Publications

Found 1263 results
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Balleza E, Alvarez-Buylla ER, Chaos A, Kauffman S, Shmulevich I, Aldana M.  2008.  Critical dynamics in genetic regulatory networks: examples from four kingdoms. PLoS OnePLoS ONE. 3:e2456.
Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I.  2008.  Critical networks exhibit maximal information diversity in structure-dynamics relationships. Phys Rev Lett. 100:058702.
Chung Y, Chang SH, Martinez GJ, Yang XO, Nurieva R, Kang HS, Ma L, Watowich SS, Jetten AM, Tian Q et al..  2009.  Critical regulation of early Th17 cell differentiation by interleukin-1 signaling. Immunity. 30:576-87.
Torres-Sosa C, Huang S, Aldana M.  2012.  Criticality is an emergent property of genetic networks that exhibit evolvability.. PLoS Comput Biol. 8(9):e1002669.
Chambers MC, Maclean B, Burke R, Amodei D, Ruderman DL, Neumann S, Gatto L, Fischer B, Pratt B, Egertson J et al..  2012.  A cross-platform toolkit for mass spectrometry and proteomics. Nature biotechnology. 30:918-20.
Yang T, Espenshade PJ, Wright ME, Yabe D, Gong Y, Aebersold R, Goldstein JL, Brown MS.  2002.  Crucial step in cholesterol homeostasis: sterols promote binding of SCAP to INSIG-1, a membrane protein that facilitates retention of SREBPs in ER. Cell. 110:489-500.
Kemp CJ, Moore J.M, Moser R., Bernard B, Teater M., Smith L.E, Rabaia N.A, Gurley K.E, Guinney J., Busch S.E et al..  2014.  CTCF Haploinsufficiency Destabilizes DNA Methylation and Predisposes to Cancer. Cell reports.
Kemp CJ, Moore JM, Moser R, Bernard B, Teater M, Smith LE, Rabaia NA, Gurley KE, Guinney J, Busch SE et al..  2014.  CTCF haploinsufficiency destabilizes DNA methylation and predisposes to cancer.. Cell Rep. 7(4):1020-9.
Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish J, Krumm A.  2008.  CTCF physically links cohesin to chromatin. Proc Natl Acad Sci U S A. 105:8309-14.
Hoopmann MR, Moritz RL.  2012.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Current opinion in biotechnology.
Hoopmann MR, Moritz RL.  2013.  Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol. 24:31-8.
Liu X, Alexiou M, Martin-Orozco N, Chung Y, Nurieva RI, Ma L, Tian Q, Kollias G, Lu S, Graf D et al..  2009.  Cutting edge: A critical role of B and T lymphocyte attenuator in peripheral T cell tolerance induction. J Immunol. 182:4516-20.
Bochud PY, Hawn TR, Aderem A.  2003.  Cutting edge: a Toll-like receptor 2 polymorphism that is associated with lepromatous leprosy is unable to mediate mycobacterial signaling. J Immunol. 170:3451-4.
Warren SE, Armstrong A, Hamilton MK, Mao DP, Leaf IA, Miao EA, Aderem A.  2010.  Cutting edge: Cytosolic bacterial DNA activates the inflammasome via Aim2. J Immunol. 185:818-21.
Hajjar AM, O'Mahony DS, Ozinsky A, Underhill DM, Aderem A, Klebanoff SJ, Wilson CB.  2001.  Cutting edge: functional interactions between toll-like receptor (TLR) 2 and TLR1 or TLR6 in response to phenol-soluble modulin. J Immunol. 166:15-9.
Andersen-Nissen E, Hawn TR, Smith KD, Nachman A, Lampano AE, Uematsu S, Akira S, Aderem A.  2007.  Cutting edge: Tlr5-/- mice are more susceptible to Escherichia coli urinary tract infection. J Immunol. 178:4717-20.
Miao EA, Alpuche-Aranda CM, Dors M, Clark AE, Bader MW, Miller SI, Aderem A.  2006.  Cytoplasmic flagellin activates caspase-1 and secretion of interleukin 1beta via Ipaf. Nat Immunol. 7:569-75.
Killcoyne S, Carter GW, Smith J, Boyle J.  2009.  Cytoscape: a community-based framework for network modeling. Methods Mol Biol. 563:219-39.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.  2003.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-504.
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Deutsch EW, Lam H, Aebersold R.  2008.  Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics. 33:18-25.
Nykter M, Lahdesmaki H, Rust A, Thorsson V, Shmulevich I.  2009.  A data integration framework for prediction of transcription factor targets. Ann N Y Acad Sci. 1158:205-14.
Hwang D, Rust AG, Ramsey S, Smith JJ, Leslie DM, Weston AD, de Atauri P, Aitchison JD, Hood L, Siegel AF et al..  2005.  A data integration methodology for systems biology. Proc Natl Acad Sci U S A. 102:17296-301.
Hwang D, Smith JJ, Leslie DM, Weston AD, Rust AG, Ramsey S, de Atauri P, Siegel AF, Bolouri H, Aitchison JD et al..  2005.  A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A. 102:17302-7.
Picotti P, Lam H, Campbell D, Deutsch EW, Mirzaei H, Ranish J, Domon B, Aebersold R.  2008.  A database of mass spectrometric assays for the yeast proteome. Nat Methods. 5:913-4.
Yan W, Lee H, Deutsch EW, Lazaro CA, Tang W, Chen E, Fausto N, Katze MG, Aebersold R.  2004.  A dataset of human liver proteins identified by protein profiling via isotope-coded affinity tag (ICAT) and tandem mass spectrometry. Mol Cell Proteomics. 3:1039-41.
Gizzatkulov NM, Goryanin II, Metelkin EA, Mogilevskaya EA, Peskov KV, Demin OV.  2010.  DBSolve Optimum: a software package for kinetic modeling which allows dynamic visualization of simulation results. BMC Syst Biol. 4:109.
Hood L.  2001.  Deciphering Heredity. The Alfred Deakin Lectures: Ideas for the Future of a Civil Society. :164-176.
Yazbek SN, Buchner DA, Geisinger JM, Burrage LC, Spiezio SH, Zentner GE, Hsieh CW, Scacheri PC, Croniger CM, Nadeau JH.  2011.  Deep congenic analysis identifies many strong, context-dependent QTLs, one of which, Slc35b4, regulates obesity and glucose homeostasis. Genome Res.
Lin B, White JT, Wu J, Lele S, Old LJ, Hood L, Odunsi K.  2009.  Deep depletion of abundant serum proteins reveals low-abundant proteins as potential biomarkers for human ovarian cancer. Proteomics Clin Appl. 3:853-861.
Andalis AA, Storchova Z, Styles C, Galitski T, Pellman D, Fink GR.  2004.  Defects arising from whole-genome duplications in Saccharomyces cerevisiae. Genetics. 167:1109-21.
Portis JL, Askovich P, Austin J, Gutierrez-Cotto Y, McAtee FJ.  2009.  The degree of folding instability of the envelope protein of a neurovirulent murine retrovirus correlates with the severity of the neurological disease. J Virol. 83:6079-86.
Brewster JL, Martin SL, Toms J, Goss D, Wang K, Zachrone K, Davis A, Carlson G, Hood L, Coffin JD.  2000.  Deletion of Dad1 in mice induces an apoptosis-associated embryonic death. Genesis. 26:271-8.
Romagnoli G, Knijnenburg TA, Liti G, Louis EJ, Pronk JT, Daran J-M.  2014.  Deletion of the Saccharomyces cerevisiae ARO8 gene, encoding an aromatic amino acid transaminase, enhances phenylethanol production from glucose.. Yeast.
Hood L, Price ND.  2014.  Demystifying disease, democratizing health care. Science translational medicine. 6:225ed5.
Stanford JL, Fitzgerald LM, McDonnell SK, Carlson EE, McIntosh LM, Deutsch K, Hood L, Ostrander EA, Schaid DJ.  2009.  Dense genome-wide SNP linkage scan in 301 hereditary prostate cancer families identifies multiple regions with suggestive evidence for linkage. Hum Mol Genet. 18:1839-48.
Fu E, Ramsey SA, Yager P.  2007.  Dependence of the signal amplification potential of colloidal gold nanoparticles on resonance wavelength in surface plasmon resonance-based detection. Anal Chim Acta. 599:118-23.
Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, Galitski T.  2005.  Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol. 6:R38.
Spellman PT, Miller M, Stewart J, Troup C, Sarkans U, Chervitz S, Bernhart D, Sherlock G, Ball C, Lepage M et al..  2002.  Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol. 3:RESEARCH0046.
Bottari P, Aebersold R, Turecek F, Gelb MH.  2004.  Design and synthesis of visible isotope-coded affinity tags for the absolute quantification of specific proteins in complex mixtures. Bioconjug Chem. 15:380-8.
Kutlu B, Burdick D, Baxter D, Rasschaert J, Flamez D, Eizirik DL, Welsh N, Goodman N, Hood L.  2009.  Detailed transcriptome atlas of the pancreatic beta cell. BMC Med Genomics. 2:3.
Craig TA, Zhang Y, Magis AT, Funk CC, Price ND, Ekker SC, Kumar, iv R.  2014.  Detection of 1α,25-dihydroxyvitamin D-regulated miRNAs in zebrafish by whole transcriptome sequencing.. Zebrafish.
Price ND, Papin JA, Palsson BO.  2002.  Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome research. 12:760-9.
Shmulevich I, Aitchison JD.  2009.  Deterministic and stochastic models of genetic regulatory networks. Methods Enzymol. 467:335-56.
Lam H, Deutsch EW, Eddes JS, Eng JK, King N, Stein SE, Aebersold R.  2007.  Development and validation of a spectral library searching method for peptide identification from MS/MS. Proteomics. 7:655-67.
Wang Y, Li X, Milne CB, Janssen H, Lin W, Phan G, Hu H, Jin Y-S, Price ND, Blaschek HP.  2013.  Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii.. Appl Environ Microbiol. 79(19):5853-63.
Lee H, Griffin TJ, Gygi SP, Rist B, Aebersold R.  2002.  Development of a multiplexed microcapillary liquid chromatography system for high-throughput proteome analysis. Anal Chem. 74:4353-60.
Z Chen J, Wang J, Tian L, Lee H-S, Wang JJ, Chen M, Lee JJ, Josefsson C, Madlung A, Watson B et al..  2004.  The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects.. Biol J Linn Soc Lond. 82(4):689-700.
Palsson BO, Price ND, Papin JA.  2003.  Development of network-based pathway definitions: the need to analyze real metabolic networks. Trends in biotechnology. 21:195-8.
Deutsch EW, Ball CA, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen J, Davidson D, Eichner LJ et al..  2006.  Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). OMICS. 10:205-8.
Chan TM, Longabaugh W, Bolouri H, Chen HL, Tseng WF, Chao CH, Jang TH, Lin YI, Hung SC, Wang HD et al..  2009.  Developmental gene regulatory networks in the zebrafish embryo. Biochim Biophys Acta. 1789:279-98.
Wheeler TJ, Clements J, Eddy SR, Hubley R, Jones TA, Jurka J, Smit AF, Finn RD.  2013.  Dfam: a database of repetitive DNA based on profile hidden Markov models. Nucleic acids research. 41:D70-82.
Xu D, Caballero J, Glusman G, Tian Q.  2013.  Diagnostic Perspectives in the Epoch of Next-Generation Sequencing.. Next-Generation Sequencing & Molecular Diagnostics. .
Park IK, He Y, Lin F, Laerum OD, Tian Q, Bumgarner R, Klug CA, Li K, Kuhr C, Doyle MJ et al..  2002.  Differential gene expression profiling of adult murine hematopoietic stem cells. Blood. 99:488-98.
Letarte S, Brusniak MY, Campbell D, Eddes J, Kemp CJ, Lau H, Mueller L, Schmidt A, Shannon P, Kelly-Spratt KS et al..  2008.  Differential Plasma Glycoproteome of p19 Skin Cancer Mouse Model Using the Corra Label-Free LC-MS Proteomics Platform. Clin Proteomics. 4:105.
Lightfield KL, Persson J, Trinidad NJ, Brubaker SW, Kofoed EM, Sauer JD, Dunipace EA, Warren SE, Miao EA, Vance RE.  2011.  Differential requirements for NAIP5 in activation of the NLRC4 inflammasome. Infect Immun. 79:1606-14.
Marr KA, Balajee SA, Hawn TR, Ozinsky A, Pham U, Akira S, Aderem A, Liles WC.  2003.  Differential role of MyD88 in macrophage-mediated responses to opportunistic fungal pathogens. Infect Immun. 71:5280-6.
Goodlett DR, Keller A, Watts J, Newitt R, Yi EC, Purvine S, Eng JK, von Haller P, Aebersold R, Kolker E.  2001.  Differential stable isotope labeling of peptides for quantitation and de novo sequence derivation. Rapid Commun Mass Spectrom. 15:1214-21.
Chen F, Rowen L, Hood L, Rothenberg EV.  2001.  Differential transcriptional regulation of individual TCR V beta segments before gene rearrangement. J Immunol. 166:1771-80.
Liu G, Yang D, Sun Y, Shmulevich I, Xue F, Sood AK, Zhang W.  2012.  Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer. Pharmacogenomics. 13:1523-35.
Hood L, Galas DJ.  2003.  The digital code of DNA. Nature. 421:444-8.
Marotti, L. A. J., Newitt R, Wang Y, Aebersold R, Dohlman HG.  2002.  Direct identification of a G protein ubiquitination site by mass spectrometry. Biochemistry. 41:5067-74.
Geiss GK, Bumgarner RE, Birditt B, Dahl T, Dowidar N, Dunaway DL, Fell HP, Ferree S, George RD, Grogan T et al..  2008.  Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat Biotechnol. 26:317-25.
Kabak S, Skaggs BJ, Gold MR, Affolter M, West KL, Foster MS, Siemasko K, Chan AC, Aebersold R, Clark MR.  2002.  The direct recruitment of BLNK to immunoglobulin alpha couples the B-cell antigen receptor to distal signaling pathways. Mol Cell Biol. 22:2524-35.
Lee HJ, Suk JE, Patrick C, Bae EJ, Cho JH, Rho S, Hwang D, Masliah E, Lee SJ.  2010.  Direct transfer of alpha-synuclein from neuron to astroglia causes inflammatory responses in synucleinopathies. J Biol Chem. 285:9262-72.
Tabb DL, Ma ZQ, Martin DB, Ham AJ, Chambers MC.  2008.  DirecTag: accurate sequence tags from peptide MS/MS through statistical scoring. J Proteome Res. 7:3838-46.
Schmidt A, Claassen M, Aebersold R.  2009.  Directed mass spectrometry: towards hypothesis-driven proteomics. Curr Opin Chem Biol. 13:510-7.
Shaw S, Bourne T., Meier C., Carrington B., Gelinas R, Henry A., Popplewell A., Adams R., Baker T., Rapecki S. et al..  2014.  Discovery and characterization of olokizumab: A humanized antibody targeting interleukin-6 and neutralizing gp130-signaling. mAbs. 6:773-81.
Yoo C, Thorsson V, Cooper GF.  2002.  Discovery of causal relationships in a gene-regulation pathway from a mixture of experimental and observational DNA microarray data. Pac Symp Biocomput. :498-509.
Ideker TE, Thorsson V, Karp RM.  2000.  Discovery of regulatory interactions through perturbation: inference and experimental design. Pac Symp Biocomput. :305-16.
del Sol A, Balling R, Hood L, Galas DJ.  2010.  Diseases as network perturbations. Curr Opin Biotechnol. 21:566-71.
Carter GW, Rupp S, Fink GR, Galitski T.  2006.  Disentangling information flow in the Ras-cAMP signaling network. Genome Res. 16:520-6.
Park H, Li Z, Yang XO, Chang SH, Nurieva R, Wang YH, Wang Y, Hood L, Zhu Z, Tian Q et al..  2005.  A distinct lineage of CD4 T cells regulates tissue inflammation by producing interleukin 17. Nat Immunol. 6:1133-41.
McBride CM, Pollak KI, Garst J, Keefe F, Lyna P, Fish L, Hood L.  2003.  Distress and motivation for smoking cessation among lung cancer patients' relatives who smoke. J Cancer Educ. 18:150-6.
Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS.  2009.  Diurnally entrained anticipatory behavior in archaea. PLoS ONEPLoS ONE. 4:e5485.
Ramsey S, Orrell D, Bolouri H.  2005.  Dizzy: stochastic simulation of large-scale genetic regulatory networks (supplementary material). J Bioinform Comput Biol. 3:437-54.
Foltz G, Yoon JG, Lee H, Ryken TC, Sibenaller Z, Ehrich M, Hood L, Madan A.  2009.  DNA methyltransferase-mediated transcriptional silencing in malignant glioma: a combined whole-genome microarray and promoter array analysis. Oncogene. 28:2667-77.
Heilig R, Eckenberg R, Petit JL, Fonknechten N, Da Silva C, Cattolico L, Levy M, Barbe V, de Berardinis V, Ureta-Vidal A et al..  2003.  The DNA sequence and analysis of human chromosome 14. Nature. 421:601-7.
Deriemer K, Garcia-Garcia L, Bobadilla-del-Valle M, Palacios-Martinez M, Martinez-Gamboa A, Small PM, Sifuentes-Osornio J, Ponce-de-Leon A.  2005.  Does DOTS work in populations with drug-resistant tuberculosis? Lancet. 365:1239-45.
de Jong BC, Onipede A, Pym AS, Gagneux S, Aga RS, Deriemer K, Small PM.  2005.  Does resistance to pyrazinamide accurately indicate the presence of Mycobacterium bovis? J Clin Microbiol. 43:3530-2.
Moore RC, Mastrangelo P, Bouzamondo E, Heinrich C, Legname G, Prusiner SB, Hood L, Westaway D, Dearmond SJ, Tremblay P.  2001.  Doppel-induced cerebellar degeneration in transgenic mice. Proc Natl Acad Sci U S A. 98:15288-93.
Westaway D, Genovesi S, Daude N, Brown R, Lau A, Lee I, Mays CE, Coomaraswamy J, Canine B, Pitstick R et al..  2011.  Down-regulation of Shadoo in prion infections traces a pre-clinical event inversely related to PrP(Sc) accumulation. PLoS pathogens. 7:e1002391.
Loevenich SN, Brunner E, King NL, Deutsch EW, Stein SE, FlyBase C, Aebersold R, Hafen E.  2009.  The Drosophila melanogaster PeptideAtlas facilitates the use of peptide data for improved fly proteomics and genome annotation. BMC Bioinformatics. 10:59.
Ramsey SA, Smith JJ, Orrell D, Marelli M, Petersen TW, de Atauri P, Bolouri H, Aitchison JD.  2006.  Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet. 38:1082-7.
Chaturvedi CP, Hosey AM, Palii C, Perez-Iratxeta C, Nakatani Y, Ranish J, Dilworth FJ, Brand M.  2009.  Dual role for the methyltransferase G9a in the maintenance of beta-globin gene transcription in adult erythroid cells. Proc Natl Acad Sci U S A. 106:18303-8.
Taylor RJ, Falconnet D, Niemisto A, Ramsey SA, Prinz S, Shmulevich I, Galitski T, Hansen CL.  2009.  Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform. Proc Natl Acad Sci U S A. 106:3758-63.
Jung S, Marelli M, Rachubinski RA, Goodlett DR, Aitchison JD.  2010.  Dynamic changes in the subcellular distribution of Gpd1p in response to cell stress. J Biol Chem. 285:6739-49.
Brand M, Ranish J, Kummer NT, Hamilton J, Igarashi K, Francastel C, Chi TH, Crabtree GR, Aebersold R, Groudine M.  2004.  Dynamic changes in transcription factor complexes during erythroid differentiation revealed by quantitative proteomics. Nat Struct Mol Biol. 11:73-80.
Nesvizhskii AI, Roos FF, Grossmann J, Vogelzang M, Eddes JS, Gruissem W, Baginsky S, Aebersold R.  2006.  Dynamic spectrum quality assessment and iterative computational analysis of shotgun proteomic data: toward more efficient identification of post-translational modifications, sequence polymorphisms, and novel peptides. Mol Cell Proteomics. 5:652-70.
Marelli M, Dilworth DJ, Wozniak RW, Aitchison JD.  2001.  The dynamics of karyopherin-mediated nuclear transport. Biochem Cell Biol. 79:603-12.
Vizeacoumar FJ, Vreden WN, Fagarasanu M, Eitzen GA, Aitchison JD, Rachubinski RA.  2006.  The dynamin-like protein Vps1p of the yeast Saccharomyces cerevisiae associates with peroxisomes in a Pex19p-dependent manner. J Biol Chem. 281:12817-23.
Majeti R, Becker MW, Tian Q, Lee TL, Yan X, Liu R, Chiang JH, Hood L, Clarke MF, Weissman IL.  2009.  Dysregulated gene expression networks in human acute myelogenous leukemia stem cells. Proc Natl Acad Sci U S A. 106:3396-401.
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Auffray C, Hood L.  2012.  Editorial: Systems biology and personalized medicine - the future is now.. Biotechnol J. 7(8):938-9.
Price ND, Lee S.Y.  2010.  Editorial: Systems biology for biotech applications. Biotechnology journal. 5:636-7.
Costa KC, Yoon SH, Pan M, Burn JA, Baliga NS, Leigh JA.  2013.  Effects of H2 and formate on growth yield and regulation of methanogenesis in Methanococcus maripaludis. Journal of bacteriology.
Han MH, Han DK, Aebersold R, Glomset JA.  2001.  Effects of protein kinase CK2, extracellular signal-regulated kinase 2, and protein phosphatase 2A on a phosphatidic acid-preferring phospholipase A1. J Biol Chem. 276:27698-708.
Zhu X-M, Yin L, Hood L, Galas DJ, Ao P.  2007.  Efficiency, Robustness, and Stochasticity of Gene Regulatory Networks in Systems Biology: λ Switch as a Working Example. Introduction to Systems Biology. :336-371.
Powell S., Forslund K., Szklarczyk D., Trachana K., Roth A., Huerta-Cepas J., Gabaldon T., Rattei T., Creevey C., Kuhn M. et al..  2014.  eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic acids research. 42:D231-9.
Bunimovich YL, Ge G, Beverly KC, Ries RS, Hood L, Heath JR.  2004.  Electrochemically programmed, spatially selective biofunctionalization of silicon wires. Langmuir. 20:10630-8.
Domon B, Bodenmiller B, Carapito C, Hao Z, Huehmer A, Aebersold R.  2009.  Electron transfer dissociation in conjunction with collision activation to investigate the Drosophila melanogaster phosphoproteome. J Proteome Res. 8:2633-9.
Chung TW, Moss CL, Zimnicka M, Johnson RS, Moritz RL, Turecek F.  2011.  Electron-capture and -transfer dissociation of peptides tagged with tunable fixed-charge groups: structures and dissociation energetics. J Am Soc Mass Spectrom. 22:13-30.

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