B.S., Biology, 1994, Cedar Crest College
Ph.D., Molecular Biology, 2002, Lehigh University
Computational Systems Biology
The value of computational approaches to biology may be summarized in three categories: (1) interpretation, or the analysis of biological data for the purpose of uncovering hidden relationships using an accepted model, (2) prediction, or using models to formulate computational hypotheses that may be further explored with bench experiments, and (3) model generation, or producing a new model by fitting known constraints on an in silico system in order to generate known results and new hypotheses.
Our group has two main interests that span the above approaches: (1) reconstruction of biological networks from data-derived theoretical networks and (2) modeling the emergent behavior of stochastic biological systems. With regard to network reconstruction, we are currently focusing our attention on the problems associated with comparing theoretical networks, or so-called relevance networks derived from high-throughput screening or other data streams, to networks built using traditional reductionist methods. Our goal is to reconstruct transcriptional regulatory networks involved in murine cardiac development. With regard to modeling, we are interested in modeling the emergent behavior of our reconstructed networks, as well as the emergent behavior of self-assembling cellular structures such as microtubules.
Several projects feed into these two main interests. To build reliable networks from high-throughput data, the data must be carefully annotated and curated, and for microarray data, it is highly desirable to obtain estimates of absolute transcript abundance. We are developing data-handling SOPs and transcript abundance estimation methods to address these important issues. Additionally, we are constructing a suitable systems biology database for murine cardiac development in order to aid our efforts in comparing our reconstructed networks to “known” networks. It is expected that our development of a public database for this purpose will be of value to the scientific community at large.
VanBuren V. (2011) Computational Modeling of Microtubule Structure and Assembly: A Pseudo-Mechanical Model and a Mechanical Model (Book), 152 pp, VDM Verlag Dr. Müller, Saarbrücken.
Jupiter D, Sahutoglu J, VanBuren V. (2010) TreeHugger: A new test for enrichment and depletion of GO Terms. INFORMS Journal on Computing. 2010 Volume: 22 Issue: 2 Pages: 210-221
Huang HC, Jupiter D, VanBuren V. (2010) Classification of Genes and Putative Biomarker Identification Using Distribution Metrics on Expression Profiles. PLoS ONE 2010 Feb 4; 5(2): e9056.
Huang HC, Zheng S, VanBuren V, Zhao Z. (2010) Discovering disease-specific biomarker genes for cancer diagnosis and prognosis. Technol Cancer Res Treat. 2010 Jun; 9(3): 219-30.
Jupiter D, Chen H, VanBuren V. (2009) StarNet 2: A Web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. BMC Bioinformatics 2009, 10:332 (**classified by BMC as Highly Accessed, **reviewed by Faculty of 1000 (F1000)).
Jupiter, D.C. and VanBuren, V. A Visual Data Mining Tool that Facilitates Reconstruction of Transcription Regulatory Networks. PLoS ONE 2008 Mar 5;3(3):e1717.
Huang, H.C., Jupiter, D., Qiu M., Briggs, J.M., and VanBuren, V. Cluster analysis of hydration waters around the active sites of bacterial alanine racemase using a 2-ns MD simulation. Biopolymers 2008 Mar;89(3):210-9. (* Article featured on the journal cover) .
VanBuren, V., Cassimeris, L., Odde, D.J. (2005) A mechanochemical model for microtubule structure and self-assembly kinetics. Biophysical Journal 89:2911-2926. [June 10 Epub ahead of print] New and Notable commentary: Schek, H.T. III, and Hunt A.J. (2005) Microtubules: Mechanical meets chemical. Biophysical Journal 89:2909-2910.
VanBuren, V. and Ko, M.S.H. (2005) Principles and applications of embryogenomics (invited encyclopedia section). Encyclopedia of Molecular Cell Biology and Molecular Medicine. Wiley-VCH, Berlin. 529-556.
VanBuren, V. and Ko, M.S.H. (2005) Regulation of genome activity and genetic networks in mammals (invited book chapter). Mammalian Genomics.CAB International Publishing, Cambridge, Massachusetts. 201-220.
VanBuren, V., Yoshikawa, T., Hamatani, T., Ko, M.S.H. (2003) Probe Design for Large-Scale Molecular Biology Applications. IEEE CSB Proceedings (CSB2003). 502-503.
VanBuren, V., Piao, Y., Dudekula, D.B., Qian, Y., Carter, M.G., Martin, P.R., Stagg, C.A., Bassey, U.C., Aiba, K., Hamatani, T., Kargul, G.J., Luo, A.G., Kelso, J., Hide, W., Ko, M.S.H. (2002) Assembly, Verification, and Initial Annotation of the NIA Mouse 7.4K cDNA Clone Set. Genome Research, 12:1999-2003.
VanBuren, V., Odde, D.J., Cassimeris, L. (2002) Estimates of Lateral and Longitudinal Bond Energies within the Microtubule Lattice. Proc Natl Acad Sci USA, 99(9): 6035-40.