Graduate Studies

Graduate Publications


Guise AJ, Budayeva HG, Diner BA, Cristea IM. Histone deacetylases in herpesvirus replication and virus-stimulated host defense. Viruses. Jul, 2013;5(7):1607-32. PMCID: PMC3738950

Schwalm J, Mahoney TF, Soltes GR, Silhavy TJ. Role for Skp in LptD assembly in Escherichia coli. J Bacteriol. Aug, 2013;195(16):3734-42. PMCID: PMC3754580

Grady SL, Purdy JG, Rabinowitz JD, Shenk T. (2013) “Argininosuccinate synthetase 1 depletion produces a metabolic state conducive to herpes simplex virus 1 infection.” Proc Natl Acad Sci U S A. Dec 17;110(51) PMCID: 3870743

Li T, Chen J, Cristea IM. (2013) “Human cytomegalovirus tegument protein pUL83 inhibits IFI16-mediated DNA sensing for immune evasion.” Cell Host Microbe. Nov 13;14(5) PMCID: 3876934

Wan L, Kang Y. (2013) “Pleiotropic roles of AEG-1/MTDH/LYRIC in breast cancer.” Adv Cancer Res.;120:113-34. PMID: 23889989 [PubMed - in process]

Bracht JR, Fang W, Goldman AD, Dolzhenko E, Stein EM, Landweber LF. (2013)“Genomes on the edge: programmed genome instability in ciliates.” Cell. Jan 31;152(3):406-16. PMCID: 3725814

Bloom JS, Ehrenreich IM, Loo WT, Lite TL, Kruglyak L. (2013) “Finding the sources of missing heritability in a yeast cross.” Nature. Feb 14;494(7436):234-7. PMID: 23376951 [PubMed - indexed for MEDLINE]

Tennen RI, Haye JE, Wijayatilake HD, Arlow T, Ponzio D, Gammie AE. (2013) “Cell-cycle and DNA damage regulation of the DNA mismatch repair protein Msh2 occurs at the transcriptional and post-transcriptional level.” DNA Repair (Amst). Feb 1;12(2):97-109. PMCID: 3749301

Fang W, Landweber LF. (2013) “RNA-mediated genome rearrangement: hypotheses and evidence.” Bioessays. Feb;35(2):84-7. PMCID: 3821980

Kramer T, Enquist LW. (2013) “Directional spread of alphaherpesviruses in the nervous system.” Viruses. Feb 11;5(2):678-707. PMCID: 3640521

Rigel NW, Ricci DP, Silhavy TJ. (2013) “Conformation-specific labeling of BamA and suppressor analysis suggest a cyclic mechanism for β-barrel assembly in Escherichia coli.” Proc Natl Acad Sci U S A. Mar 26;110(13):5151-6. PMCID: 3612609

Brunton BW, Botvinick MM, Brody CD. 2013 “Rats and humans can optimally accumulate evidence for decision-making.” Science. Apr 5;340(6128):95-8. PMID: 23559254 [PubMed - indexed for MEDLINE]

Chahal JS, Gallagher C, DeHart CJ, Flint SJ. (2013) “The repression domain of the E1B 55-kilodalton protein participates in countering interferon-induced inhibition of adenovirus replication.” J Virol. Apr;87(8):4432-44 PMCID: 3624377

Park J, Schwarzbauer JE. (2013) “Mammary epithelial cell interactions with fibronectin stimulate epithelial-mesenchymal transition.” Oncogene. Apr 29. PMID: 23624917 [PubMed - as supplied by publisher]

Chahal JS, Flint SJ. (2013) “The p53 protein does not facilitate adenovirus type 5 replication in normal human cells.”J Virol. May;87(10):6044-6 PMCID: 3648133

Xu YF, Létisse F, Absalan F, Lu W, Kuznetsova E, Brown G, Caudy AA, Yakunin AF, Broach JR, Rabinowitz JD. (2013) Nucleotide degradation and ribose salvage in yeast. Mol Syst Biol. May 14;9:665 PMID: 23670538 [PubMed - indexed for MEDLINE]

Carraher CL, Schwarzbauer JE. (2013) “Regulation of matrix assembly through rigidity-dependent fibronectin conformational changes.” J Biol Chem. May 24;288(21):14805-14. PMCID: 3663504

Granstedt AE, Brunton BW, Enquist LW. (2013) “Imaging the transport dynamics of single alphaherpesvirus particles in intact peripheral nervous system explants from infected mice.” MBio. Jun 4;4(3):e00358-13. PMCID: 3685211

Petrenko N, Chereji RV, McClean MN, Morozov AV, Broach JR. (2013) “Noise and interlocking signaling pathways promote distinct transcription factor dynamics in response to different stresses.” Mol Biol Cell. Jun;24(12):2045-57. PMCID: 3681706

Kratchmarov R, Kramer T, Greco TM, Taylor MP, Ch'ng TH, Cristea IM, Enquist LW. (2013) “Glycoproteins gE and gI are required for efficient KIF1A-dependent anterograde axonal transport of alphaherpesvirus particles in neurons.” J Virol. Jun 26. PMCID: 3754139

Gibney PA, Hickman MJ, Bradley PH, Matese JC, Botste in D. (2013) “Phylogenetic Portrait of the Saccharomyces cerevisiae Functional Genome.” G3 (Bethesda) Aug 7;3(8):1335-40. PMCID: 37371732013

Schwalm J, Mahoney TF, Soltes GR, Silhavy TJ. (2013) “Role for Skp in LptD Assembly in Escherichia coli.” J Bacteriol. Aug;195(16):3734-42. PMCID: 3754580

Bharucha N, Liu Y, Papanikou E, McMahon C, Esaki M, Jeffrey PD, Hughson FM, Glick BS. (2013) “Sec16 influences transitional ER sites by regulating rather than organizing COPII.” Mol Biol Cell. Sep 4. PMCID: 3814151

Granstedt AE, Bosse JB, Thiberge SY, Enquist LW. (2013) “In vivo imaging of alphaherpesvirus infection reveals synchronized activity dependent on axonal sorting of viral proteins.” Proc Natl Acad Sci U S A. Sep 10;110(37):E3516-25. PMCID: 3773797

Xu X, Brechbiel JL, Gavis ER. (2013) “Dynein-Dependent Transport of nanos RNA in Drosophila Sensory Neurons Requires Rumpelstiltskin and the Germ Plasm Organizer Oskar.”J Neurosci. Sep 11;33(37):14791-800. PMCID: 3771026

Reaves ML, Young BD, Hosios AM, Xu YF, Rabinowitz JD. (2013) “Pyrimidine homeostasis is accomplished by directed overflow metabolism.” Nature. Aug 8;500(7461):237-41 PMID: 23903661 [PubMed - indexed for MEDLINE]

Sun XR, Badura A, Pacheco DA, Lynch LA, Schneider ER, Taylor MP, Hogue IB, Enquist LW, Murthy M, Wang SS. (2013) “Fast GCaMPs for improved tracking of neuronal activity. Nat Commun. Jul 17;4:2170. PMCID: 3824390

Yakhnina AA, Gitai Z. (2013) “Diverse functions for six glycosyltransferases in Caulobacter crescentus cell wall assembly.” J Bacteriol. Aug 9. PMCID: 3807455

Hottes AK, Freddolino PL, Khare A, Donnell ZN, Liu JC, Tavazoie S. (2013) “Bacterial Adaptation through Loss of Function.” PLoS Genet. Jul;9(7):e1003617. PMCID: 3708842

Aoki T, Wolle D, Ben Noon EP, Dai Q, Lai EC, Schedl P. (2013) “Bi-functional cross-linking reagents efficiently capture protein-DNA complexes in Drosophila embryos.” Fly (Austin). Oct 17;8(1). PMID: 24135698 [PubMed - as supplied by publisher]

Ell B, Kang Y. (2013) “MicroRNAs as regulators of tumor-associated stromal cells.” Oncotarget. Dec;4(12):2166-7. PMCID: 3926815

Ell B, Mercatali L, Ibrahim T, Campbell N, Schwarzenbach H, Pantel K, Amadori D, Kang Y. (2013) “Tumor-Induced Osteoclast miRNA Changes as Regulators and Biomarkers of Osteolytic Bone Metastasis.” Cancer Cell. Oct 14;24(4):542-56. PMCID: 3832956

Ell B, Kang Y. (2013) “Transcriptional control of cancer metastasis.” Trends Cell Biol. Jul 6. PMCID: 3815486

Miteva YV, Budayeva HG, Cristea IM. (2013) “Proteomics-based methods for discovery, quantification, and validation of protein-protein interactions.” Anal Chem. Jan 15;85(2):749-68. PMCID: 3666915

Wan L, Pantel K, Kang Y. (2013) “Tumor metastasis: moving new biological insights into the clinic.” Nat Med. Nov;19(11):1450-64. PMID: 24202397 [PubMed - indexed for MEDLINE]

Zee BM, Garcia BA. (2013) “Validation of protein acetylation by mass spectrometry.” Methods Mol Biol.;981:1-11. PMID: 23381849 [PubMed - indexed for MEDLINE]

Cao XJ, Zee BM, Garcia BA. (2013) “Heavy methyl-SILAC labeling coupled with liquid chromatography and high-resolution mass spectrometry to study the dynamics of site-specific histone methylation.” Methods Mol Biol.;977:299-313. PMID: 23436372 [PubMed - indexed for MEDLINE]

Chen EY, Marre O, Fisher C, Schwartz G, Levy J, da Silveira RA, Berry MJ 2nd. (2013) “Alert response to motion onset in the retina.” J Neurosci. Jan 2;33(1):120-32. PMCID: 3711149

Baker RW, Jeffrey PD, Hughson FM. 2013) “Crystal Structures of the Sec1/Munc18 (SM) Protein Vps33, Alone and Bound to the Homotypic Fusion and Vacuolar Protein Sorting (HOPS) Subunit Vps16*” PLoS One. Jun 26;8(6):e67409. PMCID: 3693963

Dwyer RS, Ricci DP, Colwell LJ, Silhavy TJ, Wingreen NS. (2013) “Predicting Functionally Informative Mutations in Escherichia coli BamA Using Evolutionary Covariance Analysis.” Genetics. Aug 9.PMCID: 3781972

Shao Y, Feng L, Rutherford ST, Papenfort K, Bassler BL. (2013) “Functional determinants of the quorum-sensing non-coding RNAs and their roles in target regulation.” EMBO J. Jul 31;32(15):2158-71.PMCID: 3730234

van Kessel JC, Rutherford ST, Shao Y, Utria AF, Bassler BL. (2013). "Individual and combined roles of the master regulators AphA and LuxR in control of the Vibrio harveyi quorum-sensing regulon." J Bacteriol 195(3): 436-443. PMCID: 3554009

Joshi P, Greco TM, Guise AJ, Luo Y, Yu F, Nesvizhskii AI, Cristea IM. (2013) “The functional interactome landscape of the human histone deacetylase family.” Mol Syst Biol.;9:672. PMID: 23752268 [PubMed - indexed for MEDLINE]

Guise AJ, Budayeva HG, Diner BA, Cristea IM. (2013) “Histone deacetylases in herpesvirus replication and virus-stimulated host defense.” Viruses. Jun 27;5(7):1607-32. PMCID: 3738950

McIsaac RS, Oakes BL, Wang X, Dummit KA, Botstein D, Noyes MB. (2013) “Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast.” Nucleic Acids Res. Feb 1;41(4):e57 PMCID: 3575806

Wilson MZ, Gitai Z. (2013) “Beyond the cytoskeleton: mesoscale assemblies and their function in spatial organization.” Curr Opin Microbiol. Apr;16(2):177-83. PMID: 23601587 [PubMed - indexed for MEDLINE]

Di Talia S, She R, Blythe SA, Lu X, Zhang QF, Wieschaus EF. (2013). Posttranslational control of Cdc25 degradation terminates Drosophila's early cell-cycle program." Curr Biol 23(2): 127-132. PMCID: 3622868

Donovan J, Dufner M, Korennykh A. (2013). "Structural basis for cytosolic double-stranded RNA surveillance by human oligoadenylate synthetase 1." Proc Natl Acad Sci U S A 110(5): 1652-1657. PMCID: 3562804

Lenhart KF, Holtzman NG, Williams JR, Burdine RD. (2013) “Integration of nodal and BMP signals in the heart requires FoxH1 to create left-right differences in cell migration rates that direct cardiac asymmetry.” PLoS Genet.;9(1):e1003109. PMCID: 3554567

Evertts AG, Zee BM, Dimaggio PA, Gonzales-Cope M, Coller HA, Garcia BA. (2013) “Quantitative dynamics Of the link between cellular metabolism and histone acetylation.” J Biol Chem. Apr 26;288(17):12142-51 PMCID: 3636898

Britton LM, Newhart A, Bhanu NV, Sridharan R, Gonzales-Cope M, Plath K, Janicki SM, Garcia BA. (2013) “Initial characterization of histone H3 serine 10 O-acetylation.” Epigenetics. Aug 15;8(10). PMCID: 3891691

Park CY, Wong AK, Greene CS, Rowland J, Guan Y, Bongo LA, Burdine RD, Troyanskaya OG. (2013) “Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.” PLoS Comput Biol.;9(3):e1002957. PMCID: 3597527

Arlow, T., Scott, K., Wagenseller, A., and Gammie, A.E. (2013) The proteasome inhibitor Bortezomib rescues clinically identified unstable missense variants of the DNA mismatch repair protein Msh2. Proc Natl Acad Sci U S A. Jan 2;110(1):246-51 PMCID: 3538226

Rogers JV, Arlow T, Inkellis ER, Koo TS, Rose MD. (2013) “ER-associated SNAREs and Sey1p mediate nuclear fusion at two distinct steps during yeast mating” Mol Biol Cell. Oct 23 PMID: 24152736 [PubMed - in process]

O'Loughlin CT, Miller LC, Siryaporn A, Drescher K, Semmelhack MF, Bassler BL. (2013) “A quorum-sensing inhibitor blocks Pseudomonas aeruginosa virulence and biofilm formation” Proc Natl Acad Sci U S A. Oct 18. PMCID: 3816427

Ricci DP, Schwalm J, Gonzales-Cope M, Silhavy TJ. (2013) “The Activity and Specificity of the Outer Membrane Protein Chaperone SurA Are Modulated by a Proline Isomerase Domain.” MBio. Aug 13;4(4). PMCID: 3747590

Mahoney TF, Silhavy TJ. (2013) “The Cpx stress response confers resistance to some, but not all, bactericidal antibiotics.”J Bacteriol. May;195(9):1869-74. PMCID: 3624577

Swart EC, Bracht JR, Magrini V, Minx P, Chen X, Zhou Y, Khurana JS, Goldman AD, Nowacki M, Schotanus K, Jung S, Fulton RS, Ly A, McGrath S, Haub K, Wiggins JL, Storton D, Matese JC, Parsons L, Chang WJ,Bowen MS, Stover NA, Jones TA, Eddy SR, Herrick GA, Doak TG, Wilson RK, Mardis ER, Landweber LF.(2013) “The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS Biol.;11(1):e1001473. PMCID: 3558436 

Rowles DL., Terhune SS., and Cristea IM. (2013) “Discovery of host-viral protein complexes during infection.” Methods Mol Biol. 2013;1064:43-70. PMID: 23996249 [PubMed - in process]

Evertts AG, Manning AL, Wang X, Dyson NJ, Garcia BA, Coller HA. (2013) “H4K20 METHYLATION REGULATES QUIESCENCE AND CHROMATIN COMPACTION.” Mol Biol Cell. Oct;24(19):3025-37. PMCID: 3784377       

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