Publications

  1. Stojakovic A, Trushin S, Sheu A, Khalili L, Chang SY, Li X, Christensen T, Salisbury JL, Geroux RE, Gateno B, Flannery PJ, Dehankar M, Funk CC, Wilkins J, Stepanova A, O'Hagan T, Galkin A, Nesbitt J, Zhu X, Tripathi U, Macura S, Tchkonia T, Pirtskhalava T, Kirkland JL, Kudgus RA, Schoon RA, Reid JM, Yamazaki Y, Kanekiyo T, Zhang S, Nemutlu E, Dzeja P, Jaspersen A, Kwon YIC, Lee MK, Trushina E. Partial inhibition of mitochondrial complex I ameliorates Alzheimer's disease pathology and cognition in APP/PS1 female mice. Commun Biol. 2021 Jan 8; 4 (1):61 Epub 2021 Jan 08
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  2. Theis JL, Vogler G, Missinato MA, Li X, Nielsen T, Zeng XI, Martinez-Fernandez A, Walls SM, Kervadec A, Kezos JN, Birker K, Evans JM, O'Byrne MM, Fogarty ZC, Terzic A, Grossfeld P, Ocorr K, Nelson TJ, Olson TM, Colas AR, Bodmer R. Patient-specific genomics and cross-species functional analysis implicate LRP2 in hypoplastic left heart syndrome. Elife. 2020 Oct 2; 9 Epub 2020 Oct 02
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  3. Kleinstern G, O'Brien DR, Li X, Tian S, Kabat BF, Rabe KG, Norman AD, Yan H, Vachon CM, Boddicker NJ, Call TG, Parikh SA, Bruins L, Bonolo de Campos C, Leis JF, Shanafelt TD, Ding W, Cerhan JR, Kay NE, Slager SL, Braggio E. Tumor mutational load predicts time to first treatment in chronic lymphocytic leukemia (CLL) and monoclonal B-cell lymphocytosis beyond the CLL international prognostic index. Am J Hematol. 2020 Aug; 95 (8):906-917 Epub 2020 May 07
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  4. Biendarra-Tiegs SM, Li X, Ye D, Brandt EB, Ackerman MJ, Nelson TJ. Single-Cell RNA-Sequencing and Optical Electrophysiology of Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveal Discordance Between Cardiac Subtype-Associated Gene Expression Patterns and Electrophysiological Phenotypes. Stem Cells Dev. 2019 May 15; 28 (10):659-673 Epub 2019 Apr 17
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  5. Secreto FJ, Li X, Smith AJ, Bruinsma ES, Perales-Clemente E, Oommen S, Hawse G, Hrstka SCL, Arendt BK, Brandt EB, Wigle DA, Nelson TJ. Quantification of Etoposide Hypersensitivity: A Sensitive, Functional Method for Assessing Pluripotent Stem Cell Quality. Stem Cells Transl Med. 2017 Oct; 6 (10):1829-1839 Epub 2017 Sept 19
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  6. Hrstka SC, Li X, Nelson TJ, Wanek Program Genetics Pipeline Group. NOTCH1-Dependent Nitric Oxide Signaling Deficiency in Hypoplastic Left Heart Syndrome Revealed Through Patient-Specific Phenotypes Detected in Bioengineered Cardiogenesis. Stem Cells. 2017 Apr; 35 (4):1106-1119 Epub 2017 Mar 05
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  7. Li X, Campbell KA, Biendarra SM, Terzic A, Nelson TJ. Mapping transcriptome profiles of in vitro iPSC-derived cardiac differentiation to in utero heart development. Genom Data. 2016 Mar; 7:129-30 Epub 2015 Dec 30
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  8. Wyles SP, Li X, Hrstka SC, Reyes S, Oommen S, Beraldi R, Edwards J, Terzic A, Olson TM, Nelson TJ. Modeling structural and functional deficiencies of RBM20 familial dilated cardiomyopathy using human induced pluripotent stem cells. Hum Mol Genet. 2016 Jan 15; 25 (2):254-65 Epub 2015 Nov 24
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  9. Campbell KA, Li X, Biendarra SM, Terzic A, Nelson TJ. Nos3-/- iPSCs model concordant signatures of in utero cardiac pathogenesis. J Mol Cell Cardiol. 2015 Oct; 87:228-36.
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  10. Wyles SP, Faustino RS, Li X, Terzic A, Nelson TJ. Systems-based technologies in profiling the stem cell molecular framework for cardioregenerative medicine. Stem Cell Rev. 2015 Jun; 11: (3)501-10.
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  11. Cantero Peral S, Burkhart HM, Oommen S, Yamada S, Nyberg SL, Li X, O'Leary PW, Terzic A, Cannon BC, Nelson TJ, Wanek Program Porcine Pipeline Group. Safety and feasibility for pediatric cardiac regeneration using epicardial delivery of autologous umbilical cord blood-derived mononuclear cells established in a porcine model system. Stem Cells Transl Med. 2015 Feb; 4 (2):195-206 Epub 2015 Jan 05
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  12. Li X, Nair A, Wang S, Wang L. Quality control of RNA-seq experiments. Methods Mol Biol. 2015; 1269:137-46
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  13. Bi Y, Mukhopadhyay D, Drinane M, Ji B, Li X, Cao S, Shah VH. Endocytosis of collagen by hepatic stellate cells regulates extracellular matrix dynamics. Am J Physiol Cell Physiol. 2014 Oct 1; 307 (7):C622-33 Epub 2014 July 30
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  14. Hartjes KA, Li X, Martinez-Fernandez A, Roemmich AJ, Larsen BT, Terzic A, Nelson TJ. Selection via pluripotency-related transcriptional screen minimizes the influence of somatic origin on iPSC differentiation propensity. Stem Cells. 2014 Sep; 32 (9):2350-9
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  15. Suresh R, Li X, Chiriac A, Goel K, Terzic A, Perez-Terzic C, Nelson TJ. Transcriptome from circulating cells suggests dysregulated pathways associated with long-term recurrent events following first-time myocardial infarction. J Mol Cell Cardiol. 2014 Sep; 74:13-21 Epub 2014 May 04
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  16. Beraldi R, Li X, Martinez Fernandez A, Reyes S, Secreto F, Terzic A, Olson TM, Nelson TJ. Rbm20-deficient cardiogenesis reveals early disruption of RNA processing and sarcomere remodeling establishing a developmental etiology for dilated cardiomyopathy. Hum Mol Genet. 2014 Jul 15; 23 (14):3779-91 Epub 2014 Feb 28
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  17. Li X, Martinez-Fernandez A, Hartjes KA, Kocher JP, Olson TM, Terzic A, Nelson TJ. Transcriptional atlas of cardiogenesis maps congenital heart disease interactome. Physiol Genomics. 2014 Jul 1; 46 (13):482-95 Epub 2014 May 06
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  18. Bazil JN, Stamm KD, Li X, Thiagarajan R, Nelson TJ, Tomita-Mitchell A, Beard DA. The inferred cardiogenic gene regulatory network in the mammalian heart. PLoS One. 2014; 9 (6):e100842 Epub 2014 June 27
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  19. Martinez-Fernandez A, Li X, Hartjes KA, Terzic A, Nelson TJ. Natural cardiogenesis-based template predicts cardiogenic potential of induced pluripotent stem cell lines. Circ Cardiovasc Genet. 2013 Oct; 6 (5):462-71 Epub 2013 Sept 14
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  20. Folmes CD, Martinez-Fernandez A, Perales-Clemente E, Li X, McDonald A, Oglesbee D, Hrstka SC, Perez-Terzic C, Terzic A, Nelson TJ. Disease-causing mitochondrial heteroplasmy segregated within induced pluripotent stem cell clones derived from a patient with MELAS. Stem Cells. 2013 Jul; 31 (7):1298-308
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  21. Bailey K, Kirk A, Naik S, Nace R, Steele MB, Suksanpaisan L, Li X, Federspiel MJ, Peng KW, Kirk D, Russell SJ. Mathematical model for radial expansion and conflation of intratumoral infectious centers predicts curative oncolytic virotherapy parameters. PLoS One. 2013; 8 (9):e73759 Epub 2013 Sept 11
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  22. Sun Z, Baheti S, Middha S, Kanwar R, Zhang Y, Li X, Beutler AS, Klee E, Asmann YW, Thompson EA, Kocher JP. SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing. Bioinformatics. 2012 Aug 15; 28 (16):2180-1 Epub 2012 June 10
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  23. Asmann YW, Necela BM, Kalari KR, Hossain A, Baker TR, Carr JM, Davis C, Getz JE, Hostetter G, Li X, McLaughlin SA, Radisky DC, Schroth GP, Cunliffe HE, Perez EA, Thompson EA. Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer. Cancer Res. 2012 Apr 15; 72(8):1921-8. Epub 2012 Apr 10.
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  24. Zacharias WJ, Madison BB, Kretovich KE, Walton KD, Richards N, Udager AM, Li X, Gumucio DL. Hedgehog signaling controls homeostasis of adult intestinal smooth muscle. Dev Biol. 2011 Jul 01; 355: (1)152-62.
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  25. Zacharias WJ, Li X, Madison BB, Kretovich K, Kao JY, Merchant JL, Gumucio DL. Hedgehog is an anti-inflammatory epithelial signal for the intestinal lamina propria. Gastroenterology. 2010 Jun; 138: (7)2368-77, 2377.e1-4.
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  26. Li X, Udager AM, Hu C, Qiao XT, Richards N, Gumucio DL. Dynamic patterning at the pylorus: formation of an epithelial intestine-stomach boundary in late fetal life. Dev Dyn. 2009 Dec; 238: (12)3205-17.
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  27. Gudjonsson JE, Ding J, Li X, Nair RP, Tejasvi T, Qin ZS, Ghosh D, Aphale A, Gumucio DL, Voorhees JJ, Abecasis GR, Elder JT. Global gene expression analysis reveals evidence for decreased lipid biosynthesis and increased innate immunity in uninvolved psoriatic skin. J Invest Dermatol. 2009 Dec; 129: (12)2795-804.
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  28. Li X, Madison BB, Zacharias W, Kolterud A, States D, Gumucio DL. Deconvoluting the intestine: molecular evidence for a major role of the mesenchyme in the modulation of signaling cross talk. Physiol Genomics. 2007 May 11; 29: (3)290-301.
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