2014 Publications –
  1. Akiyoshi B, Nelson CR, Duggan N, Ceto S, Ranish JA, Biggins S (2013). The Mub1/Ubr2 ubiquitin ligase complex regulates the conserved Dsn1 kinetochore protein. PLoS Genet. PMID: 23408894; PMCID: PMC3567142.
  2. Beer KD, Orellana MV, Baliga NS (2013). Modeling the evolution of C4 photosynthesis. Cell. PMID: 23791172; PMCID: PMC3832052.
  3. Chen WM, Danziger SA, Chiang JH, Aitchison JD (2013). PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. Bioinformatics. PMID: 23832245; PMCID: PMC3777105.
  4. Cromie GA, Hyma KE, Ludlow CL, Garmendia-Torres C, Gilbert TL, May P, Huang AA, Dudley AM, Fay JC (2013). Genomic sequence diversity and population structure of Saccharomyces cerevisiae assessed by RAD-seq. G3 (Bethesda). PMID: 24122055; PMCID: PMC3852379.
  5. Farrah T, Deutsch EW, Hoopmann MR, Hallows JL, Sun Z, Huang CY, Moritz RL (2013). The state of the human proteome in 2012 as viewed through PeptideAtlas. J Proteome Res. PMID: 23215161; PMCID: PMC3928036.
  6. Farrah T, Deutsch EW, Omenn GS, Sun Z, Watts JD, Yamamoto T, Shteynberg D, Harris MM, Moritz RL (2013). State of the human proteome in 2013 as viewed through PeptideAtlas: comparing the kidney, urine, and plasma proteomes for the biology-and disease-driven Human Proteome Project. J Proteome Res. PMID: 24261998; PMCID: PMC3951210.
  7. Jung S, Smith JJ, von Haller PD, Dilworth DJ, Sitko KA, Miller LR, Saleem RA, Goodlett DR, Aitchison JD (2013). Global analysis of condition-specific subcellular protein distribution and abundance. Mol Cell Proteomics. PMID: 23349476; PMCID: PMC3650349.
  8. Heavner BD, Smallbone K, Price ND, Walker LP (2013). Version 6 of the consensus yeast metabolic network refines biochemical coverage and improves model performance. Database (Oxford). PMID: 23935056; PMCID: PMC3739857.
  9. Hood L, Rowen L (2013). The human genome project: big science transforms biology and medicine. Genome Med. PMID: 24040834. “Publisher provided directly to PMC.”
  10. Hoopmann MR, Moritz RL (2013). Current algorithmic solutions for peptide-based proteomics data generation and identification. Curr Opin Biotechnol. PMID: 23142544; PMCID: PMC3857305.
  11. Hüttenhain R, Surinova S, Ossola R, Sun Z, Campbell D, Cerciello F, Schiess R, Bausch-Fluck D, Rosenberger G, Chen J, Rinner O, Kusebauch U, Hajdúch M, Moritz RL, Wollscheid B, Aebersold R (2013). N-glycoprotein SRMAtlas: a resource of mass spectrometric assays for N-glycosites enabling consistent and multiplexed protein quantification for clinical applications. Mol Cell Proteomics. PMID: 23408683; PMCID: PMC3617325.
  12. Lindner SE, Swearingen KE, Harupa A, Vaughan AM, Sinnis P, Moritz RL, Kappe SH (2013). Total and putative surface proteomics of malaria parasite salivary gland sporozoites. Mol Cell Proteomics. PMID: 23325771; PMCID: PMC3650326.
  13. Mayer G, Montecchi-Palazzi L, Ovelleiro D, Jones AR, Binz PA, Deutsch EW, Chambers M, Kallhardt M, Levander F, Shofstahl J, Orchard S, Vizcaíno JA, Hermjakob H, Stephan C, Meyer HE, Eisenacher M; HUPO-PSI Group (2013). The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary. Database (Oxford). PMID: 23482073; PMCID: PMC3594986.
  14. Mercier SK, Donaghy H, Botting RA, Turville SG, Harman AN, Nasr N, Ji H, Kusebauch U, Mendoza L, Shteynberg D, Sandgren K, Simpson RJ, Moritz RL, Cunningham AL (2013). The microvesicle component of HIV-1 inocula modulates dendritic cell infection and maturation and enhances adhesion to and activation of T lymphocytes. PLoS Pathog. PMID: 24204260; PMCID: PMC3798598.
  15. Mirzaei H, Knijnenburg TA, Kim B, Robinson M, Picotti P, Carter GW, Li S, Dilworth DJ, Eng JK, Aitchison JD, Shmulevich I, Galitski T, Aebersold R, Ranish J (2013). Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins. Proc Natl Acad Sci U S A. PMID: 23388641; PMCID: PMC3587231.
  16. Moruz L, Hoopmann MR, Rosenlund M, Granholm V, Moritz RL, Käll L (2013). Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times. J Proteome Res. PMID: 24074221; PMCID: PMC3860378.
  17. Orellana MV, Pang WL, Durand PM, Whitehead K, Baliga NS (2013). A role for programmed cell death in the microbial loop. PLoS One. PMID: 23667496; PMCID: PMC3648572.
  18. Pang WL, Kaur A, Ratushny AV, Cvetkovic A, Kumar S, Pan M, Arkin AP, Aitchison JD, Adams MW, Baliga NS (2013). Metallochaperones regulate intracellular copper levels. PLoS Comput Biol. PMID: 23349626; PMCID: PMC3551603.
  19. Picotti P, Clément-Ziza M, Lam H, Campbell DS, Schmidt A, Deutsch EW, Röst H, Sun Z, Rinner O, Reiter L, Shen Q, Michaelson JJ, Frei A, Alberti S, Kusebauch U, Wollscheid B, Moritz RL, Beyer A, Aebersold R (2013). A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis. Nature. PMID: 23334424; PMCID: PMC3951219.
  20. Shteynberg D, Nesvizhskii AI, Moritz RL, Deutsch EW (2013). Combining results of multiple search engines in proteomics. Mol Cell Proteomics. PMID: 23720762; PMCID: PMC3769318.
  21. Smith JJ, Aitchison JD (2013). Peroxisomes take shape. Nat Rev Mol Cell Biol. PMID: 24263361. PMC Journal – In Process.
  22. Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L (2013). N glycoproteome of E14.Tg2a mouse embryonic stem cells. PLoS One. PMID: 23405203; PMCID: PMC3565968.
  23. Sun B, Utleg AG, Hu Z, Qin S, Keller A, Lorang C, Gray L, Brightman A, Lee D, Alexander VM, Ranish JA, Moritz RL, Hood L (2013). Glycocapture-assisted global quantitative proteomics (gagQP) reveals multiorgan responses in serum toxicoproteome. J Proteome Res. PMID: 23540550. PMC Journal – In Process.
  24. Tauro BJ, Mathias RA, Greening DW, Gopal SK, Ji H, Kapp EA, Coleman BM, Hill AF, Kusebauch U, Hallows JL, Shteynberg D, Moritz RL, Zhu HJ, Simpson RJ (2013). Oncogenic H-ras reprograms Madin-Darby canine kidney (MDCK) cell-derived exosomal proteins following epithelial-mesenchymal transition. Mol Cell Proteomics. PMID: 23645497; PMCID: PMC3734576.
  25. 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. PMID: 23452847; PMCID: PMC3690833.
  26. Wang C, Funk CC, Eddy JA, Price ND (2013). Transcriptional analysis of aggressiveness and heterogeneity across grades of astrocytomas. PLoS One. PMID: 24146911; PMCID: PMC3795736.
  27. Yoon SH, Turkarslan S, Reiss DJ, Pan M, Burn JA, Costa KC, Lie TJ, Slagel J, Moritz RL, Hackett M, Leigh JA, Baliga NS (2013). A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen. Genome Res. PMID: 24089473; PMCID: PMC3814884.