Publications

2024

78. Dong Y*, Yang Y*, Wang H, Feng D, Nist E, Yapundich N, Spurlock B, Craft M, Qian L, Liu J. (2024). Single-cell chromatin profiling reveals genetic programs activating pro-regenerative states in non-myocyte cells. Science Advances. 2024 Feb 23;10(8):eadk4694. doi: 10.1126/sciadv.adk4694. Epub 2024 Feb 21. PMID: 38381829. (*co-first authors).

77. Garbutt TA*, Wang Z*, Wang H*, Ma H, Ruan H, Dong Y, Xie Y, Tan L, Phookan R, Stouffer J, Vedantham V, Yang Y^#, Qian L^#, Liu J^#. (2024). Epigenetic regulation of cardiac maturation by arginine methyltransferase CARM1. Circulation. 2024 Jan 15. doi: 10.1161/CIRCULATIONAHA.121.055738. (*co-first authors, #co-correspondents).

2023

76. Zhu Q, Combs M, Liu J, Wang W, Moy S, Batrakova E, Herring L, Liu J, Locasale J, Mack C, Taylor J. (2023). GRAF1 phosphorylation integrates PINK1-Parkin signaling and actin dynamics to mediate mitochondrial homeostasis. Nat Commun. 14, 8187 (2023). https://doi.org/10.1038/s41467-023-43889-6.

75. Xie Y*, Yang Y*, Wang Q*, Near D, Wang H, Slattery C, Keepers B, Farber G, Liu J^#, Qian L^#. (2023). Translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition. Nat Cardiovasc Res. 2, 1060–1077 (2023). https://doi.org/10.1038/s44161-023-00344-5 (*co-first authors, #co-correspondents)

74. Spurlock B, Liu J, Qian L. Can we stop one heart from breaking: triumphs and challenges in cardiac reprogramming. Curr Opin Genet Dev. (2023) Dec;83:102116. doi: 10.1016/j.gde.2023.102116. Epub 2023 Oct 3. PMID: 37797568.

73. Wang Q, Spurlock B, Liu J, Qian J. Fibroblast reprogramming in cardiac repair. (2003). J Am Coll Cardiol Basic Trans Science. 2023 Sep 21. Epublished DOI: 10.1016/j.jacbts.2023.06.012

72. Wang H., Keepers B., Liu J,Qian L. (2023). Optimized protocol for direct cardiac reprogramming in mice using Ascl1 and Mef2c. STAR Protocols. 2023 Mar 28;4(2):102204. doi: 10.1016/j.xpro.2023.102204.

71. Chen J, Luo T, Jiang M, Liu J, Gupta G, Li Y. (2023). Cell composition inference and identification of layer-specific transcriptional profiles with POLARIS. Science Advances. 2023 Mar;9(9):eadd9818. doi: 10.1126/sciadv.add9818.

2022

70. Wang H, Keepers B, Qian Y, Xie Y, Colon M, Liu J, Qian L. (2022). Cross-lineage potential of Ascl1 uncovered by comparing diverse reprogramming regulatomes. Cell Stem Cell. 2022 Oct 6;29(10):1491-1504.e9. doi: 10.1016/j.stem.2022.09.006.

69. Ellis JL, Evason KJ, Zhang C, Fourman MN, Liu J, Ninov N, Delous M, Vanhollebeke B, Fiddes I, Otis JP, Houvras Y, Farber SA, Xu X, Lin X, Stainier DYR, Yin C. (2002). A missense mutation in the proprotein convertase gene furinb causes hepatic cystogenesis during liver development in zebrafish. Hepatol Commun. 2022 Aug 26. doi: 10.1002/hep4.2038.

68. Farber G, Liu J, Qian L. (2022). OSKM-mediated reversible reprogramming of cardiomyocytes regenerates injured myocardium. Cell Regeneration. 11, Article number: 6 2022.

67. Xie Y., Liu J, Qian L. (2022). Direct cardiac reprogramming comes of age: recent advance and remaining challenges. Semin. Cell Dev. Biol. 122, 37-43

66. Wang H., Yang Y., Qian Y., Liu J, Qian L. (2022). Delineating Chromatin Accessibility Re-patterning at Single Cell Level during Early Stage of Direct Cardiac Reprogramming. J Mol Cell Cardiol. 162, 62-71

2021

65.Karim AN., Maciej M., Quinn TA., Kar-Lai P., Maciej L., Agata S., Liu J., Mondal SS., Michal P., Lukasz B., Katarzyna P., Thomas B., Peter K., Vladimir K., Ceceilia W. (2021). Genomic and physiological analyses of the zebrafish atrioventricular canal reveals molecular building blocks of the secondary pacemaker region. Cell. Mol. Life Sci. 2021 Sep 23. doi.org/10.1007/s00018-021-03939-y.

64. Ma H., Liu Z., Yang Y., Feng D., Dong Y., Garbutt TA., Hu Z., Wang L., Luan, C., Cooper CD., Li Y., Welch JD., Qian L., Liu J. (2021). Functional coordination of non-myocytes plays a key role in adult zebrafish heart regeneration. EMBO R. (2021) 22: e52901.

63. Li G., Luan C., Dong Y., Xie Y., Zentz S., Zelt R., Roach J., Liu J., Qian L, Li Y., Yang Y. (2021). ExpressHeart: Web Portal to Visualize Transcriptome Profiles of Non-Cardiomyocyte Cells. Int J Mol Sci. 22, 8943. https://doi.org/10.3390/ijms22168943.

62. Dong Y., Qian L., Liu J. (2021). Molecular and cellular basis of cardiac chamber maturation. Semin. Cell Dev. Biol. (2021). May 11; S1084-9521(21)00095-1. doi: 10.1016/j.semcdb.2021.04.022.

61. Wang L., Yang Y., Ma H., Xie Y., Xu J., Near D., Wang H., Garbutt T., Li Y., Liu J^#., Qian L^#. (2021). Single cell dual-omics of cardiac non-myocyte reveals functional states at transcriptomic and epigenomic levels. Cardiovasc. Res. 2021 Apr 11:cvab134. doi: 10.1093/cvr/cvab134. (# co-correspondents)

60. Yang Y., Li G., Xie Y., Wang L., Lagler TM., Yang Y., Liu J., Qian L., Li Y. (2021). iSMNN: batch effect correction for single-cell RNA-seq data via iterative supervised mutual nearest neighbor refinement. Brief Bioinform. 2021 Apr 12:bbab122. doi: 10.1093/bib/bbab122.

59. Wang H., Yang Y., Liu J., Qian L. (2021). Direct Cell Reprogramming: approaches, mechanisms and progress. Nat. Rev. Mol. Cell Biol. 2021 Feb 22.https://doi.org/10.1038/s41580-021-00335-z.

2020

58. Peng X., Lai K., She P., Kang J., Wang T., Li G., Zhou Y., Sun J., Jin D., Xu X., Liao L., Liu J., Lee E., Poss KD., Zhong TP. (2020). Induction of Wnt signaling antagonists and P21-activated kinase enhances cardiomyocyte proliferation during zebrafish heart regeneration. Journal of Molecular Cell Biology. mjaa046, https://doi.org/10.1093/jmcb/mjaa04.

57.Wang L., Ma H., Huang P., Xie Y., Near D., Xu J., Yang Y., Xu Y., Garbutt T., Zhou Y., Liu Z., Yin C., Bressan M., Taylor JM., Liu J., Qian L. (2020). Beclin1 shapes cardiomyocyte cell identity independent of its autophagic function during cardiac reprogramming. Science Translational Medicine. 12(566):eaay7856. doi: 10.1126/scitranslmed.aay7856.

56. Xu J., Wang L, Liu J., Qian L. (2020). In Vitro Conversion of Murine Fibroblasts into Cardiomyocyte-like Cells. Cardiac Regeneration: Methods and Protocols, Methods in Molecular Biology, vol. 2158, Kenneth Poss and Bernhard Ku¨ hn (eds.), https://doi.org/10.1007/978-1-0716-0668-1_12, © Springer Science+Business Media, LLC, part of Springer Nature 2020.

55. Teranikar T., Messerchmidt V., Lim J., Bailey Z., Chiao J., Cao H., Liu J., Lee J. (2020). Correcting anisotropic intensity in light sheet images using dehazing and image morphology. APL Bioeng. 2020 Jul 1;4(3):036103. doi: 10.1063/1.5144613. eCollection 2020 Sep.

54. Wang L.*, Huang P.*, Near D., Ravi K., Xu Y., Liu J., and Qian L. (2020). Isoform Specific Effects of Mef2C during Direct Cardiac Reprogramming. Cells. 9(2): 268.

53. Garbutt T.A.*, Zhou Y.*, Keepers B., Liu J., Qian L.^# (2020). An Optimized Protocol for Human Direct Cardiac Reprogramming. STAR Protocols. DOI: 10.1016/j.xpro.2019.100010.

2019

51. Tian X-Q., Yang Y-J., Li Q., Xu J., Huang P-S., Xiong Y-Y., Li X-D., Jin C., Qi K., Jiang L-P., Chen G-H., Qian L., Liu J., Geng Y-J. (2019). Combined therapy with atorvastatin and atorvastatin-pretreated mesenchymal stem cells enhances cardiac performance after acute myocardial infarction by activating SDF-1/CXCR4 axis. Am J Transl Res.11(7): 4214–4231.

50. Xu J., Xiong Y-Y., Li Q., Hu M-J., Huang P-S., Xu J-Y., Tian X-Q., Jin C., Liu J., Qian L^#., Yang Y.^# (2019). Optimization of Timing and Times for Administration of Atorvastatin-pretreated Mesenchymal Stem Cells in a Preclinical Model of Acute Myocardial Infarction. Stem Cells Transl Med.  2019;8:1068–1083.

49. Zhou Y.*, Liu Z.*, Welch J.D., Gao X., Wang L., Garbutt T., Keepers B., Ma H., Prins J.F., Shen W., Liu J., Qian L. (2019). Singe cell transcriptomic analyses of cell fate transitions during human cardiac reprogramming. Cell Stem Cell. 25: 149-164.

48. Keepers B., Liu J. and Qian L. (2019). What’s in a cardiomyocyte – And how do we make one through reprogramming? Biochim Biophys Acta Mol Cell Res. pii: S0167-4889(18)30396-3. doi: 10.1016/j.bbamcr.2019.03.011.

47. Battista N., Douglas D., Lane AN., Samsa LA., Liu J., Miller L. (2019). Vortex dynamics in trabeculated embryonic ventricles. J. Cardiovasc. Dev. Dis. 6(1). pii: E6. doi: 10.3390/jcdd6010006.

46. Ma H., Yu S., Liu X., Zhang Y., Fakadej T., Liu Z., Yin C., Locasale JW., Taylor JM., Qian L., Liu J. (2019). Lin28a Regulates Pathological Cardiac Hypertrophic Growth through Pck2-mediated Enhancement of Anabolic Synthesis. Circulation. 139:1725–1740.

45. Su T, Huang K, Ma H, Liang H, Dinh PU, Chen J, Shen D, Allen TA, Qiao L, Li Z, Hu S, Cores J, Frame BN., Young AT., Yin Q., Liu J., Qian L., Caranasos TG., Brudno Y., Ligler FS., Cheng K. (2019). Platelet-Inspired Nanocells for Targeted Heart Repair After Ischemia/Reperfusion Injury. Adv Funct Mater. 29, 1803567.

2018

44. Chrispell JD., Dong E., Osawa S., Liu J., Cameron DJ., Weiss ER. (2018). Grk1b and Grk7a both contribute to the recovery of the isolated cone photoresponse in larval zebrafish. Invest ophthalmol Vis Sci. 59:5116-5124.

43. Liu J., Renz M., Hassel D. (2018). Interrogating cardiovascular genetics in zebrafish. In Genetic Causes of Cardiac Disease. J. Erdmann and A. Moretti, editors. London: Springer. pp 313-339.

42. Fleming N., Samsa L.A., Hassel D., Qian L. and Liu J. (2018). Rapamycin attenuates pathological hypertrophy caused by an absence of trabecular formation. Sci Rep. 8:8584. doi:10.1038/s41598-018-26843-1.

41. Miao L., Li J., Li J., Tian X., Lu Y., Hu S., Shieh D., Kanai R., Zhou B., Zhou B., Liu J., Firulli A., Martin J., Singer H., Zhou B., Xin H., Wu M. (2018). Notch signaling regulates Hey2 expression in a spatiotemporal dependent manner during cardiac morphogenesis and trabecular specification. Sci Rep. 8(1):2678. doi: 10.1038/s41598-018-20917-w.

40.  Zhou Y., Alimohamadi S., Wang L., Liu Z., Wall J.B., Yin C., Liu J., Qian L. (2018). A Loss of Function Screen of Epigenetic Modifiers and Splicing Factors during Early Stage of Cardiac Reprogramming. Stem Cells Int. 2018:3814747. doi: 10.1155/2018/3814747.

39. Wang L., Liu J., Qian L. (2018). In vivo Lineage Reprogramming of Fibroblasts to Cardiomyocytes for Heart Regeneration. In: In Vivo Reprogramming in Regenerative Medicine (Stem Cell Biology and Regenerative Medicine) (Yilmazer ed) Springer International Publishing AG. p45-63.

38. Brown D.R., Samsa L.A., Ito C., Ma H., Batres K., Arnaout R., Qian L., Liu J. (2018). Neuregulin-1 is essential for nerve plexus formation during cardiac maturation. J Cell Mol Med. 22: 2007-2017.

2017

37. Liu Z*., Wang L.*, Welch J.*, Ma H., Zhou Y., Vaseghi H.R., Yu S., Wall J.B., Alimohamadi S., Zheng M., Yin C., Shen W., Prins J., Liu J.,^# Qian L.^# (2017). Single cell transcriptomics reconstructs fate conversion from fibroblast to cardiomyocyte. Nature. 551:100–104. (# co-correspondents)

36. Zhou Y., Wang L., Liu Z., Alimohamadi S., Liu J.,  Qian L. (2017). Comparative gene expression analyses reveal distinct molecular signature between induced cardiomyocytes and induced pluripotent stem cell-derived cardiomyocytes. Cell Reports. 20: 3014-3024.

35. Haskell G.T., Jensen B.C., Samsa L.A., Marchuk D., Huang W., Skrzynia C., Tilley C., Seifert B.A., Rivera-Muñoz E.A., Koller B., Wilhelmsen K.C., Liu J., Alhosaini H., Weck K.E., Evans J.P., Berg J.S. (2017). Whole exome sequencing identifies truncating variants in nuclear envelope genes in patients with cardiovascular disease.  Circ Cardiovasc Genet. pii:e001443.doi:10.1161/CIRCGENETICS.116.001443.

34. Liu Z., Chen O., Wall J., Zheng M., Zhou Y., Wang L., Vaseghi H., Qian L., Liu J. (2017). Systematic comparison of 2A peptides for cloning multi-genes in a polycistronic vector. Sci Rep. 7, 2193 DOI:10.1038/s41598-017-02460-2.

33. Vaseghi H., Liu J., Qian L. (2017). Molecular barriers to direct cardiac reprogramming. Protein & Cell. doi: 10.1007/s13238-017-0402-x.

32. Ma H., Wang L, Liu J., Qian L. (2017) Direct cardiac reprogramming as a novel therapeutic strategy for treatment of myocardial infarction. Methods Mol Biol. 1521:69-88.

2016

31. Samsa, L.A., Cade, I.E., Brown D.R., Qian L., Liu J. (2016). IgG-containing isoforms of Neuregulin-1 are dispensable for cardiac trabeculation in zebrafish. Plos One. 1(11):e0166734. doi: 10.1371/journal.pone.0166734.

30. Mouillesseaux K., Wiley D., Saunders L., Wylie L., Kushner E., Chong D., Citrin K., Barber A., Park Y., Kim J., Samsa L.A., Kim J., Liu J., Jin W., Bautch V. (2016). Notch Regulates BMP Responsiveness and Lateral Branching in Vessel Networks via SMAD6. Nature Communications. 7:13247. doi: 10.1038/ncomms13247.

29.Kechele D.O., Dunworth W.P., Trincot C.E., Wetzel-Strong S.E., Li M., Ma H., Liu J., Caron K.M. (2016). Endothelial restoration of receptor activity-modifying protein 2 is sufficient to rescue lethality, but survivors develop dilated cardiomyopathy. Hypertension. 68:667-777.

28. Ma H., Yin C., Zhang Y., Qian L., Liu J. (2016). ErbB2 is required for cardiomyocyte proliferation in murine neonatal hearts. Gene. 592:325-330.

27. Vaseghi H., Zhou Y., Wang L., Yin C., Liu J., Qian L. (2016). Generation of an inducible fibroblast cell line for studying direct cardiac reprogramming. Genesis. 54:398-406.

26. Ma H., Liu J., Qian L. (2016). Fat for Fostering: Regenerating Injured Heart Using Local Adipose Tissue. EBioMedicine. 7:25-26.

25. Brown D.R., Samsa L.A., Qian L., Liu J. (2016). Advances in the study of heart development and disease using zebrafish. J. Cardiovasc. Dev. Dis. 3(2), 13; doi:10.3390/jcdd3020013.

24. Liu Z., Chen O., Zheng M., Wang L., Zhou Y., Yin C., Liu J., Qian L. (2016). Re-patterning of H3K27me3, H3K4me3 and DNA methylation during fibroblast conversion into induced cardiomyocytes. Stem Cell Research. 16:507-518.

23. Samsa L.A., Fleming D., Magness S., Qian L., Liu J. (2016). Isolation and characterization of single cells from zebrafish embryos. J Vis Exp. (109), e53877, doi:10.3791/53877.

22. Zhou Y., Wang L., Vaseghi H.R., Liu Z., Lu R., Alimohamadi S., Yin C., Fu J., Wang G.G., Liu J., Qian L. (2016). Bmi1 is a key epigenetic barrier to direct cardiac reprogramming. Cell Stem Cell. 18:382–395.

2015

21. Samsa L.A., Givens C., Tzima E., Stainier D.Y.R., Qian L., Liu J. (2015). Cardiac contraction activates Notch signaling to modulate chamber maturation. Dev. 142: 4080-4091.

20. Wang L., Liu Z., Yin C., Zhou Y., Liu J. Qian L. (2015). Improved generation of induced cardiomyocytes using a polycistronic construct expressing optimal ratio of Gata4, Mef2c and Tbx5. J Vis Exp. (105), e53426, doi:10.3791/53426.

19. Zou et al., (2015). An internal promoter underlies the difference in disease severity between N- and C-terminal truncations of Titin in zebrafish. elife. doi:10.7554/eLife.09406.

18. Ma H., Wang L., Yin C., Liu J^#., Qian L^#. (2015). In vivo cardiac reprogramming using an optimal single polycistronic construct. Cardiovasc Res. 108:217-219. (# co-correspondents)

17. Guo C., Deng Y., Liu J., Qian L. (2015). Cardiomyocyte-specific role of miR-24 in promoting cell survival. J Cell Mol Med. 19:103-112.

16. Wang L., Liu Z., Yin C., Asfour H., Chen OM., Li Y., Bursac N., Liu J., Qian L. (2015). Stoichiometry of Gata4, Mef2c, and Tbx5 Influences the Efficiency and Quality of Induced Cardiac Myocyte Reprogramming. Circ Res. 116:237-244.

2014

15. Vogler G., Liu J., Iafe T.W., Migh E., Mihály J., Bodmer R. (2014). Cdc42 and formin activity control non-muscle myosin dynamics during Drosophila heart morphogenesis. J Cell Biol. 206:909-922.

14. Staudt D.W., Liu J., Thorn K.S., Stuurman N., Liebling M., Stainier D.Y. (2014). High- resolution imaging of cardiomyocyte behavior reveals two distinct steps in ventricular trabeculation. Development. 141:585-593.

2013

13. Samsa L.A., Yang B., Liu J. (2013). Embryonic cardiac chamber maturation: Trabeculation, conduction, and cardiomyocyte proliferation. Am J Med Genet C Semin Med Genet. 163:157-168.

2012

12. Liu J. and Stainier D.Y. (2012). Zebrafish in the study of early cardiac development. Circ Res. 110:870-874.

2011

11. Qian L., Wythe J.D., Liu J., Cartry J., Vogler G., Mohapatra B., Otway R.T., Huang Y., King I.N., Maillet M., Zheng Y., Crawley T., Taghli-Lamallem O., Semsarian C., Dunwoodie S., Winlaw D., Harvey R.P., Fatkin D., Towbin J.A., Molkentin J.D., Srivastava D., Ocorr K., Bodmer R. (2011). Tinman/Nkx2-5 acts via miR-1 and upstream of Cdc42 to regulate heart function across species. J Cell Biol. 193:1181-1196.

2010

10. Liu J., Bressan M., Hassel D., Huisken J., Staudt D., Kikuchi K., Poss K.D., Mikawa T., Stainier D.Y. (2010). A dual role for ErbB2 signaling in cardiac trabeculation. Development. 137:3867-3875.

9. Liu J., Stainier D.Y. (2010). Tbx5 and Bmp signaling are essential for proepicardium specification in zebrafish. Circ Res. 106:1818-1828.

2008

8. Qian L., Mohapatra B., Akasaka T., Liu J., Ocorr K., Towbin J.A., Bodmer R. (2008). Transcription factor neuromancer/TBX20 is required for cardiac function in Drosophila with implications for human heart disease. Proc Natl Acad Sci U S A. 105:19833-19838.

7. Liu J., Qian L., Han Z., Wu X., Bodmer R. (2008). Spatial specificity of mesodermal even-skipped expression relies on multiple repressor sites. Dev Biol. 313:876-886.

6. Qian L., Liu J., Bodmer R. (2008). Heart development in Drosophila. In: Cardiovascular Development, Advances in Developmental Biology (Volume 18). Elsevier press. (pp. 1-29)

2006

5. Liu J., Qian L., Wessells R.J., Bidet Y., Jagla K., Bodmer R. (2006). Hedgehog and RAS pathways cooperate in the anterior-posterior specification and positioning of cardiac progenitor cells. Dev Biol. 290:373-385.

4. Wang D., Qian L., Xiong H., Liu J., Neckameyer W.S., Oldham S., Wang J., Xia K., Bodmer R., Zhang Z. (2006). Antioxidants protect PINK1-dependent dopaminergic neurons in Drosophila. Proc Natl Acad Sci U.S.A. 103:13520-13525.

2005

3. Qian L., Liu J., Bodmer R. (2005). Slit and Robo control cardiac cell polarity and morphogenesis. Curr Biol. 15:2271-2278.

2. Fujioka M., Wessells R.J., Han Z., Liu J., Fitzgerald K., Yusibova G.L., Zamora M., Ruiz- Lozano P., Bodmer R., Jaynes JB (2005). Embryonic Even Skipped-Dependent Muscle and Heart Cell Fates Are Required for Normal Adult Activity, Heart Function, and Lifespan. Circ Res. 97:1108-1114.

1. Qian L., Liu J., Bodmer R. (2005). Neuromancer (H15/midline) T-box20-related genes promote cell fate specification and morphogenesis of the Drosophila heart. Dev Biol. 279:509–524.