroenterol Hepatol. 2017 Mar 15;3(3):301-302.
  • Bigorgne AE, John B, Ebrahimkhani MR, Shimizu-Albergine M, Campbell JS, Crispe IN. TLR4-Dependent Secretion by Hepatic Stellate Cells of the Neutrophil-Chemoattractant CXCL1 Mediates Liver Response to Gut Microbiota. PLoS ONE. 2016 Mar 22;11(3):e0151063.
  • Mohar I, Brempelis KJ, Murray SA, Ebrahimkhani MR, Crispe IN. Isolation of Non-parenchymal Cells from the Mouse Liver. Methods Mol Biol. 2015;1325:3-17
  • Kiani S*, Chavez A*, Tuttle M, Hall RN, Chari R, Ter-Ovanesyan D, Qian J, Pruitt BW, Beal J, Vora S, Buchthal J, Kowal EJ, Ebrahimkhani MR, Collins JJ, Weiss R, Church G. Cas9 gRNA engineering for genome editing, activation and repression. Nat Methods. 2015 Sep 7. doi: 10.1038 (* co-first authors)
  • Sarkar U, Rivera-Burgos D, Large EM, Hughes DJ, Ravindra KC, Dyer RL, Ebrahimkhani MR, Wishnok JS, Griffith LG, Tannenbaum SR. Metabolite profiling and pharmacokinetic evaluation of hydrocortisone in a perfused three-dimensional human liver bioreactor. Drug Metab Dispos. 2015 Jul;43(7):1091-9
  • Ebrahimkhani MR, Daneshmand A, Mazumder A, Allocca M, Calvo JA, Abolhassani N, Jhun I, Muthupalani S, Cenk A, Samson LD. Aag-Initiated Base Excision Repair Promotes Ischemia Reperfusion Injury In Liver, Brain And Kidney. Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):E4878-86
  • Kiani S, Beal J, Ebrahimkhani MR, Huh J, Hall RN, Xie Z, Li Y, Weiss R. CRISPR transcriptional repression devices and layered circuits in mammalian cells. Nat Methods. 2014 Jul;11(7):723-6

  • Guye P*, Ebrahimkhani MR*, Kipniss N, Velazquez JJ, Schoenfeld E, Kiani S, Griffith LG, Weiss R. Genetically engineering self-organization of human pluripotent stem cells into a liver bud-like tissue using Gata6. Nature communications. 2016 Jan 6;7(1):1-2. (* co-first authors)

  • Ebrahimkhani MR, Shepard JA, Raredon MSB, Griffith LG. Bioreactor Technologies to Support Liver Function In Vitro.  Adv Drug Deliv Rev. 2014 Apr; 69-70:132-57
  • Ebrahimkhani MR, Young CL, Lauffenburger DA, Griffith LG, Borenstein JT. Approaches To In Vitro Tissue Regeneration With Application For Human Disease Modeling And Drug Development. Drug Discov Today. 2014 Jun;19(6):754-62.
  • Probert P, Ebrahimkhani MR, Oakley F, Mann J, Burt AD, Mann DA, Wright MC. A Reversible Model For Periportal Fibrosis And A Refined Alternative To Bile Duct Ligation. Toxicol. Res. 2014 Mar 1;3(2):98-109.
  • Wheeler S, Borenstein JT, Clark A, Ebrahimkhani MR, Fox IJ, Griffith LG, Inman W, Lauffenburger DA, Nguyen T, Pillai V, Prantil-Baun R, Stolz DB, Taylor D, Ulrich T, Venkataramanan R, Wells A, Young CA. All-Human Microphysical Model Of Metastasis Therapy. Stem Cell Research & Therapy. 2013; 4 S1:S11.
  • Ebrahimkhani MR, Oakley F, Murphy L, Mann J, Ellis E, Burt A, Douglass A, Wright M, White S, Jaffré F, Maroteaux L, Mann DA. Stimulating Healthy Tissue Regeneration By Targeting The 5-Ht2b Receptor In Chronic Liver Disease. Nat. Medicine. 2011; 17 (12): 1668-73.
  • Ebrahimkhani MR, Mohar I, Crispe IN. Antigen Cross-Presentation By Different Subset Of Liver Cells. Hepatology. 2011; 54: 1379-87
  • Gieling RG, ElsharkawyAM , Caamano JH ,Cowie DE, Wright MC, Ebrahimkhani MR, Burt AD, Raychaudhuri P, Hsiou-Chi L, Oakley F, Mann DA. The c-Rel Subunit of Nuclear Factor-kB Regulates Murine Liver Inflammation, Wound-Healing and Hepatocyte Proliferation. Hepatology. 2010; 51(3):922-31.
  • Wu F, Wuensch SA, Azadniv M, Ebrahimkhani MR, Crispe IN.A Novel Targeting Delivery System To Deliver Antigen to Macrophages and Enhance Antigen Specific T Cell Responses. Galactosylated LDL Nanoparticles:  Mol Pharm. 2009 Aug 10.
  • Ebrahimkhani   MR, Elsharkawy AM, Mann DA. Wound Healing And Local Neuroendocrine Regulation In The Injured Liver. Expert Rev Mol Med. 2008 Apr 29;10.
  • Ebrahimkhani MR, Kiani S, Oakley F, Kendall T, Shariftabrizi A, Tavangar SM, Payabvash S, L Moezi L, 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(11): 1606-16.
  • Mani AR, Ebrahimkhani MR, Ippolito S, Ollosson R, Moore KP. Metalloprotein Dependent Decomposition Of S-Nitrosothiols: Studies On The Stabilization And Measurement Of S-Nitrosothiols In Tissues. Free Radic Biol Med. 2006 May 1;40(9):1654-63.
  • Shariftabrizi A, Nifli AP, Ansari M, Saadat F, Ebrahimkhani MR, Alizadeh N, Nasseh A, Alexaki VI, Dehpour AR, Castanas E, Khorramizadeh MR. Nitric Oxide Modulates Morphine Induced Inhibition Of Matrix-Metalloproteinase-2 Secretion From Mice Fibrosarcoma Cells. Eur J Pharmacol. 2006 Jan 13;530(1-2):33-9.
  • Ebrahimkhani MR, Mani AR, Moore K. Hydrogen Sulphide And The Hyperdynamic Circulation In Cirrhosis: A Hypothesis. Gut. 2005 Dec;54(12):1668-71
  • Shariftabrizi A, Khorramizadeh MR, Saadat F, Alimoghadam K, Safavifar F, Ebrahimkhani MR. Concomitant Reduction Of Matrix Metalloproteinase-2 Secretion And Intracellular Reactive Oxygen Species Following Anti-Sense Inhibition Of Telomerase Activity In PC-3 Prostate Carcinoma Cells. Molecular Cell Biochem. 2005; 109-116
  • Ebrahimkhani MR, Sadeghipour H, Dehghani M, Kiani S, Payabvash S, Riazi K, Honar H, Mirazi N, Pasalar P, Amanlou M, Farsam H, Dehpour AR. Homocysteine alterations in experimental cholestasis and subsequent cirrhosis. Life Sciences. 2005; 76, 2497-2512.
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