2012 Publications –
  1. Austin RJ, Kuestner RE, Chang DK, Madden KR, Martin DB (2011). SILAC compatible strain of Pichia pastoris for expression of isotopically labeled protein standards and quantitative proteomics. J Proteome Res. PMID: 21942632; PMCID: PMC3361967.
  2. Baumgardner LA, Shanmugam AK, Lam H, Eng JK, Martin DB (2011). Fast parallel tandem mass spectral library searching using GPU hardware acceleration. J Proteome Res. PMID: 21545112; PMCID: PMC3107871.
  3. Brooks AN, Turkarslan S, Beer KD, Lo FY, Baliga NS (2011). Adaptation of cells to new environments. Wiley Interdiscip Rev Syst Biol Med. PMID: 21197660; PMCID: PMC3081528.
  4. Brusniak MY, Kwok ST, Christiansen M, Campbell D, Reiter L, Picotti P, Kusebauch U, Ramos H, Deutsch EW, Chen J, Moritz RL, Aebersold R (2011). ATAQS: A computational software tool for high throughput transition optimization and validation for selected reaction monitoring mass spectrometry. BMC Bioinformatics. PMID: 21414234. Book chapter.
  5. Cho JH, Gelinas R, Wang K, Etheridge A, Piper MG, Batte K, Dakhallah D, Price J, Bornman D, Zhang S, Marsh C, Galas D (2011). Systems biology of interstitial lung diseases: integration of mRNA and microRNA expression changes. BMC Med Genomics. PMID: 21241464; PMCID: PMC3035594.
  6. Farrah T, Deutsch EW, Aebersold R (2011). Using the Human Plasma PeptideAtlas to study human plasma proteins. Methods Mol Biol. PMID: 21468960. Book chapter.
  7. Farrah, T, Deutsch, EW, Omen, GS, Campbell, DS, Sun, Z, Bletz, JA, Mallick, P, Katz, JE, Malmstrom, J, Ossola, R, Watts, JD, Lin, B, Zhang, H, Mortiz, RL, Aebersold, R (2011) A high-confidence human plasma proteome reference set with estimated concentrations in PeptidleAtlas. Mol Cell Proteomics. PMCID: PMC3186192.
  8. Helsens, K, Brusniak, M, Deutsch, E, Moritz, R, Martens, L (2011). jTraML: An open source Java API for TraML, the PSI standard for sharing SRM transitions. J of Proteome Research. PMID: 21967198; PMCID: PMC3208355.
  9. Ideker T, Dutkowski J, Hood L (2011). Boosting signal-to-noise in complex biology: prior knowledge is power. Cell. PMID: 21414478; PMCID: PMC3102020.
  10. Knijnenburg TA, Lin J, Rovira H, Boyle J, Shmulevich I (2011). EPEPT: a web service for enhanced P-value estimation in permutation tests. BMC Bioinformatics. PMID: 22024252; PMCID: PMC3277916.
  11. 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. Mol Syst Biol. PMID: 21952134; PMCID: PMC3202802.
  12. Moussay E, Wang K, Cho JH, van Moer K, Pierson S, Paggetti J, Nazarov PV, Palissot V, Hood LE, Berchem G, Galas DJ (2011). MicroRNA as biomarkers and regulators in B-cell chronic lymphocytic leukemia. Proc Natl Acad Sci. PMID: 21460253; PMCID: PMC3081030.
  13. Nadeau JH, Dudley AM (2011). Genetics. Systems genetics. Science. PubMed PMID: 21350153. Review
  14. Orchard S, Albar JP, Deutsch EW, Eisenacher M, Vizcaíno JA, Hermjakob H (2011). Enabling BioSharing – a report on the Annual Spring Workshop of the HUPO-PSI April 11-13, 2011, EMBL-Heidelberg, Germany. Proteomics. PMID: 22045680. Report..
  15. Panchaud A, Jung S, Shaffer SA, Aitchison JD, Goodlett DR (2011). Faster, quantitative, and accurate precursor acquisition independent from ion count. Anal Chem. PMID: 21341720; PMCID: PMC3217585.
  16. Plaisier CL, Bare JC, Baliga NS (2011). miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profiling. Nucleic Acids Res. PMID: 21602264; PMCID: PMC3125776.
  17. Ratushny AV, Ramsey SA, Aitchison JD (2011). Mathematical modeling of biomolecular network dynamics. Methods Mol Biol. PMID: 21877294. PMC – In Process
  18. Ratushny AV, Shmulevich I, Aitchison JD (2011). Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues. PLoS Comput Biol. PMID: 21738459; PMCID: PMC3127798.
  19. Roach JC, Glusman G, Hubley R, Montsaroff SZ, Holloway AK, Mauldin DE, Srivastava D, Garg V, Pollard KS, Galas DJ, Hood L, Smit AF (2011). Chromosomal haplotypes by genetic phasing of human families. Am J Hum Genet. PMID: 21855840; PMCID: PMC3169815.
  20. Robinson CK, Webb K, Kaur A, Jaruga P, Dizdaroglu M, Baliga NS, Place A, Diruggiero J. (2011). A major role for nonenzymatic antioxidant processes in the radioresistance of Halobacterium salinarum. J Bacteriol. 2011 PMID: 21278285; PMCID: PMC3067647.
  21. Robinson T, Killcoyne S, Bressler R, Boyle J (2011). SAMQA: error classification and validation of high-throughput sequenced read data. BMC Genomics. PMID: 21851633; PMCID: PMC3170309.
  22. Schmid AK, Pan M, Sharma K, Baliga NS (2011). Two transcription factors are necessary for iron homeostasis in a salt-dwelling archaeon. Nucleic Acids Res. PMID: 21109526; PMCID: PMC3074139.
  23. Shteynberg D, Deutsch EW, Lam H, Eng JK, Sun Z, Tasman N, Mendoza L, Moritz RL, Aebersold R, Nesvizhskii AI (2011). iProphet: Multi-level integrative analysis of shotgun proteomic data improves peptide and protein identification rates and error estimates. Mol Cell Proteomics. PMID: 21876204; PMCID: PMC3237071.
  24. Smith JJ, Miller LR, Kreisberg R, Vazquez L, Wan Y, Aitchison JD (2011). Environment-responsive transcription factors bind subtelomeric elements and regulate gene silencing. Mol Syst Biol. PMID: 21206489; PMC3049408.
  25. Smith JJ, Saleem RA, Aitchison JD (2011). Statistical analysis of dynamic transcriptional regulatory network structure. Methods Mol Biol. PMID: 21877289. PMC – In Process.
  26. Swearingen KE, Hoopmann MR, Johnson RS, Saleem RA, Aitchison JD, Moritz RL (2011). Nanospray FAIMS fractionation provides significant increases in proteome coverage of unfractionated complex protein digests. Mol Cell Proteomics. PMID: 22186714. PMC – In Process.
  27. Turkarslan S, Reiss DJ, Gibbins G, Su WL, Pan M, Bare JC, Plaisier CL, Baliga NS (2011). Niche adaptation by expansion and reprogramming of general transcription factors. Mol Syst Biol. PMID: 22108796; PMCID: PMC3261711.
  28. 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. Review. PMID: 21305702; PMCID: PMC3050641.
  29. Yan W, Luo J, Robinson M, Eng J, Aebersold R, Ranish J (2011). Index-ion triggered MS2 ion quantification: a novel proteomics approach for reproducible detection and quantification of targeted proteins in complex mixtures. Mol Cell Proteomics. PMID: 21169564; PMCID: PMC3047164.
  30. Yan X, Ma L, Yi D, Yoon JG, Diercks A, Foltz G, Price ND, Hood LE, Tian Q (2011). A CD133-related gene expression signature identifies an aggressive glioblastoma subtype with excessive mutations. Proc Natl Acad Sci U S A. PMID: 21220328; PMC3029739.