Alan Aderem's Group

Smith KD, Andersen-Nissen E, Hayashi F, Strobe K, Bergman MA, Barrett SL, Cookson BT, Aderem A. 2003. Toll-like receptor 5 recognizes a conserved site on flagellin required for protofilament formation and bacterial motility. Nat Immunol. (12):1247-53.

Hawn TR, Verbon A, Lettinga KD, Zhao LP, Li SS, Laws RJ, Skerrett SJ, Beutler B, Schroeder L, Nachman A, Ozinsky A, Smith KD, Aderem A. 2003. A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to legionnaires' disease. J. Exp. Med. 198:1563-72.

Flo TH, Smith KD, Sato S, Rodriguez DJ, Holmes MA, Strong RK, Akira S, and Aderem A. 2004. Lipocalin 2 mediates a novel innate immune response to bacterial infection by sequestrating iron. Nature. 16:917:21.

Gold ES, Simmons RM, Petersen TW, Campbell LA, Kuo CC, Aderem A. 2004. Amphiphysin IIm Is Required for Survival of Chlamydia pneumoniae in Macrophages. J Exp Med 200:581-6

Andersen-Nissen E, Smith KD, Strobe KL, Barrett SL, Cookson BT, Logan SM, Aderem A. 2005. Evasion of Toll-like receptor 5 by flagellated bacteria. Proc Natl Acad Sci USA. 102:9247-52.

Roach JC, Glusman G, Rowen L, Kaur A, Purcell MK, Smith KD, Hood LE, Aderem A. 2005. The evolution of vertebrate Toll-like receptors. Proc Natl Acad Sci USA. 102:9577-82.

Hawn TR, Wu H, Grossman JM, Hahn BH, Tsao BP, Aderem A. 2005. A TLR5 stop codon polymorphism is associated with resistance to systemic lupus erythematosus. Proc Natl Acad Sci USA. 102: 10593-10597.

Aderem A. 2005. Systems biology: its practice and challenges. Cell. 121:511-13.

Gilchrist M, Thorsson V, Li B, Rust AG, Korb M, Kennedy K, Hai T, Bolouri H, Aderem A. 2006. Systems Biology Approaches Identify ATF3 as a Negative Regulator of Innate Immunity. Nature. 441:173-8.

Miao, EA, CM Alpuche-Aranda, M Dors, AE Clark, MW Bader, SI Miller, and A Aderem. 2006. Cytoplasmic flagellin activates Caspase 1 and IL–1ß secretion through Ipaf. Nature Immunology. 7:569-75.

Hawn TR, Dunstan SJ, Thwaites GE, Simmons CP, Thuong NT, Lan NT, Quy HT, Chau TT, Hieu NT, Rodrigues S, Janer M, Zhao LP, Hien TT, Farrar, JJ, Aderem A. 2006. A polymorphism in toll-interleukin 1 receptor domain containing adaptor protein is associated with susceptibility to meningeal tuberculosis. J Infect Dis. 194:1127-34.

Andersen-Nissen E, Smith KD, Bonneau R, Strong RK, Aderem A.2007. A conserved surface on Toll-like receptor 5 recognized bacterial flagellin. J Exp Med. 204:393-403.

Bochud PY, Hersberger M, Taffe P, Bochud M, Stein CM, Rodrigues SD, Calandra T, Francioli P, Telenti A, Speck RF, Aderem A. 2007. Polymorphisms in Toll-like receptor 9 influence the clinical course of HIV-1 infection. AIDS 21:441-446.

Roach JC, Smith KD, Strobe KL, Nissen SM, Haudenschild CD, Zhou D, Vasicek TJ, Held GA, Stolovitzky GA, Hood LE, Aderem A. Transcription factor expression in lipopolysaccharide-activated peripheral-blood-derived mononuclear cells. Proc Natl Acad Sci U S A. 104:16245-50.

Aderem A. 2008. Alan Aderem: from molecules to megabytes. Interviewed by Nicole LeBrasseur. J Cell Biol. 180:252-3.

Rosenberger CM, Clark AE, Treuting PM, Johnson CD, Aderem A. 2008. ATF3 regulates MCMV infection in mice by modulating IFN-{gamma} expression in natural killer cells. Proc Natl Acad Sci U S A. 105:2544-9.

Ramsey SA, Klemm SL, Zak DE, Kennedy KA, Thorsson V, Li B, Gilchrist M, Gold ES, 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 Comput Biol. 21:4

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Ruedi Aebersold's Group

Zhang J, Goodlett DR, Quinn JF, Peskind E, Kaye JA, Zhou Y, Pan C, Yi E, Eng J, Wang Q, Aebersold RH, Montine TJ. Quantitative proteomics of cerebrospinal fluid from patients with Alzheimer disease. J Alzheimers Dis. 2005 Apr;7(2):125-33.

Chen R, Pan S, Brentnall TA, Aebersold R. Proteomic profiling of pancreatic cancer for biomarker discovery. Mol Cell Proteomics. 2005 Apr;4(4):523-33. Epub 2005 Jan 31.

Yi EC, Li XJ, Cooke K, Lee H, Raught B, Page A, Aneliunas V, Hieter P, Goodlett DR, Aebersold R. Increased quantitative proteome coverage with (13)C/(12)C-based, acid-cleavable isotope-coded affinity tag reagent and modified data acquisition scheme. Proteomics. 2005 Feb;5(2):380-7.

Desiere F, Deutsch EW, Nesvizhskii AI, Mallick P, King NL, Eng JK, Aderem A, Boyle R, Brunner E, Donohoe S, Fausto N, Hafen E, Hood L, Katze MG, Kennedy KA, Kregenow F, Lee H, Lin B, Martin D, Ranish JA, Rawlings DJ, Samelson LE, Shiio Y, Watts JD, Wollscheid B, Wright ME, Yan W, Yang L, Yi EC, Zhang H, Aebersold R. Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol. 2005;6(1):R9. Epub 2004 Dec 10.

Pan S, Zhang H, Rush J, Eng J, Zhang N, Patterson D, Comb MJ, Aebersold R. High throughput proteome screening for biomarker detection. Mol Cell Proteomics. 2005 Feb;4(2):182-90. Epub 2005 Jan 5.

Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R. A common open representation of mass spectrometry data and its application to proteomics research. Nat Biotechnol. 2004 Nov;22(11):1459-66.

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John Aitchison's Group

David J. Dilworth, Alan J. Tackett, Richard S. Rogers, Eugene C. Yi, Rowan H. Christmas, Jennifer J. Smith, Andrew F. Siegel, Brian T. Chait, Richard W. Wozniak and John D. Aitchison The mobile nucleoporin Nup2p and chromatin-bound Prp20p function in endogenous NPC-mediated transcriptional control J. Cell Biology, Accepted for Publication

Scott RJ, Lusk CP, Dilworth DJ, Aitchison JD, Wozniak RW. Interactions between Mad1p and the Nuclear Transport Machinery in the Yeast Saccharomyces cerevisiae. Mol Biol Cell. 2005 Sep;16(9):4362-74. Epub 2005 Jul 6.

Fagarasanu M, Fagarasanu A, Tam YY, Aitchison JD, Rachubinski RA.Inp1p is a peroxisomal membrane protein required for peroxisome inheritance in Saccharomyces cerevisiae. J Cell Biol. 2005 Jun 6;169(5):765-75. Epub 2005 May 31.

Tackett AJ, Dilworth DJ, Davey MJ, O'Donnell M, Aitchison JD, Rout MP, Chait BT. Proteomic and genomic characterization of chromatin complexes at a boundary. J Cell Biol. 2005 Apr 11;169(1):35-47.

Marelli M, Smith JJ, Jung S, Yi E, Nesvizhskii AI, Christmas RH, Saleem RA, Tam YY, Fagarasanu A, Goodlett DR, Aebersold R, Rachubinski RA, Aitchison JD. Quantitative mass spectrometry reveals a role for the GTPase Rho1p in actin organization on the peroxisome membrane. J Cell Biol. 2004 Dec 20;167(6):1099-112. Epub 2004 Dec 13.

Leslie DM, Zhang W, Timney BL, Chait BT, Rout MP, Wozniak RW, Aitchison JD. Characterization of karyopherin cargoes reveals unique mechanisms of Kap121p-mediated nuclear import. Mol Cell Biol. 2004 Oct;24(19):8487-503. Erratum in: Mol Cell Biol. 2004 Nov;24(22):10099.

Makhnevych T, Lusk CP, Anderson AM, Aitchison JD, Wozniak RW. Cell cycle regulated transport controlled by alterations in the nuclear pore complex. Cell. 2003 Dec 26;115(7):813-23.

Rout MP, Aitchison JD, Magnasco MO, Chait BT. Virtual gating and nuclear transport: the hole picture. Trends Cell Biol. 2003 Dec;13(12):622-8. Review.

Tam YY, Torres-Guzman JC, Vizeacoumar FJ, Smith JJ, Marelli M, Aitchison JD, Rachubinski RA. Pex11-related proteins in peroxisome dynamics: a role for the novel peroxin Pex27p in controlling peroxisome size and number in Saccharomyces cerevisiae. Mol Biol Cell. 2003 Oct;14(10):4089-102. Epub 2003 May 18.

Aitchison JD, Galitski T. Inventories to insights. J Cell Biol. 2003 May 12;161(3):465-9. Review.

Smith JJ, Marelli M, Christmas RH, Vizeacoumar FJ, Dilworth DJ, Ideker T, Galitski T, Dimitrov K, Rachubinski RA, Aitchison JD. Transcriptome profiling to identify genes involved in peroxisome assembly and function. J Cell Biol. 2002 Jul 22;158(2):259-71. Epub 2002 Jul 22.

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Nitin Baliga's Group

Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, Baliga NS, Thorsson V. The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol. 2006 May 10;7(5):R36

Kaur A, Pan M, Meislin M, Facciotti MT, El-Geweley R, Baliga NS. A systems view of haloarchaeal strategies to withstand stress from transition metals. Genome Res. 2006 Jun 2

Reiss DJ, Baliga NS, Bonneau R. Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics. 2006 Jun 2;7(1):280

Shannon P, Reiss D, Bonneau R, Baliga N Gaggle: An open-source software system for integrating bioinformatics software and data sources. BMC Bioinformatics, 2006 Mar 28; 7(1):176

Baliga NS, Bonneau R, Facciotti MT, Pan M, Glusman G, Deutsch EW, Shannon P, Chiu Y, Weng RS, Gan RR, Hung P, Date SV, Marcotte E, Hood L, Ng WV. Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res. 2004 Nov;14(11):2221-34. Erratum in: Genome Res. 2004 Dec;14(12):2510.

Bonneau R, Baliga NS, Deutsch EW, Shannon P, Hood L. Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1. Genome Biol. 2004;5(8):R52. Epub 2004 Jul 12.

Weston AD, Baliga NS, Bonneau R, Hood L. Systems approaches applied to the study of Saccharomyces cerevisiae and Halobacterium sp. Cold Spring Harb Symp Quant Biol. 2003;68:345-57.

Facciotti, MT, Boneau, R., Hood, L., Baliga, NS. Systems Biology Experimental Design--Considerations for building predictive gene regulatory network models for prokaryotic systems. Current Genomics 2004;5:527-544.

Baliga NS, Bjork SJ, Bonneau R, Pan M, Iloanusi C, Kottemann MC, Hood L, DiRuggiero J. Systems level insights into the stress response to UV radiation in the halophilic archaeon Halobacterium NRC-1. Genome Res. 2004 Jun;14(6):1025-35. Epub 2004 May 12.

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Aimee Dudley's Group

Lee, S., D. Pe´er, A. M. Dudley, G. M. Church, and D. Koller.
Identifying regulatory mechanisms using individual variation reveals key role for chromatin modification. (2006) PNAS 103:14062-7.

Dudley, A. M., D. M. Janse, A. Tanay, R. Shamir, and G. M. Church.
A global view of pleiotropy and phenotypically derived gene function in yeast. Mol. Systems Biol. msb4100004:E1. Supplemental materials.

Dudley, A. M. and D. L. Cardozo.
Introduction to biological research: a laboratory course. American Biology Teacher 68: 14-24.

Dudley, A. M., J. Aach, M. A. Steffen, and G. M. Church.
Measuring absolute expression with microarrays using a calibrated reference sample and an extended signal intensity range. (2002) PNAS 99:7554-9. Supplemental materials.

Dudley, A. M., C. Rougeulle, and F. Winston.
The Spt components of SAGA facilitate TBP binding to a promoter at a post-activator-binding step in vivo. (1999) Genes & Dev. 13: 2940-2945.

Dudley, A. M., L. J. Gansheroff, and F. Winston.
Specific components of the SAGA complex are required for Gcn4- and Gcr1-mediated activation of the his4-912?promoter in Saccharomyces cerevisiae. (1999) Genetics 151: 1365-1378.

Pinkham, J. L., A. M. Dudley, and T. L. Mason.
T7 RNA polymerase-dependent expression of COXII in yeast mitochondria. (1994) Mol. Cell. Biol. 14: 4643-4652.

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Tim Galitski's Group

Carter GW, Rupp S, Fink GR, Galitski T. Disentangling information flow in the Ras-cAMP signaling network. Genome Res. 2006 Apr;16(4):520-6. Epub 2006 Mar 13.

Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T. Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. BMC Bioinformatics. 2005 Jun 20;6(1):154.

Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, Galitski T. erivation of genetic interaction networks from quantitative phenotype data. Genome Biol. 2005;6(4):R38. Epub 2005 Mar 31.

Galitski T. Molecular networks in model systems. Annu Rev Genomics Hum Genet. 2004;5:177-87.

Yan W, Lee H, Yi EC, Reiss D, Shannon P, Kwieciszewski BK, Coito C, Li XJ, Keller A, Eng J, Galitski T, Goodlett DR, Aebersold R, Katze MG. System-based proteomic analysis of the interferon response in human liver cells. Genome Biol. 2004;5(8):R54. Epub 2004 Jul 22.

Andalis AA, Storchova Z, Styles C, Galitski T, Pellman D, Fink GR. Defects arising from whole-genome duplications in Saccharomyces cerevisiae. Genetics. 2004 Jul;167(3):1109-21.

Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T. Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res. 2004 Mar;14(3):380-90.

Drees BL, Thorsson V, Carter GW, Rives AW, Raymond MZ, Avila-Campillo I, Shannon P, Galitski T. Derivation of genetic interaction networks from quantitative phenotype data. Genome Biol. 2005;6(4):R38. Epub 2005 Mar 31.

Galitski T. Molecular networks in model systems. Annu Rev Genomics Hum Genet. 2004;5:177-87. Review.

Reiss DJ, Avila-Campillo I, Thorsson V, Schwikowski B, Galitski T. Tools enabling the elucidation of molecular pathways active in human disease: Application to Hepatitis C Virus infection. BMC Bioinformatics. 2005 Jun 20;6(1):154 [Epub ahead of print]

Prinz S, Avila-Campillo I, Aldridge C, Srinivasan A, Dimitrov K, Siegel AF, Galitski T. Control of yeast filamentous-form growth by modules in an integrated molecular network. Genome Res. 2004 Mar;14(3):380-90.

Aitchison JD, Galitski T. Inventories to insights. J Cell Biol. 2003 May 12;161(3):465-9. Review.

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Leroy Hood's Lab

Lin B, White JT, Lu W, Xie T, Utleg AG, Yan X, Yi EC, Shannon P, Khrebtukova I, Lange PH, Goodlett DR, Zhou D, Vasicek TJ, Hood L. Evidence for the presence of disease-perturbed networks in prostate cancer cells by genomic and proteomic analyses: a systems approach to disease. Cancer Res. 2005 Apr 15;65(8):3081-91.

Hood L, Heath JR, Phelps ME, Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science. 2004 Oct 22;306(5696):640-3.

Bunimovich YL, Ge G, Beverly KC, Ries RS, Hood L, Heath JR. Electrochemically programmed, spatially selective biofunctionalization of silicon wires. Langmuir. 2004 Nov 23;20(24):10630-8.

Tian Q, Stepaniants SB, Mao M, Weng L, Feetham MC, Doyle MJ, Yi EC, Dai H, Thorsson V, Eng J, Goodlett D, Berger JP, Gunter B, Linseley PS, Stoughton RB, Aebersold R, Collins SJ, Hanlon WA, Hood LE. Integrated genomic and proteomic analyses of gene expression in Mammalian cells. Mol Cell Proteomics. 2004 Oct;3(10):960-9. Epub 2004 Jul 6.

Lausted C, Dahl T, Warren C, King K, Smith K, Johnson M, Saleem R, Aitchison J, Hood L, Lasky SR. POSaM: a fast, flexible, open-source, inkjet oligonucleotide synthesizer and microarrayer. Genome Biol. 2004;5(8):R58. Epub 2004 Jul 27.

Weston AD, Hood L. Systems biology, proteomics, and the future of health care: toward predictive, preventative, and personalized medicine. J Proteome Res. 2004 Mar-Apr;3(2):179-96. Review.

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Adrian Ozinsky's Group

Hawn TR, Verbon A, Lettinga KD, Zhao LP, Li SS, Laws RJ, Skerrett SJ, Beutler B, Schroeder L, Nachman A, Ozinsky A, Smith KD, Aderem A. A common dominant TLR5 stop codon polymorphism abolishes flagellin signaling and is associated with susceptibility to legionnaires' disease. J Exp Med. 2003 Nov 17;198(10):1563-72.

Marr KA, Balajee SA, Hawn TR, Ozinsky A, Pham U, Akira S, Aderem A, Liles WC. Differential role of MyD88 in macrophage-mediated responses to opportunistic fungal pathogens. Infect Immun. 2003 Sep;71(9):5280-6.

Underhill DM, Ozinsky A. Toll-like receptors: key mediators of microbe detection. Curr Opin Immunol. 2002 Feb;14(1):103-10. Review.

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Jeff Ranish's Group

Rubio, E. D., Reiss, D. J., Welcsh, P. L., Disteche, C. M., Filippova, G. N., Baliga, N. S., Aebersold, R., Ranish, J. A., Krumm, A. (2008) Proc Natl Acad Sci U S A. 2008 Jun 11. Epub ahead of print

Ranish, J.A., Hahn, S., Lu, Y., Yi, E.C., Li, X-J., Eng, J., Aebersold, R. Quantitative proteomic identification of TFB5, a new component of general transcription/DNA repair factor IIH. Nature Genetics 36: 707-713, 2004.

Giglia-Mari, G., Coin, F., Ranish, J.A., Stefanini, M., Hoogstraten, D., Theil, A., Wijgers, N., Jaspers, N.G.J., Raams, A., Argentini, M., van der Spek, P.J., Botta, E., Egly, J-M., Aebersold, R. Hoeijmakers, J.H.J., and W.Vermeulen. A new, tenth subunit of TFIIH is responsible for the DNA repair syndrome trichothiodystrophy group A and stabilizes TFIIH. Nature Genetics 36: 714-719, 2004.

Warfield, L. Ranish, J.A., and S. Hahn. Positive and Negative functions of the SAGA complex mediated through interaction of Spt8 with TBP and the N-terminal domain of TFIIA. Genes & Development 18:1022-1034, 2004.

Himeda, C.L., Ranish, J.A., Angello, J.C., Maire, P., Aebersold, R.A., and S.D. Hauschka. Quantitative Proteomic Identification of Six4 as the Trex-Binding Factor in the Muscle Creatine Kinase Enhancer. Molecular and Cellular Biology 24:2132-2143, 2004.

Rani, P.G., Ranish, J.A., and S. Hahn. RNA Polymerase II (Pol II)-TFIIF and Pol II-Mediator Complexes: the Major Stable Pol II Complexes and Their Activity in Transcription Initiation and Reinitiation. Molecular and Cellular Biology 24:1709-1720, 2004.

Brand, M., Ranish, J.A., Kummer, N.T., Igarashi, K., Francastel, C., Chi, T.H., Crabtree, G.R., Aebersold, R.A., and M. Groudine. Dynamic changes in transcription factors complexes during erythroid differentiation revealed by quantitative proteomics. Nature Structural and Molecular Biology 11: 73- 80, 2004.

Li, X-j., Zhang, H., Ranish, J.A., and R. Aebersold. Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry. Analytical Chemistry 75: 6648-6657, 2003.

Ranish, J.A., Yi, E.C., Leslie, D.M., Purvine, S.O., Goodlett, D.R., Eng, J., Aebersold, R. The study of macromolecular complexes by quantitative proteomics. Nature Genetics 33:349-355, 2003.

Zhou, H., Ranish, J.A., Watts, J.D., Aebersold, R. Quantitative proteome analysis by solid-phase isotope tagging and mass spectrometry. Nature Biotechnology 19:512-515, 2002.

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Ilya Shmulevich's Group

J. Boyle, C. Cavnor, S. Killcoyne, I. Shmulevich, "Systems biology driven software design for the research enterprise," BMC Bioinformatics, Vol. 9, No. 295, 2008.

H. Lähdesmäki, I. Shmulevich, "Learning the Structure of Dynamic Bayesian Networks from Time Series and Steady State Measurements," Machine Learning, Vol. 71, pp. 185-217, 2008.

H. Lähdesmäki, A. G. Rust, I. Shmulevich, "Probabilistic inference of transcription factor binding from multiple data sources," PLoS ONE, Vol. 3, No. 3, e1820, 2008.

S. A. Ramsey, S. L. Klemm, D. E. Zak, K. A. Kennedy, V. Thorsson, B. Li, M. Gilchrist, E. Gold, C. D. Johnson, V. Litvak, G. Navarro, J. C. Roach, C. M. Rosenberger, A. G. 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.

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.

M. Nykter, N. D. Price, M. Aldana, S. A. Ramsey, S. A. Kauffman, L. 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.

S. A. Kauffman, R. K. Logan, R. Este, R. Goebel, D. Hobill, I. Shmulevich, "Propagating Organization: An Enquiry," Biology and Philosophy, Vol. 23, No. 1, pp. 27-45, 2007.

R. Vêncio, I. Shmulevich, "ProbCD: enrichment analysis accounting for categorization uncertainty," BMC Bioinformatics, Vol. 8, No. 383, 2007.

P. Krawitz, I. Shmulevich, "Entropy of complex relevant components in Boolean networks," Physical Review E, Vol. 76, 036115, 2007.

N. D. Price, I. Shmulevich, "Biochemical and statistical network models for systems biology," Current Opinion in Biotechnology, Vol. 18, pp. 365-370, 2007.

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.

P. Krawitz, I. Shmulevich, "Basin Entropy in Boolean Network Ensembles," Physical Review Letters, Vol. 98, No. 15, pp. 158701, 2007.

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.

I. Shmulevich, S. A. Kauffman, M. Aldana, "Eukaryotic cells are dynamically ordered or critical but not chaotic" Proceedings of the National Academy of Sciences of the USA, Vol. 102, No. 38, pp. 13439-13444, 2005.

Niemisto A, Dunmire V, Yli-Harja O, Zhang W, Shmulevich I. Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans Med Imaging. 2005 Apr;24(4):549-53.

Lähdesmäki H, Hao X, Sun B, Hu L, Yli-Harja O, Shmulevich I, Zhang W. Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis. Int J Oncol. 2004 Jun;24(6):1589-96.

Hashimoto RF, Kim S, Shmulevich I, Zhang W, Bittner ML, Dougherty ER. Growing genetic regulatory networks from seed genes. Bioinformatics. 2004 May 22;20(8):1241-7. Epub 2004 Feb 10.

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