MS in Biochemistry and Molecular Medicine

Publications

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Representative publications resulting from students’ thesis projects

  • C Poulard, D Bittencourt, DY Wu, Y Hu, DS Gerke, MR Stallcup (2017). A post-translational modification switch controls coactivator function of histone methyltransferases G9a and GLP. EMBO Rep. 18, 1442-1459.
  • Z Luo, SK Rhie, FD Lay, PJ Farnham (2017). A Prostate Cancer Risk Element Functions as a Repressive Loop that Regulates HOXA13. Cell Rep. 21, 1411-1417.​
  • A Martin, J Yu, J Xiong, AB Khalid, B Katzenellenbogen, SH Kim, JA Katzenellenbogen, S Malaivijitnond, Y Gabet, SA Krum, B Frenkel (2017). Estrogens and androgens inhibit association of RANKL with the pre-osteoblast membrane through post-translational mechanisms. J. Cell. Physiol. 232, 3798-3807. ​
  • ​MA Soria, SA Cervantes, TH Bajakian, AB Siemer (2017). The Functional Amyloid Orb2A Binds to Lipid Membranes. Biophys. J. 113, 37-47.
  • YG Tak, Y Hung, L Yao, MR Grimmer, A Do, MS Bhakta, H O’Geen, DJ Segal, PJ Farnham (2016). Effects on the transcriptome upon deletion of a distal element cannot be predicted by the size of the H3K27Ac peak in human cells. Nucleic Acids Res. 44, 4123-4133.
  • ​MA Pulido, MK DerHartunian, P Sehgal, IA Laird-Offringa (2016). Data on isoaspartylation of neuronal ELAVL proteins. Data Brief 9, 1052-1055.
  • SA Cervantes, TH Bajakian, MA Soria, AS Falk, RJ Service, R Langen, AB Siemer (2016). Identification and Structural Characterization of the N-terminal Amyloid Core of Orb2 isoform A. Sci. Rep. 6, 38265.
  • X Song, N Zhang, P Han, BS Moon, RK Lai, K Wang, W Lu (2016). Circular RNA profile in gliomas revealed by identification tool UROBORUS. Nucleic Acids Res. 44, e87.​
  • JL Yu, H Adisetiyo, GH Little, CT Vangsness, J Jiang, H Sternberg, MD West, B Frenkel (2015). Initial Characterization of Osteoblast Differentiation and Loss of RUNX2 Stability in the Newly Established SK11 Human Embryonic Stem Cell-Derived Cell Line. J. Cell. Physiol. 230, 237-241.
  • A Blattler, L Yao, H Witt, Y Guo, CM Nicolet, BP Berman, PJ Farnham (2014). Global loss of DNA methylation uncovers intronic enhancers in genes showing expression changes. Genome Biol. 15, 469.
  • SB Lokappa, JE Suk, A Balasubramanian, S Samanta, AJ Situ, TS Ulmer (2014). Sequence and membrane determinants of the random coil-helix transition of alpha-synuclein. J. Mol. Biol. 426, 2130-2144.
  • MJ Law, DS Lee, CS Lee, PP Anglim, IS Haworth, IA Laird-Offringa (2013). The role of the C-terminal helix of U1A protein in the interaction with U1hpII RNA. Nucleic Acids Res. 41, 7092-7100.
  • Y Chen, DL Bates, R Dey, PH Chen, AC Machado, IA Laird-Offringa, R Rohs, L Chen (2012). DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation. Cell Rep. 2, 1197-1206.
  • ​TJ Pemberton, FY Li, EK Hanson, NU Mehta, S Choi, J Ballantyne, JW Belmont, NA Rosenberg, C Tyler-Smith, PI Patel (2012). Impact of restricted marital practices on genetic variation in an endogamous Gujarati group. Am. J. Phys. Anthropol. 149, 92-103.
  • S Frietze, R Wang, L Yao, YG Tak, Z Ye, M Gaddis, H Witt, PJ Farnham, VX Jin (2012). Cell type-specific binding patterns reveal that TCF7L2 can be tethered to the genome by association with GATA3. Genome Biol. 13, r52.
  • RO Minea, CM Helchowski, SJ Zidovetzki, FK Costa, SD Swenson, FS Markland (2010). Vicrostatin – an anti-invasive multi-integrin targeting chimeric disintegrin with tumor anti-angiogenic and pro-apoptotic activities. PLoS One 5, e10929.
  • S Vikman, RM Brena, P Armstrong, J Hartiala, CB Stephensen, H Allayee (2009). Functional analysis of 5-lipoxygenase promoter repeat variants. Hum. Mol. Genet. 18, 4521-4529.
  • ​T Noh, Y Gabet, J Cogan, Y Shi, A Tank, T Sasaki, B Criswell, A Dixon, C Lee, J Tam, T Kohler, E Segev, L Kockeritz, J Woodgett, R Muller, Y Chai, E Smith, I Bab, B Frenkel (2009). Lef1 haploinsufficient mice display a low turnover and low bone mass phenotype in a gender- and age-specific manner. PLoS One 4, e5438.
  • RL Rich, GA Papalia, PJ Flynn, J Furneisen, J Quinn, JS Klein, PS Katsamba, MB Waddell, M Scott, J Thompson, J Berlier, S Corry, M Baltzinger, G Zeder-Lutz, A Schoenemann, A Clabbers, S Wieckowski, MM Murphy, P Page, TE Ryan, J Duffner, T Ganguly, J Corbin, S Gautam, G Anderluh, A Bavdek, D Reichmann, SP Yadav, E Hommema, E Pol, A Drake, S Klakamp, T Chapman, D Kernaghan, K Miller, J Schuman, K Lindquist, K Herlihy, MB Murphy, R Bohnsack, B Andrien, P Brandani, D Terwey, R Millican, RJ Darling, L Wang, Q Carter, J Dotzlaf, J Lopez-Sagaseta, I Campbell, P Torreri, S Hoos, P England, Y Liu, Y Abdiche, D Malashock, A Pinkerton, M Wong, E Lafer, C Hinck, K Thompson, CD Primo, A Joyce, J Brooks, F Torta, AB Bagge Hagel, J Krarup, J Pass, M Ferreira, S Shikov, M Mikolajczyk, Y Abe, G Barbato, AM Giannetti, G Krishnamoorthy, B Beusink, D Satpaev, T Tsang, E Fang, J Partridge, S Brohawn, J Horn, O Pritsch, G Obal, S Nilapwar, B Busby, G Gutierrez-Sanchez, RD Gupta, S Canepa, K Witte, Z Nikolovska-Coleska, YH Cho, R D’Agata, K Schlick, R Calvert, EM Munoz, MJ Hernaiz, T Bravman, M Dines, MH Yang, A Puskas, E Boni, J Li, M Wear, A Grinberg, J Baardsnes, O Dolezal, M Gainey, H Anderson, J Peng, M Lewis, P Spies, Q Trinh, S Bibikov, J Raymond, M Yousef, V Chandrasekaran, Y Feng, A Emerick, S Mundodo, R Guimaraes, K McGirr, YJ Li, H Hughes, H Mantz, R Skrabana, M Witmer, J Ballard, L Martin, P Skladal, G Korza, I Laird-Offringa,  CS Lee, A Khadir, F Podlaski, P Neuner, J Rothacker, A Rafique, N Dankbar, P Kainz, E Gedig, M Vuyisich, C Boozer, N Ly, M Toews, A Uren, O Kalyuzhniy, K Lewis, E Chomey, BJ Pak, DG Myszka (2009). A global benchmark study using affinity-based biosensors. Anal. Biochem. 386, 194-216.
  • KR Julien, M Sumita, PH Chen, IA Laird-Offringa, CG Hoogstraten (2008). Conformationally restricted nucleotides as a probe of structure-function relationships in RNA. RNA 14, 1632-1643.
  • TJ Pemberton, NU Mehta, D Witonsky, A Di Rienzo, H Allayee, DV Conti, PI Patel (2008). Prevalence of common disease-associated variants in Asian Indians. BMC Genet. 9, 13.
  • ​Z Wang, PS Lecane, P Thiemann, Q Fan, C Cortez, X Ma, D Tonev, D Miles, L Naumovski, RA Miller, D Magda, DG Cho, JL Sessler, BL Pike, SM Yeligar, MW Karaman, JG Hacia (2007). Synthesis and biologic properties of hydrophilic sapphyrins, a new class of tumor-selective inhibitors of gene expression. Mol. Cancer. 6, 9.​
  • MJ Law, ME Linde, EJ Chambers, C Oubridge, PS Katsamba, L Nilsson, IS Haworth, IA Laird-Offringa (2006). The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res. 34, 275-285.
  • C Mao, WC Tai, Y Bai, C Poizat, AS Lee (2006). In vivo regulation of Grp78/BiP transcription in the embryonic heart: role of the endoplasmic reticulum stress response element and GATA-4. J. Biol. Chem. 281, 8877-8887.​
  • C Teyssier, CY Ou, K Khetchoumian, R Losson, MR Stallcup (2006). Transcriptional intermediary factor 1alpha mediates physical interaction and functional synergy between the coactivator-associated arginine methyltransferase 1 and glucocorticoid receptor-interacting protein 1 nuclear receptor coactivators. Mol. Endocrinol. 20, 1276-1286.
  • ​M Hong, MY Lin, JM Huang, P Baumeister, S Hakre, AL Roy, AS Lee (2005). Transcriptional regulation of the Grp78 promoter by endoplasmic reticulum stress: role of TFII-I and its tyrosine phosphorylation. J. Biol. Chem. 280, 16821-16828.
  • M Hong, S Luo, P Baumeister, JM Huang, RK Gogia, M Li, AS Lee (2004). Underglycosylation of ATF6 as a novel sensing mechanism for activation of the unfolded protein response. J. Biol. Chem. 279, 11354-11363.
  • JA Tsou, JA Hagen, CL Carpenter, IA Laird-Offringa (2002). DNA methylation analysis: a powerful new tool for lung cancer diagnosis. Oncogene 21, 5450-5461.
  • ​RK Reddy, L Dubeau, H Kleiner, T Parr, P Nichols, B Ko, D Dong, H Ko, C Mao, J DiGiovanni, AS Lee (2002). Cancer-inducible transgene expression by the Grp94 promoter: spontaneous activation in tumors of various origins and cancer-associated macrophages. Cancer Res. 62, 7207-7212.​
  • AK Virmani, JA Tsou, KD Siegmund, LY Shen, TI Long, PW Laird, AF Gazdar, IA Laird-Offringa (2002). Hierarchical clustering of lung cancer cell lines using DNA methylation markers. Cancer Epidemiol. Biomarkers Prev. 11, 291-297.
  • NL Bernasconi, TA Wormhoudt, IA Laird-Offringa (2000). Post-transcriptional deregulation of myc genes in lung cancer cell lines. Am. J. Respir. Cell Mol. Biol. 23, 560-565.