Publications

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Meyer AL, Benson J, Song F, Javed N, Gienapp IE, Goverman J, Brabb TA, Hood L, Whitacre CC.  2001.  Rapid depletion of peripheral antigen-specific T cells in TCR-transgenic mice after oral administration of myelin basic protein. J Immunol. 166:5773-81.
Sherwood CA, Eastham A, Lee LW, Risler J, Mirzaei H, Falkner JA, Martin DB.  2009.  Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets. J Proteome Res. 8:3746-51.
Kinsinger CR, Apffel J, Baker M, Bian X, Borchers CH, Bradshaw R, Brusniak MY, Chan DW, Deutsch EW, Domon B et al..  2012.  Recommendations for Mass Spectrometry Data Quality Metrics for Open Access Data (Corollary to the Amsterdam Principles). Journal of proteome research. 11:1412-1419.
Wang Y, Eddy JA, Price ND.  2012.  Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC systems biology. 6:153.
Knijnenburg TA, Roda O, Wan Y, Nolan GP, Aitchison JD, Shmulevich I.  2011.  A regression model approach to enable cell morphology correction in high-throughput flow cytometry. Molecular systems biology. 7:531.
de Atauri P, Orrell D, Ramsey S, Bolouri H.  2005.  Is the regulation of galactose 1-phosphate tuned against gene expression noise? Biochem J. 387:77-84.
Knudsen BS, Lucas JM, Fazli L, Hawley S, Falcon S, Coleman IM, Martin DB, Xu C, True LD, Gleave ME et al..  2005.  Regulation of hepatocyte activator inhibitor-1 expression by androgen and oncogenic transformation in the prostate. Am J Pathol. 167:255-66.
Cook MS, Munger SC, Nadeau JH, Capel B.  2011.  Regulation of male germ cell cycle arrest and differentiation by DND1 is modulated by genetic background. Development. 138:23-32.
Smith JJ, Aitchison JD.  2009.  Regulation of peroxisome dynamics. Curr Opin Cell Biol. 21:119-26.
Sumara G, Formentini I, Collins S, Sumara I, Windak R, Bodenmiller B, Ramracheya R, Caille D, Jiang H, Platt KA et al..  2009.  Regulation of PKD by the MAPK p38delta in insulin secretion and glucose homeostasis. Cell. 136:235-48.
Morrison DL, Yee A, Paddon HB, Vilimek D, Aebersold R, Pelech SL.  2000.  Regulation of the meiosis-inhibited protein kinase, a p38(MAPK) isoform, during meiosis and following fertilization of seastar oocytes. J Biol Chem. 275:34236-44.
Davidson EH, McClay DR, Hood L.  2003.  Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A. 100:1475-80.
Kastenmüller W, Gasteiger G, Subramanian N, Sparwasser T, Busch DH, Belkaid Y, Drexler I, Germain RN.  2011.  Regulatory T cells selectively control CD8+ T cell effector pool size via IL-2 restriction.. J Immunol. 187(6):3186-97.
Li H, Glusman G, Hu H, , Caballero J, Hubley R, Witherspoon D., Guthery S.L, Mauldin DE, Jorde LB et al..  2014.  Relationship estimation from whole-genome sequence data. PLoS genetics. 10:e1004144.
Lahdesmaki H, Hautaniemi S, Shmulevich I, Yli-Harja O.  2006.  Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Processing. 86:814-834.
Eddy JA, Geman D, Price ND.  2009.  Relative expression analysis for identifying perturbed pathways. Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference. 2009:5456-9.
Eddy JA, Sung J, Geman D, Price ND.  2010.  Relative expression analysis for molecular cancer diagnosis and prognosis. Technology in cancer research & treatment. 9:149-59.
Sims A.C, Tilton S.C, Menachery V.D, Gralinski L.E, Schafer A., Matzke M.M, Webb-Robertson B.J, Chang J., Luna M.L, Long C.E et al..  2013.  Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. J Virol. 87:3885-902.
Ozinsky A, Underhill DM, Fontenot JD, Hajjar AM, Smith KD, Wilson CB, Schroeder L, Aderem A.  2000.  The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between toll-like receptors. Proc Natl Acad Sci U S A. 97:13766-71.
Aebersold R, Auffray C, Baney E, Barillot E, Brazma A, Brett C, Brunak S, Butte A, Califano A, Celis J et al..  2009.  Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008). Mol Oncol. 3:9-17.
Bradshaw RA, Burlingame AL, Carr S, Aebersold R.  2006.  Reporting protein identification data: the next generation of guidelines. Mol Cell Proteomics. 5:787-8.
Bodenmiller B, Mueller LN, Mueller M, Domon B, Aebersold R.  2007.  Reproducible isolation of distinct, overlapping segments of the phosphoproteome. Nat Methods. 4:231-7.
Huttenhain R, Soste M, Selevsek N, Rost H, Sethi A, Carapito C, Farrah T, Deutsch EW, Kusebauch U, Moritz RL et al..  2012.  Reproducible quantification of cancer-associated proteins in body fluids using targeted proteomics. Science translational medicine. 4:142ra94.
Thyme S.B, Boissel S.J, S. Quadri A, Nolan T., Baker D.A, Park R.U, Kusak L., Ashworth J, Baker D..  2013.  Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic Acids Res.
Thyme S.B, Boissel S.J, S. Quadri A, Nolan T., Baker D.A, Park R.U, Kusak L., Ashworth J, Baker D..  2014.  Reprogramming homing endonuclease specificity through computational design and directed evolution. Nucleic acids research. 42:2564-76.
Craig TA, Zhang Y, McNulty MS, Middha S, Ketha H, Singh RJ, Magis AT, Funk C, Price ND, Ekker SC et al..  2012.  Research resource: whole transcriptome RNA sequencing detects multiple 1alpha,25-dihydroxyvitamin d3-sensitive metabolic pathways in developing zebrafish. Molecular endocrinology. 26:1630-42.
Diercks A, Kostner H, Ozinsky A.  2009.  Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS OnePLoS ONE. 4:e6326.
Fu E, Ramsey SA, Chen J, Chinowsky TM, Wiley B, Xia Y, Yager P.  2007.  Resonance wavelength-dependent signal of absorptive particles in surface plasmon resonance-based detection. Sens Actuators B Chem. 123:606-613.
Thorsson V, Hornquist M, Siegel AF, Hood L.  2005.  Reverse engineering galactose regulation in yeast through model selection. Stat Appl Genet Mol Biol. 4:Article28.
Ashworth J, Wurtmann EJ, Baliga NS.  2011.  Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Current opinion in biotechnology.
Gomes C.P, Cho JH, Hood L, Franco O.L, Pereira R.W, Wang K.  2013.  A Review of Computational Tools in microRNA Discovery. Front Genet. 4:81.
Hood L, Balling R, Auffray C.  2012.  Revolutionizing medicine in the 21(st) century through systems approaches. Biotechnology journal.
Orellana MV, Hansell DA.  2012.  Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO): A long-lived protein inthe deep ocean. Limnology & Oceanography. 57:826-834.
Rani PG, Ranish J, Hahn S.  2004.  RNA polymerase II (Pol II)-TFIIF and Pol II-mediator complexes: the major stable Pol II complexes and their activity in transcription initiation and reinitiation. Mol Cell Biol. 24:1709-20.
Mandin P., Toledo-Arana A., A. d'Hérouel F, Repoila F..  2013.  RNA-mediated Control of Bacterial Gene Expression: Role of Regulatory non-Coding RNAs. Encyclopedia of Molecular Cell Biology and Molecular Medicine. :1–36.
Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE.  2012.  RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. Nucleic acids research. 40:e42.
Aitchison JD, Rout MP.  2000.  The road to ribosomes. Filling potholes in the export pathway. J Cell Biol. 151:F23-6.
Ahdesmaki M, Lahdesmaki H, Gracey A, Shmulevich I, Yli-Harja O.  2007.  Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics. 8:233.
Zhu XM, Yin L, Hood L, Ao P.  2004.  Robustness, stability and efficiency of phage lambda genetic switch: dynamical structure analysis. J Bioinform Comput Biol. 2:785-817.
Nirodi C, NagDas S, Gygi SP, Olson G, Aebersold R, Richmond A.  2001.  A role for poly(ADP-ribose) polymerase in the transcriptional regulation of the melanoma growth stimulatory activity (CXCL1) gene expression. J Biol Chem. 276:9366-74.
Orellana MV, Pang WL, Durand P.M, Whitehead K, Baliga NS.  2013.  A role for programmed cell death in the microbial loop. PLoS One. 8:e62595.
Ptak C, Anderson AM, Scott RJ, Van de Vosse D, Rogers RS, Sydorskyy Y, Aitchison JD, Wozniak RW.  2009.  A role for the karyopherin Kap123p in microtubule stability. Traffic. 10:1619-34.
Van de Vosse DW, Wan Y, Lapetina DL, Chen WM, Chiang JH, Aitchison JD, Wozniak RW.  2013.  A role for the nucleoporin nup170p in chromatin structure and gene silencing. Cell. 152:969-83.
Makhnevych T, Ptak C, Lusk CP, Aitchison JD, Wozniak RW.  2007.  The role of karyopherins in the regulated sumoylation of septins. J Cell Biol. 177:39-49.
Koide T, Pang WL, Baliga NS.  2009.  The role of predictive modelling in rationally re-engineering biological systems. Nat Rev Microbiol. 7:297-305.
Gershenson C, Kauffman SA, Shmulevich I.  2005.  The role of redundancy in the robustness of random Boolean networks. Arxiv preprint nlin/0511018.
Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD.  2009.  Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes. Mol Cell Biol. 29:2346-58.
Van de Vosse DW, Wan Y, Wozniak RW, Aitchison JD.  2011.  Role of the nuclear envelope in genome organization and gene expression. Wiley Interdiscip Rev Syst Biol Med. 3:147-66.
Aderem A.  2001.  Role of Toll-like receptors in inflammatory response in macrophages. Crit Care Med. 29:S16-8.
Ostrowski J, Schullery DS, Denisenko ON, Higaki Y, Watts J, Aebersold R, Stempka L, Gschwendt M, Bomsztyk K.  2000.  Role of tyrosine phosphorylation in the regulation of the interaction of heterogenous nuclear ribonucleoprotein K protein with its protein and RNA partners. J Biol Chem. 275:3619-28.
Iouk TL, Aitchison JD, Maguire S, Wozniak RW.  2001.  Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome biosynthesis. Mol Cell Biol. 21:1260-71.