Recent Publications

2015

Mitchell, CJ., Kim, MS., Na, CH., and Pandey, A., 2015, ” PyQuant: a versatile framework for analysis of quantitative mass spectrometry data,” Mol Cell Proteomics. pii: mcp.O115.056879  PubMed​
Prasad, M., Wang, X., He, L., Cai, D., and Montell, DJ., 2015, “Border Cell Migration: A Model System for Live Imaging and Genetic Analysis of Collective Cell Movement,”  Methods Mol Biol. 1328:89-97.  PubMed
de la Peña, AH., Suarez, A., Duong-Ly, KC., Schoeffield, AJ., Pizarro-Dupuy, MA., Zarr, M., Pineiro, SA., Amzel, LM. and Gabelli, SB., 2015, "Structural and Enzymatic Characterization of a Nucleoside Diphosphate Sugar Hydrolase from Bdellovibrio bacteriovorus," PLoS One, PMID: 26524597 PubMed
Baras, AS., Mitchell, CJ., Myers, JR., Gupta, S., Weng, LC., Ashton, JM., Cornish, TC., Pandey, A. and  Halushka, MK., 2015, "miRge - A Multiplexed Method of Processing Small RNA-Seq Data to Determine MicroRNA Entropy," PLoS One. PMID: 26571139  PubMed
Mitchell, CJ., Getnet, D., Kim, MS., Manda, SS., Kumar, P., Huang, TC., Pinto, SM., Nirujogi, RS., Iwasaki, M., Shaw, PG., Wu, X., Zhong, J., Chaerkady, R., Marimuthu, A., Muthusamy, B., Sahasrabuddhe, NA., Raju, R., Bowman, C., Danilova, L., Cutler, J., Kelkar, DS., Drake, CG., Prasad, TS., Marchionni, L., Murakami, PN., Scott, AF., Shi, L., Thierry-Mieg, J., Thierry-Mieg, D., Irizarry, R., Cope, L., Ishihama, Y., Wang, C., Gowda, H. and Pandey, A., 2015, "A multi-omic analysis of human naïve CD4+ T cells," BMC Syst Biol. 9:75. PMID: 26542228 PubMed
Zhou, Y., Williams, J., Smallwood, PM. and Nathans, J., 2015, "Sox7, Sox17, and Sox18 Cooperatively Regulate Vascular Development in the Mouse Retina," PLoS One. 10(12):e0143650. PMID: 26630461 PubMed
Phua, SC., Lin, YC. and Inoue, T., 2015, "An intelligent nano-antenna: Primary cilium harnesses TRP channels to decode polymodal stimuli," Cell Calcium. 58(4):415-22. Review. PMID: 25828566 PubMed​
Lim, C., Gandhi, S., Biniossek, ML., Feng, L., Schilling, O., Urban, S., Chen, X., 2015, An Aminopeptidase in the Drosophila Testicular Niche Acts in Germline Stem Cell Maintenance and Spermatogonial Dedifferentiation. Cell Rep. 13(2):315-25. PMID: 26440886  PubMed
Sundararajan, K.*, Miguel, A., Desmarais, SM., Meier, EL*., Casey, Huang, K. and Goley, ED.*, 2015, "The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction," Nat Commun. 6:7281. PMCID: PMC4532373 *equal contribution​ PubMed
Kurbanov, F., Kim, Y., Latanich, R., Chaudhari, P., El-Diwany, R., Knabel, M., Kandathil, AJ., Cameron, A., Cox, A., Jang, YY., Thomas, DL. and Balagopal, A., 2015, "IFNL3 genotype is associated with differential induction of IFNL3 in primary human hepatocytes," Antivir Ther. doi: 10.3851/IMP2974. [Epub ahead of print]  PMCID: unknown PubMed
Greenspan, LJ., de Cuevas, M. and Matunis, E., 2015, "Genetics of gonadal stem cell renewal," Annu Rev Cell Dev Biol. 31:291-315. PMID: 26355592 PubMed​
Lee, CF., Lo, YC., Cheng, CH., Furtmüller, GJ., Oh, B., Andrade-Oliveira, V., Thomas, AG., Bowman, CE., Slusher, BS., Wolfgang, MJ., Brandacher, G., Powell, JD., 2015, "Preventing Allograft Rejection by Targeting Immune Metabolism," Cell Rep. 13(4):760-70. PMID: 26489460 PubMed
Moyer, TC. and Holland, AJ., 2015, "Generation of a conditional analog-sensitive kinase in human cells using CRISPR/Cas9-mediated genome engineering," Methods Cell Biol. 129:19-36.​ ​ PubMed​
Ward, MD. and Leahy, DJ., 2015, "Kinase activator-receiver preference in ErbB heterodimers is determined by intracellular regions and is not coupled to extracellular asymmetry," J Biol Chem. 290(3):1570-9. PMCID: PMC4340403 PubMed
Deng, K., Pertea, M., Rongvaux, A., Wang, L., Durand, CM., Ghiaur, G., Lai, J., McHugh, HL., Hao, H., Zhang, H., Margolick, JB., Gurer, C., Murphy, AJ., Valenzuela, DM., Yancopoulos, GD., Deeks, SG., Strowig, T., Kumar, P., Siliciano, JD., Salzberg, SL., Flavell, RA., Shan, L. and Siliciano, RF, 2015, "Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations," Nature.15;517(7534):381-5. PMCID: PMC4406054  PubMed
Multhaup, ML., Seldin, MM., Jaffe, AE., Lei, X., Kirchner, H., Mondal, P., Li, Y., Rodriguez, V., Drong, A., Hussain, M., Lindgren, C., McCarthy, M., Näslund, E., Zierath, JR., Wong, GW. and Feinberg, AP., 2015, "Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes," Cell Metab. 21(1):138-49. PMCID: PMC4340475  PubMed
Dancy, BM. and Cole, PA., 2015, "Protein Lysine Acetylation by p300/CBP," Chem Rev, 115(6):2419-52. PMCID: PMC4378506 PubMed
Goodrich, AC. and Frueh, DP., 2015, "A Nuclear Magnetic Resonance Method for Probing Molecular Influences of Substrate Loading in Nonribosomal Peptide Synthetase Carrier Proteins. Biochemistry, 54, 1154-6.  PMCID: PMC4378656 PubMed
Harr, JC.*, Luperchio, TR.*, Wong, X.*, Cohen, E*., Wheelan, SJ. and Reddy, KL., 2015, "Directed targeting of chromatin to the nuclear lamina is mediated by chromatin state and A-type lamins," J Cell Biol. 208(1):33-52. PMCID: PMC4284222 *equal contribution.​ PubMed​
Surcel, A., Ng, WP., West-Foyle, H., Zhu, Q., Ren, Y., Avery, LB., Krenc, AK., Meyers, DJ., Rock, RS., Anders, RA., Freel, Meyers, CL. and Robinson, DN., 2015, "Pharmacological activation of myosin II paralogs to correct cell mechanics defects," Proc Natl Acad Sci USA, 112(5):1428-33.  PMCID: PMC4321244 PubMed​
Clister, T., Mehta, S. and Zhang, J., 2015, "Single-cell Analysis of G-protein Signal Transduction," J Biol Chem, 290(11):6681-8. PMCID: PMC4358091 PubMed
Koutmou, K.S., Schuller, A.P., Brunelle, J.L., Radhakrishnan, A., Djuranovic, S. & Green, R. Ribosomes slide on lysine-encoding homopolymeric A stretches. eLife, e05534 (2015). . PMCID: PMC4363877 PubMed​
Lu, YW. and Claypool, SM., 2015, "Disorders of phospholipid metabolism: an emerging class of mitochondrial disease due to defects in nuclear genes," Front Genet. 2015 Feb 3;6:3 PMCID: PMC4315098  PubMed​
Lei, X.*, Li, Q., Rodriguez, S.*, Tan, SY.*, Seldin, MM.*, McLenithan, JC., Jia, W. and Wong, GW., 2015, "Thromboxane synthase deficiency improves insulin action and attenuates adipose tissue fibrosis," Am J Physiol Endocrinol Metab. 308(9):E792-804 *equal contribution PubMed
Cox, E., Uzoma, I., Guzzo, C., Jeong, JS., Matunis, M., Blackshaw, S. and Zhu, H., 2015, "Identification of SUMO E3 Ligase-Specific Substrates Using the HuProt Human Proteome Microarray," Methods Mol Biol. 1295:455-63. PMCID: unknown PubMed
Zhou, X.*, Clister, TL.*, Lowry, PR.*, Seldin, MM., Wong, GW. and Zhang, J., 2015, "Dynamic Visualization of mTORC1 Activity in Living Cells," Cell Rep. pii: S2211-1247(15)00177-1. PMCID: PMC4567530 *equal contribution PubMed
Eginton C, Cressman WJ, Bachas S, Wade H, Beckett D. Allosteric Coupling via Distant Disorder-to-Order Transitions. J Mol Biol. 2015 Apr 24;427(8):1695-1704. doi: 10.1016/j.jmb.2015.02.021. Epub 2015 Mar 4. PubMed Eginton C, Cressman WJ, Bachas S, Wade H, Beckett D. Allosteric Coupling via Distant Disorder-to-Order Transitions. J Mol Biol. 2015 Apr 24;427(8):1695-1704. doi: 10.1016/j.jmb.2015.02.021. Epub 2015 Mar 4. PubMed
Deng, H., Wang, W., Yu, J., Zheng, Y., Qing, Y., and Pan, D., 2015, "Spectrin regulates Hippo signaling by modulating cortical actomyosin activity,"  ELife, 4:e06567.  PMCID: PMC4412106  PubMed
Shamir, ER. and Ewald, AJ., 2015, "Adhesion in mammary development: novel roles for e-cadherin in individual and collective cell migration," Curr Top Dev Biol. 112:353-82. PMCID: unknown PubMed
Zhang, W., Wu, J., Ward, MD., Yang, S., Chuang, YA., Xiao, M., Li, R., Leahy, DJ. and Worley, PF., 2015, "Structural basis of arc binding to synaptic proteins: implications for cognitive disease," Neuron. 86(2):490-500. PMCID: PMC4409568 PubMed
Yoo, SW.*, Motari, MG.*, Susuki, K.*, Prendergast, J.*, Mountney, A.*, Hurtado, A.* and Schnaar, RL., 2015 "Sialylation regulates brain structure and function," FASEB J. 29(7):3040-53. PMCID: PMC4478807 *equal contribution PubMed​
Metcalf, Pate, KA., Pohlmeyer, CW., Walker-Sperling, VE., Foote, JB., Najarro, KM., Cryer, CG., Salgado, M., Gama, L., Engle, EL., Shirk, EN., Queen, SE., Chioma, S., Vermillion, MS., Bullock, B., Li, M., Lyons, CE., Adams, RJ., Zink, MC., Clements, JE., Mankowski, JL. and Blankson, JN., 2015, "A murine viral outgrowth assay to detect residual HIV-1 in patients with undetectable viral loads," J Infect Dis. 212:1387-1396. PMCID: PMC4601916 ​ PubMed
Onguka, O.*, Calzada, E.*, Ogunbona, OB*. and Claypool, SM., 2015, "Phosphatidylserine Decarboxylase 1 Autocatalysis and Function Does Not Require a Mitochondrial-specific Factor," J Biol Chem, 290: 12744-52  PMCID: PMC4432291 *equal contribution PubMed​
Li, Z., He, SQ., Tseng, PY., Xu, Q., Tiwari, V., Yang, F., Shu, B., Zhang, T., Tang, Z., Raja, SN., Wang, Y., Dong, X. and Guan, Y., 2015, "The inhibition of high-voltage-activated calcium current by activation of MrgC11 involves phospholipase C-dependent mechanisms," Neuroscience, 300:393-403. PMCID: PMC4485588  PubMed​
Zhang, W., Wu, J., Ward, MD., Yang, S., Chuang, YA., Xiao, M., Li, R., Leahy, DJ. and Worley, PF., 2015, “Structural basis of arc binding to synaptic proteins: implications for cognitive disease.” Neuron. 22;86(2):490-500. PMCID: PMC4409568 PubMed
Kurbanov, F., Kim, Y., Latanich, R., Chaudhari, P., El-Diwany, R., Knabel, M., Kandathil, AJ., Cameron, A., Cox, A., Jang, YY., Thomas, DL. and Balagopal, A., 2015, "IFNL3 genotype is associated with differential induction of IFNL3 in primary human hepatocytes," Antivir Ther. doi: 10.3851/IMP2974. [Epub ahead of print]  PMCID: unknownPubMed
Echeverria, I., Liu, Y., Gabelli, SB. and Amzel, LM., 2015, "PI3Kα oncogenic mutations weaken the interactions that stabilize the p110α/p85α heterodimer," FEBS J., 282(18):3528-42  PMCID: PMC4573839  PubMed
Hasan, S., Hétié, P amd Matunis, EL., 2015, "Niche signaling promotes stem cell survival in the Drosophila testis via the JAK-STAT target DIAP1," Dev Biol, 404(1):27-39 PMCID: PMC4469572 PubMed
Morris, M., Knudsen, GM., Maeda, S., Trinidad, JC., Ioanoviciu, A., Burlingame, AL. and Mucke, L., 2015, "Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice," Nat Neurosci. 18(8):1183-9. PubMed
Maruotti, J.*, Sripathi, SR.*, Bharti, K.*, Fuller, J.*, Wahlin, KJ.*, Ranganathan, V.*, Sluch, VM.*, Berlinicke, CA.*, Davis, J., Kim, C.*, Zhao, L.*, Wan, J.*, Qian, J.*, Corneo, B., Temple, S., Dubey, R., Olenyuk, BZ., Bhutto, I.*, Lutty, GA.* and Zack, DJ.*, 2015, "Small-molecule-directed, efficient generation of retinal pigment epithelium from human pluripotent stem cells," Proc Natl Acad Sci U S A. 112(35):10950-5. PMCID: PMC4568212 *equal contribution PubMed
Westerbeck, JW. and Machamer, CE., 2015, "A Coronavirus E Protein is Present in Two Distinct Pools with Different Effects on Assembly and the Secretory Pathway," J Virol., 89:18.  PMCID: PMC4542375  PubMed
Sun, G. j*, Zhou, Y.*, Stadel, R. p*, Moss, J., Yong, J.H. a, Ito, S., Kawasaki, N. k, Phan, A. t, Oh, J. h, Modak, N., Reed, R. r, Toni, N., Song, H., Ming, G.-L. Tangential migration of neuronal precursors of glutamatergic neurons in the adult mammalian brain. Proc Natl Acad Sci U S A. 2015 Jul 28;112(30):9484-9 (*equal contributions) PMID: 26170290 PubMed
Moyer, TC., Clutario, KM., Lambrus, BG., Daggubati, V. and Holland, AJ., 2015, "Binding of STIL to Plk4 activates kinase activity to promote centriole assembly," J Cell Biol. 209(6):863-78. PMCID: PMC4477857  PubMed
Vanhollebeke, B., Stone, OA., Bostaille, N., Cho, C., Zhou, Y., Maquet, E., Gauquier, A., Cabochette, P., Fukuhara, S., Mochizuki, N., Nathans and J. and Stainier, DY., 2015, "Tip cell-specific requirement for an atypical Gpr124- and Reck-dependent Wnt/β-catenin pathway during brain angiogenesis," Elife. 4. PMCID: PMC4456509 PubMed
Durand, CM., Buckheit, RW 3rd., Salgado, M., Pohlmeyer, CW., Walker-Sperling, VE., Hegarty, RW., Ambinder, RF. and Blankson, JN., 2015, "A Human Immunodeficiency Virus Controller With a Large Population of CD4(+)CD8(+) Double-Positive T Cells," Open Forum Infect Dis. 2(2):ofv039. PMCID: PMC4567082 PubMed
Hanlon, C.D. and Andrew, D.J., 2015, "Outside – In Signaling: a review of the Drosophila GPCR family," J Cell Sci. 2015 Oct 1;128(19):3533-42. Review. PMCID: PMC4610211 .PubMed
Julian, TR., Baugher, JD., Rippinger, C., Pinekenstein, R., Kolawole, AO., Mehoke, T., Wobus, CE., Feldman, A., Pineda, FJ. and Schwab, KJ., 2015, "Murine norovirus (MNV-1) exposure in vitro to the purine nucleoside analog Ribavirin increases quasispecies diversity," Virus Res, 211:165-73.      [PubMed - in process] PubMed​
Morris, M., Knudsen, GM., Maeda, S., Trinidad, JC., Ioanoviciu, A., Burlingame, AL. and Mucke, L., 2015, "Tau post-translational modifications in wild-type and human amyloid precursor protein transgenic mice," Nat Neurosci. 18(8):1183-9.   PubMed
Nguyen-Ngoc, KV., Shamir, ER., Huebner, RJ., Beck, JN., Cheung, KJ. and Ewald, AJ., 2015, "3D culture assays of murine mammary branching morphogenesis and epithelial invasion," Methods Mol Biol. 1189:135-62.  PubMed​
Li,  W., Koutmou, KS., Leahy, DJ. and Li, M., 2015, "Systemic RNA Interference Deficiency-1 (SID-1) Extracellular Domain Selectively Binds Long Double-stranded RNA and Is Required for RNA Transport by SID-1.," J Biol Chem. 290(31):18904-13. PMCID: PMC4521010 PubMed

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