2010 Publications –
  1. Akiyoshi B, Nelson CR, Ranish JA, Biggins S (2009). Analysis of Ipl1-mediated phosphorylation of the Ndc80 kinetochore protein in Saccharomyces cerevisiae. Genetics. 183(4):1591-5. PMID: 19822728; PMCID: PMC2787442.
  2. 2. Akiyoshi B, Nelson CR, Ranish JA, Biggins S (2009). Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit. Genes Dev. 23(24):2887-99. PMID: 19948764; PMCID: PMC2800092.
  3. Boyle J, Rovira H, Cavnor C, Burdick D, Killcoyne S, Shmulevich I (2009). Adaptable data management for systems biology investigations. BMC Bioinformatics. 10:79. PMID: 19265554.
  4. Carter GW, Galas DJ, Galitski T (2009). Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol. 5(4):e1000347. PMID: 19343223.
  5. Diercks A, Kostner H, Ozinsky A (2009). Resolving cell population heterogeneity: real-time PCR for simultaneous multiplexed gene detection in multiple single-cell samples. PLoS One. 4(7):e6326. PMID: 19633712.
  6. Diercks AH, Ozinsky A, Hansen CL, Spotts JM, Rodriguez DJ, Aderem A (2009). A microfluidic device for multiplexed protein detection in nano-liter volumes. Anal Biochem. 386(1):30-5. PMID: 19133224.
  7. Ghosh D, Yan X, Tian Q (2009). Gene regulatory networks in embryonic stem cells and brain development. Birth Defects Res C Embryo Today, 87(2):182-91.
  8. Hohmann L, Sherwood C, Eastham A, Peterson A, Eng JK, Eddes JS, Shteynberg D, Martin DB (2009). Proteomic analyses using Grifola frondosa metalloendoprotease Lys-N. J Proteome Res. 8(3):1415-22. PMID: 19195997.
  9. Huang AC, Hu L, Kauffman SA, Zhang W, Shmulevich I (2009). Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst Biol. 18;3:20. PMCID: 2652435.
  10. Hwang D, Lee IY, Yoo H, Gehlenborg N, Cho JH, Petritis B, Baxter D, Pitstick R, Young R, Spicer D, Price ND, Hohmann JG, Dearmond SJ, Carlson GA, Hood LE (2009). A systems approach to prion disease. Mol Syst Biol. 5:252. PubMed PMID: 19530135.
  11. Killcoyne S, Boyle J (2009). Managing Chaos: Lessons Learned Developing Software in the Life Sciences. Comput Sci Eng. 11(6):20-29. PMID: 20700479; PMCID: PMC2917833.
  12. Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I (2009). Fewer permutations, more accurate P-values. Bioinformatics. 25(12):i161-8. PMID: 19477983.
  13. Koide T, Pang WL, Baliga NS (2009). The role of predictive modeling in rationally re-engineering biological systems. Nat Rev Microbiol. 7(4):297-305. PMID: 19252506.
  14. Koide T, Reiss DJ, Bare JC, Pang WL, Facciotti MT, Schmid AK, Pan M, Marzolf B, Van PT, Lo FY, Pratap A, Deutsch EW, Peterson A, Martin D, Baliga NS (2009). Prevalence of transcription promoters within archaeal operons and coding sequences. Mol Syst Biol. 5:285. PMID: 19536208.
  15. Lin B, Wang J, Hong X, Yan X, Hwang D, Cho JH, Yi D, Utleg AG, Fang X, Schones DE, Zhao K, Omenn GS, Hood L (2009). Integrated expression profiling and ChIP-seq analyses of the growth inhibition response program of the androgen receptor. PLoS One. 4(8):e6589. PMID: 19668381.
  16. Liu Y, Warfield L, Zhang C, Luo J, Allen J, Lang WH, Ranish J, Shokat KM, Hahn S (2009). Phosphorylation of the transcription elongation factor Spt5 by yeast Bur1 kinase stimulates recruitment of the PAF complex. Mol Cell Biol. 29(17):4852-63. PMID: 19581288; PMCID: 2725703.
  17. Nykter M, Lähdesmäki 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. PMID: 19348642.
  18. Pan S, Cheng L, White JT, Lu W, Utleg AG, Yan X, Urban ND, Drescher CW, Hood L, Lin B (2009). Quantitative proteomics analysis integrated with microarray data reveals that extracellular matrix proteins, catenins, and p53 binding protein 1 are important for chemotherapy response in ovarian cancers. OMICS. 13(4):345-54. PMID: 19422301.
  19. Pascal LE, Goo YA, Vêncio RZ, Page LS, Chambers AA, Liebeskind ES, Takayama TK, True LD, Liu AY (2009). Gene expression down-regulation in CD90+ prostate tumor-associated stromal cells involves potential organ-specific genes. BMC Cancer. 9:317. PMID: 19737398; PMCID: PMC2745432.
  20. Pascal LE, Vêncio RZ, Goo YA, Page LS, Shadle CP, Liu AY (2009). Temporal expression profiling of the effects of secreted factors from prostate stromal cells on embryonal carcinoma stem cells. Prostate. 69(12):1353-65. PMID: 19455603.
  21. Peterson A, Hohmann L, Huang L, Kim B, Eng JK, Martin DB (2009). Analysis of RP-HPLC loading conditions for maximizing peptide identifications in shotgun proteomics. J Proteome Res. 8(8):4161-8. PMID: 19601632.
  22. Saleem RA, Aitchison JD. Quantitative phosphoproteomics in fatty acid stimulated Saccharomyces cerevisiae (2009). J Vis Exp. 12;(32). PMID: 19823167, PMC – In Progress.
  23. Schmid AK, Reiss DJ, Pan M, Koide T, Baliga NS (2009). A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability. Mol Syst Biol. 5:282. PMID: 19536205.
  24. Shmulevich I, Aitchison JD. Deterministic and stochastic models of genetic regulatory networks (2009). Methods Enzymol. 467:335-56. PMID: 19897099, PMC – In Progress.
  25. Selinummi J, Ruusuvuori P, Podolsky I, Ozinsky A, Gold E, Yli-Harja O, Aderem A, Shmulevich I (2009). Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images. PLoS One 22;4(10):e7497. PMCID: 2760782.
  26. Sherwood CA, Eastham A, Lee LW, Peterson A, Eng JK, Shteynberg D, Mendoza L, Deutsch EW, Risler J, Tasman N, Aebersold R, Lam H, Martin DB (2009). MaRiMba: a software application for spectral library-based MRM transition list assembly. J Proteome Res. 8(10):4396-405. PMID: 19603829.
  27. Sherwood CA, Eastham A, Lee LW, Risler J, Vitek O, Martin DB (2009). Correlation between y-type ions observed in ion trap and triple quadrupole mass spectrometers. J Proteome Res. 8(9):4243-51. PMID: 19603825.
  28. Sherwood CA, Eastham A, Lee LW, Risler J, Mirzaei H, Falkner JA, Martin DB (2009). Rapid optimization of MRM-MS instrument parameters by subtle alteration of precursor and product m/z targets. J Proteome Res. 8(7):3746-51. PMID: 19405522.
  29. 26. Smith JJ, Aitchison JD (2009). Regulation of peroxisome dynamics. Curr Opin Cell Biol.:119-26. Review. PMID: 19188056; PMCID: PMC2681484.
  30. Taylor RJ, Falconnet D, Niemistö 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(10):3758-63. PMID: 19223588.
  31. Tu LC, Foltz G, Lin E, Hood L, Tian Q (2009). Targeting stem cells-clinical implications for cancer therapy. Curr Stem Cell Res Ther. 4(2):147-53. PMID: 19442199.
  32. Wan Y, Saleem RA, Ratushny AV, Roda O, Smith JJ, Lin CH, Chiang JH, Aitchison JD (2009). Role of the histone variant H2A.Z/Htz1p in TBP recruitment, chromatin dynamics, and regulated expression of oleate-responsive genes. Mol Cell Biol. 29(9):2346-58. PMID: 19273605.
  33. Wang K, Zhang S, Marzolf B, Troisch P, Brightman A, Hu Z, Hood LE, Galas DJ (2009). Circulating microRNAs, potential biomarkers for drug-induced liver injury. Proc Natl Acad Sci U S A.106(11):4402-7. PMID: 19246379.
  34. Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS (2009). Diurnally entrained anticipatory behavior in archaea. PLoS One. 4(5):e5485. PMID: 19424498.