Baxevanis Group

Andreas D. Baxevanis, Ph.D.

Head, Computational Genomics Unit
Director, Bioinformatics and Scientific Programming Core
Associate Investigator, Computational and Statistical Genomics Branch
Assistant Director for Computational Biology, NIH Office of Intramural Research

Selected Publications

Ryan, J.F., Mazza, M.E., Pang, K., Matus, D. Q., Baxevanis, A.D., Martindale, M.Q., and Finnerty, J.R. Pre-Bilaterian Origins of the Hox Cluster and the Hox code: Evidence from the Sea Anemone Nematostella vectensis. PLoS ONE, 2:e153. 2007. [PubMed]

Ryan, J.F. and Baxevanis, A.D. Hox, Wnt, and the Evolution of the Primary Body Axis: Insights from the Early-Divergent Phyla. Biol. Direct,  2:37. 2007. [PubMed]

Moreland, R.T., Ryan, J.F., Pan, C., and Baxevanis, A.D.  The Homeodomain Resource: A Comprehensive Collection of Sequence, Structure, Interaction, Genomic, and Functional Information on the Homeodomain Protein Family. Database, doi:10.1093/database/bap004. 2009. [PubMed]
Ryan, J.R., Pang, K., NISC Comparative Sequencing Program, Mullikin, J.C., Martindale, M.Q., and Baxevanis, A.D.  The Homeodomain Complement of the Ctenophore Mnemiopsis leidyi Suggests that Ctenophora and Porifera Diverged Prior to the ParaHoxozoa.  EvoDevo, 1:9. 2010. [PubMed]

Pang, K., Ryan, J.F., NIH Intramural Sequencing Program, Mullikin, J.C., Baxevanis, A.D., and Martindale, M.Q.  Genomic Insights into Wnt Signaling in an Early Diverging Metazoan, the Ctenophore Mnemiopsis leidyi. EvoDevo, 1:10. 2010. [PubMed]

Reitzel, A.M., Pang, K., Ryan, J.F., Mullikin, J.C., Martindale, M.Q., Baxevanis, A.D., and Tarrant, A.M.  Nuclear Receptors from the Ctenophore Mnemiopsis leidyi Lack a Zinc-Finger DNA-Binding Domain: Lineage-Specific Loss or Ancestral Condition in the Emergence of the Nuclear Receptor Superfamily?  EvoDevo, 2:3. 2011. [PubMed]

Pang, K., Ryan, J.F., Baxevanis, A.D., and Martindale, M.Q.  Evolution of the TGF-beta Signaling Pathway and its Potential Role in the Ctenophore, Mnemiopsis leidyi.  PLoS ONE, 6:e24152. 2011. [PubMed]

Pett, W., Ryan, J.F., Pang, K., NISC Comparative Sequencing Program, Martindale, M.Q., Baxevanis, A.D., and Lavrov, D.V.  Extreme Mitochondrial Evolution in the Ctenophore Mnemiopsis leidyi:  Insights from mtDNA and the Nuclear Genome. Mitochondrial DNA, 22:130-142. 2011. [PubMed]

Mariño-Ramírez, L., Levine, K.M., Morales, M., Zhang, S., Moreland, T.M., Baxevanis, A.D., and Landsman, D.  The Histone Database: An Integrated Resource for Histones and Histone-Fold Proteins. Database doi: 10.1093/database/bar048, 2011. [PubMed]
Koch, B.J., Ryan, J.F., and Baxevanis, A.D.  The Expansion of the LIM Superclass at the Base of the Metazoa Increased Subcellular Complexity and Promoted Multicellular Specialization. PLoS One, 7:e32261. 2012. [PubMed]

Maxwell, E.K., Ryan, J.F., Schnitzler, C.E., Browne, W.E., and Baxevanis, A.D.  MicroRNAs and Essential Components of the microRNA Processing Machinery are Not Encoded in the Genome of the Ctenophore Mnemiopsis leidyi. BMC Genomics, 13:714. 2012. [PubMed]

Schnitzler, C.E., Pang, K., Powers, M.L., Reitzel, A.M., Ryan, J.F., Simmons, D.K., Park, M., Gupta, J., Brooks, S.Y., Blakesley, R.W., Haddock, S.H.D., Martindale, M.Q., and Baxevanis, A.D.  Genomic Organization, Evolution, and Expression of Photoprotein and Opsin Genes in Mnemiopsis leidyi: A New View of Ctenophore Photocytes.  BMC Biol, 10:107. 2012. [PubMed]
Ryan, J.F., Pang, K., Schnitzler, C.E., Nguyen, A.D., Moreland, R.T., Simmons, D.K., Koch, B.J., Francis, W.R., Havlak, P., NISC Comparative Sequencing Program, Smith, S.A., Putnam, N.H., Haddock, S.H.D., Dunn, C.W., Wolfsberg, T.G., Mullikin, J.C., Martindale, M.Q., and Baxevanis, A.D.  The Genome of the Ctenophore Mnemiopsis leidyi and its Implications for Cell Type Evolution.  Science, 342:1242592. 2013. [PubMed]
LaFave, M.C., Varshney, G.K., Gildea, D.E., Wolfsberg, T.G., Baxevanis, A.D., and Burgess, S.M.  MLV Integration Site Selection is Driven by Strong Enhancers and Active Promoters.  Nucleic Acids Res, 1-13. 2014. [PubMed]
Schnitzler, C.E., Simmons, D.K., Pang, K., Martindale, M.Q., and Baxevanis, A.D.  Expression of Multiple Sox Genes Through Embryonic Development in the Ctenophore Mnemiopsis leidyi is Spatially Restricted to Zones of Cell Proliferation. EvoDevo, 5:15. 2014. [PubMed]

Moreland, R.T., Nguyen, A.-D., Ryan, J.F., Schnitzler, C.E., Koch, B.J., Siewert, K., Wolfsberg, T.G., and Baxevanis, A.D.  A Customized Web Portal for the Genome of the Ctenophore Mnemiopsis leidyi.  BMC Genomics, 15:316. 2014. [PubMed

Instructional Videos

Current Topics in Genome Analysis 2014 Series
Biological Sequence Analysis I 
Biological Sequence Analysis II

Books and Guides

Wolfsberg T.G., Wetterstrand K.A., Guyer M.S., Collins F.S., and Baxevanis A.D. A User's Guide to the Human Genome II. Nature Genetics: Supplement 35: 1-79. 2003. [Full Text]

Baxevanis, A.D, Ouellette B.F.F. (Eds). Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 3rd ed. John Wiley & Sons, 2005.

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Last Updated: December 5, 2014