Publication in Revised Chronological Order

2016

  1. 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 Suppl 1:S103 link
  2. Kuokkanen S, Polotsky AJ, Chosich J, Bradford AP, Jasinska A, Phang T, Santoro N, Appt SE. Corpus luteum as a novel target of weight changes that contribute to impaired female reproductive physiology and function. Syst Biol Reprod Med. 2016:1-16 link

2015

  1. Walter, N. D., M. A. Miller, J. Vasquez, M. Weiner, A. Chapman, M. Engle, M. Higgins, A. M. Quinones, V. Roselli, E. Canono, C. Yoon, A. Cattamanchi, J. L. Davis, T. Phang, R. S. Stearman, G. Datta, B. J. Garcia, C. L. Daley, M. Strong, K. Kechris, T. E. Fingerlin, R. Reves and M. W. Geraci (2015). ”Blood transcriptional biomarkers for active TB among US patients: A case-control study with systematic cross-classifier evaluation.” J Clin Microbiol link
  2. Sasse, S. K., Z. Zuo, V. Kadiyala, L. Zhang, M. A. Pufall, M. K. Jain, T. L. Phang, G. D. Stormo and A. N. Gerber (2015). ”Response Element Composition Governs Correlations between Binding Site Affinity and Transcription in Glucocorticoid Receptor Feed-forward Loops.” J Biol Chem 290(32): 19756-19769. link
  3. Merhi, Z., A. J. Polotsky, A. P. Bradford, E. Buyuk, J. Chosich, T. Phang, S. Jindal and N. Santoro (2015). ”Adiposity Alters Genes Important in Inflammation and Cell Cycle Division in Human Cumulus Granulosa Cell.” Reprod Sci 22(10): 1220-1228. link
  4. Green, R. M., W. Feng, T. Phang, J. L. Fish, H. Li, R. A. Spritz, R. S. Marcucio, J. Hooper, H. Jamniczky, B. Hallgrimsson and T. Williams (2015). ”Tfap2a-dependent changes in mouse facial morphology result in clefting that can be ameliorated by a reduction in Fgf8 gene dosage.” Dis Model Mech 8(1): 31-43. link
  5. Baumgartner, H. K., K. M. Trinder, C. E. Galimanis, A. Post, T. Phang, R. G. Ross and V. D. Winn (2015). ”Characterization of choline transporters in the human placenta over gestation.” Placenta 36(12): 1362-1369. link
  6. Al-Safi, Z. A., H. Liu, N. E. Carlson, J. Chosich, J. Lesh, C. Robledo, A. P. Bradford, N. A. Gee, T. Phang, N. Santoro, W. Kohrt and A. J. Polotsky (2015). ”Estradiol Priming Improves Gonadotrope Sensitivity and Pro-inflammatory Cytokines in Obese Women.” J Clin Endocrinol Metab: jc20151946.link

2014

  1. Altonsy, M. O., S. K. Sasse, T. L. Phang and A. N. Gerber (2014). ”Context-dependent cooperation between nuclear factor kappaB (NF-kappaB) and the glucocorticoid receptor at a TNFAIP3 intronic enhancer: a mechanism to maintain negative feedback control of inflammation.” J Biol Chem 289(12): 8231-8239. link

2013

  1. Reisdorph, N., R. Stearman, K. Kechris, T. L. Phang, R. Reisdorph, J. Prenni, D. J. Erle, C. Coldren, K. Schey, A. Nesvizhskii and M. Geraci (2013). ”Hands-on workshops as an effective means of learning advanced technologies including genomics, proteomics and bioinformatics.” Genomics Proteomics Bioinformatics 11(6): 368-377. link
  2. Frantz, A. M., A. L. Sarver, D. Ito, T. L. Phang, A. Karimpour-Fard, M. C. Scott, V. E. Valli, K. Lindblad-Toh, K. E. Burgess, B. D. Husbands, M. S. Henson, A. Borgatti, W. C. Kisseberth, L. E. Hunter, M. Breen, T. D. O'Brien and J. F. Modiano (2013). ”Molecular Profiling Reveals Prognostically Significant Subtypes of Canine Lymphoma.” Veterinary pathology. link
  3. Darlington, T. M., M. A. Ehringer, C. Larson, T. L. Phang and R. A. Radcliffe (2013). ”Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice.” Genes, brain, and behavior 12(2): 263-274. link

2012

  1. Wang, J., M. P. Nikrad, E. A. Travanty, B. Zhou, T. Phang, B. Gao, T. Alford, Y. Ito, P. Nahreini, K. Hartshorn, D. Wentworth, C. A. Dinarello and R. J. Mason (2012). ”Innate immune response of human alveolar macrophages during influenza A infection.” Plos One 7(3): e29879. link
  2. Shaw, L. A., A. L. Stefanski, L. K. Peterson, K. K. Rumer, A. Vondracek, T. L. Phang, S. Sakaguchi, V. D. Winn and L. L. Dragone (2012). ”Pregnancy amelioration of arthritis in SKG mice corresponds with alterations in serum amyloid A3 levels.” Am J Clin Exp Immunol 1(1): 12-19. link
  3. Kiseljak-Vassiliades, K., S. Shafi, J. M. Kerr, T. L. Phang, B. K. Kleinschmidt-Demasters and M. E. Wierman (2012). ”Clinical implications of growth hormone-secreting tumor subtypes.” Endocrine 42(1): 18-28. link
  4. Shaw, L. A., Stefanski, A. L., Peterson, L. K., Rumer, K. K., Vondracek, A., Phang, T. L., … Dragone, L. L. (2012). ”Pregnancy amelioration of arthritis in SKG mice corresponds with alterations in serum amyloid A3 levels.” American Journal of Clinical and Experimental Immunology, 1(1), 12–19. link

2011

  1. Clark, D. W., T. Phang, M. G. Edwards, M. W. Geraci and M. N. Gillespie (2012). ”Promoter G-quadruplex sequences are targets for base oxidation and strand cleavage during hypoxia-induced transcription.” Free radical biology & medicine 53(1): 51-59. link
  2. Wang, J. R., M. P. Nikrad, T. Phang, B. F. Gao, T. Alford, Y. Ito, K. Edeen, E. A. Travanty, B. Kosmider, K. Hartshorn and R. J. Mason (2011). ”Innate Immune Response to Influenza A Virus in Differentiated Human Alveolar Type II Cells.” American Journal of Respiratory Cell and Molecular Biology 45(3): 582-591. link
  3. Phang, T. L., P. Y. Zeng and E. F. de Zoeten (2011). “Exploring and Profiling Long Non-coding RNA in T cell Development Using Next Generation Sequencing and Bioinformatics approaches” Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO.
  4. Phang, T. L., W. Feng, R. A. Radcliffe and K. Kechris (2011). ”Post-processing multi-treatment time-course microarray studies using the Johnson-Neyman procedure.” Biostatistics, Bioinformatics and Biomathematics 2: 107-126.
  5. Olincy, A., R. House, B. Gao, P. Recksiek, T. L. Phang, B. Sullivan, J. P. Hollis, J. Hopkins, T. Shade, M. G. Edwards, R. Vianzon, C. Griffiths, J. Ceilley, R. W. Helfrich, J. Ritvo, E. Weis, D. Weiss and J. Gault (2011). ”Elevated DISC1 transcript levels in PBMCs during acute psychosis in patients with schizophrenia.” Translational biomedicine 2(1). link
  6. Kim, H., J. Kim, H. Selby, D. Gao, T. Tong, T. L. Phang and A. C. Tan (2011). "A short survey of computational analysis methods in analysing ChIP-seq data." Human genomics 5(2): 117-123. link
  7. Burnham, E. L., T. L. Phang, R. House, R. W. Vandivier, M. Moss and J. Gaydos (2011). "Alveolar Macrophage Gene Expression Is Altered in the Setting of Alcohol Use Disorders." Alcoholism-Clinical and Experimental Research 35(2): 284-294. link

2010

  1. Tyler, K. L., J. S. Leser, T. L. Phang and P. Clarke (2010). ”Gene expression in the brain during reovirus encephalitis.” Journal of neurovirology 16(1): 56-71. link
  2. Tamburini, B. A., T. L. Phang, S. P. Fosmire, M. C. Scott, S. C. Trapp, M. M. Duckett, S. R. Robinson, J. E. Slansky, L. C. Sharkey, G. R. Cutter, J. W. Wojcieszyn, D. Bellgrau, R. M. Gemmill, L. E. Hunter and J. F. Modiano (2010). ”Gene expression profiling identifies inflammation and angiogenesis as distinguishing features of canine hemangiosarcoma.” Bmc Cancer 10. link
  3. Phang, T. L., H. Kim, J. Kim, D. Gao, T. Tong, H. Selby and A. C. Tan (2010). AN ANALYSIS WORKFLOW FOR LOSS-­‐OF-­‐FUNCTION RNA INTERFERENCE WHOLE-­‐ GENOME SCREENING USING THE NEXT GENERATION SEQUENCING TECHNOLOGY. Aspen Lung Conference, Aspen, CO.
  4. Phang, T. L., H. Kim, J. Kim, D. Gao, T. Tong, H. Selby, M. A. Gregory, J. DeGregori and A. C. Tan (2010). BiNGS!SL-Seq: A Computational Analysis Workflow for Whole-Genome RNA Interference Screening Using the Next Generation Sequencing Technology. Intelligent Systems for Molecular Biology, Boston, MA.
  5. Phang, T. L., A. Hunter, P. Y. Zeng, T. Kerbowski and E. F. de Zoeten (2010). Analysis workflow of Methylation and Gene Expression microarray in Pediatric Crohn Disease. Annual Rocky Mountain Bioinformatics Conference, Snowmass, CO.
  6. Karimpour-Fard, A., L. Dumas, T. Phang, J. M. Sikela and L. E. Hunter (2010). ”A survey of analysis software for array-comparative genomic hybridisation studies to detect copy number variation.” Human genomics 4(6): 421-427. link
  7. Gregory, M. A., T. L. Phang, P. Neviani, F. Alvarez-Calderon, C. A. Eide, T. O'Hare, V. Zaberezhnyy, R. T. Williams, B. J. Druker, D. Perrotti and J. DeGregori (2010). ”Wnt/Ca2+/NFAT Signaling Maintains Survival of Ph+ Leukemia Cells upon Inhibition of Bcr-Abl.” Cancer Cell 18(1): 74-87.
  8. Gao, D., J. Kim, H. Kim, T. L. Phang, H. Selby, A. C. Tan and T. Tong (2010). "A survey of statistical software for analysing RNA-seq data." Human genomics 5(1): 56-60. link
  9. Calverley, D. C., T. L. Phang, Q. G. Choudhury, B. Gao, A. B. Oton, M. J. Weyant and M. W. Geraci (2010). ”Significant downregulation of platelet gene expression in metastatic lung cancer.” Clinical and translational science 3(5): 227-232. link
  10. Calverley, D. C., I. P. Casserly, Q. G. Choudhury, T. L. Phang, B. Gao, J. C. Messenger and M. W. Geraci (2010). ”Platelet Gene Expression as a Biomarker Risk Stratification Tool in Acute Myocardial Infarction: A Pilot Investigation.” Clinical Medicine Insights: Blood Disorders 3: 9-15. link

2009

  1. Woo, D. K., T. L. Phang, J. D. Trawick and R. O. Poyton (2009). ”Multiple pathways of mitochondrial-nuclear communication in yeast: Intergenomic signaling involves ABF1 and affects a different set of genes than retrograde regulation.” Biochimica Et Biophysica Acta-Gene Regulatory Mechanisms 1789(2): 135-145. link
  2. Tamburini, B. A., S. Trapp, T. L. Phang, J. T. Schappa, L. E. Hunter and J. F. Modiano (2009). ”Gene Expression Profiles of Sporadic Canine Hemangiosarcoma Are Uniquely Associated with Breed.” Plos One 4(5). link
  3. Phang, T. (2009). ”R and Bioconductor solutions for alternative splicing detection.” Human genomics 4(2): 131-135. link
  4. Liu, L. Y. D., C. Y. Chen, M. J. M. Chen, M. S. Tsai, C. H. S. Lee, T. L. Phang, L. Y. Chang, W. H. Kuo, H. L. Hwa, H. C. Lien, S. M. Jung, Y. S. Lin, K. J. Chang and F. J. Hsieh (2009). ”Statistical identification of gene association by CID in application of constructing ER regulatory network.” Bmc Bioinformatics 10. link
  5. Feng, W. G., S. M. Leach, H. Tipney, T. Phang, M. Geraci, R. A. Spritz, L. E. Hunter and T. Williams (2009). ”Spatial and Temporal Analysis of Gene Expression during Growth and Fusion of the Mouse Facial Prominences.” Plos One 4(12). link

2008

  1. Harvell, D. M., N. S. Spoelstra, M. Singh, J. L. McManaman, C. Finlayson, T. Phang, S. Trapp, L. Hunter, W. W. Dye, V. F. Borges, A. Elias, K. B. Horwitz and J. K. Richer (2008). ”Molecular signatures of neoadjuvant endocrine therapy for breast cancer: characteristics of response or intrinsic resistance.” Breast cancer research and treatment 112(3): 475-488. link

2007

  1. Rudolph, M. C., J. L. McManaman, T. Phang, T. Russell, D. J. Kominsky, N. J. Serkova, T. Stein, S. M. Anderson and M. C. Neville (2007). ”Metabolic regulation in the lactating mammary gland: a lipid synthesizing machine.” Physiological genomics 28(3): 323-336. link
  2. Bhave, S. V., C. Hornbaker, T. L. Phang, L. Saba, R. Lapadat, K. Kechris, J. Gaydos, D. McGoldrick, A. Dolbey, S. Leach, B. Soriano, A. Ellington, E. Ellington, K. Jones, J. Mangion, J. K. Belknap, R. W. Williams, L. E. Hunter, P. L. Hoffman and B. Tabakoff (2007). ”The PhenoGen informatics website: tools for analyses of complex traits.” BMC genetics 8: 59. link

2006

  1. Guzelian, J., J. L. Barwick, L. Hunter, T. L. Phang, L. C. Quattrochi and P. S. Guzelian (2006). ”Identification of genes controlled by the pregnane X receptor by microarray analysis of mRNAs from pregnenolone 16alpha-carbonitrile-treated rats.” Toxicological sciences : an official journal of the Society of Toxicology 94(2): 379-387. link

2003

  1. Shenkar, R., J. P. Elliott, K. Diener, J. Gault, L. J. Hu, R. J. Cohrs, T. Phang, L. Hunter, R. E. Breeze and I. A. Awad (2003). ”Differential gene expression in human cerebrovascular malformations.” Neurosurgery 52(2): 465-477; discussion 477-468. link
  2. Rudolph, M. C., J. L. McManaman, L. Hunter, T. Phang and M. C. Neville (2003). ”Functional development of the mammary gland: Use of expression profiling and trajectory clustering to reveal changes in gene expression during pregnancy, lactation, and involution.” Journal of Mammary Gland Biology and Neoplasia 8(3): 287-307. link
  3. Phang, T. L., M. C. Neville, M. Rudolph and L. Hunter (2003). ”Trajectory clustering: a non-parametric method for grouping gene expression time courses, with applications to mammary development.” Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing: 351-362. link
  4. Lewis, G. S., J. E. Jewell, T. Phang and K. W. Miller (2003). ”Mutational and sequence analysis of transmembrane segment 6 orientation in TetA proteins.” Biochemical and biophysical research communications 305(4): 1067-1072. link
  5. Hoshikawa, Y., P. Nana-Sinkam, M. D. Moore, S. Sotto-Santiago, T. Phang, R. L. Keith, K. G. Morris, T. Kondo, R. M. Tuder, N. F. Voelkel and M. W. Geraci (2003). ”Hypoxia induces different genes in the lungs of rats compared with mice.” Physiological genomics 12(3): 209-219. link

2002

  1. Lewis, G. S., J. E. Jewell, T. Phang and K. W. Miller (2002). ”Mutational analysis of tetracycline resistance protein transmembrane segment insertion.” Archives of biochemistry and biophysics 404(2): 317-325. link

2001

  1. Zeng, H., T. Phang, Y. S. Song, I. Ji and T. H. Ji (2001). ”The role of the hinge region of the luteinizing hormone receptor in hormone interaction and signal generation.” The Journal of biological chemistry 276(5): 3451-3458. link
  2. Jeoung, M., T. Phang, Y. S. Song, I. Ji and T. H. Ji (2001). ”Hormone interactions to Leu-rich repeats in the gonadotropin receptors. III. Photoaffinity labeling of human chorionic gonadotropin with receptor Leu-rich repeat 4 peptide.” The Journal of biological chemistry 276(5): 3443-3450. link

1998

  1. Phang, T., G. Kundu, S. H. Hong, I. H. Ji and T. H. Ji (1998). ”The amino-terminal region of the luteinizing hormone choriogonadotropin receptor contacts both subunits of human choriogonadotropin II. Photoaffinity labeling.” Journal of Biological Chemistry 273(22): 13841-13847. link
  2. Hong, S. H., T. Phang, I. H. Ji and T. H. Ji (1998). ”The amino-terminal region of the luteinizing hormone choriogonadotropin receptor contacts both subunits of human choriogonadotropin I. Mutational analysis.” Journal of Biological Chemistry 273(22): 13835-13840. link

1996

  1. Phang, T. L., I. H. Ji and T. H. Ji (1996). ”No need of acetic acid for processing polyacrylamide gels.” Analytical Biochemistry 234(1): 96-97. link

1995

  1. Ji, I., Y. N. Pan, Y. M. Lee, T. Phang and T. H. Ji (1995). ”Receptor binding dependent structural changes in human choriogonadotropin: photochemical inter-subunit crosslinking.” Endocrine 3(12): 907-911. link