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Center for Systems Biology Publications

2008 | 2007 | 2006


The following publications reference the Center for Systems Biology. Center publications are updated at the end of each quarter: March, June, September, and December.

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 2008. The following publications reference the P50GMO76547/Center for Systems Biology
  1. M Korb, AG Rust, V Thorsson, C Battail, B Li, D Hwang, K Kennedy, JC Roach, CM Rosenberger, M Gilchrist, D Zak, C Johnson, B Marzolf, A Aderem, I Shmulevich, H Bolouri, The Innate Immune Database (IIDB), BMC Immunology, Vol. 9, No. 7, 2008.
  2. H Lähdesmäki, AG Rust, I Shmulevich, Probabilistic inference of transcription factor binding from multiple data sources, PLoS ONE, Vol. 3, No. 3, e1820, 2008.
  3. R Li, Y Guo, B Ming Han, X Yan, AG Utleg, W Li, L Chun Tu, J Wang, LE Hood, S Xia, B Lin. Proteomics cataloguing analysis of human expressed prostatic secretions reveals rich source of biomarker candidates. Proteomics-Clinical Applications. Volume 2, Issue 4 , Pages 543 – 555. Epub Mar 7, 2008.
  4. 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, March 1, 2008. doi: 10.1158/1078-0432.CCR-07-1535.
  5. M Nykter, ND Price, M Aldana, SA Ramsey, SA Kauffman, LE Hood, O Yli-Harja, I Shmulevich, Gene Expression Dynamics in the Macrophage Exhibit Criticality, Proceedings of the National Academy of Sciences of the USA, Vol. 105, No. 6, pp. 1897-1900, 2008.
  6. M. Nykter, N. D. Price, A. Larjo, T. Aho, S. A. Kauffman, O. Yli-Harja, I. Shmulevich, Critical networks exhibit maximal information diversity in structure-dynamics relationships, Physical Review Letters, Vol. 100, 058702, 2008.
  7. RA Saleem , B Knoblach , FD Mast , JJ Smith , J Boyle , CM Dobson , R Long-O ’ Donnell , RA Rachubinski , and JD Aitchison. Genome-wide analysis of signaling networks regulating fatty acid- induced gene expression and organelle biogenesis. The Journal of Cell Biology, April 2008. In press.
  8. SA Ramsey, SL Klemm, DE Zak, KA Kennedy, V Thorsson, B Li, M Gilchrist, E Gold, CD Johnson, V Litvak, G Navarro, JC Roach, CM Rosenberger, AG Rust, N Yudkovsky, A Aderem, I Shmulevich, Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics, PLoS Computational Biology, Vol. 4, No. 3, e1000021, 2008.

 2007. The following publications reference the P50GMO76547/Center for Systems Biology
  1. Bare JC, Shannon P, Schmid A, Baliga NS. The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics. 2007 Nov 19; 8(1), 456. PMID: 18021453.
  2. Bong K, Nesvizhskii AI, Rani PG, Hahn S, Aebersold R, Ranish, JA. The transcription elongation factor TFIIS is a component of RNA polymerase II preinitiation complexes. (2007). PNAS 41(104): 16068-73.
  3. Bonneau R, Facciotti MT, Reiss DJ, Schmid AK, Pan M, Kaur A, Thorsson T, Shannon P, Johnson MH, Bare CJ, Longabaugh W, Vuthoori M, Whitehead K, Madar A, Suzuki L, Mori T, Chang DE, DiRuggiero J, Johnson CH, Hood L, Baliga NS. A predictive model for transcriptional control of physiology in a free living cell. Cell. 2007 Dec 28; 131 (7): 1354-65. PMID: 18160043.
  4. Carter GW, Prinz S, Neou C, Shelby JP, Marzolf B, Thorsson V, Galitski T. (2007). Prediction of phenotype and gene expression for combinations of mutations. Mol. Syst. Biol. 3:96.
  5. Carter GW, Thorsson V, Galitski T. (2007). Integrated network modeling of molecular and genetic interactions. In, Sourcebook of Models for Biomedical Research, (ed. M Conn, Humana). Book chapter.
  6. Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS. General transcription factor specified global gene regulation in archaea. Proc Natl Acad Sci U S A. 2007; 104(11): 4630-4635. PMID: 17360575.
  7. P. Krawitz, I. Shmulevich, Basin Entropy in Boolean Network Ensembles, Physical Review Letters, Vol. 98, No. 15, pp. 158701(1-4), 2007.
  8. P. Krawitz, I. Shmulevich, Entropy of complex relevant components in Boolean networks, Physical Review E, Vol. 76, 036115, 2007.
  9. Makhnevych, T., Ptak, C., Lusk, C. P., Aitchison, J. D., Wozniak, R. W. (2007). The role of karyopherins in the regulated sumoylation of septins. J Cell Biol 177, 39-49.
  10. A. Niemisto, T. Korpelainen, R. Saleem, O. Yli-Harja, J. Aitchison, I. Shmulevich, A K-Means Segmentation Method for Finding 2-D Object Areas Based on 3-D Image Stacks Obtained by Confocal Microscopy, 29th International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France, August 23-26, 2007.
  11. Oeffinger, M, Wei, KE, Rogers, R, Degrasse, JA, Chait, BT, Aitchison, JD, Rout, MP. (2007). Comprehensive analysis of diverse ribonucleoprotein complexes. Nat Methods 4, 951-956.
  12. N. D. Price, J. Trent, A. K. El-Naggar, D. Cogdell, E. Taylor, K. K. Hunt, R. E. Pollock, L. Hood, I. Shmulevich, W. Zhang, Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas, Proceedings of the National Academy of Sciences of the USA, Vol. 104, No. 9, pp- 3414-3419, 2007.
  13. Prinz S, Aldridge C, Ramsey SA, Taylor RJ, Galitski T. (2007). Control of Signaling in a MAP-kinase Pathway by an RNA-Binding Protein. PLoS ONE 2:e249.
  14. Reiss DJ, Facciotti MT, Baliga NS. Model-based deconvolution of genome-wide DNA binding. Bioinformatics. 2008 Feb1: 24(3):396-403. PMID: 18056063.
  15. Schmid AK, Reiss DJ, Kaur A, Pan M, King N, Van PT, Hohmann L, Martin DB, Baliga NS. The anatomy of microbial cell state transitions in response to oxygen. Genome Research. 2007 Oct; 17(10): 1399-413. Epub 2007 Sep 4. PMID: 17785531.
  16. J. Selinummi, A. Niemistö, R. Saleem, G. W. Carter, J. Aitchison, O. Yli-Harja, I. Shmulevich, and J. Boyle, A Case Study on 3-D Reconstruction and Shape Description of Peroxisomes in Yeast, IEEE International Conference on Signal Processing and Communication (ICSPC07), Dubai, United Arab Emirates (UAE), November 24-27, 2007.
  17. Smith, J. J., Ramsey, S. A., Marelli, M., Marzolf, B., Hwang, D., Saleem, R. A., Rachubinski, R. A., Aitchison, J. D. (2007). Transcriptional responses to fatty acid are coordinated by combinatorial control. Mol Syst Biol 3, 115.
  18. Sun B, Ranish J.A., Utleg A.G., White J.T., Yan X., Lin B, Hood L.E. (2007). Shotgun Glycopeptide-Capture Approach Coupled With Mass Spectrometry for Comprehensive Glycoproteomics. Molecular Cellular Proteomics 6:141-149.
  19. Taylor RJ, Siegel AF, Galitski T. (2007). Network motif analysis of multi-mode genetic-interaction networks. Genome Biology 2007 8:R160.
  20. Tu L.C., Yan X., Hood L.E., Lin B. (2007). Proteomic analysis of the interactome of N-myc downstream regulated gene 1 and its interaction with the androgen program in prostrate cancer cells. Mol Cell Proteomics, 6(4): 575-588. Epub 2007.
  21. R. Vencio, I. Shmulevich, ProbCD: enrichment analysis accounting for categorization uncertainty, BMC Bioinformatics, Vol 8, No. 383, 2007.
  22. R. Vêncio, L. Varuzza, C. Pereira, H. Brentani, I. Shmulevich, Simcluster: clustering enumeration gene expression data on the simplex space, BMC Bioinformatics, Vol. 8, No. 246, 2007.


 2006. The following publications reference the P50GMO76547/Center for Systems Biology
  1. Ramsey, S. A., Smith, J. J., Orrell, D., Marelli, M., Petersen, T. W., de Atauri, P., Bolouri, H., Aitchison, J. D. (2006). Dual feedback loops in the GAL regulon suppress cellular heterogeneity in yeast. Nat Genet 38, 1082-1087. Full text pdf provided in Addenda.
  2. Saleem, R. A., Smith, J. J., Aitchison, J. D. (2006). Proteomics of the peroxisome. Biochim Biophys Acta 1763, 1541-1551. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1858641
  3. Taverna, S. D., Ilin, S., Rogers, R. S., Tanny, J. C., Lavender, H., Li, H., Baker, L., Boyle, J., Blair, L. P., Chait, B. T., Patel, D. J., Aitchison, J. D., Tackett, A. J., Allis, C. D. (2006). Yng1 PHD finger binding to H3 trimethylated at K4 promotes NuA3 HAT activity at K14 of H3 and transcription at a subset of targeted ORFs. Mol Cell 24, 785-796. http://www.rockefeller.edu/labheads/chait/pdf/06/06_taverna_mol-cell.pdf
  4. Whitehead K., Kish A., Pan M., Kaur A., Reiss D.J., King N., Hohmann L., DiRuggiero J., Baliga N. (2006). An integrated systems approach for understanding cellular responses to gamma radiation. Mol Syst Biol, 2, 47. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1681521

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