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Computational Genomics Unit


Bioinformatics and Scientific Programming Core

Senior Scientist

Computational and Statistical Genomics Branch

Director of Computational Biology

NIH Office of Intramural Research


B.S. Cornell University, 1984

Ph.D. The Johns Hopkins University, 1991


Dr. Baxevanis is the director of Computational Biology for the National Institutes of Health's (NIH) Intramural Research Program. He is also a senior scientist leading the Computational Genomics Unit at the National Human Genome Research Institute (NHGRI).

Dr. Baxevanis' research program uses computational approaches to understand the molecular innovations that drove the surge of diversity in early animal evolution. His research group focuses on the analysis of genomes of early branching metazoan phyla to understand the relationship between genomic and morphological complexity, as well as the evolution of novel cell types. Dr. Baxevanis' group focuses specifically on invertebrate species with the potential to serve as "emerging model organisms" that can yield insights of relevance to human health.

Dr. Baxevanis received his Bachelor of Science in biological sciences from Cornell University and his Ph.D. in the Department of Biology at The Johns Hopkins University. He was a post-doctoral fellow at the National Center for Biotechnology Information at NIH, after which he joined the NHGRI faculty.

Dr. Baxevanis is co-author of the textbook Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, now in its third edition. His involvement in educational activities have included teaching bioinformatics at The Johns Hopkins University, serving as an adjunct faculty member at Boston University, and serving as the director of NHGRI's Intramural Training Office. He has also served as the co-director of the Boston University/NIH Graduate Partnerships Program in Bioinformatics.

Dr. Baxevanis is the recipient of the Bodossaki Foundation's 2000 Academic Prize in Medicine and Biology, Greece's highest honor for young academics and scientists of Greek heritage throughout the world. In 2007, Dr. Baxevanis was awarded the IEEE Computer Society's Outstanding Achievement Award for his outstanding contributions to the field of bioinformatics. In 2014, he was elected to membership in the Johns Hopkins Society of Scholars, which recognizes alumni who have achieved marked distinction in their field of study. Dr. Baxevanis was the recipient of the NIH's Ruth L. Kirschstein Mentoring Award in 2015, in recognition of his commitment to scientific training, education and mentoring. In 2016, Dr. Baxevanis was elected as a senior member of the International Society for Computational Biology for his sustained contributions to the field, and, in 2018, he was elected as a Fellow of the American Association for the Advancement of Science for his distinguished contributions to the field of comparative genomics.

Scientific Summary

Dr. Baxevanis' research focuses on the use of phylogenetic and comparative genomic techniques to study developmental proteins that play a fundamental role in the specification of body plan, pattern formation and cell fate determination during metazoan development. His group uses a variety of bioinformatic approaches to understand the evolution and function of these proteins and their ultimate role in human disease.

Building upon his prior work on the origin and early evolution of the Hox genes, Dr. Baxevanis' focus has turned to analyzing the genomes of early branching metazoan phyla in an effort to better understand the relationship between genomic and morphological complexity, as well as the molecular basis for the evolution of novel cell types. Thematically, Dr. Baxevanis' current research interests are centered on probing the interface between genomics and developmental biology and conducting comparative, genomics-based research with an evolutionary point of view. These themes were elucidated in the 2011 document from the National Human Genome Research Institute (NHGRI) outlining a vision for the future of genomic research.

Until recently, only three of the four non-bilaterian metazoan lineages (Porifera, Placozoa, and Cnidaria) had at least one species whose genome had been sequenced. Ctenophora - the comb jellies - remained as the last non-bilaterian animal phylum without a sequenced genome, and its phylogenetic position remained uncertain. With the goal of understanding the molecular innovations that drove the surge in diversity and increasing complexity in early animal evolution, Dr. Baxevanis' group sequenced, assembled, annotated and analyzed the 150-megabase genome of the ctenophore, Mnemiopsis leidyi. By addressing the void in the availability of high-quality, genome-scale sequence data in a critical part of the evolutionary tree, Dr. Baxevanis' group resolved the question of the phylogenetic position of the ctenophores. The results of their phylogenomic analyses strongly suggest that ctenophores are the sister group to all other animals. Based on analyses of gene content, their results also suggest that neural and mesodermal cell types were either lost in Porifera and Placozoa or that to some extent these cell types evolved independently in the ctenophore lineage. These findings challenge long-held ideas regarding not only the phylogenetic position of the ctenophores, but of the evolution of the aforementioned cell types as well.

The availability of these data has also enabled Dr. Baxevanis' group to answer important questions regarding phylogenetic diversity and the evolution of protein families that play a fundamental role in metazoan development. For example, his group showed that Mnemiopsis contains a reduced set of homeodomains, supporting the placement of ctenophores at the base of the Metazoa. His group's work on the Wnt family showed that Wnt antagonists appear to be scarce in Mnemiopsis, suggesting that complex regulation of this pathway probably emerged later in animal evolution. Studies on the evolution of LIM proteins revealed a significant expansion of the LIM superclass at the base of the Metazoa, allowing for the increase in complexity required for the transition from a unicellular to multicellular lifestyle. A comprehensive phylogenetic analysis of the Sox family has provided strong evidence that the ancient primary function of Sox genes was to regulate the maintenance of stem cells and function in cell fate determination. His group also determined that there are no discernible microRNAs in Mnemiopsis and that key components of the microprocessor complex are missing, perhaps indicating a point in evolutionary time that pre-dated the development of additional plasticity in developmental signaling networks.Finally, as part of an in-depth study yielding the first metazoan phylogeny for the photoprotein gene family, Dr. Baxevanis' group was able to demonstrate co-localized expression of photoprotein genes and two putative opsin genes in developing Mnemiopsis photocytes, showing that these cells have the capacity to both sense and respond to stimuli. This finding is the first reported instance of photoreception and light production being functionally linked in the same cell type of a given organism, which may shed new light on the evolution of the eye.

Dr. Baxevanis' current work is focused on learning how these early branching animals could be used in the context of human disease research. Using a comparative genomics approach based on sequence data from animals across the metazoan tree, his group has found that non-bilaterian genomes contain a surprisingly high number of human disease gene homologs, despite their evolutionarily distant position with respect to humans. The findings from this study support the proposition that non-bilaterian animals have the potential to serve as viable models for studying various important classes of human diseases.

In related work, Dr. Baxevanis is now leading an international effort to sequence two Hydractinia species. The regenerative abilities of these hydrozoan cnidarians make them excellent models for the study of key questions related to pluripotency, allorecognition and stem cell biology, work that will be significantly advanced by the availability of high quality whole-genome sequencing data from these organisms.


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]

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]

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]

Maxwell, E.K., Schnitzler, C.E., Havlak, P., Putnam, N.H., Nguyen, A.-D., Moreland, R.T., and Baxevanis, A.D. Evolutionary Profiling Reveals the Heterogeneous Origins of Classes of Human Disease Genes: Implications for Modeling Disease Genetics in Animals. BMC Evol. Biol. 14: 212. 2014. [PubMed]

Török, A., Schiffer, P.H., Schnitzler, C.E., Ford, K., Mullikin, J.C., Baxevanis, A.D., Bacic, A., Frank, U., and Gornik, S.G. The Cnidarian Hydractinia Employs Canonical and Highly Adapted Histones to Pack its DNA. Epigenetics & Chromatin 9: 36. 2016. [PubMed]

Flici, H., Schnitzler, C.E., Millane, R.C., Govinden, G., Houlihan, A., Baxevanis, A.D., and Frank, U. An Evolutionarily Conserved SoxB-Hdac2 Crosstalk Regulates Neurogenesis in a Cnidarian. Cell Rep. 18: 1395-1409. 2017. [PubMed]

Bond, S.R., Keat, K.E., Barreira, S.N., and Baxevanis, A.D. BuddySuite: Command-Line Toolkits for Manipulating Sequences, Alignments, and Phylogenetic Trees. Mol. Biol. Evol. 34: 1543-1546. 2017. [In Process]

Gahan, J.M., Schnitzler, C.E., Doonan, L.B., Kanska, J., Gornik, S.G., Barreira, S., Thompson, K., Schiffer, P., Baxevanis, A.D., and Frank, U. Functional Studies on the Role of Notch Signaling in Hydractinia Development. Dev. Biol. 428: 224-231. 2017. [PubMed]

Instructional Videos

Current Topics in Genome Analysis 2016 Series
Biological Sequence Analysis I (2016)
Biological Sequence Analysis II (2016)

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.

Computational Genomics Unit Staff

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Sofia De Pereira Barreira, Ph.D.
  • Postdoctoral Fellow
  • Computational Genomics Unit
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Stephen R. Bond, Ph.D.
  • Postdoctoral Fellow
  • Computational Genomics Unit
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Christine Schintzler, Ph.D.
  • Guest Researcher
  • Computational Genomics Unit

Last updated: May 24, 2018