Penn State Science
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Biological Networks
Large Networks
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The remarkable progress in molecular biology has lead to a complete map of the building blocks of life. The next major challenge is to understand the interactions between the myriad of sub-cellular components that form the network structure of biological systems. My main research goal is studying and modeling these biological networks, and finding the fundamental principles that govern their topology, function and evolution.

More information on current projects

This research area provides opportunities for undergraduate research.

Publications

«  2008 · 2009 · 2010 · 2011 · 2012 · All
J. Thakar, A. Pathak, L. Murphy, R. Albert and I. Cattadori, "Network Model of Immune Responses Reveals Key Effectors to Single and Co-infection Dynamics by a Respiratory Bacterium and a Gastrointestinal Helminth," PLoS Comp. Biol. 8, e1002345 (2012)
C. Campbell, S. Yang, R. Albert and K. Shea, "A network model for plant–pollinator community assembly," Proc. Natl. Acad. Sci. U.S.A 108, 197 – 202 (2011)
A. Saadatpour Moghaddam, R. Wang, T. Loughran, I. Albert and R. Albert, "Dynamical and Structural Analysis of a T Cell Survival Network Identifies Novel Candidate Therapeutic Targets for Large Granular Lymphocyte Leukemia," PLoS Comp. Biol. 7, e1002267 (2011)
R. Wang and R. Albert, "Elementary signaling modes predict the essentiality of signal transduction network components," BMC Syst. Biol. 5, 44 (2011)
R. Zhang, T. Loughran and R. Albert, "Network model of survival signaling in T-cell large granular lymphocyte leukemia", in Cancer Systems Biology, Ed.: E. Wang (Chapman and Hall, 2010) p.
A. Saadatpour Moghaddam, I. Albert and R. Albert, "Attractor analysis of asynchronous Boolean models of signal transduction networks," J. Theor. Biol. 266, 641 – 656 (2010)
R. Wang, R. Albert and S. M. Assmann, "Boolean modeling of transcriptome data reveals novel modes of heterotrimeric G-protein action,," Mol. Syst. Biol. 6, 372 (2010)
R. Albert and S. M. Assmann, "Discrete dynamic modeling with asynchronous update or, how to model complex systems in the absence of quantitative information", in Methods in Molecular Biology 553: Plant Systems Biology, Ed.: D. Belostotsky (Humana Press, 2009) p. 207-225
J. Thakar, A. Saadatpour Moghaddam, E. Harvill and R. Albert, "Constraint-Based Network Model of Pathogen-Immune System Interactions," J. R. Soc. Interface 6, 599 – 612 (2009)
R. Zhang, M. Shah, J. Yang, S. B. Nyland, Y. K. Yun, R. Albert and T. Loughran, "Network model of survival signaling in large granular lymphocyte leukemia," Proc. Natl. Acad. Sci. U.S.A 105, 16308 – 16313 (2008)
S. Kachalo, R. Zhang, E. Sontag, R. Albert and B. DasGupta, "NET-SYNTHESIS: A software for synthesis, inference and simplification of signal transduction networks," Bioinformatics 24, 293 – 295 (2008)
M. Chaves and R. Albert, "Studying the effect of cell division on expression patterns of the segment polarity genes," J. R. Soc. Interface 5, S71 – S84 (2008)
J. Joo, E. Harvill and R. Albert, "Effects of noise in bacteriophage-mediated competition," J. Stat. Phys. 128, 229 – 256 (2007)
R. Albert and Z. N. Oltvai, "Shaping specificity in signaling networks," Nature 39, 286 – 287 (2007)
C. Christensen, A. Gupta, C. Maranas and R. Albert, "Inference and graph-theoretical analysis of Bacillus Subtilis gene regulatory networks," Physica A 373, 796 – 810 (2007)
C. Christensen, J. Thakar and R. Albert, "Systems-level insights into cellular regulation: inferring, analyzing, and modeling intracellular networks," IET Syst. Biol. 1, 61 – 77 (2007)
J. Thakar, M. Pilione, G. Kirimanjeswara, E. Harvill and R. Albert, "Modeling Systems-Level Regulation of Host Immune Responses," PLoS Comp. Biol. 6, e109 (2007)
J. Joo, M. Gunny, M. Cases, P. Hudson, R. Albert and E. Harvill, "Bacteriophage-mediated competition in Bordetella bacteria," Proc. R. S. London 273, 1843 – 1848 (2006)
A. Gupta, C. Maranas and R. Albert, "Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites," Bioinformatics 22, 209 – 214 (2006)
W. Chung, R. Albert, I. Albert, A. Nekrutenko and K. Makova, "Rapid and asymmetric divergence of duplicate genes in the human gene coexpression network," BMC Bioinformatics 7, 46 (2006)
M. Chaves, E. Sontag and R. Albert, "Methods of robustness analysis for Boolean models of gene regulatory networks," IEE Proc., Syst. Biol. 153, 154 – 156 (2006)
S. Li, S. M. Assmann and R. Albert, "Predicting essential components of signal transduction networks: dynamic model of guard cell abscisic acid signaling," PLoS Biology 4, e312 (2006)
M. Chaves, R. Albert and E. Sontag, "Robustness and fragility of Boolean models for genetic regulatory networks," J. Theor. Biol. 235, 431 – 449 (2005)
R. Albert, "Scale - free networks in cell biology," J. Cell Sci. 118, 4947 – 4957 (2005)
I. Albert and R. Albert, "Conserved network motifs allow protein-protein interaction prediction," Bioinformatics 20, 3346 – 3352 (2005)
R. Albert, H. G. Othmer, R. Dillon and C. Gadgil, "Spatial Pattern Formation and Morphogenesis in Development: Recent Progress for Two Model Systems", in Morphogenesis and Pattern Formation in Biological Systems: Experiments and Models, Ed.: T. Sekimura, S. Noji, N. Ueno and P.K. Maini (Springer Verlag, 2004) p.
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R. Albert : Biological Networks