Graduate Studies
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Graduate Publications

2014

Esposito M, Kang Y. Targeting tumor-stromal interactions in bone metastasis. Pharmacol Ther. Feb, 2014;141(2):222-33. PMCID: PMC3947254

Guise AJ, Mathias RA, Rowland EA, Yu F, Cristea IM. Probing phosphorylation-dependent protein interactions within functional domains of histone deacetylase 5 (HDAC5). Proteomics. Oct, 2014;14(19):2156-66. PMCID: PMC4184959

Ha JY, Pokrovskaya ID, Climer LK, Shimamura GR, Kudlyk T, Jeffrey PD, Lupashin VV, Hughson FM. Cog5-Cog7 crystal structure reveals interactions essential for the function of a multisubunit tethering complex. Proc Natl Acad Sci U S A. Nov 4, 2014;111(44):15762-7. PMCID: PMC4226102

Han Y, Donovan J, Rath S, Whitney G, Chitrakar A, Korennykh A. Structure of human RNase L reveals the basis for regulated RNA decay in the IFN response. Science. Mar 14, 2014;343(6176):1244-8. PMCID: PMC4731867

Li W, Kang Y. A new Lnc in metastasis: long noncoding RNA mediates the prometastatic functions of TGF-beta. Cancer Cell. May 12, 2014;25(5):557-9. PMCID: PMC4091806

Domanitskaya, E, Anllo, L, Schupbach, T. 2014. Phantom, a cytochrome P450 enzyme essential for ecdysone biosynthesis, plays a critical role in the control of border cell migration in Drosophila. Developmental Biology. 386: 408-418.e: http://www.ncbi.nlm.nih.gov/pubmed/24373956

Zheng H, Shen M, Zha YL, Li W, Wei Y, Blanco MA, Ren G, Zhou T, Storz P, Wang HY, Kang Y. PKD1 phosphorylation-dependent degradation of SNAIL by SCF-FBXO11 regulates epithelial-mesenchymal transition and metastasis. Cancer Cell. Sep 8, 2014;26(3):358-73. PMCID: PMC4159622

Shi C, Murphy CT. Mating induces shrinking and death in Caenorhabditis mothers. Science. Jan 31, 2014;343(6170):536-40. Pubmed

Perez LJ, Karagounis TK, Hurley A, Bassler BL, Semmelhack MF. Highly Potent, Chemically Stable Quorum Sensing Agonists for. Chem Sci. Jan 1, 2014;5(1):151-5. PMCID: PMC3890260

Mathias RA, Greco TM, Oberstein A, Budayeva HG, Chakrabarti R, Rowland EA, Kang Y, Shenk T, Cristea IM. Sirtuin 4 is a lipoamidase regulating pyruvate dehydrogenase complex activity. Cell. Dec 18, 2014;159(7):1615-25. PMCID: PMC4344121

Polyakov O, He B, Swan M, Shaevitz JW, Kaschube M, Wieschaus E. Passive mechanical forces control cell-shape change during Drosophila ventral furrow formation. Biophys J. Aug 19, 2014;107(4):998-1010. PMCID: PMC4142243

Nguyen UT, Bittova L, Muller MM, Fierz B, David Y, Houck-Loomis B, Feng V, Dann GP, Muir TW. Accelerated chromatin biochemistry using DNA-barcoded nucleosome libraries. Nat Methods. Aug, 2014;11(8):834-40. PMCID: PMC4130351

Jean Beltran PM, Cristea IM. The life cycle and pathogenesis of human cytomegalovirus infection: lessons from proteomics. Expert Rev Proteomics. Dec, 2014;11(6):697-711. PMCID: PMC4604749

Amato SM, Fazen CH, Henry TC, Mok WW, Orman MA, Sandvik EL, Volzing KG, Brynildsen MP. The role of metabolism in bacterial persistence. Front Microbiol. 2014;5:70. PMCID: PMC3939429

Chakrabarti R, Wei Y, Hwang J, Hang X, Andres Blanco M, Choudhury A, Tiede B, Romano RA, DeCoste C, Mercatali L, Ibrahim T, Amadori D, Kannan N, Eaves CJ, Sinha S, Kang Y. (2014) “ΔNp63 promotes stem cell activity in mammary gland development and basal-like breast cancer by enhancing Fzd7 expression and Wnt signalling.” Nat Cell Biol. Oct;16(10):1004-15. PMCID: 4183725.

Guise AJ, Mathias RA, Rowland EA, Yu F, Cristea IM. (2014) “Probing phosphorylation-dependent protein interactions within functional domains of histone deacetylase 5 (HDAC5).” Proteomics. Oct;14(19):2156-66. PMCID: 4184959

Britton LM, Sova P, Belisle S, Liu S, Chan EY, Katze MG, Garcia BA. (2014) “A proteomic glimpse into the initial global epigenetic changes during HIV infection.” Proteomics. Oct;14(19):2226-30.PMCID: 4198388.

Sutterlin HA, Zhang S, Silhavy TJ. (2014) “Accumulation of phosphatidic acid increases vancomycin resistance in Escherichia coli.” J Bacteriol. Sep;196(18):3214-20. PMCID: 4135694

Fan J, Shan C, Kang HB, Elf S, Xie J, Tucker M, Gu TL, Aguiar M, Lonning S, Chen H, Mohammadi M, Britton LM, Garcia BA, Aleckovic M, Kang Y, Kaluz S, Devi N, Van Meir EG, Hitosugi T, Seo JH, Lonial S, Gaddh M, Arellano M, Khoury HJ, Khuri FR, Boggon TJ, Kang S, Chen J. Tyr phosphorylation of PDP1 toggles recruitment between ACAT1 and SIRT3 to regulate the pyruvate dehydrogenase complex. Mol Cell. Feb 20, 2014;53(4):534-48. PMCID: PMC3943932

Wan L, Hu G, Wei Y, Yuan M, Bronson RT, Yang Q, Siddiqui J, Pienta KJ, Kang Y. (2014) “Genetic ablation of metadherin inhibits autochthonous prostate cancer progression and metastasis” Cancer Res. Sep 15;74(18):5336-47. PMCID: 4167565.

Zheng H, Shen M, Zha YL, Li W, Wei Y, Blanco MA, Ren G, Zhou T, Storz P, Wang HY, Kang Y. (2014) “PKD1 phosphorylation-dependent degradation of SNAIL by SCF-FBXO11 regulates epithelial-mesenchymal transition and metastasis.” Cancer Cell. Sep 8;26(3):358-73. PMCID: 4159622.

Hjeij R, Onoufriadis A, Watson CM, Slagle CE, Klena NT, Dougherty GW, Kurkowiak M, Loges NT, Diggle CP, Morante NF, Gabriel GC, Lemke KL, Li Y, Pennekamp P, Menchen T, Konert F, Marthin JK, Mans DA, Letteboer SJ, Werner C, Burgoyne T, Westermann C, Rutman A, Carr IM, O'Callaghan C, Moya E, Chung EM; UK10K Consortium, Sheridan E, Nielsen KG, Roepman R, Bartscherer K, Burdine RD, Lo CW, Omran H, Mitchison HM. (2014) “CCDC151 mutations cause primary ciliary dyskinesia by disruption of the outer dynein arm docking complex formation.” Am J Hum Genet. Sep 4;95(3):257-74.PMCID: 4157146.

Dwyer RS, Malinverni JC, Boyd D, Beckwith J, Silhavy TJ. (2014) “Folding LacZ in the periplasm of Escherichia coli.” J Bacteriol.Sep;196(18):3343-50. PMCID: 4135689.

Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. (2014) “The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development”.Cell. Aug 28;158(5):1187-98. PMCID: 4199391.

Miller CG, Pozzi A, Zent R, Schwarzbauer JE.( 2014) “Effects of High Glucose on Integrin Activity and Fibronectin Matrix Assembly by Mesangial Cells.” Mol Biol Cell. Aug 15;25(16):2342-50. PMCID:4142608

Polyakov O, He B, Swan M, Shaevitz JW, Kaschube M, Wieschaus E. (2014) “Passive mechanical forces control cell-shape change during Drosophila ventral furrow formation.” Biophys J. Aug 19;107(4):998-1010. PMCID: 4142243.

Ell B, Qiu Q, Wei Y, Mercatali L, Ibrahim T, Amadori D, Kang Y. (2014) “The microRNA-23b/27b/24 cluster promotes breast cancer lung metastasis by targeting metastasis-suppressive gene prosaposin.” J Biol Chem. Aug 8;289(32):21888-95. PMCID: 4139207. 

Wang SS, Kloth AD, Badura A. (2014) “The cerebellum, sensitive periods, and autism.” Neuron. Aug 6;83(3):518-32. PMCID: 4135479.

Barry RM, Bitbol AF, Lorestani A, Charles EJ, Habrian CH, Hansen JM, Li HJ, Baldwin EP, Wingreen NS, Kollman JM, Gitai Z. (2014) “Large-scale filament formation inhibits the activity of CTP synthetase” Elife. Jul 16;3:e03638. PMCID: 4126345.

Wan L, Lu X, Yuan S, Wei Y, Guo F, Shen M, Yuan M, Chakrabarti R, Hua Y, Smith HA, Blanco MA, Chekmareva M, Wu H, Bronson RT, Haffty BG, Xing Y, Kang Y. (2014) “MTDH-SND1 interaction is crucial for expansion and activity of tumor-initiating cells in diverse oncogene- and carcinogen-induced mammary tumors.” Cancer Cell. Jul 14;26(1):92-105. PMCID: 4101059.

Ell B, Kang Y. (2014) MicroRNAs as regulators of bone homeostasis and bone metastasis.” Bonekey Rep. Jul 2;3:549. PMCID: 4119205.

Li W, Kang Y. (2014) “A new Lnc in metastasis: long noncoding RNA mediates the prometastatic functions of TGF-β” Cancer Cell. May 12;25(5):557-9. PMCID: 4091806.

Khurana JS, Wang X, Chen X, Perlman DH, Landweber LF. (2014) “Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax.” Genetics. May 1;197(3):839-849. PMCID: 4096365.

McIsaac RS, Gibney PA, Chandran SS, Benjamin KR, Botstein D. (2014) “Synthetic biology tools for programming gene expression without nutritional perturbations in Saccharomyces cerevisiae.” Nucleic Acids Res. Apr 1;42(6):e48. PMCID: 3973312

Shao Y, Bassler BL. (2014) “Quorum regulatory small RNAs repress type VI secretion in Vibrio cholerae.” Mol Microbiol. Apr 3. PMCID: 4038675

O'Hara JK, Kerwin LJ, Cobbold SA, Tai J, Bedell TA, Reider PJ, Llinás M. (2014) ”Targeting NAD+ metabolism in the human malaria parasite Plasmodium falciparum” PLoS One. Apr 18;9(4):e94061. PMCID: P3991606.

Breunig JS, Hackett SR, Rabinowitz JD, Kruglyak L. (2014) “Genetic basis of metabolome variation in yeast”. PLoS Genet. Mar 6;10(3):e1004142. PMCID: 3945093

Aoki T, Wolle D, Ben Noon EP, Dai Q, Lai EC, Schedl P. (2014) “Bi-functional cross-linking reagents efficiently capture protein-DNA complexes in Drosophila embryos.” Fly (Austin). Jan-Mar;8(1):43-51. PMCID: 3974894

Park J, Schwarzbauer JE. (2014) “Mammary epithelial cell interactions with fibronectin stimulate epithelial-mesenchymal transition”. Oncogene. Mar 27;33(13):1649-57. PMCID: 3934944

Zhou J, Troyanskaya OG. (2014) “Global quantitative modeling of chromatin factor interactions.” PLoS Comput Biol. Mar 27;10(3):e1003525. PMCID: 3967939

Ke X, Miller LC, Ng WL, Bassler BL. (2014) “CqsA-CqsS quorum-sensing signal-receptor specificity in Photobacterium angustum.” Mol Microbiol. 2014 Feb;91(4):821-33. PMCID: 3959898

Esposito M, Kang Y. (2014) “Targeting tumor-stromal interactions in bone metastasis.” Pharmacol Ther. Feb;14 1(2):222-33 PMCID: 3947254

Domanitskaya E, Anllo L, Schupbach T. Phantom, a cytochrome P450 enzyme essential for ecdysone biosynthesis, plays a critical role in the control of border cell migration in Drosophila. Dev Biol. Feb 15, 2014;386(2):408-18. PMCID: PMC4028970

Fan J, Shan C, Kang HB, Elf S, Xie J, Tucker M, Gu TL, Aguiar M, Lonning S, Chen H, Mohammadi M, Britton LM, Garcia BA4, Alečković M, Kang Y, Kaluz S, Devi N, Van Meir EG, Hitosugi T, Seo JH, Lonial S, Gaddh M, Arellano M, Khoury HJ1 Khuri FR, Boggon TJ, Kang S, Chen J. (2014) “Tyr Phosphorylation of PDP1 Toggles Recruitment between ACAT1 and SIRT3 to Regulate the Pyruvate Dehydrogenase Complex.” Mol Cell. Feb 20;53(4):534-48. PMCID: 3943932

Andersen EC, Bloom JS, Gerke JP, Kruglyak L. (2014) “A variant in the neuropeptide receptor npr-1 is a major determinant of Caenorhabditis elegans growth and physiology.” PLoS Genet.Feb 27;10(2):e1004156. PMCID: 3937155

Smadbeck J, Peterson MB, Zee BM, Garapaty S, Mago A, Lee C, Giannis A, Trojer P, Garcia BA, Floudas CA (2014) “De novo peptide design and experimental validation of histone methyltransferase inhibitors.” PLoS One. Feb 28;9(2):e90095. PMCID: 3938834

Desai VD, Hsia HC, Schwarzbauer JE. (2014) “Reversible modulation of myofibroblast differentiation in adipose-derived mesenchymal stem cells.” PLoS One. Jan 23;9(1):e86865. PMCID: 3900664

DeHart CJ, Chahal JS, Flint SJ, Perlman DH. (2014) “Extensive post-translational modification of active and inactivated forms of endogenous p53.” Mol Cell Proteomics. Jan;13(1):1-17. PMCID: 3879606

Miteva YV, Cristea IM. (2014) “A Proteomic Perspective of Sirtuin 6 (SIRT6) Phosphorylation and Interactions and Their Dependence on Its Catalytic Activity.” Mol Cell Proteomics. Jan;13(1):168-83. PMCID: 3879612

Perez LJ, Karagounis TK, Hurley A, Bassler BL, Semmelhack MF (2014) “Highly potent, chemically stable quorum sensing agonists for vibrio Cholerae” Chem. Sci. Jan. 1;5(1):151-155 PMCID: 3890260

Berman GJ, Choi DM, Bialek W, Shaevitz JW. Mapping the stereotyped behaviour of freely moving fruit flies. J R Soc Interface. Oct 6, 2014;11(99). PMCID: PMC4233753

Barry RM, Bitbol AF, Lorestani A, Charles EJ, Habrian CH, Hansen JM, Li HJ, Baldwin EP, Wingreen NS, Kollman JM, Gitai Z. Large-scale filament formation inhibits the activity of CTP synthetase. Elife. 2014;3:e03638. PMCID: PMC4126345

Chen X, Bracht JR, Goldman AD, Dolzhenko E, Clay DM, Swart EC, Perlman DH, Doak TG, Stuart A, Amemiya CT, Sebra RP, Landweber LF. The architecture of a scrambled genome reveals massive levels of genomic rearrangement during development. Cell. Aug 28, 2014;158(5):1187-98. PMCID: PMC4199391

de Jong YP, Dorner M, Mommersteeg MC, Xiao JW, Balazs AB, Robbins JB, Winer BY, Gerges S, Vega K, Labitt RN, Donovan BM, Giang E, Krishnan A, Chiriboga L, Charlton MR, Burton DR, Baltimore D, Law M, Rice CM, Ploss A. Broadly neutralizing antibodies abrogate established hepatitis C virus infection. Sci Transl Med. Sep 17, 2014;6(254):254ra129. PMCID: PMC4312107

 

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