DOE Systems Biology Knowledgebase
Sergei Maslov leads the team of scientists at BNL, Cold Spring Harbor Laboratory, and Yale University constructing Systems
Biology Knowledgebase. In addition to Brookhaven this DOE-wide effort involves scientists from Lawrence Berkley, Argonne, and Oak
Ridge National Labs. Systems Biology Knowledgebase is aimed to integrate and make broadly accessible everything we know or can learn
about plants and microbes from the genetic and molecular to the organism and systems level. The BNL-led effort concentrates on
genotype-to-phenotype relations and complex biomolecular networks in plants.
Research in the Maslov lab is focused on selected topics in systems, computational, and evolutionary biology with particular emphasis
on large-scale properties of complex biomolecular networks. These networks operate inside living cells on multiple levels including
protein-protein binding interactions, transcriptional regulation, signaling, metabolic reactions, etc. We are interested in a broad
range of questions including:
- How biological networks minimize the undesirable crosstalk and limit the effects of non-specific interactions
(PNAS 2011, MSB 2008, PNAS 2007, NJP 2007, Science 2002)?
- How they achieve robustness against noise and perturbations (PNAS 2007, PRL 2008, Science 2002)?
- How topological properties of these networks affect their functioning inside living cells
(Nucleic Acids Research 2005, Phys. Biol. 2007, BMC Bioinformatics 2006, PRL 2004, Science 2002)?
- How bio-molecular networks and underlying genomes change in the course of evolution
(PLoS Comb Bio 2011, PNAS 2009, JMB 2009, BMC Evol. Biol. 2004, Nucleic Acids Research 2005, Biol. Direct 2007)?
Genome-scale networks involve interactions among 1000s of genes/proteins. High-throughput experimental data describing these interactions are
often noisy and incomplete. Statistical physics with its emphasis on scaling laws, general trends and correlations has many of the right tools to
approach this type of data. In addition to genome-scale network models Maslov lab is also interested in detailed understanding of temporal dynamics
of relatively small pathways (tens of genes). For example, Dr. Maslov and his collaborators modeled the time course of SOS response to UV-induced DNA
damage in E. coli (PLoS Comp Bio 2007).
Grilli J., Bassetti B., Maslov S., and Cosentino Lagomarsino M.
Joint scaling laws in functional and evolutionary categories in prokaryotic genomes.
Nucleic Acids Research (in press 2011).
Pang T.Y., and Maslov S.
A toolbox model of evolution of metabolic pathways on networks of arbitrary topology.
PLoS Comput. Biol,. 7(5):e1001137 (2011).
Heo M., Maslov S., and Shakhnovich E.
Topology of protein interaction network shapes protein abundances and strengths of their functional and nonspecific interactions.
Proceedings of the National Academy of Sciences, 108(10):4258-4263 (2011).
Studier F.W., Daegelen P., Lenski R.E., Maslov S., and Kim J.F.
Understanding the differences between genome sequences of Escherichia coli B strains REL606 and BL21(DE3) and comparison of the E. coli B and K-12 genomes.
J. Mol. Biol., 394(4):653-680 (2009).
Maslov S., Krishna S., Pang T.Y., and Sneppen K.
Toolbox model of evolution of prokaryotic metabolic networks and their regulation.
Proc. Natl. Acad. Sci. U.S.A., 106:9743-9748 (2009).
Yan K.-K., Walker D., and Maslov S.
Fluctuations in mass-action equilibrium of protein binding networks.
Phys. Rev. Lett., 101(26):268102 (2008).
Zhang J., Maslov S., and Shakhnovich E.I.
Constraints imposed by non-functional protein-protein interactions on gene expression and proteome size.
Mol. Syst. Biol., 4:210 (2008).
Ispolatov I., and Maslov S.
Detection of the dominant direction of information flow and feedback links in densely interconnected regulatory networks.
BMC Bioinformatics, 9:424 (2008).
Maslov S., and Ispolatov I.
Propagation of large concentration changes in reversible protein-binding networks.
Proc. Natl. Acad. Sci. U.S.A., 104(34):13655-13660 (2007).
Krishna S., Maslov S., and Sneppen K.
UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model.
PLoS Comput. Biol., 3(3):e41 (2007).
Kotelnikova E., Kalinin A., Yuryev A., and Maslov S.
Prediction of Protein-protein Interactions on the Basis of Evolutionary Conservation of Protein Functions.
Evol. Bioinform. Online, 3:197-206 (2007).
Axelsen J.B., Yan K.-K., and Maslov S.
Parameters of proteome evolution from histograms of amino-acid sequence identities of paralogous proteins.
Biol. Direct., 2:32 (2007).
Yuryev A. et al.
Automatic pathway building in biological association networks.
BMC Bioinformatics, 7:171 (2006).
Maslov S., and Sneppen K.
Computational architecture of the yeast regulatory network.
Phys Biol., 2(4):S94-100 (2005).
Ispolatov I., Yuryev A., Mazo I., and Maslov S.
Binding properties and evolution of homodimers in protein-protein interaction networks.
Nucleic Acids Res., 33(11):3629-3635 (2005).
Maslov S., Sneppen K., Eriksen K.A., and Yan K.-K.
Upstream plasticity and downstream robustness in evolution of molecular networks.
BMC Evol. Biol., 4:9 (2004).
Maslov S., and Sneppen K.
Specificity and stability in topology of protein networks.
Science, 296(5569):910-913 (2002).
Maslov S., and Zhang Y.C.
Extracting hidden information from knowledge networks.
Phys. Rev. Lett., 87:(24)8701 (2001).
Selected Book Chapters
S. Simakov, I. Ispolatov, S. Maslov, and A. Nikitin
“Algorithmic basis for pathway visualization”, book chapter in the "Pathway Analysis for drug discovery"
edited by A. Yuryev, Wiley, New York (2008).
“Topological and dynamical properties of protein interaction networks”
book chapter in the "Protein-protein interactions and networks: Identification, Analysis and Prediction",
A. R. Panchenko and T. M. Przytycka (eds.), Springer-Verlag, New York (2008).
S. Maslov, and K. Sneppen
“Large-scale topological properties of molecular networks”, book chapter in the "Power Laws, Scale-free Networks and Genome Biology"
Eugene Koonin, Yuri Wolf and Georgy Karev (eds.), Landes Biosciences, Georgetown, Texas (2005).
S. Maslov, and K. Sneppen
“Detection of topological patterns in protein networks”
book chapter in the "Genetic Engineering, Principles and Methods", vol. 26,
Jane K. Setlow (ed.), Kluwer Academic/ Plenum Publishers, Dordrecht, The Netherlands (2004).
S. Maslov, K. Sneppen, and U. Alon
“Correlation Profiles and Circuit Motifs in Complex Networks”
book chapter in the "Handbook of Graphs and Networks",
S. Bornholdt, and H.-G. Schuster, (eds.), Wiley-VCH, Weinheim, (2003).