Institute for Systems Biology  CSB Home
Center for Systems Biology Publications

2009 | 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.

We are happy to try to provide full text copies of any Center publication . Please contact .

 2009. The following publications reference the P50GMO76547/Center for Systems Biology
  1. 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.
  2. Carter GW, Galas DJ, Galitski T (2009). Maximal extraction of biological information from genetic interaction data. PLoS Comput Biol. 5(4):e1000347. PMID: 19343223.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. Knijnenburg TA, Wessels LF, Reinders MJ, Shmulevich I (2009). Fewer permutations, more accurate P-values. Bioinformatics. 25(12):i161-8. PMID: 19477983.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. Whitehead K, Pan M, Masumura K, Bonneau R, Baliga NS (2009). Diurnally entrained anticipatory behavior in archaea. PLoS One. 4(5):e5485. PMID: 19424498.

 2008. The following publications reference the P50GMO76547/Center for Systems Biology
  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. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. Reiss DJ, Facciotti MT, Baliga NS (2008). Model-based deconvolution of genome-wide DNA binding. Bioinformatics. 24(3):396-403. PMID: 18056063.
  22. 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
  23. 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.
  24. 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.

 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. 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.
  15. 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.
  16. 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.
  17. 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.
  18. Taylor RJ, Siegel AF, Galitski T. (2007). Network motif analysis of multi-mode genetic-interaction networks. Genome Biology 2007 8:R160.
  19. 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.
  20. R. Vencio, I. Shmulevich, ProbCD: enrichment analysis accounting for categorization uncertainty, BMC Bioinformatics, Vol 8, No. 383, 2007.
  21. 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.
  2. Saleem, R. A., Smith, J. J., Aitchison, J. D. (2006). Proteomics of the peroxisome. Biochim Biophys Acta 1763, 1541-1551.
  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.
  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.

Institute for Systems BiologyCenter for Systems Biology at the Institute for Systems Biology
1441 N. 34th Street, Seattle, WA 98103
Phone: 206.732.1200 | Fax: 206.732.1299 | Email:
© 2007, Institute for Systems Biology, All Rights Reserved