Updated 4/13/16, 1/12/17, 6/26/17, 2/26/18

  1. Craciun FL, Bijol V, Ajay AK, Rao P, Kumar RK, Hutchinson J, Hofmann O, Joshi N, Luyendyk JP, Kusebauch U, Moss CL, Srivastava A, Himmelfarb J, Waikar SS, Moritz RL, Vaidya VS (2016). RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis. J Am Soc Nephrol. PMID: 26449608; PMCID: PMC4884105.
  2. Chevillet JR, Khokhlova TD, Giraldez MD, Schade GR, Starr F, Wang YN, Gallichotte EN, Wang K, Hwang JH, Tewari M (2016). Release of Cell-free MicroRNA Tumor Biomarkers into the Blood Circulation with Pulsed Focused Ultrasound: A Noninvasive, Anatomically Localized, Molecular Liquid Biopsy. Radiology. PMID: 27802108; PMCID: PMC5375625.
  3. Deutsch EW, Csordas A, Sun Z, Jarnuczak A, Perez-Riverol Y, Ternent T, Campbell DS, Bernal-Llinares M, Okuda S, Kawano S, Moritz RL, Carver JJ, Wang M, Ishihama Y, Bandeira N, Hermjakob H, Vizcaíno JA. The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition. Nucleic Acids Res. PMID: 27924013; PMCID: PMC5210636.
  4. Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL (2016). Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics. J Proteome Res. PMID: 27577934; PMCID: PMC5096980.
  5. Gatto L, Hansen KD, Hoopmann MR, Hermjakob H, Kohlbacher O, Beyer A (2016). Testing and Validation of Computational Methods for Mass Spectrometry. J Proteome Res. PMID: 26549429; PMCID: PMC4804830.
  6. Hesselager MO, Codrea MC, Sun Z, Deutsch EW, Bennike TB, Stensballe A, Bundgaard L, Moritz RL, Bendixen E (2016). The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine. Proteomics. PMID: 26699206; PMCID: PMC4786621.
  7. Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian WJ, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk JE, Wong SH, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, Paulovich AG (2016). Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clin Chem. PMID: 26719571; PMCID: PMC4830481.
  8. Hoopmann MR, Mendoza L, Deutsch EW, Shteynberg D, Moritz RL (2016). An Open Data Format for Visualization and Analysis of Cross-Linked Mass Spectrometry Results. J Am Soc Mass Spectrom. PMID: 27469004; PMCID: PMC5061604.
  9. Keller A, Bader SL, Kusebauch U, Shteynberg D, Hood L, Moritz RL (2016). Opening a SWATH Window on Posttranslational Modifications: Automated Pursuit of Modified Peptides. Mol Cell Proteomics. PMID: 26704149; PMCID: PMC4813695.
  10. Kusebauch U, Campbell DS, Deutsch EW, Chu CS, Spicer DA, Brusniak MY, Slagel J, Sun Z, Stevens J, Grimes B, Shteynberg D, Hoopmann MR, Blattmann P, Ratushny AV, Rinner O, Picotti P, Carapito C, Huang CY, Kapousouz M, Lam H, Tran T, Demir E, Aitchison JD, Sander C, Hood L, Aebersold R, Moritz RL (2016). Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome. Cell. PMID: 27453469; PMCID: PMC5245710.
  11. Maixner F, Krause-Kyora B, Turaev D, Herbig A, Hoopmann MR, Hallows JL, Kusebauch U, Vigl EE, Malfertheiner P, Megraud F, O’Sullivan N, Cipollini G, Coia V, Samadelli M, Engstrand L, Linz B, Moritz RL, Grimm R, Krause J, Nebel A, Moodley Y, Rattei T, Zink A (2016). The 5300-year-old Helicobacter pylori genome of the Iceman. Science. PMID: 26744403; PMCID: PMC4775254.
  12. Mast FD, Jamakhandi A, Saleem RA, Dilworth DJ, Rogers RS, Rachubinski RA, Aitchison JD (2016). Peroxins Pex30 and Pex29 Dynamically Associate with Reticulons to Regulate Peroxisome Biogenesis from the Endoplasmic Reticulum. J Biol Chem. PMID: 27129769; PMCID: PMC4957030.
  13. Mojtahedi M, Skupin A, Zhou J, Castaño IG, Leong-Quong RY, Chang H, Trachana K, Giuliani A, Huang S (2017). Cell Fate Decision as High-Dimensional Critical State Transition. PLoS Biol. PMID: 28027308; PMCID: PMC5189937.
  14. McDermott SM, Luo J, Carnes J, Ranish JA, Stuart K (2016). The Architecture of Trypanosoma brucei editosomes. Proc Natl Acad Sci U S A. PMID: 27708162; PMCID: PMC5081628.
  15. Peterson EJ, Ma S, Sherman DR, Baliga NS (2016). Network analysis identifies Rv0324 and Rv0880 as regulators of bedaquiline tolerance in Mycobacterium tuberculosis. Nat Microbiol. PMID: 27573104; PMCID: PMC5010021.
  16. Plaisier CL, O’Brien S, Bernard B, Reynolds S, Simon Z, Toledo CM, Ding Y, Reiss DJ, Paddison PJ, Baliga NS (2016). Causal Mechanistic Regulatory Network for Glioblastoma Deciphered Using Systems Genetics Network Analysis. Cell Syst. PMID: 27426982; PMCID: PMC5001912.
  17. Vialas V, Sun Z, Reales-Calderón JA, Hernáez ML, Casas V, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Moritz RL, Gil C (2016). A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage. J Proteomics. PMID: 26493587; PMCID: PMC4670622.
  18. Warfield L, Luo J, Ranish J, Hahn S (2016). Function of Conserved Topological Regions within the Saccharomyces cerevisiae Basal Transcription Factor TFIIH. Mol Cell Biol. PMID: 27381459; PMCID: PMC5021372.
  19. Winget JM, Finlay D, Mills KJ, Huggins T, Bascom C, Isfort RJ, Moritz RL (2016). Quantitative Proteomic Analysis of Stratum Corneum Dysfunction in Adult Chronic Atopic Dermatitis. J Invest Dermatol. PMID: 27091361; PMCID: PMC5018406.
  20. Xue T, Liu P, Zhou Y, Liu K, Yang L, Moritz RL, Yan W, Xu LX (2016). Interleukin-6 Induced “Acute” Phenotypic Microenvironment Promotes Th1 Anti-Tumor Immunity in Cryo-Thermal Therapy Revealed By Shotgun and Parallel Reaction Monitoring Proteomics. Theranostics. PMID: 27162549; PMCID: PMC4860887.
  21. Zhou JX, Samal A, d’Hérouël AF, Price ND, Huang S (2016). Relative stability of network states in Boolean network models of gene regulation in development. Biosystems. PMID: 26965665; PMCID: PMC5149109.