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Tzu Lip Phang

TitleAssociate Professor
InstitutionUniversity of Colorado Denver - Anschutz Medical Campus
DepartmentSOM-PEDS

    Collapse Overview 
    Collapse overview
    Dr. Phang primary activities include microarray and Next Generation Sequencing data analysis, specializing in developing methods for multivariate time course microarray data and Alternative Splicing detection algorithm. He is also interested in studying the roles of long non-coding RNAs that is pervasively expressed in the genome. He is involved in establishing the Bioinformatics Consultation and Analysis Core (BCAC) that serves the general bioinformatics needs for the University of Colorado and the Rocky Mountain regions scientific communities. He is also interested in developing multi-media approaches to disseminate translational science education to the scientific community. He is the creator of 5X5, where scientist create a 5 minutes video to discuss 5 important aspects of a topic of interest. (cctsi.ucdenver.edu/5x5)

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Wiley LK, Shortt JA, Roberts ER, Lowery J, Kudron E, Lin M, Mayer D, Wilson M, Brunetti TM, Chavan S, Phang TL, Pozdeyev N, Lesny J, Wicks SJ, Moore ET, Morgenstern JL, Roff AN, Shalowitz EL, Stewart A, Williams C, Edelmann MN, Hull M, Patton JT, Axell L, Ku L, Lee YM, Jirikowic J, Tanaka A, Todd E, White S, Peterson B, Hearst E, Zane R, Greene CS, Mathias R, Coors M, Taylor M, Ghosh D, Kahn MG, Brooks IM, Aquilante CL, Kao D, Rafaels N, Crooks KR, Hess S, Barnes KC, Gignoux CR. Building a vertically integrated genomic learning health system: The biobank at the Colorado Center for Personalized Medicine. Am J Hum Genet. 2024 01 04; 111(1):11-23. PMID: 38181729.
      View in: PubMed
    2. Roark CL, Ho BE, Aubrey MT, Anobile C, Israeli S, Phang TL, Braxton D, Ho AP, Freed BM. HLA homozygosity is associated with Non-Hodgkin lymphoma. Hum Immunol. 2022 Oct; 83(10):730-735. PMID: 35953408.
      View in: PubMed
    3. Mickler EA, Zhou H, Phang TL, Geraci MW, Stearman RS, Sears CR. Low-Coverage Whole Genome Sequencing Using Laser Capture Microscopy with Combined Digital Droplet PCR: An Effective Tool to Study Copy Number and Kras Mutations in Early Lung Adenocarcinoma Development. Int J Mol Sci. 2021 Nov 06; 22(21). PMID: 34769463.
      View in: PubMed
    4. Stearman RS, Cornelius AR, Young LR, Conklin DS, Mickler EA, Lu X, Hara N, Fettig LM, Phang TL, Geraci MW. Familial Pulmonary Fibrosis and Hermansky-Pudlak Syndrome Rare Missense Mutations in Context. Am J Respir Crit Care Med. 2019 07 15; 200(2):253-256. PMID: 30985222.
      View in: PubMed
    5. Sasse SK, Kadiyala V, Danhorn T, Panettieri RA, Phang TL, Gerber AN. Glucocorticoid Receptor ChIP-Seq Identifies PLCD1 as a KLF15 Target that Represses Airway Smooth Muscle Hypertrophy. Am J Respir Cell Mol Biol. 2017 08; 57(2):226-237. PMID: 28375666.
      View in: PubMed
    6. Hooper JE, Feng W, Li H, Leach SM, Phang T, Siska C, Jones KL, Spritz RA, Hunter LE, Williams T. Systems biology of facial development: contributions of ectoderm and mesenchyme. Dev Biol. 2017 06 01; 426(1):97-114. PMID: 28363736.
      View in: PubMed
    7. Kadiyala V, Sasse SK, Altonsy MO, Berman R, Chu HW, Phang TL, Gerber AN. Cistrome-based Cooperation between Airway Epithelial Glucocorticoid Receptor and NF-?B Orchestrates Anti-inflammatory Effects. J Biol Chem. 2016 Jun 10; 291(24):12673-12687. PMID: 27076634.
      View in: PubMed
    8. Kadiyala V, Sasse SK, Altonsy MO, Phang TL, Gerber AN. Cistrome Analysis of Glucocorticoid Receptor Activity in Bronchial Epithelial Cells Defines Novel Mechanisms of Steroid Efficacy. Ann Am Thorac Soc. 2016 Mar; 13 Suppl 1:S103. PMID: 27027943.
      View in: PubMed
    9. Sasse SK, Zuo Z, Kadiyala V, Zhang L, Pufall MA, Jain MK, Phang TL, Stormo GD, Gerber AN. Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops. J Biol Chem. 2015 Aug 07; 290(32):19756-69. PMID: 26088140.
      View in: PubMed
    10. Green RM, Feng W, Phang T, Fish JL, Li H, Spritz RA, Marcucio RS, Hooper J, Jamniczky H, Hallgr?msson B, Williams T. Tfap2a-dependent changes in mouse facial morphology result in clefting that can be ameliorated by a reduction in Fgf8 gene dosage. Dis Model Mech. 2015 Jan; 8(1):31-43. PMID: 25381013.
      View in: PubMed
    11. Altonsy MO, Sasse SK, Phang TL, Gerber AN. Context-dependent cooperation between nuclear factor ?B (NF-?B) and the glucocorticoid receptor at a TNFAIP3 intronic enhancer: a mechanism to maintain negative feedback control of inflammation. J Biol Chem. 2014 Mar 21; 289(12):8231-9. PMID: 24500711.
      View in: PubMed
    12. Reisdorph N, Stearman R, Kechris K, Phang TL, Reisdorph R, Prenni J, Erle DJ, Coldren C, Schey K, Nesvizhskii A, Geraci M. Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics. Genomics Proteomics Bioinformatics. 2013 Dec; 11(6):368-77. PMID: 24316330.
      View in: PubMed
    13. Darlington TM, Ehringer MA, Larson C, Phang TL, Radcliffe RA. Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. Genes Brain Behav. 2013 Mar; 12(2):263-74. PMID: 23433184.
      View in: PubMed
    14. Frantz AM, Sarver AL, Ito D, Phang TL, Karimpour-Fard A, Scott MC, Valli VE, Lindblad-Toh K, Burgess KE, Husbands BD, Henson MS, Borgatti A, Kisseberth WC, Hunter LE, Breen M, O'Brien TD, Modiano JF. Molecular profiling reveals prognostically significant subtypes of canine lymphoma. Vet Pathol. 2013 Jul; 50(4):693-703. PMID: 23125145.
      View in: PubMed
    15. Shaw LA, Stefanski AL, Peterson LK, Rumer KK, Vondracek A, Phang TL, Sakaguchi S, Winn VD, Dragone LL. Pregnancy amelioration of arthritis in SKG mice corresponds with alterations in serum amyloid A3 levels. Am J Clin Exp Immunol. 2012 Jun 30; 1(1):12-19. PMID: 23097751.
      View in: PubMed
    16. Kiseljak-Vassiliades K, Shafi S, Kerr JM, Phang TL, Kleinschmidt-DeMasters BK, Wierman ME. Clinical implications of growth hormone-secreting tumor subtypes. Endocrine. 2012 Aug; 42(1):18-28. PMID: 22434413.
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    17. Wang J, Nikrad MP, Travanty EA, Zhou B, Phang T, Gao B, Alford T, Ito Y, Nahreini P, Hartshorn K, Wentworth D, Dinarello CA, Mason RJ. Innate immune response of human alveolar macrophages during influenza A infection. PLoS One. 2012; 7(3):e29879. PMID: 22396727.
      View in: PubMed
    18. Phang TL, Feng W., Radcliffe R.A. and Kechris K. Biostatistics, Bioinformatics and Biomathematics. Post-processing multi-treatment time-course microarray studies using the Johnson-Neyman procedure. 2012; (2):107-126.
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    19. Wang J, Nikrad MP, Phang T, Gao B, Alford T, Ito Y, Edeen K, Travanty EA, Kosmider B, Hartshorn K, Mason RJ. Innate immune response to influenza A virus in differentiated human alveolar type II cells. Am J Respir Cell Mol Biol. 2011 Sep; 45(3):582-91. PMID: 21239608.
      View in: PubMed
    20. Olincy A, House R, Gao B, Recksiek P, Phang TL, Sullivan B, Hollis JP, Hopkins J, Shade T, Edwards MG, Vianzon R, Griffiths C, Ceilley J, Helfrich RW, Ritvo J, Weis E, Weiss D, Gault J. Elevated DISC1 transcript levels in PBMCs during acute psychosis in patients with schizophrenia. Transl Biomed. 2011; 2(1). PMID: 22319686.
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    21. Kim H, Kim J, Selby H, Gao D, Tong T, Phang TL, Tan AC. A short survey of computational analysis methods in analysing ChIP-seq data. Hum Genomics. 2011 Jan; 5(2):117-23. PMID: 21296745.
      View in: PubMed
    22. Burnham EL, Phang TL, House R, Vandivier RW, Moss M, Gaydos J. Alveolar macrophage gene expression is altered in the setting of alcohol use disorders. Alcohol Clin Exp Res. 2011 Feb; 35(2):284-94. PMID: 21121937.
      View in: PubMed
    23. Tamburini BA, Phang TL, Fosmire SP, Scott MC, Trapp SC, Duckett MM, Robinson SR, Slansky JE, Sharkey LC, Cutter GR, Wojcieszyn JW, Bellgrau D, Gemmill RM, Hunter LE, Modiano JF. Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma. BMC Cancer. 2010 Nov 09; 10:619. PMID: 21062482.
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    24. Gao D, Kim J, Kim H, Phang TL, Selby H, Tan AC, Tong T. A survey of statistical software for analysing RNA-seq data. Hum Genomics. 2010 Oct; 5(1):56-60. PMID: 21106489.
      View in: PubMed
    25. Calverley DC, Phang TL, Choudhury QG, Gao B, Oton AB, Weyant MJ, Geraci MW. Significant downregulation of platelet gene expression in metastatic lung cancer. Clin Transl Sci. 2010 Oct; 3(5):227-32. PMID: 21500395.
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    26. Karimpour-Fard A, Dumas L, Phang T, Sikela JM, Hunter LE. A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation. Hum Genomics. 2010 Aug; 4(6):421-7. PMID: 20846932.
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    27. Gregory MA, Phang TL, Neviani P, Alvarez-Calderon F, Eide CA, O'Hare T, Zaberezhnyy V, Williams RT, Druker BJ, Perrotti D, Degregori J. Wnt/Ca2+/NFAT signaling maintains survival of Ph+ leukemia cells upon inhibition of Bcr-Abl. Cancer Cell. 2010 Jul 13; 18(1):74-87. PMID: 20609354.
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    28. Tyler KL, Leser JS, Phang TL, Clarke P. Gene expression in the brain during reovirus encephalitis. J Neurovirol. 2010 Feb; 16(1):56-71. PMID: 20158406.
      View in: PubMed
    29. Gaydos J, Phang TL, House R, Vandivier RW, Moss M, Burnham EL. Alveolar Macrophage Gene Expression is altered in the Setting of Alcohol Use Disorders. Alcoholism: Clinical and Experimental Research. 2010; 2(35):284-294.
    30. Calverley DC, Casserly IP, Choudhury QG, Phang TL, Gao B, Messenger JC, Geraci MW. Platelet Gene Expression as a Biomarker Risk Stratification Tool in Acute Myocardial Infarction: A Pilot Investigation. Clinical Medicine Insights: Blood Disorders. 2010; (3):9-15.
    31. Feng W, Leach SM, Tipney H, Phang T, Geraci M, Spritz RA, Hunter LE, Williams T. Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences. PLoS One. 2009 Dec 16; 4(12):e8066. PMID: 20016822.
      View in: PubMed
    32. Phang T. R and Bioconductor solutions for alternative splicing detection. Hum Genomics. 2009 Dec; 4(2):131-5. PMID: 20038500.
      View in: PubMed
    33. Tamburini BA, Trapp S, Phang TL, Schappa JT, Hunter LE, Modiano JF. Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed. PLoS One. 2009 May 20; 4(5):e5549. PMID: 19461996.
      View in: PubMed
    34. Liu LY, Chen CY, Chen MJ, Tsai MS, Lee CH, Phang TL, Chang LY, Kuo WH, Hwa HL, Lien HC, Jung SM, Lin YS, Chang KJ, Hsieh FJ. Statistical identification of gene association by CID in application of constructing ER regulatory network. BMC Bioinformatics. 2009 Mar 17; 10:85. PMID: 19292896.
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    35. Woo DK, Phang TL, Trawick JD, Poyton RO. Multiple pathways of mitochondrial-nuclear communication in yeast: intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation. Biochim Biophys Acta. 2009 Feb; 1789(2):135-45. PMID: 18977319.
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    36. Harvell DM, Spoelstra NS, Singh M, McManaman JL, Finlayson C, Phang T, Trapp S, Hunter L, Dye WW, Borges VF, Elias A, Horwitz KB, Richer JK. Molecular signatures of neoadjuvant endocrine therapy for breast cancer: characteristics of response or intrinsic resistance. Breast Cancer Res Treat. 2008 Dec; 112(3):475-88. PMID: 18327671.
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    37. Bhave SV, Hornbaker C, Phang TL, Saba L, Lapadat R, Kechris K, Gaydos J, McGoldrick D, Dolbey A, Leach S, Soriano B, Ellington A, Ellington E, Jones K, Mangion J, Belknap JK, Williams RW, Hunter LE, Hoffman PL, Tabakoff B. The PhenoGen informatics website: tools for analyses of complex traits. BMC Genet. 2007 Aug 30; 8:59. PMID: 17760997.
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    38. Rudolph MC, McManaman JL, Phang T, Russell T, Kominsky DJ, Serkova NJ, Stein T, Anderson SM, Neville MC. Metabolic regulation in the lactating mammary gland: a lipid synthesizing machine. Physiol Genomics. 2007 Feb 12; 28(3):323-36. PMID: 17105756.
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    39. Guzelian J, Barwick JL, Hunter L, Phang TL, Quattrochi LC, Guzelian PS. Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats. Toxicol Sci. 2006 Dec; 94(2):379-87. PMID: 16997903.
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    40. Rudolph MC, McManaman JL, Hunter L, Phang T, Neville MC. Functional development of the mammary gland: use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution. J Mammary Gland Biol Neoplasia. 2003 Jul; 8(3):287-307. PMID: 14973374.
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    41. Lewis GS, Jewell JE, Phang T, Miller KW. Mutational and sequence analysis of transmembrane segment 6 orientation in TetA proteins. Biochem Biophys Res Commun. 2003 Jun 13; 305(4):1067-72. PMID: 12767939.
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    42. Hoshikawa Y, Nana-Sinkam P, Moore MD, Sotto-Santiago S, Phang T, Keith RL, Morris KG, Kondo T, Tuder RM, Voelkel NF, Geraci MW. Hypoxia induces different genes in the lungs of rats compared with mice. Physiol Genomics. 2003 Feb 06; 12(3):209-19. PMID: 12464684.
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    43. Shenkar R, Elliott JP, Diener K, Gault J, Hu LJ, Cohrs RJ, Phang T, Hunter L, Breeze RE, Awad IA. Differential gene expression in human cerebrovascular malformations. Neurosurgery. 2003 Feb; 52(2):465-77; discussion 477-8. PMID: 12535382.
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    44. Phang TL, Neville MC, Rudolph M, Hunter L. Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development. Pac Symp Biocomput. 2003; 351-62. PMID: 12603041.
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    45. Lewis GS, Jewell JE, Phang T, Miller KW. Mutational analysis of tetracycline resistance protein transmembrane segment insertion. Arch Biochem Biophys. 2002 Aug 15; 404(2):317-25. PMID: 12147271.
      View in: PubMed
    46. Zeng H, Phang T, Song YS, Ji I, Ji TH. The role of the hinge region of the luteinizing hormone receptor in hormone interaction and signal generation. J Biol Chem. 2001 Feb 02; 276(5):3451-8. PMID: 10964934.
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    47. Jeoung M, Phang T, Song YS, Ji I, Ji TH. Hormone interactions to Leu-rich repeats in the gonadotropin receptors. III. Photoaffinity labeling of human chorionic gonadotropin with receptor Leu-rich repeat 4 peptide. J Biol Chem. 2001 Feb 02; 276(5):3443-50. PMID: 10880517.
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    48. Phang T, Kundu G, Hong S, Ji I, Ji TH. The amino-terminal region of the luteinizing hormone/choriogonadotropin receptor contacts both subunits of human choriogonadotropin. II. Photoaffinity labeling. J Biol Chem. 1998 May 29; 273(22):13841-7. PMID: 9593729.
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    49. Hong S, Phang T, Ji I, Ji TH. The amino-terminal region of the luteinizing hormone/choriogonadotropin receptor contacts both subunits of human choriogonadotropin. I. Mutational analysis. J Biol Chem. 1998 May 29; 273(22):13835-40. PMID: 9593728.
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    50. Phang T, Ji I, Ji TH. No need of acetic acid for processing polyacrylamide gels. Anal Biochem. 1996 Feb 01; 234(1):96-7. PMID: 8742087.
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    51. Ji I, Pan YN, Lee YM, Phang T, Ji TH. Receptor binding dependent structural changes in human choriogonadotropin: photochemical inter-subunit crosslinking. Endocrine. 1995 Dec; 3(12):907-11. PMID: 21153219.
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