2009 Publications –
  1. Balleza E, Alvarez-Buylla E, Chaos A, Kauffman SA, Shmulevich I, Aldana M (2008). Critical Dynamics in Genetic Regulatory Networks: Examples from Four Kingdoms, PLoS ONE, Vol. 3, No. 6, e2456.
  2. Boyle J, Cavnor C, Killcoyne S, Shmulevich I (2008). Systems biology driven software design for the research enterprise, BMC Bioinformatics, Vol. 9, No. 295.
  3. Deutsch EW, Lam H, Aebersold R (2008). Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics. Physiol Genomics 33(1):18-25. PMID: 18212004.
  4. Deutsch EW, Lam H, Aebersold R (2008). PeptideAtlas: a resource for target selection for emerging targeted proteomics workflows. EMBO Rep. 9(5):429-34. PMID: 18451766; PMCID: 2373374.
  5. Gradolatto A, Rogers RS, Lavender H, Taverna SD, Allis CD, Aitchison JD, Tackett AJ (2008). Saccharomyces cerevisiae Yta7 Regulates Histone Gene Expression, Genetics. DOI: 10.1534.
  6. Himeda CL, Ranish JA, Hauschka SD (2008). Quantitative proteomic identification of MAZ as a transcriptional regulator of muscle-specific genes in skeletal and cardiac myocytes, Mol. Cell Biol. PMID: 18710939.
  7. Hood LE, Rowen L, Galas DJ, Aitchison JD (2008). Systems Biology and the Institute for Systems Biology, Briefings in Functional Genomics and Proteomics.
  8. Korb M, Rust AG, Thorsson V, Battail C, Li B, Hwang D, Kennedy K, Roach JC, Rosenberger CM, Gilchrist M, Zak D, Johnson C, Marzolf B, Aderem A, Shmulevich I, Bolouri H (2008). The Innate Immune Database (IIDB), BMC Immunology, Vol. 9, No. 7.
  9. Lähdesmäki H, Shmulevich I (2008). Learning the Structure of Dynamic Bayesian Networks from Time Series and Steady State Measurements, Machine Learning, Vol. 71, 185-217.
  10. Lähdesmäki H, Rust AG, Shmulevich I (2008). Probabilistic inference of transcription factor binding from multiple data sources, PLoS ONE, Vol. 3, No. 3, e1820.
  11. Li R, Guo Y, Ming Han B, Yan X, Utleg AG, Li W, Chun Tu L, Wang J, Hood LE, Xia S, Lin B (2008). Proteomics cataloguing analysis of human expressed prostatic secretions reveals rich source of biomarker candidates. Proteomics-Clinical Applications. Volume 2, Issue 4, 543 – 555.
  12. Lin B, Utleg A, Gravdal K, White J, Halvorsen O, Lu W, True L, Vessella R, Lange P, Nelson P, Hood LE, Kalland K, Akslen L (2007). WDR19 expression is increased in prostate cancer compared to normal cells, but low intensity expression in cancers is associated with shorter time to biochemical failures and local recurrence. Clinical Cancer Research 14, 1397-1406.
  13. Liu W, Lähdesmäki H, Dougherty ER, Shmulevich I (2008). Inference of Boolean Networks using Sensitivity Regularization, EURASIP Journal on Bioinformatics and Systems Biology, Vol. 2008, Article ID 780541.
  14. Marelli M, Nesvizhskii AI, Aitchison JD. Identifying bona fide components of an organelle by isotope-coded labeling of subcellular fractions: an example in peroxisomes (2008). Methods Mol Biol. 432:357-71. PMID: 18370030, PMC – Progress.
  15. Martin DB, Holzman T, May D, Peterson A, Eastham A, Eng J, McIntosh M (2008). MRMer, an interactive open source and cross-platform system for data extraction and visualization of multiple reaction monitoring experiments. Mol Cell Proteomics. 7(11):2270-8. PMID: 18641041.
  16. Nykter M, Price ND, Aldana M, Ramsey SA, Kauffman SA, Hood LE, Yli-Harja O, Shmulevich I (2008). Gene Expression Dynamics in the Macrophage Exhibit Criticality, Proceedings of the National Academy of Sciences of the USA, Vol. 105, No. 6, 1897-1900.
  17. Nykter M, Price ND, Larjo A, Aho T, Kauffman SA, Yli-Harja O, Shmulevich I (2008). Critical networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, Vol. 100, 058702.
  18. Pascal LE, True LD, Campbell DS, Deutsch EW, Risk M, Coleman IM, Eichner LJ, Nelson PS, Liu AY (2008). Correlation of mRNA and protein levels: cell type-specific gene expression of cluster designation antigens in the prostate. BMC Genomics. 9:246. PMID: 18501003; PMCID: 2413246.
  19. Saleem RA, Knoblach B, Mast FD, Smith JJ, Boyle J, Dobson CM , Long-O’Donnell R, Rachubinski RA, Aitchison JD (2008). Genome-wide analysis of signaling networks regulating fatty acid- induced gene expression and organelle biogenesis. The Journal of Cell Biology.
  20. Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold E, Johnson CD, Litvak V, Navarro G, Roach JC, Rosenberger CM, Rust AG, Yudkovsky N, Aderem A, Shmulevich I (2008). Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics, PLoS Computational Biology, Vol. 4, No. 3, e1000021.
  21. Ratushny AV, Ramsey SA, Roda O, Wan Y, Smith JJ, Aitchison JD (2008). Control of Transcriptional Variability by Overlapping Feed-Forward Regulatory Motifs, Biophys J. PMID: 18621837.
  22. Reiss DJ, Facciotti MT, Baliga NS (2008). Model-based deconvolution of genome-wide DNA binding. Bioinformatics. 24(3):396-403. PMID: 18056063.
  23. Rubio ED, Reiss DJ, Welcsh PL, Disteche CM, Filippova GN, Baliga NS, Aebersold R, Ranish JA, Krumm A (2008). CTCF physically links cohesin to chromatin, Proc Natl Acad Sci U S A, 105(24):8309-14. PMID: 18550811
  24. Tabb DL, Ma ZQ, Martin DB, Ham AJ L, Chambers MC (2008). DirecTag: Accurate Sequence Tags from Peptide MS/MS through Statistical Scoring, Journal of Proteome Research.
  25. Van PT, Schmid AK, King NL, Kaur A, Pan M, Whitehead K, Koide T, Facciotti MT, Goo YA, Deutsch EW, Reiss DJ, Mallick P, Baliga NS (2008). Halobacterium salinarum NRC-1 Peptide Atlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage. J Proteome Res.