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    Neil Chi

    TitleAssociate Professor In Residence
    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0613-J
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Regulatory Mechanisms of Myocardial Reprogramming in Zebrafish
      NIH/NHLBI R01HL132298Apr 1, 2017 - Mar 31, 2021
      Role: Principal Investigator
      Reconstruction of cardiovascular regulatory networks from large-scale single-cell analyses of cardiovascular lineages
      NIH/NICHD R01HD085902Mar 1, 2016 - Feb 28, 2021
      Role: Principal Investigator
      GPCR Cytoprotective Signaling Mechanisms
      NIH/NIGMS R01GM116597Sep 1, 2015 - Jul 31, 2019
      Role: Principal Investigator
      Developmental Regulatory Genomics of Human Cardiovascular Lineages
      NIH/NHLBI UM1HL128773Aug 1, 2015 - Jul 31, 2020
      Role: Principal Investigator
      Electrical Biophysical Forces Impact Cardiac Morphogenesis
      NIH/NICHD R01HD069305Sep 10, 2011 - Jun 30, 2016
      Role: Principal Investigator
      NIH/NHLBI U01HL107442Jul 15, 2011 - Jun 30, 2017
      Role: Principal Investigator
      Molecular and genetic mechanisms of cardiac conduction development and disease
      NIH/NHLBI R01HL104239Jul 1, 2011 - Jun 30, 2015
      Role: Principal Investigator
      Directed Cardiac Cellular Programming: A New Paradigm for Cardiac Regeneration
      NIH DP2OD007464Sep 30, 2010 - Jun 30, 2015
      Role: Principal Investigator
      Zebrafish Heart Mutants:Physiological &Genetic Analyses
      NIH/NHLBI K08HL074891Mar 1, 2004 - Feb 28, 2010
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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      1. Hu Z, Liu Y, Huarng MC, Menegatti M, Reyon D, Rost MS, Norris ZG, Richter CE, Stapleton AN, Chi N, Peyvandi F, Joung JK, Shavit JA. Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathway. Blood. 2017 Aug 03; 130(5):666-676. PMID: 28576875.
        View in: PubMed
      2. Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi N, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA. iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. Stem Cell Reports. 2017 Apr 11; 8(4):1086-1100. PMID: 28410642.
        View in: PubMed
      3. Pradhan A, Zeng XI, Sidhwani P, Marques SR, George V, Targoff KL, Chi N, Yelon D. FGF signaling enforces cardiac chamber identity in the developing ventricle. Development. 2017 Apr 01; 144(7):1328-1338. PMID: 28232600.
        View in: PubMed
      4. Lardelli RM, Schaffer AE, Eggens VR, Zaki MS, Grainger S, Sathe S, Van Nostrand EL, Schlachetzki Z, Rosti B, Akizu N, Scott E, Silhavy JL, Heckman LD, Rosti RO, Dikoglu E, Gregor A, Guemez-Gamboa A, Musaev D, Mande R, Widjaja A, Shaw TL, Markmiller S, Marin-Valencia I, Davies JH, de Meirleir L, Kayserili H, Altunoglu U, Freckmann ML, Warwick L, Chitayat D, Blaser S, Çaglayan AO, Bilguvar K, Per H, Fagerberg C, Christesen HT, Kibaek M, Aldinger KA, Manchester D, Matsumoto N, Muramatsu K, Saitsu H, Shiina M, Ogata K, Foulds N, Dobyns WB, Chi N, Traver D, Spaccini L, Bova SM, Gabriel SB, Gunel M, Valente EM, Nassogne MC, Bennett EJ, Yeo GW, Baas F, Lykke-Andersen J, Gleeson JG. Biallelic mutations in the 3' exonuclease TOE1 cause pontocerebellar hypoplasia and uncover a role in snRNA processing. Nat Genet. 2017 Mar; 49(3):457-464. PMID: 28092684.
        View in: PubMed
      5. Bloomekatz J, Galvez-Santisteban M, Chi N. Myocardial plasticity: cardiac development, regeneration and disease. Curr Opin Genet Dev. 2016 Oct; 40:120-130. PMID: 27498024.
        View in: PubMed
      6. Lee J, Fei P, Sevag Packard RR, Kang H, Xu H, Baek KI, Jen N, Chen J, Yen H, Kuo CC, Chi N, Ho CM, Li R, Hsiai TK. 4-Dimensional light-sheet microscopy to elucidate shear stress modulation of cardiac trabeculation. J Clin Invest. 2016 Aug 01; 126(8):3158. PMID: 27479748; PMCID: PMC4966324.
      7. Reischauer S, Stone OA, Villasenor A, Chi N, Jin SW, Martin M, Lee MT, Fukuda N, Marass M, Witty A, Fiddes I, Kuo T, Chung WS, Salek S, Lerrigo R, Alsiö J, Luo S, Tworus D, Augustine SM, Mucenieks S, Nystedt B, Giraldez AJ, Schroth GP, Andersson O, Stainier DY. Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification. Nature. 2016 07 14; 535(7611):294-8. PMID: 27411634.
        View in: PubMed
      8. Han P, Bloomekatz J, Ren J, Zhang R, Grinstein JD, Zhao L, Burns CG, Burns CE, Anderson RM, Chi N. Coordinating cardiomyocyte interactions to direct ventricular chamber morphogenesis. Nature. 2016 06 30; 534(7609):700-4. PMID: 27357797.
        View in: PubMed
      9. Lee J, Fei P, Packard RR, Kang H, Xu H, Baek KI, Jen N, Chen J, Yen H, Kuo CC, Chi N, Ho CM, Li R, Hsiai TK. 4-Dimensional light-sheet microscopy to elucidate shear stress modulation of cardiac trabeculation. J Clin Invest. 2016 May 02; 126(5):1679-90. PMID: 27018592; PMCID: PMC4855946.
      10. Palencia-Desai S, Rost MS, Schumacher JA, Ton QV, Craig MP, Baltrunaite K, Koenig AL, Wang J, Poss KD, Chi N, Stainier DY, Sumanas S. Myocardium and BMP signaling are required for endocardial differentiation. Development. 2015 Jul 01; 142(13):2304-15. PMID: 26092845; PMCID: PMC4510589.
      11. Guemez-Gamboa A, Nguyen LN, Yang H, Zaki MS, Kara M, Ben-Omran T, Akizu N, Rosti RO, Rosti B, Scott E, Schroth J, Copeland B, Vaux KK, Cazenave-Gassiot A, Quek DQ, Wong BH, Tan BC, Wenk MR, Gunel M, Gabriel S, Chi N, Silver DL, Gleeson JG. Inactivating mutations in MFSD2A, required for omega-3 fatty acid transport in brain, cause a lethal microcephaly syndrome. Nat Genet. 2015 Jul; 47(7):809-13. PMID: 26005868; PMCID: PMC4547531.
      12. Yang H, Fang L, Zhan R, Hegarty JM, Ren J, Hsiai TK, Gleeson JG, Miller YI, Trejo J, Chi N. Polo-like kinase 2 regulates angiogenic sprouting and blood vessel development. Dev Biol. 2015 Aug 15; 404(2):49-60. PMID: 26004360; PMCID: PMC4515213.
      13. Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi N, Adler ED. Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. Stem Cells. 2015 Jul; 33(7):2343-50. PMID: 25826782; PMCID: PMC4651661.
      14. Kametani Y, Chi N, Stainier DY, Takada S. Notch signaling regulates venous arterialization during zebrafish fin regeneration. Genes Cells. 2015 May; 20(5):427-38. PMID: 25810153; PMCID: PMC4996968.
      15. Mishra-Gorur K, Çaglayan AO, Schaffer AE, Chabu C, Henegariu O, Vonhoff F, Akgümüs GT, Nishimura S, Han W, Tu S, Baran B, Gümüs H, Dilber C, Zaki MS, Hossni HA, Rivière JB, Kayserili H, Spencer EG, Rosti RÖ, Schroth J, Per H, Çaglar C, Çaglar Ç, Dölen D, Baranoski JF, Kumandas S, Minja FJ, Erson-Omay EZ, Mane SM, Lifton RP, Xu T, Keshishian H, Dobyns WB, Chi N, Šestan N, Louvi A, Bilgüvar K, Yasuno K, Gleeson JG, Günel M. Mutations in KATNB1 cause complex cerebral malformations by disrupting asymmetrically dividing neural progenitors. Neuron. 2014 Dec 17; 84(6):1226-39. PMID: 25521378; PMCID: PMC5024344.
      16. Li R, Beebe T, Jen N, Yu F, Takabe W, Harrison M, Cao H, Lee J, Yang H, Han P, Wang K, Shimizu H, Chen J, Lien CL, Chi N, Hsiai TK. Shear stress-activated Wnt-angiopoietin-2 signaling recapitulates vascular repair in zebrafish embryos. Arterioscler Thromb Vasc Biol. 2014 Oct; 34(10):2268-75. PMID: 25147335; PMCID: PMC4169303.
      17. Cao H, Yu F, Zhao Y, Zhang X, Tai J, Lee J, Darehzereshki A, Bersohn M, Lien CL, Chi N, Tai YC, Hsiai TK. Wearable multi-channel microelectrode membranes for elucidating electrophysiological phenotypes of injured myocardium. Integr Biol (Camb). 2014 Aug; 6(8):789-95. PMID: 24945366; PMCID: PMC4124744.
      18. Dickover M, Hegarty JM, Ly K, Lopez D, Yang H, Zhang R, Tedeschi N, Hsiai TK, Chi N. The atypical Rho GTPase, RhoU, regulates cell-adhesion molecules during cardiac morphogenesis. Dev Biol. 2014 May 15; 389(2):182-91. PMID: 24607366; PMCID: PMC4101123.
      19. Samson SC, Ferrer T, Jou CJ, Sachse FB, Shankaran SS, Shaw RM, Chi N, Tristani-Firouzi M, Yost HJ. 3-OST-7 regulates BMP-dependent cardiac contraction. PLoS Biol. 2013 Dec; 11(12):e1001727. PMID: 24311987; PMCID: PMC3849020.
      20. Zhang K, Deacon DC, Rao F, Schork AJ, Fung MM, Waalen J, Schork NJ, Nievergelt CM, Chi N, O'Connor DT. Human heart rate: heritability of resting and stress values in twin pairs, and influence of genetic variation in the adrenergic pathway at a microribonucleic acid (microrna) motif in the 3'-UTR of cytochrome b561 [corrected]. J Am Coll Cardiol. 2014 Feb 04; 63(4):358-68. PMID: 24140660; PMCID: PMC3946708.
      21. Lee J, Moghadam ME, Kung E, Cao H, Beebe T, Miller Y, Roman BL, Lien CL, Chi N, Marsden AL, Hsiai TK. Moving domain computational fluid dynamics to interface with an embryonic model of cardiac morphogenesis. PLoS One. 2013; 8(8):e72924. PMID: 24009714; PMCID: PMC3751826.
      22. Yoshioka N, Gros E, Li HR, Kumar S, Deacon DC, Maron C, Muotri AR, Chi N, Fu XD, Yu BD, Dowdy SF. Efficient generation of human iPSCs by a synthetic self-replicative RNA. Cell Stem Cell. 2013 Aug 01; 13(2):246-54. PMID: 23910086; PMCID: PMC3845961.
      23. Page DM, Wittamer V, Bertrand JY, Lewis KL, Pratt DN, Delgado N, Schale SE, McGue C, Jacobsen BH, Doty A, Pao Y, Yang H, Chi N, Magor BG, Traver D. An evolutionarily conserved program of B-cell development and activation in zebrafish. Blood. 2013 Aug 22; 122(8):e1-11. PMID: 23861249; PMCID: PMC3750348.
      24. Zhang R, Han P, Yang H, Ouyang K, Lee D, Lin YF, Ocorr K, Kang G, Chen J, Stainier DY, Yelon D, Chi N. In vivo cardiac reprogramming contributes to zebrafish heart regeneration. Nature. 2013 Jun 27; 498(7455):497-501. PMID: 23783515; PMCID: PMC4090927.
      25. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi N, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013 May 23; 153(5):1134-48. PMID: 23664764; PMCID: PMC3786220.
      26. Hegarty JM, Yang H, Chi N. UBIAD1-mediated vitamin K2 synthesis is required for vascular endothelial cell survival and development. Development. 2013 Apr; 140(8):1713-9. PMID: 23533172; PMCID: PMC3621489.
      27. Dickover MS, Zhang R, Han P, Chi N. Zebrafish cardiac injury and regeneration models: a noninvasive and invasive in vivo model of cardiac regeneration. Methods Mol Biol. 2013; 1037:463-73. PMID: 24029953; PMCID: PMC4159160.
      28. Tu S, Chi N. Zebrafish models in cardiac development and congenital heart birth defects. Differentiation. 2012 Jul; 84(1):4-16. PMID: 22704690; PMCID: PMC4099249.
      29. Yu F, Zhao Y, Gu J, Quigley KL, Chi N, Tai YC, Hsiai TK. Flexible microelectrode arrays to interface epicardial electrical signals with intracardial calcium transients in zebrafish hearts. Biomed Microdevices. 2012 Apr; 14(2):357-66. PMID: 22124886; PMCID: PMC3322508.
      30. Yoruk B, Gillers BS, Chi N, Scott IC. Ccm3 functions in a manner distinct from Ccm1 and Ccm2 in a zebrafish model of CCM vascular disease. Dev Biol. 2012 Feb 15; 362(2):121-31. PMID: 22182521.
        View in: PubMed
      31. Hong TT, Smyth JW, Chu KY, Vogan JM, Fong TS, Jensen BC, Fang K, Halushka MK, Russell SD, Colecraft H, Hoopes CW, Ocorr K, Chi N, Shaw RM. BIN1 is reduced and Cav1.2 trafficking is impaired in human failing cardiomyocytes. Heart Rhythm. 2012 May; 9(5):812-20. PMID: 22138472; PMCID: PMC3306544.
      32. Palencia-Desai S, Kohli V, Kang J, Chi N, Black BL, Sumanas S. Vascular endothelial and endocardial progenitors differentiate as cardiomyocytes in the absence of Etsrp/Etv2 function. Development. 2011 Nov; 138(21):4721-32. PMID: 21989916; PMCID: PMC3190385.
      33. Zhang SS, Kim KH, Rosen A, Smyth JW, Sakuma R, Delgado-Olguín P, Davis M, Chi N, Puviindran V, Gaborit N, Sukonnik T, Wylie JN, Brand-Arzamendi K, Farman GP, Kim J, Rose RA, Marsden PA, Zhu Y, Zhou YQ, Miquerol L, Henkelman RM, Stainier DY, Shaw RM, Hui CC, Bruneau BG, Backx PH. Iroquois homeobox gene 3 establishes fast conduction in the cardiac His-Purkinje network. Proc Natl Acad Sci U S A. 2011 Aug 16; 108(33):13576-81. PMID: 21825130; PMCID: PMC3158173.
      34. Amigo JD, Yu M, Troadec MB, Gwynn B, Cooney JD, Lambert AJ, Chi N, Weiss MJ, Peters LL, Kaplan J, Cantor AB, Paw BH. Identification of distal cis-regulatory elements at mouse mitoferrin loci using zebrafish transgenesis. Mol Cell Biol. 2011 Apr; 31(7):1344-56. PMID: 21248200; PMCID: PMC3135305.
      35. Yu F, Huang J, Adlerz K, Jadvar H, Hamdan MH, Chi N, Chen JN, Hsiai TK. Evolving cardiac conduction phenotypes in developing zebrafish larvae: implications to drug sensitivity. Zebrafish. 2010 Dec; 7(4):325-31. PMID: 20958244; PMCID: PMC3005146.
      36. Chi N, Bussen M, Brand-Arzamendi K, Ding C, Olgin JE, Shaw RM, Martin GR, Stainier DY. Cardiac conduction is required to preserve cardiac chamber morphology. Proc Natl Acad Sci U S A. 2010 Aug 17; 107(33):14662-7. PMID: 20675583; PMCID: PMC2930423.
      37. Bertrand JY, Chi N, Santoso B, Teng S, Stainier DY, Traver D. Haematopoietic stem cells derive directly from aortic endothelium during development. Nature. 2010 Mar 04; 464(7285):108-11. PMID: 20154733; PMCID: PMC2858358.
      38. Smyth JW, Hong TT, Gao D, Vogan JM, Jensen BC, Fong TS, Simpson PC, Stainier DY, Chi N, Shaw RM. Limited forward trafficking of connexin 43 reduces cell-cell coupling in stressed human and mouse myocardium. J Clin Invest. 2010 Jan; 120(1):266-79. PMID: 20038810; PMCID: PMC2798685.
      39. Anderson RM, Bosch JA, Goll MG, Hesselson D, Dong PD, Shin D, Chi N, Shin CH, Schlegel A, Halpern M, Stainier DY. Loss of Dnmt1 catalytic activity reveals multiple roles for DNA methylation during pancreas development and regeneration. Dev Biol. 2009 Oct 01; 334(1):213-23. PMID: 19631206; PMCID: PMC2759669.
      40. Hogan BM, Bos FL, Bussmann J, Witte M, Chi N, Duckers HJ, Schulte-Merker S. Ccbe1 is required for embryonic lymphangiogenesis and venous sprouting. Nat Genet. 2009 Apr; 41(4):396-8. PMID: 19287381.
        View in: PubMed
      41. De Val S, Chi N, Meadows SM, Minovitsky S, Anderson JP, Harris IS, Ehlers ML, Agarwal P, Visel A, Xu SM, Pennacchio LA, Dubchak I, Krieg PA, Stainier DY, Black BL. Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell. 2008 Dec 12; 135(6):1053-64. PMID: 19070576; PMCID: PMC2782666.
      42. Chi N, Shaw RM, Jungblut B, Huisken J, Ferrer T, Arnaout R, Scott I, Beis D, Xiao T, Baier H, Jan LY, Tristani-Firouzi M, Stainier DY. Genetic and physiologic dissection of the vertebrate cardiac conduction system. PLoS Biol. 2008 May 13; 6(5):e109. PMID: 18479184; PMCID: PMC2430899.
      43. Chi N, Shaw RM, De Val S, Kang G, Jan LY, Black BL, Stainier DY. Foxn4 directly regulates tbx2b expression and atrioventricular canal formation. Genes Dev. 2008 Mar 15; 22(6):734-9. PMID: 18347092; PMCID: PMC2275426.
      44. Arnaout R, Ferrer T, Huisken J, Spitzer K, Stainier DY, Tristani-Firouzi M, Chi N. Zebrafish model for human long QT syndrome. Proc Natl Acad Sci U S A. 2007 Jul 03; 104(27):11316-21. PMID: 17592134; PMCID: PMC2040896.
      45. Jin SW, Herzog W, Santoro MM, Mitchell TS, Frantsve J, Jungblut B, Beis D, Scott IC, D'Amico LA, Ober EA, Verkade H, Field HA, Chi N, Wehman AM, Baier H, Stainier DY. A transgene-assisted genetic screen identifies essential regulators of vascular development in vertebrate embryos. Dev Biol. 2007 Jul 01; 307(1):29-42. PMID: 17531218; PMCID: PMC2695512.
      46. Scott EK, Mason L, Arrenberg AB, Ziv L, Gosse NJ, Xiao T, Chi N, Asakawa K, Kawakami K, Baier H. Targeting neural circuitry in zebrafish using GAL4 enhancer trapping. Nat Methods. 2007 Apr; 4(4):323-6. PMID: 17369834.
        View in: PubMed
      47. Chi N, Karliner JS. Molecular determinants of responses to myocardial ischemia/reperfusion injury: focus on hypoxia-inducible and heat shock factors. Cardiovasc Res. 2004 Feb 15; 61(3):437-47. PMID: 14962475.
        View in: PubMed
      48. Milewski RC, Chi N, Li J, Brown C, Lu MM, Epstein JA. Identification of minimal enhancer elements sufficient for Pax3 expression in neural crest and implication of Tead2 as a regulator of Pax3. Development. 2004 Feb; 131(4):829-37. PMID: 14736747.
        View in: PubMed
      49. Chi N, Epstein JA. Getting your Pax straight: Pax proteins in development and disease. Trends Genet. 2002 Jan; 18(1):41-7. PMID: 11750700.
        View in: PubMed
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