2013 Publications –
  1. Aitchison JD, Rout MP (2012). The yeast nuclear pore complex and transport through it. Genetics. PMID: 22419078; PMCID: PMC3296253.
  2. Ashworth J, Wurtmann EJ, Baliga NS (2012). Reverse engineering systems models of regulation: discovery, prediction and mechanisms. Curr Opin Biotechnol. PMID: 22209016; PMCID: PMC3477774.
  3. Austin RJ, Smidansky HM, Holstein CA, Chang DK, Epp A, Josephson NC, Martin DB (2012). Proteomic analysis of the androgen receptor via MS-compatible purification of biotinylated protein on streptavidin resin. Proteomics. PMID: 22116683; PMCID: PMC3544294.
  4. Bislev SL, Kusebauch U, Codrea MC, Beynon RJ, Harman VM, Røntved CM, Aebersold R, Moritz RL, Bendixen E (2012). Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus uberis. J Proteome Res. PMID: 22256911; PMCID: PMC3342530.
  5. Boyle J, Kreisberg R, Bressler R, Killcoyne S (2012). Methods for visual mining of genomic and proteomic data atlases. BMC Bioinformatics. PMID: 22524279; PMCID: PMC3352268.
  6. Brusniak MY, Chu CS, Kusebauch U, Sartain MJ, Watts JD, Moritz RL (2012). An assessment of current bioinformatic solutions for analyzing LC-MS data acquired by selected reaction monitoring technology. Proteomics.  PMID: 22577019; PMC – In Process.
  7. Carter GW, Hays M, Sherman A, Galitski T (2012). Use of pleiotropy to model genetic interactions in a population. PLoS Genet.  PMID: 23071457; PMCID: PMC3469415.
  8. Chen LY, Wei KC, Huang AC, Wang K, Huang CY, Yi D, Tang CY, Galas DJ, Hood LE (2011). RNASEQR–a streamlined and accurate RNA-seq sequence analysis program. Nucleic Acids Res. PMID: 22199257; PMCID: PMC3315322.
  9. Deutsch EW (2012). File formats commonly used in mass spectrometry proteomics. Mol Cell Proteomics. PMID: 22956731; PMCID: PMC3518119.
  10. DuBois KN, Alsford S, Holden JM, Buisson J, Swiderski M, Bart JM, Ratushny AV, Wan Y, Bastin P, Barry JD, Navarro M, Horn D, Aitchison JD, Rout MP, Field MC (2012). NUP-1 Is a Large Coiled-Coil Nucleoskeletal Protein in Trypanosomes with Lamina-Like Functions. PLOS Biology. PMID: 22479148; PMCID: PMC3313915.
  11. Edgar RS, Green EW, Zhao Y, van Ooijen G, Olmedo M, Qin X, Xu Y, Pan M, Valekunja UK, Feeney KA, Maywood ES, Hastings MH, Baliga NS, Merrow M, Millar AJ, Johnson CH, Kyriacou CP, O’Neill JS, Reddy AB (2012). Peroxiredoxins are conserved markers of circadian rhythms. Nature.  PMID: 22622569; PMCID: PMC3398137.
  12. Hood L, Balling R, Auffray C (2012). Revolutionizing medicine in the 21st century through systems approaches. Biotechnol J. PMID: 22815171; PMC – In Process.
  13. Hood L, Tian Q (2012). Systems approaches to biology and disease enable translational systems medicine. Genomics Proteomics Bioinformatics. PMID: 23084773; PMC – In Process.
  14. Jones AR, Eisenacher M, Mayer G, Kohlbacher O, Siepen J, Hubbard SJ, Selley JN, Searle BC, Shofstahl J, Seymour SL, Julian R, Binz PA, Deutsch EW, Hermjakob H, Reisinger F, Griss J, Vizcaíno JA, Chambers M, Pizarro A, Creasy D (2012). The mzIdentML data standard for mass spectrometry-based proteomics results. Mol Cell Proteomics. PMID: 22375074; PMCID: PMC3394945.
  15. Lewis S, Csordas A, Killcoyne S, Hermjakob H, Hoopmann MR, Moritz RL, Deutsch EW, Boyle J (2012). Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework. BMC Bioinformatics. PMID: 23216909; PMCID: PMC3538679.
  16. London N, Ceto S, Ranish JA, Biggins S (2012). Phosphoregulation of Spc105 by Mps1 and PP1 regulates Bub1 localization to kinetochores. Curr Biol. PMID: 22521787; PMC – In Process.
  17. Luo J, Fishburn J, Hahn S, Ranish J (2012). An Integrated Chemical Cross-linking and Mass Spectrometry Approach to Study Protein Complex Architecture and Function. Mol Cell Proteomics. PMID: 22067100; PMCID: PMC3277749.
  18. Plaisier CL, Pan M, Baliga NS (2012). A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res. PMID: 22745231; PMCID: PMC3483559.
  19. Plaisier CL, Baliga NS (2012). Harnessing the power of human tumor-derived cell lines for the rational design of cancer therapies. Pigment Cell Melanoma Res. PMID: 22781216.
  20. Ratushny AV, Saleem RA, Sitko K, Ramsey SA, Aitchison JD (2012). Asymmetric Positive Feedback Loops Reliably Control Biological Responses. Mol Syst Biol.PMID: 22531117; PMCID: PMC3361002.
  21. Swearingen KE, Moritz RL (2012). High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics. Expert Rev Proteomics. PMID: 23194268; PMC – In Process.
  22. Thompson EG, Galitski T (2012). Quantifying and analyzing the network basis of genetic complexity. PLoS Comput Biol.  PMID: 22792055; PMCID: PMC3390359.