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PMM Graduate Student Publications (2009-2018)


Venkatesan, A.M., Vyas, R., Dresser, K., Gujja, S., Bhatnagar, S., Chhangawala, S., Gomes, C., Xi, H.S., Lian, C.G., Houvras, Y., Edwards, Y.J.K., Deng, A., Green, M. and Ceol, C.J. Ligand-activated BMP signaling inhibits cell differentiation and death to promote melanoma.    J Clin Invest. 2018 Jan 2;128(1):294-308. doi: 10.1172/JCI92513.  PMID: 29202482.

Neto, A. and Ceol, C.J.  Melanoma-associated GRM3 variants dysregulate melanosome trafficking and cAMP signaling.  Pigment Cell Melanoma Res. 2018 Jan;31(1):115-119. doi: 10.1111/pcmr.12610. PMID: 28646617.

Mir, A., Edraki, A., Lee, J., and Sontheimer, E. J.  Type II-C CRISPR-Cas9 biology, mechanism and application. ACS Chem Biol. 2018 Feb 16;13(2):357-365. doi: 10.1021/acschembio.7b00855. Epub 2017 Dec 20. PMID:29202216.

Sanchez-Ramos J, Song S, Kong X, Foroutan P, Martinez G, Dominguez-Viqueria W, Mohapatra S, Mohapatra S, Haraszti RA, Khvorova A, Aronin N, Sava V. Chitosan-Mangafodipir nanoparticles designed for intranasal delivery of siRNA and DNA to brain. J Drug Deliv Sci Technol. 2018 Feb;43:453-460. doi: 10.1016/j.jddst.2017.11.013. Epub 2017 Nov 21. PubMed PMID: 29805475; PubMed Central PMCID: PMC5967853.

Edraki, A., and Sontheimer, E. J. CRISPRs from scratch. Nature Microbiology 3, 261-262.  Nat Microbiol. 2018 Mar;3(3):261-262. doi: 10.1038/s41564-018-0115-9. PMID: 29463924.

Hassler MR, Turanov AA, Alterman JF, Haraszti RA, Coles AH, Osborn MF, Echeverria D, Nikan M, Salomon WE, Roux L, Godinho BMDC, Davis SM, Morrissey DV, Zamore PD, Karumanchi SA, Moore MJ, Aronin N, Khvorova A. Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivo. Nucleic Acids Res. 2018 Mar 16;46(5):2185-2196. doi: 10.1093/nar/gky037. PubMed PMID: 29432571; PubMed Central PMCID: PMC5861422.

Girnius, N. Edwards, Y. J. K. and Davis, R. J.  The cJun NH2-terminal kinase (JNK) pathway contributes to mouse mammary gland remodeling during involution.  Cell Death Differ. 2018 Sep;25(9):1702-1715. doi: 10.1038/s41418-018-0081-z. Epub 2018 Mar 6. PMID: 29511338.

Gao, X. D., Tu, L.-C., Mir, A., Rodriguez, T., Ding, Y., Leszyk, J., Dekker, J., Shaffer, S. A., Zhu, L. J., Wolfe, S. A., and Sontheimer, E. J. C-BERST: Defining subnuclear proteomic landscapes at genomic elements with dCas9-APEX2. Nat Methods. 2018 May 7. doi: 10.1038/s41592-018-0006-2. [Epub ahead of print].PMID:29735996.

Girnius, N., Edwards, Y. J. K., Garlick, D. S. and Davis, R. J.  The cJUN NH2-terminal kinase (JNK) signaling pathway promotes genome stability and prevents tumor initiation.   Elife. 2018 Jun 1;7. pii: e36389. doi: 10.7554/eLife.36389.  PMID:29856313.

Biscans A, Haraszti RA, Echeverria D, Miller R, Didiot MC, Nikan M, Roux L, Aronin N, Khvorova A. Hydrophobicity of Lipid-Conjugated siRNAs Predicts Productive Loading to Small Extracellular Vesicles. Mol Ther. 2018 Jun 6;26(6):1520-1528. doi:0.1016/j.ymthe.2018.03

Stone, N., Hilbert, B. J., Hidalgo, D., Halloran, K. T., Lee, J., Sontheimer, E. J., and Kelch, B. A. A hyperthermophilic phage decoration protein suggests common evolutionary origin with herpesvirus triplex proteins and an anti-CRISPR protein.  Structure. 2018 Jul 3;26(7):936-947.e3. doi: 10.1016/j.str.2018.04.008. Epub 2018 May 17. PMID: 29779790.

Sharma VK, Osborn MF, Hassler MR, Echeverria D, Ly S, Ulashchik EA, Martynenko-Makaev YV, Shmanai VV, Zatsepin TS, Khvorova A, Watts JK. Novel Cluster and Monomer-Based GalNAc Structures Induce Effective Uptake of siRNAs in Vitro and in Vivo. Bioconjug Chem. 2018 Jul 18;29(7):2478-2488. doi: 10.1021/acs.bioconjchem.8b00365. Epub 2018 Jul 2. PubMed PMID: 29898368.

Mir A, Alterman JF, Hassler MR, Debacker AJ, Hudgens E, Echeverria D, Brodsky MH, Khvorova A, Watts JK, Sontheimer EJ. Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing. Nat Commun. 2018 Jul 6;9(1):2641. doi: 10.1038/s41467-018-05073-z. PubMed PMID: 29980686; PubMed Central PMCID: PMC6035171.

Landry BD, Leete T, Richards R, Cruz-Gordillo P, Schwartz HR, Honeywell ME, Ren G, Schwartz AD, Peyton SR, and Lee MJ. Tumor-stroma interactions differentially alter drug sensitivity based on the origin of stromal cells. Mol Syst Biol. 2018 Aug 6;14(8):e8322. doi: 10.15252/msb.20188322.  PMCID: PMC6078165

Barutcu, S., Girnius, N., Vernia, S., and Davis, R. J.  Role of the MAPK/cJun NH2-terminal kinase signaling pathway in starvation-induced autophagy. Autophagy. 2018;14(9):1586-1595. doi: 10.1080/15548627.2018.1466013. Epub 2018 Aug 17.  PMID:29950132.

Godinho BMDC, Henninger N, Bouley J, Alterman JF, Haraszti RA, Gilbert JW, Sapp E, Coles AH, Biscans A, Nikan M, Echeverria D, DiFiglia M, Aronin N, Khvorova A. Transvascular Delivery of Hydrophobically Modified siRNAs: Gene Silencing in the Rat Brain upon Disruption of the Blood-Brain Barrier. Mol Ther. 2018 Nov 7;26(11):2580-2591. doi: 10.1016/j.ymthe.2018.08.005. Epub 2018 Aug 8. PubMed PMID: 30143435; PubMed Central PMCID: PMC6225091.

Mapa CE, Arsenault HE, Conti MM, Poti KE, Benanti JA.  A balance of deubiquitinating enzymes controls cell cycle entry. Mol Biol Cell. 2018 Sep 12:mbcE18070425. doi: 10.1091/mbc.E18-07-0425. [Epub ahead of print].  PMID:  30207830.

Didiot MC, Ferguson CM, Ly S, Coles AH, Smith AO, Bicknell AA, Hall LM, Sapp E, Echeverria D, Pai AA, DiFiglia M, Moore MJ, Hayward LJ, Aronin N, Khvorova A. Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin. Cell Rep. 2018 Sep 4;24(10):2553-2560.e5. doi: 10.1016/j.celrep.2018.07.106. PubMed PMID: 30184490; PubMed Central PMCID: PMC6245656.

Ibraheim, R., Song, C.-Q., Mir, A., Amrani, N., Xue, W., and Sontheimer, E. J. All-in-one Adeno-associated Virus Delivery and Genome Editing by Neisseria meningitidis Cas9 in vivo. Genome Biol. 2018 Sep 19;19(1):137. doi: 10.1186/s13059-018-1515-0. PMID: 30231914.

Haraszti RA, Miller R, Stoppato M, Sere YY, Coles A, Didiot MC, Wollacott R, Sapp E, Dubuke ML, Li X, Shaffer SA, DiFiglia M, Wang Y, Aronin N, Khvorova A. Exosomes Produced from 3D Cultures of MSCs by Tangential Flow Filtration Show Higher Yield and Improved Activity. Mol Ther. 2018 Dec 5;26(12):2838-2847. doi: 10.1016/j.ymthe.2018.09.015. Epub 2018 Sep 22. PubMed PMID: 30341012; PubMed Central PMCID: PMC6277553.

Turanov AA, Lo A, Hassler MR, Makris A, Ashar-Patel A, Alterman JF, Coles AH, Haraszti RA, Roux L, Godinho BMDC, Echeverria D, Pears S, Iliopoulos J, Shanmugalingam R, Ogle R, Zsengeller ZK, Hennessy A, Karumanchi SA, Moore MJ, Khvorova A. RNAi modulation of placental sFLT1 for the treatment of preeclampsia. Nat Biotechnol. 2018 Nov 19. doi: 10.1038/nbt.4297. [Epub ahead of print] PubMed PMID: 30451990.

Didiot MC, Haraszti RA, Aronin N, Khvorova A. Loading of Extracellular Vesicles with Hydrophobically Modified siRNAs. Methods Mol Biol. 2018;1740:199-214. doi: 10.1007/978-1-4939-7652-2_16. PubMed PMID: 29388146.

Acharya D, Nera B, Milstone ZJ, Bourke L, Yoon Y, Rivera-Pérez JA, Trivedi CM, Fazzio TG. TIP55, a splice isoform of the KAT5 acetyltransferase, is essential for developmental gene regulation and organogenesis.  Sci Rep. 2018 (in press).    


Ly S, Navaroli DM, Didiot MC, Cardia J, Pandarinathan L, Alterman JF, Fogarty K, Standley C, Lifshitz LM, Bellve KD, Prot M, Echeverria D, Corvera S, Khvorova A. Visualization of self-delivering hydrophobically modified siRNA cellular internalization. Nucleic Acids Res. 2017 Jan 9;45(1):15-25. doi: 10.1093/nar/gkw1005. Epub 2016 Nov 28. PubMed PMID: 27899655; PubMed Central PMCID: PMC5224471.

Matheson TD and Kaufman PD. The p150N domain of Chromatin Assembly Factor-1 regulates Ki-67 accumulation on the mitotic perichromosomal layer. Mol. Biol. Cell 28: 21-29 (2017). PMCID: PMC5221625. (Cover article).

Dagdeviren, S., Jung, D.Y., Friedline, R.H., Noh, H.-L., Kim, J.H., Patel, P.R., Tsitsilianos, N., Inashima, K., Tran, D.A., Hu, X., Loubato, M.L., Craige, S.M., Kwon, J.Y., Lee, K.W., and Kim, J.K. IL-10 prevents aging-associated inflammation and insulin resistance in skeletal muscle. FASEB J.  2017 Feb;31(2):701-710. doi: 10.1096/fj.201600832R. Epub 2016 Nov 3.  PMID: 27811060.  PMCID: PMC5240661.

Adkins, N.L., Swygert, S.G., Kaur, P., Niu, H., Grigoryev, S.A., Sung, P., Wang, H., and Peterson, C.L. Nucleosome-like, single-stranded DNA (ssDNA)-histone octamer complexes and the implication for DNA double strand break repair. J. Biol. Chem. 292:5271-5281.
2017 Mar 31;292(13):5271-5281. doi: 10.1074/jbc.M117.776369. Epub 2017 Feb 15. PMID: 28202543.   PMCID: PMC5392674.

Pearring JN, San Agustin JT, Lobanova ES, Gabriel CJ, Lieu EC, Monis WJ, Stuck MW, Strittmatter L, Jaber SM, Arshavsky VY, Pazour GJ.   Loss of Arf4 Causes Severe Degeneration of the Exocrine Pancreas but Not Cystic Kidney Disease or Retinal Degeneration.  PLoS Genet. 2017 Apr 14;13(4):e1006740. doi: 10.1371/journal.pgen.1006740.   PMID:28410364.   PMCID: PMC5409180. 

Acharya D, Hainer SJ, Yoon Y, Wang F, Bach I, Rivera-Pérez JA, Fazzio TG.   KAT-Independent Gene Regulation by Tip60 Promotes ESC Self-Renewal but Not Pluripotency.  Cell Rep. 2017 Apr 25;19(4):671-679. doi: 10.1016/j.celrep.2017.04.001.  PMID:  28445719.

Guilherme, A, Pedersen, DJ, Henchey, E, Henriques, FS, Danai, LV, Shen, Y, Yenilmez, B, Jung, DY, Kim, JK, Lodhi, IJ, Semenkovich, CF, Czech, MP.  Adipocyte lipid synthesis coupled to neuronal control of thermogenic programming.  Mol. Metab. 2017 May 31;6:781-796.  PMID: 28752043

Monis WJ, Faundez V, Pazour GJ.   BLOC-1 is required for selective membrane protein trafficking from endosomes to primary cilia.  J Cell Biol. 2017 Jul 3;216(7):2131-2150. doi: 10.1083/jcb.201611138. Epub 2017 Jun 2.  PMCID: PMC5496619.

Ee LS, McCannell KN, Tang Y, Fernandes N, Hardy WR, Green MR, Chu F, Fazzio TG.  An Embryonic Stem Cell-Specific NuRD Complex Functions through Interaction with WDR5. Stem Cell Reports. 2017 Jun 6;8(6):1488-1496. doi: 10.1016/j.stemcr.2017.04.020. Epub 2017 May 18. PMID: 28528697.

McFleder, R.L., Mansur, F., Richter, J.D. Dynamic Control of Dendritic mRNA Expression by CNOT7 Regulates Synaptic Efficacy and Higher Cognitive Function.  Cell Rep. 2017 Jul 18;20(3):683-696. doi: 10.1016/j.celrep.2017.06.078.  PMID:28723570.  PMCID:PMC5557029.

Haraszti RA, Roux L, Coles AH, Turanov AA, Alterman JF, Echeverria D, Godinho BMDC, Aronin N, Khvorova A. 5΄-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res. 2017 Jul 27;45(13):7581-7592. doi: 10.1093/nar/gkx507. PubMed PMID: 28591791; PubMed Central PMCID: PMC5570069.

Gioacchini, N., Peterson, C.L.  Chromatin remodeling: A complex affair. EMBO Rep., 2017 Aug 23. pii: e201744852. doi: 10.15252/embr.201744852. [Epub ahead of print].  PMID: 28835548.

Alterman JF, Coles AH, Hall LM, Aronin N, Khvorova A, Didiot MC. A High-throughput Assay for mRNA Silencing in Primary Cortical Neurons in vitro with Oligonucleotide Therapeutics. Bio Protoc. 2017 Aug 20;7(16). pii: e2501. doi: 10.21769/BioProtoc.2501. PubMed PMID: 28966945; PubMed Central PMCID: PMC5621760.

Sharma VK, Singh SK, Krishnamurthy PM, Alterman JF, Haraszti RA, Khvorova A, Prasad AK, Watts JK. Synthesis and biological properties of triazole-linked locked nucleic acid. Chem Commun (Camb). 2017 Aug 3;53(63):8906-8909. doi: 10.1039/c7cc04092j. PubMed PMID: 28736781.

Sun X, Bizhanova A, Matheson TD, Yu J, Zhu LJ, Kaufman PD. Ki-67 contributes to normal cell cycle progression and inactive X heterochromatin in p21 checkpoint-proficient human cells. Mol. Cell. Biol. 37: e00569-16 (2017). PMCID: PMC5559680. (Cover article).

Harrington, L. B., Doxzen, K. W., Ma, E., Liu, J.-J., Knott, G. J., Edraki, A., Amrani, N., Chen, J. S., Cofsky, J. C., Kranzusch, P. J., Sontheimer, E. J., Davidson, A. R., Maxwell, K., and Doudna, J. A. (2017). A broad-spectrum inhibitor of CRISPR-Cas9. Cell. 2017 Sep 7;170(6):1224-1233.e15. doi: 10.1016/j.cell.2017.07.037.  PMID:28844692.

Ichikawa Y, Connelly CF, Appleboim A, Jacobi H, Abshiru NA, Chen Y, Sharma U, Zheng Y, Thomas PM, Chen HV, Bajaj V, Kelleher NL, Friedman N, Bolon DN, Rando OJ*, and Kaufman PD*. A synthetic biology approach to probing nucleosome symmetry. Elife. 2017 Sep 12;6. pii: e28836. doi: 10.7554/eLife.28836. (*Co-corresponding authors). PMCID: PMC5626479.

Roth Flach RJ, DiStefano MT, Danai LV, Senol-Cosar O, Yawe JC, Kelly M, Garcia Menendez L, Czech MP. MAP4K4 impairs energy metabolism in endothelial cells and promotes insulin resistance in obesity. Am J Physiol Endocrinol Metab. 2017 Sep 1;313: E303-E313.  PMID: 28611026.

Hartwig C, Monis WJ, Chen X, Dickman DK, Pazour GJ, Faundez V. 2017. Neurodevelopmental Disease Mechanisms, Primary Cilia, and Endosomes Converge on the BLOC-1 and BORC Complexes.  Dev Neurobiol. 2017 Oct 7. doi: 10.1002/dneu.22542.   PMCID: PMC5816705.

Girnius, N. and Davis, R. J.  JNK promotes epithelial cell anoikis by transcriptional and post-translational regulation of BH3-only proteins.  Cell Rep. 2017 Nov 14;21(7):1910-1921. doi: 10.1016/j.celrep.2017.10.067. PMID:29141222.

Neiswender, J.V., Kortum, R.L., Bourque, C., Kasheta, M., Zon, L.I., Morrison, D.K. and Ceol, C.J. KIT suppresses BRAFV600E-mutant melanoma by attenuating RAS/MAPK signaling.  Cancer Res. 2017 Nov 1;77(21):5820-5830. doi: 10.1158/0008-5472.CAN-17-0473. Epub 2017 Sep 25.  PMID: 28947418.

Godinho BMDC, Gilbert JW, Haraszti RA, Coles AH, Biscans A, Roux L, Nikan M, Echeverria D, Hassler M, Khvorova A. Pharmacokinetic Profiling of Conjugated Therapeutic Oligonucleotides: A High-Throughput Method Based Upon Serial Blood Microsampling Coupled to Peptide Nucleic Acid Hybridization Assay. Nucleic Acid Ther. 2017 Dec;27(6):323-334. doi: 10.1089/nat.2017.0690. Epub 2017 Oct 12. PubMed PMID: 29022758; PubMed Central PMCID: PMC5706627.

Kasheta, M., Painter, C.A., Moore, F.E., Lobbardi, R., Bryll, A., Freiman, E., Stachura, D., Rogers, A.B., Houvras, Y., Langenau, D.M. and Ceol, C.J.  Identification and characterization of Treg-like cells in zebrafish.  J Exp Med. 2017 Dec 4;214(12):3519-3530. doi: 10.1084/jem.20162084.  PMID: 29066577.

Russo, L., Muturi, H.T., Ghadieh, H.E., Ghanem, S.S., Bowman, T.A., Noh, H.L., Dagdeviren, S., Dogbey, G.Y., Kim, J.K., Heinrich, G., Najjar, S.M.  Liver-specific reconstitution of CEACAM1 reverses the metabolic abnormalities caused by its global deletion in male mice.  Diabetologia. 2017 Dec;60(12):2463-2474. doi: 10.1007/s00125-017-4432-y. Epub 2017 Sep 14.


Haraszti RA, Didiot MC, Sapp E, Leszyk J, Shaffer SA, Rockwell HE, Gao F, Narain NR, DiFiglia M, Kiebish MA, Aronin N, Khvorova A. High-resolution proteomic and lipidomic analysis of exosomes and microvesicles from different cell sources. J Extracell Vesicles. 2016 Nov 17;5:32570. doi: 10.3402/jev.v5.32570. eCollection 2016. PubMed PMID: 27863537; PubMed Central PMCID: PMC5116062.

Senol-Cosar, O., Flach, R.J., DiStefano, M., Chawla, A., Nicoloro, S., Straubhaar, J., Hardy, O.T., Noh, H.L., Kim, J.K., Wabitsch, M., et al.  Tenomodulin promotes human adipocyte differentiation and beneficial visceral adipose tissue expansion.   Nat Commun. 2016 Feb 16;7:10686. doi: 10.1038/ncomms10686.  PMID: 26880100; PMCID: PMC4757769.

Cohen, J.L., Shen, Y., Aouadi, M., Vangala, P., Tencerova, M., Amano, S.U., Nicoloro, S.M., Yawe, J.C., and Czech, M.P. Peptide- and Amine-Modified Glucan Particles for the Delivery of Therapeutic siRNA.   Mol Pharm. 2016 Mar 7;13(3):964-78. doi: 10.1021/acs.molpharmaceut.5b00831. Epub 2016 Feb 11. PMID: 26815386.  

Vertii, A, Hung HF, Hehnly, H, Doxsey, S.  Human basal body basics.  Cilia. 2016 Mar 14;5:13. doi: 10.1186/s13630-016-0030-8. eCollection 2016.

Friedline, R.H., Ko, H.-J., Jung, D.Y., Lee, Y., Bortell, R., Dagdeviren, S., Patel, P.R., Hu, X., Inashima, K., Kearns, C., Tsitsilianos, N., Shafiq, U., Shultz, L.D., Lee, K.W., Greiner, D.L., and Kim, J.K.  Genetic ablation of lymphocytes and cytokine signaling in non-obese diabetic mouse background prevents diet-induced obesity and insulin resistance. FASEB J. 2016 Mar;30(3):1328-38. doi: 10.1096/fj.15-280610. Epub 2015 Dec 7. PMID:  26644351.  PMCID:PMC4750424

Liu, D., Bordicchia, M., Zhang, C., Fang, H., Wei, W., Li, J.L., Guilherme, A., Guntur, K., Czech, M.P., and Collins, S.  Activation of mTORC1 is essential for beta-adrenergic stimulation of adipose browning.    J Clin Invest. 2016 May 2;126(5):1704-16. doi: 10.1172/JCI83532. Epub 2016 Mar 28.  PMID: 27018708; PMCID: PMC4855937.

Hung, HF, Hehnly, H, Doxsey, S.  The Mother Centriole Appendage Protein Cenexin Modulates Lumen Formation through Spindle Orientation. Curr Biol. 2016 Mar 21;26(6):793-801. doi: 10.1016/j.cub.2016.01.025. Epub 2016 Mar 3. PMID:26948879.

Coles AH, Osborn MF, Alterman JF, Turanov AA, Godinho BM, Kennington L, Chase K, Aronin N, Khvorova A. A High-Throughput Method for Direct Detection of Therapeutic Oligonucleotide-Induced Gene Silencing In Vivo. Nucleic Acid Ther. 2016 Apr;26(2):86-92. doi: 10.1089/nat.2015.0578. Epub 2015 Nov 23. PubMed PMID: 26595721; PubMed Central PMCID: PMC4834514.

Ren, Z., Veksler-Lublinsky I., Morrissey D., Ambros V.  Staufen negatively modulates microRNA activity in Caenorhabditis elegans.  G3 (Bethesda).  2016 May 3;6(5):1227-37. doi: 10.1534/g3.116.027300. PMID: 26921297.  PMCID:  PMC4856075.

Roth Flach, R.J., Guo, C.A., Danai, L.V., Yawe, J.C., Gujja, S., Edwards, Y.J., and Czech, M.P.   Endothelial Mitogen-Activated Protein Kinase Kinase Kinase Kinase 4 Is Critical for Lymphatic Vascular Development and Function.    Mol Cell Biol. 2016 May 31;36(12):1740-9. doi: 10.1128/MCB.01121-15. Print 2016 Jun 15.   PMID: 27044870; PMCID: PMC4907094.

Roth Flach, R.J., Danai, L.V., DiStefano, M.T., Kelly, M., Garcia Menendez, L., Jurczyk, A., Sharma, R.B., Jung, D.Y., Kim, J.H., Kim, J.K., et al.   Protein Kinase Mitogen Activated Protein Kinase Kinase Kinase Kinase 4 (MAP4K4) Promotes Obesity-Induced Hyperinsulinemia.   J Biol Chem. 2016 May 20. pii: jbc.M116.718932. [Epub ahead of print].  PMID:  27226575; DOI: 10.1074/jbc.M116.718932.

Yu, L., Rege, M., Peterson, C.L., and Volkert, M.R.   RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Molecular Biology,  2016 Aug 30;17(1):20. doi: 10.1186/s12867-016-0074-8.  PMID: 27578267. PMCID: PMC5004267.

Nikan M, Osborn MF, Coles AH, Godinho BM, Hall LM, Haraszti RA, Hassler MR, Echeverria D, Aronin N, Khvorova A. Docosahexaenoic Acid Conjugation Enhances Distribution and Safety of siRNA upon Local Administration in Mouse Brain. Mol Ther Nucleic Acids. 2016 Aug 9;5(8):e344. doi: 10.1038/mtna.2016.50. PubMed PMID: 27504598; PubMed Central PMCID: PMC5023396.

Didiot MC, Hall LM, Coles AH, Haraszti RA, Godinho BM, Chase K, Sapp E, Ly S, Alterman JF, Hassler MR, Echeverria D, Raj L, Morrissey DV, DiFiglia M, Aronin N, Khvorova A. Exosome-mediated Delivery of Hydrophobically Modified siRNA for Huntingtin mRNA Silencing. Mol Ther. 2016 Oct;24(10):1836-1847. doi: 10.1038/mt.2016.126. Epub 2016 Jun 27. PubMed PMID: 27506293; PubMed Central PMCID: PMC5112038.

DiStefano, M.T., Flach, R.J.R., Senol-Cosar, O., Danai, L.V., Virbasiu, J.V., Nicoloro, S.M., Straubhaar, J., Dagdeviren, S., Wabitsch, M., Gupta, O.T., Kim, J.K., and Czech, M.P. Adipocyte-specific Hypoxia-inducible gene 2 promotes fat deposition and diet-induced insulin resistance. Mol Metab. 2016 Sep 28;5(12):1149-1161. eCollection 2016 Dec.   PMID: 27900258.  PMCID:  PMC5123203.

Dagdeviren, S., Jung, D.Y., Lee, E., Friedline, R.H., Noh, H.L., Kim, J.H., Patel, P.R., Tsitsilianos, N., Tsitsilianos, A., Tran, D.A., Tsougranis, G.H., Kearns, C.C., Uong, C.P., Kwon, J.Y., Muller, W., Lee, K.W., and Kim, J.K.  Altered Interleukin-10 signaling in skeletal muscle regulates obesity-mediated inflammation and insulin resistance. Mol Cell Biol. 2016 Nov 14;36(23):2956-2966. Print 2016 Dec 1.  PMID: 27644327.  PMCID:  PMC5108883


Ren Z, Ambros VR.  Caenorhabditis elegans microRNAs of the let-7 family act in innate immune response circuits and confer robust developmental timing against pathogen stress.   Proc Natl Acad Sci USA. 2015, May 5;112(18):E2366-75. doi: 10.1073/pnas.1422858112. Epub 2015 Apr 20. PMID: 25897023. PMCID:PMC4426397.

Pedersen, D.J., Guilherme, A., Danai, L.V., Heyda, L., Matevossian, A., Cohen, J., Nicoloro, S.M., Straubhaar, J., Noh, H.L., Jung, D., et al.   A major role of insulin in promoting obesity-associated adipose tissue inflammation.   Mol Metab. 2015 May 1;4(7):507-18. doi: 10.1016/j.molmet.2015.04.003. eCollection 2015.  PMID: 26137438; PMCID: PMC4481426. 

DiStefano, M.T., Danai, L.V., Roth Flach, R.J., Chawla, A., Pedersen, D.J., Guilherme, A., and Czech, M.P.  The Lipid Droplet Protein Hypoxia-inducible Gene 2 Promotes Hepatic Triglyceride Deposition by Inhibiting Lipolysis.   J Biol Chem. 2015 Jun 12;290(24):15175-84. doi: 10.1074/jbc.M115.650184. Epub 2015 Apr 28.  PMID: 25922078; PMCID:  PMC4463459. 

Hung, HF, Hehnly H, Doxsey, S.  Methods to analyze novel liaisons between endosomes and centrosomes.  Methods Cell Biol. 2015;130:47-58. doi: 10.1016/bs.mcb.2015.03.024. Epub 2015 Jun 11.  PMID:26360027

Bennett, G., and Peterson, C.L. SWI/SNF recruitment to a double strand break by the NuA4 and Gcn5 histone acetyltransferases. DNA Repair (Amst). 2015 Jun;30:38-45.  doi: 10.1016/j.dnarep.2015.03.006. Epub 2015 Mar 25. PMID:25869823 PMCID:  PMC4425604.

Malaby, A. W., Chakravarthy, S., Irving, T. C., Kathuria, S. V., Bilsel, O., Lambright, D. G.  Methods for analysis of size-exclusion chromatography-small-angle X-ray scattering and reconstruction of protein scattering.    J Appl Crystallogr.   2015  Jul 8;48(Pt 4):1102-1113. eCollection 2015 Aug 1.  PMID: 26306089

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Danai, L.V., Flach, R.J., Virbasius, J.V., Menendez, L.G., Jung, D.Y., Kim, J.H., Kim, J.K., and Czech, M.P. Inducible Deletion of Protein Kinase Map4k4 in Obese Mice Improves Insulin Sensitivity in Liver and Adipose Tissues.   Mol Cell Biol. 2015 Jul;35(13):2356-65.  PMID:  25918248; PMCID: PMC4456439.

Burke SL, Hammell M, Ambros V.  Robust distal tip cell pathfinding in the face of temperature stress is ensured by two conserved microRNAS in caenorhabditis elegans. Genetics. 2015, Aug;200(4):1201-18. doi: 10.1534/genetics.115.179184. Epub 2015 Jun 15. PMID:26078280.   PMCID:PMC4574240.

Osborn MF, Alterman JF, Nikan M, Cao H, Didiot MC, Hassler MR, Coles AH, Khvorova A. Guanabenz (Wytensin™) selectively enhances uptake and efficacy of hydrophobically modified siRNAs. Nucleic Acids Res. 2015 Oct 15;43(18):8664-72. doi: 10.1093/nar/gkv942. Epub 2015 Sep 22. PubMed PMID: 26400165; PubMed Central PMCID: PMC4605330.

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Swygert, S.G., and Peterson, C.L.  Chromatin dynamics: Interplay between remodeling enzymes and histone modifications. Biochim Biophys Acta.  2014 Aug; 1839(8): 728-736. doi: 10.1016/j.bbagrm.2014.02.013. Epub 2014 Feb 28.

Aouadi, M., Vangala, P., Yawe, J.C., Tencerova, M., Nicoloro, S.M., Cohen, J.L., Shen, Y., and Czech, M.P. Lipid storage by adipose tissue macrophages regulates systemic glucose tolerance.  Am J Physiol Endocrinol Metab. 2014 Aug 15;307(4):E374-83. doi: 10.1152/ajpendo.00187.2014. Epub 2014 Jul 1.  PMID: 24986598; PMCID: PMC4137117.

Swygert, S.G., Manning, B., Senapati, S., Kaur, P., Lindsay, S., Demeler, B., and Peterson, CL.  Solution-state conformation and stoichiometry of yeast Sir3 heterochromatin fibers. Nat Commun.  2014 Aug 28;5:4751. doi: 10.1038/ncomms5751.

Negrin, K.A., Roth Flach, R.J., DiStefano, M.T., Matevossian, A., Friedline, R.H., Jung, D., Kim, J.K., and Czech, M.P.   IL-1 signaling in obesity-induced hepatic lipogenesis and steatosis.  PLoS One. 2014 Sep 12;9(9):e107265. doi.  10.1371/journal.pone.0107265. eCollection 2014.  PMID: 25216251; PMCID: PMC4162604. 

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Manning. B. J., and Peterson, C.L.  Direct interactions promote eviction of the Sir3 heterochromatin protein by the SWI/SNF chromatin remodeling enzyme. Proc Natl Acad Sci USA.  2014 Dec 16;111:17827-17832.  doi: 10.1073/pnas.1420096111. Epub 2014 Dec 1.


Manning, B., and Peterson, C.L.  Releasing the brakes on a chromatin remodelling enzyme.  Nat Struct Molec Biol. 2013 Jan; 20(1):5-7.

Roth Flach, R.J., Matevossian, A., Akie, T.E., Negrin, K.A., Paul, M.T., and Czech, M.P. beta3-Adrenergic receptor stimulation induces E-selectin-mediated adipose tissue inflammation. J Biol Chem. 2013 Jan 25; 288(4): 2882–2892. 

Wang M, Amano SU, Roth Flach RJ, Chawla A, Aouadi M, Czech MP. Identification of Map4k4 as a novel suppressor of skeletal muscle differentiation. Mol Cell Biol.  Mol Cel Biol 2013 Feb;33(4):678-87. PMID: 23207904; PMCID: PMC3571342

Hehnly H, Hung HF, Doxsey.  One among many: ODF2 isoform 9, a.k.a. Cenexin-1, is required for ciliogenesis.  Cell Cycle. 2013 Apr 1;12(7):1021.  PMID: 23511168.  PMCID: PMC3646858.

Guo, C.A., Kogan, S., Amano, S.U., Wang, M., Dagdeviren, S., Friedline, R.H., Aouadi, M., Kim, J.K., and Czech, M.P. CD40 deficiency in mice exacerbates obesity-induced adipose tissue inflammation, hepatic steatosis, and insulin resistance.   Am J Physiol Endocrinol Metab. 2013 May 1;304(9):E951-63.  PMID: 23482447; PMCID: PMC3651645.

Aouadi, M., Tencerova, M., Vangala, P., Yawe, J.C., Nicoloro, S.M., Amano, S.U., Cohen, J.L., and Czech, M.P. Gene silencing in adipose tissue macrophages regulates whole-body metabolism in obese mice.  Proc Natl Acad Sci U S A. 2013 May 14;110(20):8278-83. doi: 10.1073/pnas.1300492110. Epub 2013 Apr 29.  PMID: 23630254; PMCID:  PMC3657808. 

Bennett, G., Papamichos-Chronakis, M., and Peterson.  DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat Commun.  2013 Jun 28;4:2084. doi: 10.1038/ncomms3084.

Malaby, A. W., van den Berg, B., & Lambright, D. G.  Structural basis for membrane recruitment and allosteric activation of cytohesin family Arf GTPase exchange factors.  2013 Aug 27;110(35):14213-8.  PMID  23940353.

Danai, L.V., Guilherme, A., Guntur, K.V., Straubhaar, J., Nicoloro, S.M., and Czech, M.P. Map4k4 suppresses Srebp-1 and adipocyte lipogenesis independent of JNK signaling.   J Lipid Res. 2013 Oct;54(10):2697-707. doi: 10.1194/jlr.M038802. Epub 2013 Aug 7.  PMID: 23924694; PMCID: PMC3770083.

Nechama M, Lin CL, Richter JD. An Unusual Two-Step Control of CPEB Destruction by Pin1. Mol Cell Biol. 2013 Jan;33(1):48-58. doi: 10.1128/MCB.00904-12. Epub 2012 Oct 22. PubMed PMID: 23090969.

Lambright, D. G., Malaby, A. W., Katurhia, S. V., Nobrega, R. P., Bilsel, O., Matthews, C. R., Muthurajan, U., Luger, K., Chopra, R., Irviing, T. C., & Chakravarthy, S. Complementary techniques enhance the quality and scope of information obtained from SAXS.   Trans. Amer. Crystallogr. Soc.  2013  44: 1-12.


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Hung CM, Garcia-Haro L, Sparks CA, Guertin DA. mTOR-Dependent Cell Survival Mechanisms. Cold Spring Harb Perspect Biol. 2012 Dec 1;4(12). doi:pii: a008771. 10.1101/cshperspect.a008771. PubMed PMID: 23124837.

Zhang F, Wang J, Xu J, Zhang Z, Koppetsch BS, Schultz N, Vreven T, Meignin C, Davis I, Zamore PD, Weng Z, Theurkauf WE. UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery. Cell. 2012 Nov 9;151(4):871-84. doi: 10.1016/j.cell.2012.09.040. PubMed PMID: 23141543; PubMed Central PMCID: PMC3499805.

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Chen CT, Doxsey SJ. An MBoC favorite: role of GTP hydrolysis in microtubule dynamics: information from a slowly hydrolyzable analogue, GMPCPP. Mol Biol Cell. 2012 Oct;23(19):3775. doi: 10.1091/mbc.E12-03-0186. PubMed PMID: 23024182; PubMed Central PMCID: PMC3459854.

Sanchez-Gurmaches J, Hung CM, Sparks CA, Tang Y, Li H, Guertin DA. PTEN loss in the Myf5 lineage redistributes body fat and reveals subsets of white adipocytes that arise from Myf5 precursors. Cell Metab. 2012 Sep 5;16(3):348-62. PubMed PMID: 22940198; PubMed Central PMCID: PMC3488151.

Chen CT, Hehnly H, Doxsey SJ. Orchestrating vesicle transport, ESCRTs and kinase surveillance during abscission. Nat Rev Mol Cell Biol. 2012 Jul 11;13(8):483-8. doi: 10.1038/nrm3395. Review. PubMed PMID: 22781903.

Shirayama M, Seth M, Lee HC, Gu W, Ishidate T, Conte D Jr, Mello CC. piRNAs initiate an epigenetic memory of nonself RNA in the C. elegans germline. Cell. 2012 Jul 6;150(1):65-77. doi: 10.1016/j.cell.2012.06.015. Epub 2012 Jun 25. PubMed PMID: 22738726.

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Cellurale C, Girnius N, Jiang F, Cavanagh-Kyros J, Lu S, Garlick DS, Mercurio AM, Davis RJ. Role of JNK in mammary gland development and breast cancer. Cancer Res. 2012 Jan 15;72(2):472-81. doi: 10.1158/0008-5472.CAN-11-1628. Epub 2011 Nov 29. PubMed PMID: 22127926; PubMed Central PMCID: PMC3261359.

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Young JL, Mora A, Cerny A, Czech MP, Woda B, Kurt-Jones EA, Finberg RW, Corvera S. CD14 deficiency impacts glucose homeostasis in mice through altered adrenal tone. PLoS One. 2012;7(1):e29688. doi: 10.1371/journal.pone.0029688. Epub 2012 Jan 13. PubMed PMID: 22253759; PubMed Central PMCID: PMC3258240.


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Fitzgibbons TP, Kogan S, Aouadi M, Hendricks GM, Straubhaar J, Czech MP. Similarity of mouse perivascular and brown adipose tissues and their resistance to diet-induced inflammation. Am J Physiol Heart Circ Physiol. 2011 Oct;301(4):H1425-37. doi: 10.1152/ajpheart.00376.2011. Epub 2011 Jul 15. PubMed PMID: 21765057; PubMed Central PMCID: PMC3197360.

Navaroli DM, Stevens ZH, Uzelac Z, Gabriel L, King MJ, Lifshitz LM, Sitte HH, Melikian HE. The plasma membrane-associated GTPase Rin interacts with the dopamine transporter and is required for protein kinase C-regulated dopamine transporter trafficking. J Neurosci. 2011 Sep 28;31(39):13758-70. doi: 10.1523/JNEUROSCI.2649-11.2011. PubMed PMID: 21957239; PubMed Central PMCID: PMC3205929.

Kuo TC, Chen CT, Baron D, Onder TT, Loewer S, Almeida S, Weismann CM, Xu P, Houghton JM, Gao FB, Daley GQ, Doxsey S. Midbody accumulation through evasion of autophagy contributes to cellular reprogramming and tumorigenicity. Nat Cell Biol. 2011 Sep 11;13(10):1214-23. doi: 10.1038/ncb2332. Erratum in: Nat Cell Biol. 2011 Dec;13(12):1467. PubMed PMID: 21909099.

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Burns DM, D'Ambrogio A, Nottrott S, Richter JD. CPEB and two poly(A) polymerases control miR-122 stability and p53 mRNA translation. Nature. 2011 May 5;473(7345):105-8. doi: 10.1038/nature09908. Epub 2011 Apr 10. PubMed PMID: 21478871; PubMed Central PMCID: PMC3088779.

Tabuchi TM, Deplancke B, Osato N, Zhu LJ, Barrasa MI, Harrison MM, Horvitz HR, Walhout AJ, Hagstrom KA. Chromosome-biased binding and gene regulation by the Caenorhabditis elegans DRM complex. PLoS Genet. 2011 May;7(5):e1002074. doi: 10.1371/journal.pgen.1002074. Epub 2011 May 12. PubMed PMID: 21589891; PubMed Central PMCID: PMC3093354.

Narasimhan SD, Yen K, Bansal A, Kwon ES, Padmanabhan S, Tissenbaum HA. PDP-1 links the TGF-β and IIS pathways to regulate longevity, development, and metabolism. PLoS Genet. 2011 Apr;7(4):e1001377. doi: 10.1371/journal.pgen.1001377. Epub 2011 Apr 21. PubMed PMID: 21533078; PubMed Central PMCID: PMC3080858.

Cellurale C, Sabio G, Kennedy NJ, Das M, Barlow M, Sandy P, Jacks T, Davis RJ. Requirement of c-Jun NH(2)-terminal kinase for Ras-initiated tumor formation. Mol Cell Biol. 2011 Apr;31(7):1565-76. doi: 10.1128/MCB.01122-10. Epub 2011 Jan 31. PubMed PMID: 21282468; PubMed Central PMCID: PMC3135291.

Delaval B, Bright A, Lawson ND, Doxsey S. The cilia protein IFT88 is required for spindle orientation in mitosis. Nat Cell Biol. 2011 Apr;13(4):461-8. doi: 10.1038/ncb2202. Epub 2011 Mar 27. PubMed PMID: 21441926; PubMed Central PMCID: PMC3073523.

Musich T, Peters PJ, Duenas-Decamp MJ, Gonzalez-Perez MP, Robinson J, Zolla-Pazner S, Ball JK, Luzuriaga K, Clapham PR. A conserved determinant in the V1 loop of HIV-1 modulates the V3 loop to prime low CD4 use and macrophage infection. J Virol. 2011 Mar;85(5):2397-405. doi: 10.1128/JVI.02187-10. Epub 2010 Dec 15. PubMed PMID: 21159865; PubMed Central PMCID: PMC3067776.

Yen K, Narasimhan SD, Tissenbaum HA. DAF-16/Forkhead box O transcription factor: many paths to a single Fork(head) in the road. Antioxid Redox Signal. 2011 Feb 15;14(4):623-34. doi: 10.1089/ars.2010.3490. Epub 2010 Nov 30. PubMed PMID: 20673162; PubMed Central PMCID: PMC3021330.

Burkart A, Shi X, Chouinard M, Corvera S. Adenylate kinase 2 links mitochondrial energy metabolism to the induction of the unfolded protein response. J Biol Chem. 2011 Feb 11;286(6):4081-9. doi: 10.1074/jbc.M110.134106. Epub 2010 Sep 27. PubMed PMID: 20876536; PubMed Central PMCID: PMC3039340.


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Khurana JS, Xu J, Weng Z, Theurkauf WE. Distinct functions for the Drosophila piRNA pathway in genome maintenance and telomere protection. PLoS Genet. 2010 Dec 16;6(12):e1001246. doi: 10.1371/journal.pgen.1001246. PubMed PMID: 21179579; PubMed Central PMCID: PMC3003142.

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Cellurale C, Weston CR, Reilly J, Garlick DS, Jerry DJ, Sluss HK, Davis RJ. Role of JNK in a Trp53-dependent mouse model of breast cancer. PLoS One. 2010 Aug 30;5(8):e12469. doi: 10.1371/journal.pone.0012469. PubMed PMID: 20814571; PubMed Central PMCID: PMC2930003.

DiNitto JP, Lee MT, Malaby AW, Lambright DG. Specificity and membrane partitioning of Grsp1 signaling complexes with Grp1 family Arf exchange factors. Biochemistry. 2010 Jul 27;49(29):6083-92. doi: 10.1021/bi1000454. PubMed PMID: 20527794; PubMed Central PMCID: PMC2912425.

Kwon ES, Narasimhan SD, Yen K, Tissenbaum HA. A new DAF-16 isoform regulates longevity. Nature. 2010 Jul 22;466(7305):498-502. doi: 10.1038/nature09184. Epub 2010 Jul 7. PubMed PMID: 20613724; PubMed Central PMCID: PMC3109862.

Duenas-Decamp MJ, Peters PJ, Repik A, Musich T, Gonzalez-Perez MP, Caron C, Brown R, Ball J, Clapham PR. Variation in the biological properties of HIV-1 R5 envelopes: implications of envelope structure, transmission and pathogenesis. Future Virol. 2010 Jul;5(4):435-451. PubMed PMID: 20930940; PubMed Central PMCID: PMC2949073.

Arda HE, Taubert S, MacNeil LT, Conine CC, Tsuda B, Van Gilst M, Sequerra R, Doucette-Stamm L, Yamamoto KR, Walhout AJ. Functional modularity of nuclear hormone receptors in a Caenorhabditis elegans metabolic gene regulatory network. Mol Syst Biol. 2010 May 11;6:367. doi: 10.1038/msb.2010.23. PubMed PMID: 20461074; PubMed Central PMCID: PMC2890327.

Walz HA, Shi X, Chouinard M, Bue CA, Navaroli DM, Hayakawa A, Zhou QL, Nadler J, Leonard DM, Corvera S. Isoform-specific regulation of Akt signaling by the endosomal protein WDFY2. J Biol Chem. 2010 May 7;285(19):14101-8. doi: 10.1074/jbc.M110.110536. Epub 2010 Feb 26. PubMed PMID:

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Vasale JJ, Gu W, Thivierge C, Batista PJ, Claycomb JM, Youngman EM, Duchaine TF, Mello CC, Conte D Jr. Sequential rounds of RNA-dependent RNA transcription drive endogenous small-RNA biogenesis in the ERGO-1/Argonaute pathway. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3582-7. doi: 10.1073/pnas.0911908107. Epub 2010 Feb 2. PubMed PMID: 20133583; PubMed Central PMCID: PMC2840456.

Conine CC, Batista PJ, Gu W, Claycomb JM, Chaves DA, Shirayama M, Mello CC. Argonautes ALG-3 and ALG-4 are required for spermatogenesis-specific 26G-RNAs and thermotolerant sperm in Caenorhabditis elegans. Proc Natl Acad Sci U S A. 2010 Feb 23;107(8):3588-93. doi: 10.1073/pnas.0911685107. Epub 2010 Feb 4. PubMed PMID: 20133686; PubMed Central PMCID: PMC2840486.

Navaroli DM, Melikian HE. Insertion of tetracysteine motifs into dopamine transporter extracellular domains. PLoS One. 2010 Feb 9;5(2):e9113. doi: 10.1371/journal.pone.0009113. PubMed PMID: 20161733; PubMed Central PMCID: PMC2817725. 

Lin CL, Evans V, Shen S, Xing Y, Richter JD. The nuclear experience of CPEB: implications for RNA processing and translational control. RNA. 2010 Feb;16(2):338-48. doi: 10.1261/rna.1779810. Epub 2009 Dec 29. PubMed PMID: 20040591; PubMed Central PMCID: PMC2811663.

Follit JA, Li L, Vucica Y, Pazour GJ. The cytoplasmic tail of fibrocystin contains a ciliary targeting sequence. J Cell Biol. 2010 Jan 11;188(1):21-8. doi: 10.1083/jcb.200910096. Epub 2010 Jan 4. PubMed PMID: 20048263; PubMed Central PMCID: PMC2812845.


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Arda HE, Walhout AJ. Gene-centered regulatory networks. Brief Funct Genomics. 2010 Jan;9(1):4-12. doi: 10.1093/bfgp/elp049. Epub 2009 Dec 13. Review. PubMed PMID: 20008400; PubMed Central PMCID: PMC3096532.

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Narasimhan SD, Mukhopadhyay A, Tissenbaum HA. InAKTivation of insulin/IGF-1 signaling by dephosphorylation. Cell Cycle. 2009 Dec;8(23):3878-84. PubMed PMID: 19901535; PubMed Central PMCID: PMC3109867.

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Claycomb JM, Batista PJ, Pang KM, Gu W, Vasale JJ, van Wolfswinkel JC, Chaves DA, Shirayama M, Mitani S, Ketting RF, Conte D Jr, Mello CC. The Argonaute CSR-1 and its 22G-RNA cofactors are required for holocentric chromosome segregation. Cell. 2009 Oct 2;139(1):123-34. doi: 10.1016/j.cell.2009.09.014. PubMed PMID: 19804758; PubMed Central PMCID: PMC2766185.

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