Publications in 2012

Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization

Baliban RC, Sakellari D, Li Z, Guzman Y, Garcia BA, Floudas CA. Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization. J Clin Periodontol. 2012, 40(2):131-9.

Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation

Wu Y, Dimaggio PA, Perlman DH, Zakian V, Garcia BA. Novel phosphorylation sites in the S. cerevisiae Cdc13 protein reveal new targets for telomere length regulation. J Proteome Res. 2012, 12(1):316-27.

Asymmetrically modified nucleosomes

Voigt P, Leroy G, Drury WJ 3rd, Zee BM, Son J, Beck DB, Young NL, Garcia BA, Reinberg D. Asymmetrically modified nucleosomes. Cell. 2012, 151(1):181-93.

Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies

Rothbart SB, Lin S, Britton LM, Krajewski K, Keogh MC, Garcia BA, Strahl BD. Poly-acetylated chromatin signatures are preferred epitopes for site-specific histone H4 acetyl antibodies. Sci Rep. 2012;2:489.

Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins

Leroy G, Chepelev I, Dimaggio PA, Blanco, MA, Zee BM, Zhao K, Garcia BA. Proteo-Genomic Characterization and Mapping of Nucleosomes Decoded by Brd and HP1 Proteins. Genome Biology, 2012, 13(8):R68.

Global secretome analysis identifies novel mediators of bone metastasis

Blanco MA, Leroy G, Khan Z, Alečković M, Zee BM, Garcia BA, Kang Y. Global secretome analysis identifies novel mediators of bone metastasis. Cell Res. 2012, 22(9):1339-55.

BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection

Lee SH, Kalejta RF, Kerry J, Semmes OJ, O’Connor CM, Khan Z, Garcia BA, Shenk T, Murphy E. BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection. PNAS, 2012, 109(24):9575-80.

SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation

Barber MF, Michishita-Kioi E, Xi Y, Tasselli L, Kioi M, Moqtaderi Z, Tennen RI, Paredes S, Young NL, Chen K, Struhl K, Garcia BA, Gozani O, Li W, Chua KF. SIRT7 links H3K18 deacetylation to maintenance of oncogenic transformation. Nature, 2012, 487(7405):114-8.

Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET

Peinado H, Alečković M, Lavotshkin S, Matei I, Costa-Silva B, Moreno-Bueno G, Hergueta-Redondo M, Williams C, García-Santos G, Ghajar CM, Nitadori-Hoshino A, Hoffman C, Badal K, Garcia BA, Callahan MK, Yuan J, Martins VR, Skog J, Kaplan RN, Brady MS, Wolchok JD, Chapman PB, Kang Y, Bromberg J, Lyden D. Melanoma exosomes educate bone marrow progenitor cells toward a pro-metastatic phenotype through MET. Nat Med. 2012, 18(6):883-91.

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence

Chicas A, Kapoor A, Wang X, Aksoy O, Evertts AG, Zhang MQ, Garcia BA, Bernstein E, Lowe SW. H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proc Natl Acad Sci U S A. 2012, 109(23):8971-6.

Origins and Formation of Histone Methylation across the Human Cell Cycle

Zee, B.M., Britton, L.M., Wolle, D., Haberman, D., Garcia, B.A. Origins and Formation of Histone Methylation across the Human Cell Cycle. Molecular and Cellular Biology, 2012, 32(13):2503-14

Analysis of histone posttranslational modification patterns by high resolution mass spectrometry

Lin, S. Garcia, B.A. Analysis of histone posttranslational modification patterns by high resolution mass spectrometry. Methods in Enzymology, 2012, 512:3-28.

PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization

Baliban, R.C.; Dimaggio, P. A.; Plazas-Mayorca, M.D.; Garcia, B. A., Floudas, C. A. PILOT_PROTEIN: Identification of Unmodified and Modified Proteins via High-Resolution Mass Spectrometry and Mixed-Integer Linear Optimization. J Proteome Res. 2012, 11(9):4615-29.

Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation

Van Aller GS, Reynoird N, Barbash O, Huddleston M, Liu S, Zmoos AF, McDevitt P, Sinnamon R, Le B, Mas G, Annan R, Sage J, Garcia BA, Tummino PJ, Gozani O, Kruger RG. Smyd3 regulates cancer cell phenotypes and catalyzes histone H4 lysine 5 methylation. Epigenetics. 2012, 1;7(4), 340-343.

Discovery of lysine post-translational modifications through mass spectrometric detection

Zee, B.M., Garcia, B.A. Discovery of lysine post-translational modifications through mass spectrometric detection. Essays in Biochemistry, 2012, 52:147-63.

ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression

Ratnakumar K, Duarte LF, Leroy G, Hasson D, Smeets D, Vardabasso C, Bönisch C, Zeng T, Xiang B, Zhang DY, Li H, Wang X, Hake SB, Schermelleh L, Garcia BA, Bernstein E. ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression. Genes Dev. 2012, 26(5):433-8.

Histone H3 Lysine 56 Methylation Regulates DNA Replication through Its Interaction with PCNA

Yu Y, Song C, Zhang Q, Dimaggio PA, Garcia BA, York A, Carey MF, Grunstein M. Histone H3 Lysine 56 Methylation Regulates DNA Replication through Its Interaction with PCNA. Mol Cell. 2012, 46(1):7-17.

Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses

Green, E.M., Mas, G., Young, N.L., Garcia, B.A., Gozani, O. Methylation of H4 lysines 5, 8 and 12 by yeast Set5 calibrates chromatin stress responses. Nat Struct Mol Biol. 2012, 19(3):361-3.

Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples

Baliban, R.C., Sakellari, D., Li, Z., DiMaggio, P.A., Garcia, B.A., Floudas, C.A. Novel protein identification methods for biomarker discovery via a proteomic analysis of periodontally healthy and diseased gingival crevicular fluid samples. Journal of Clinical Periodontology, 2012, 3, 203-12.