Duke IGSP Center for Systems Biology Publications 2008-2009
Benfey PN and T. Mitchell-Olds (2008) From genotype to phenotype: systems biology meets natural variation. Science 320:495-7. (Abstract)
Bradham CA, CM Lookingbill, J Modell, DR McClay, and A Poustka. (2009) Chordin is required for neural but not axial specification in sea urchin embryos. Dev. Biol. 328:221-233(Featured on the Cover). (Abstract)
Byrum, C.A., R. Xu, J.M. Bince, D.R. McClay, and A.H. Wikramanayake (2009) Blocking Dishevelled signaling in the non-canonical Wnt pathway in sea urchins disrupts endoderm formation and spiculogenesis, but not secondary mesoderm formation. Dev. Dyn. In Press. (Abstract)
Croce, J. C. and D.R. McClay (2008) Wnt signaling, In Methods in Molecular Biology. Volume 2, Pathways Models. (Vincan, E. ed), pg.3-18, Humana Press, USA. (Abstract)
Croce, J.C., R.C. Range, S-Y. Wu, E. Miranda, A. Wikramanayake, T. Lepage, and D. R. McClay (2008) Maternal determinants in the vegetal cortex are required to activate the sea urchin endomesoderm gene regulatory network. In Revison.
Iyer-Pascuzzi AS, Simpson J, Herrera-Estrella L and PN Benfey (2008) Functional genomics of Arabidopsis root development. Curr Opin Plant Biol. Dec 29. [Epub ahead of print] (Abstract)
Iyer-Pascuzzi AS and PN Benfey (2008) Transcriptional networks in root cell fate specification. Biochim Biophys Acta. Oct 10. (Abstract)
T. Lee, G. Yao, J. R. Nevins, and L. You, 2008 Sensing and integration of Erk and PI3K signals by Myc. PLoS Computational Biology, 4: e1000013. (Abstract)
Long TA, Brady SM and PN Benfey, (2008) Systems Approaches to Identifying Gene Regulatory Networks in Plants. Annual Review Cell Dev Biol. 24:81-103. (Abstract)
Magwene, P. M. (2008) Pleiotropy and tradeoffs in yeast development. In revision.
McClay, D .R. (2009) Cleavage and Gastrulation in the Sea Urchin. Encyclopedia of Life Sciences. In press.
Megraw M, Pereira F, Jensen ST, Ohler U, Hatzigeorgiou AG. (2009) A transcription factor affinity-based code for mammalian transcription initiation. Genome Res. 19:644-56. (Abstract)
C. Mukherjee, Y. Tanouchi, L. You and M. West, 2009 Sequential Monte Carlo in model comparison: Examples in single-cell systems biology studies. Submitted to the Joint Statistical Meetings, 2009.
J. Niemi, C.M. Tan, Q. Wang, L. You and M. West, 2009 Statistical analysis of stochastic dynamic models in single-cell fluorescence studies. Under revision.
J. Niemi and M. West, 2009 AM4: Software implementing adaptive mixture modelling Metropolis methods for analysis of non-linear time series, with applications in systems biology. To be available for download shortly.
J. Niemi and M. West, 2008 Adaptive mixture modelling MCMC for analysis of non-linear time series. To appear in the Journal of Computational & Graphical Statistics.
J. Norrell and J.E.S. Socolar, Boolean modeling of collective effects in complex networks, Physical Review E, vol. 79 (2009), pp. 061908 (Abstract)
Orlando DA, Lin CY, Bernard A, Wang, J, Socolar, JES, Iversen ES, Hartemink AJ, Haase SB. (2008) Global control of cell cycle transcription by coupled CDK and network oscillators. Nature 453:944-7. (Abstract)
Orlando, D.A., Iversen, E.S., Hartemink, A.J., and Haase, S.B. (2009) A branching process model for flow cytometry and budding index measurements in cell synchrony experiments. (Accepted) Ann. App. Statistics.
A. Pai, Y. Tanouchi, C. Collins, and L. You, 2009 Engineering multicellular systems by cell-cell communication. Invited review submitted to Current Opinions in Biotechnology.
Range, R. C. T. D. Glenn, and D. R. McClay (2008) LvNumb positively influences Notch signaling during secondary mesenchyme specification in the sea urchin embryo. Development, 135:2445-2454. (Featured on the cover). (Abstract)
Rottinger, E., A. Saudemont, V. Duboc, L. Besnardeau, D.R. McClay and T. Lepage (2008) FGF signals guide migration of mesenchymal cells, control skeletal morphogenesis of the skeleton and regulate gastrulation during sea urchin development. Development 135:353-365. (Abstract)
C. Tan, H. Song and J. Niemi and L. You, 2009 A synthetic biology challenge: Making cells compute. Molecular BioSystems 3.5, 343--353. (Abstract)
C. Tan, P. Marguet and L. You, 2009 Emergent bistability by growth-modulating positive feedback. Under revision.
Tung, J, S Mukherjee, R Haygood, and G A Wray. Genomic features that predict allelic imbalance are negatively correlated with gene density, expression evenness, and selective constraint. Molecular Biology and Evolution, in review. (Abstract)
Tung, J and G A Wray. Evolution of traits deduced from genome comparisons. Encylopedia of Life Sciences, in press.
Walton, K.D., J.F. Warner, P.H. Hertzler, and D.R. McClay (2009) Hedgehog signaling patterns mesoderm in the sea urchin. Dev. Biol. In Press. (Abstract)
Q. Wang, J. Niemi, C.M. Tan, L. You and M. West, 2009 Image segmentation and dynamic lineage analysis in single-cell fluorescent microscopy. Synthetic Biology, in press.
Q. Wang, L. You and M. West, 2008 CellTracer: Software for automated dynamic image analysis in single cell fluorescent microscopy studies. http://www.stat.duke.edu/research/software/west/celltracer/
Wray, G A and D A Garfield. The evolution of gene regulation. BioScience, in press.
Wu, S-Y., Y-P. Yang, and D.R. McClay (2008) Twist is an essential regulator of the skeletogenic gene regulatory network in the sea urchin embryo. Dev. Biol. 319:406-415. (Abstract)
G. Yao, T. Lee, S. Mori, J.R. Nevins, and L. You, 2008 A Bistable Rb-E2F Switch Underlies the Restriction Point. Nature Cell Biology, 10: 476-482. Faculty of 1000 Biology, Must Read. (Abstract)
Yokoyama, K-D, U Ohler, and G A Wray. Spatial preferences identify known and novel cis-regulatory element candidates and functional motif-pair relationships. Nucleic Acids Research, in review. (Abstract)