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Janies, Daniel

Dan Janies

Carol Grotnes Belk Distinguished Professor of Bioinformatics and Genomics
Bioinformatics and Genomics

Office: Bioinformatics 315
Email: djanies@uncc.edu
Phone: 704-687-1742
Biography: In July 2012, Daniel Janies joined the faculty of the University of North Carolina at Charlotte as The Carol Grotnes Belk Distinguished Professor of Bioinformatics and Genomics. Dr. Janies received a Bachelor of Sciences degree in Biology from the University of Michigan in 1988 and a Ph.D. in Zoology from the University of Florida in 1995. Dr. Janies worked as a postdoctoral fellow (1996 - 1999) and a principal investigator (2000-2002) at the American Museum of Natural History in New York City where he lead a team that, using off-the-shelf PC components, built one of the worlds largest computing clusters in 2001. Most recently Dr. Janies was a tenured faculty member in the College of Medicine at the Ohio State University. Dr. Janies is a national principal investigator in the Tree of Life program ( http://echinotol.org/ ) of the National Science foundation and is funded by the Defense Applied Research Projects Agency. His work involves empirical studies of organismal diversity and development of software, such as Supramap (https://supramap.renci.org/supramap/home). Supramap is used by public health scientists to put pathogen genomic data into context with geography and hosts. The results are akin to weather maps for disease.

Degree: Ph.D. Biology; University of Florida

Publications:

  • Daniel A. Janies, Laura W. Pomeroy, Chris Krueger, Yuqi Zhang, Izzet Senturk, Kamer Kaya, Ümit V. Çatalyürek. Phylogenetic visualization of the spread of H7 influenza A viruses. In press. Cladistics
  • Samuel K. Handelman, Jacob M. Aaronson, Michal Sweryn, Igor Voronkin, Jesse J. Kwiek, Wolfgang Sadee, Joseph S. Verduccie, and Daniel A. Janies. Cladograms with Path to Event (ClaPTE): A novel algorithm to detect associations between genotypes of phenotypes using phylogenies. In press. Computers in Biology and Medicine.
  • Kim, S., Miller, A., Brunson, C., Netchy, K., Clouse, R., Janies, D.,Tardy, E., Kerr, A. Shallow-water holothuroids (Echinodermata) of Yap, Federated States of Micronesia. Pacific Science vol. 68 no. 3. http://pacificscience.files.wordpress.com/2014/02/pac-sci-early-view-68-3-8.pdf
  • Goldberg, D., Cockburn, M., Hammond, T., Jacquez, G., Janies, D., Knoblock, C., Kuhn, W., Pultar, E., and Raubal, M. 2013. Envisioning a Future for a Spatial-Health CyberGIS Marketplace. HealthGIS 2013.
  • Zhang, L., Cressie, N., Pomeroy, L., Janies, D. 2013. Multi-species SIR Models from a Dynamical Bayesian Perspective. Theoretical Ecology. http://link.springer.com/article/10.1007%2Fs12080-013-0180-x
  • Mates, J., Kumar, S., Bazan, J., Mefford, M., Voronkin, I., Handelman, S., Mwapasa, V., Ackerman, W., Janies, D., Kwiek, J. 2013. Genotypic and phenotypic heterogeneity in the U3R region of HIV-1 subtype C.  AIDS Research and Human Retroviruses. http://online.liebertpub.com/doi/abs/10.1089/AID.2013.0026?mi=3yvu6q&af=R&searchText=breastfeeding&target=default&
  • Mounce, R. and Janies, D.  2013. Synergistic sharing of data and tools to enable team science.  In press in Computation for Humanity - Information Technology to Advance Society.  Justyna Zander and Pieter J. Mosterman eds.  CRC press.  http://www.crcpress.com/product/isbn/9781439883273
  • Janies, D. 2013. Xyloplax. McGraw-Hill 2013 Yearbook of Science & Technology.
  • Cai, Z., Eulenstein, O., Janies, D., Schwartz, D.  2013. Bioinformatics Research and Applications: 9th International Symposium, ISBRA 2013, Charlotte, NC, USA, May 20-22, 2013, Proceedings (Lecture Notes in Bioinformatics 7875; Springer)

  • Daniel A. Janies, Jonathon Studer, Samuel K. Handelman, Gregorio Linchangco. A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets. Cladistics. DOI: 10.1111/cla.12014. February 18, 2013. http://onlinelibrary.wiley.com/doi/10.1111/cla.12014/full.
  • Janies, D., Pomeroy, L., Aaronson, J., Handelman, S., Hardman, J., Kawalec, K., Bitterman, T., Wheeler, W.C. (2012) Analysis and visualization of H7 influenza using genomic, evolutionary and geographic information in a modular web service.Cladistics. DOI: 10.1111/j.1096-0031.2012.00401.x
  • Chakrabarty, P., Lam, C., Hardman, J., Aaronson, J., House, P., Janies, D. (2012) Speciesmap: A Web-Based Application for Determining the Effects of the 2010 Gulf Of Mexico Oil Spill on Wildlife, with a Preliminary List of Fishes Put at Risk. Biodiversity and Conservation.                                                                                                                 http://www.springerlink.com/openurl.asp?genre=article&id=doi:10.1007/s10...
  • Newman S., Hill, N., Spragens, K., Janies, D., Voronkin, I., Prosser, D., Baoping, Y., Lei, F., Batbayar, N., Tseveenmyadag, N., Bishop, C., Butler, P., Wikelski, M., Sivananinthaperumal, B., Mundkur, T., Douglas, D., and Takekawa, J. (2012) An Eco-Virological Approach for Assessing the Role of Wild Birds in the Spread of Avian Influenza H5N1 Along the Central Asian Flyway. PloS ONE. 7(2): e30636. doi:10.1371/journal.pone.0030636
  • Bokhari, S., Pomeroy, L., Janies, D. (2012) Reassortment Networks and the Evolution of Pandemic H1N1 Swine-origin Influenza. IEEE Transactions on Computational Biology and Bioinformatics.                                         http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2011.95
  • Janies D., Embi P.J., Payne P.R. Health-care hit or miss?: Collect genetic data on pathogens. Nature. Vol. 470, no. 7334. (February 17, 2011):329.                                                                                                                                                       http://www.nature.com/nature/journal/v470/n7334/full/470327a.html
  • Janies, D., Voight, J., Daly, M., (2011) Echinoderm Phylogeny including Xyloplax, a Progenetic Asteroid. Systematic Biology. 604:420-438 doi: 10.1093/sysbio/syr044
  • Studer, J. and Janies. D. (2011) Global spread and evolution of viral hemorrhagic septicemia virus. Journal of Fish Diseases. 34: 741–747. doi: 10.1111/j.1365-2761.2011.01290.x
  • Griffen, A., Beall C., Firestone, N., Gross, E., DiFranco J., Hardman, H., Vriesendorp, B., Faust, R., Janies, D., Leys, E., CORE: A Phylogenetically-Curated 16S rDNA Database of the Core Oral Microbiome. PLoS ONE 6(4):e19051. doi:10.1371/journal.pone.0019051
  • Kumar, S., Handelman, S., Voronkin I., Mwapasa V., Janies D., Rogerson S., Meshnick S., Kwiek J. (2011) Different Regions of HIV-1 Subtype C Env are Associated  with Placental Localization and in Utero Mother-to-Child Transmission. Journal of Virology.                                                                                                                                                                             http://jvi.asm.org/cgi/reprint/JVI.01955-10v1?view=long&pmid=21543508
  • Gross, E., E. Leys, S. Gasparovich, N. Firestone, J. Schwartzbaum, D. Janies, K. Asnani, A. Griffen, (2010) Bacterial 16S Sequence Analysis of Severe Caries in Young Permanent Teeth. Journal of Clinical Microbiology. 48:4121-8
    http://jcm.asm.org/cgi/content/abstract/JCM.01232-10v1
  • Bulach, D., R. Halpin, D. Spiro, L. Pomeroy, D. Janies, D. Boyle (2010) Molecular analysis of H7 avian influenza viruses from Australia and New Zealand: Genetic diversity and relationships – 1976 to 2007. Journal of Virology.
    http://jvi.asm.org/cgi/content/abstract/JVI.00930-10v1
  • Janies, D., I. Voronkin, M. Das, J. Hardman, T. Treseder, J. Studer. (2010) Genome Informatics of Influenza A. From data sharing to shared analytical capabilities.Animal Health Research Reviews. 11: 73-79
    http://journals.cambridge.org/repo_A78auyCI
  • Janies, D., T. Treseder, B. Alexandrov, F. Habib, J. Chen, R. Ferreira, Ü. Çatalyürek, A. Varón, W.C. Wheeler. (2010) The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases. Cladistics. 27: 61-
    66 http://dx.doi.org/10.1111/j.1096-0031.2010.00314.x
  • Janies, D., I. Voronkin, J. Studer, J. Hardman, B. Alexandrov, T. Treseder, C. Valson. (2010) Selection for resistance to oseltamivir in seasonal and pandemic H1N1 influenza and widespread co-circulation of the lineages. International Journal of Health Geographics. 9:13 http://dx.doi.org/10.1186/1476-072X-9-13
  • Hovmöller, R., B. Alexandrov, J. Hardman, D. Janies. (2010) Tracking the Geographic Spread of Avian Influenza (H5N1) with Multiple Phylogenetic Trees. Cladistics. 26:1–13.
    http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2009.00297.x/full
  • Bokhari, S. and D. Janies. (2010) Reassortment Networks for Investigating the Evolution of Segmented Viruses. IEEE Transactions on Computational Biology and Bioinformatics 7:288-298
    http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04585355
  • Hill, A.W., R. Guralnick, M. Wilson, F. Habib, D. Janies. (2009) Evolution of drug resistance in multiple distinct lineages of H5N1 avian influenza. Infection, Genetics, and Evolution. 9: 169-178. Top 10 most downloaded for the journal for 2009. http://linkinghub.elsevier.com/retrieve/pii/S1567134808001913
  • Yilmaz, A., M. Nishiyama, B. Garcia-Fuentes, G. Souza, D. Janies, J. Gray, E. Grotewold. (2009) GRASSIUS: A Platform for Comparative Regulatory Genomics Across the Grasses. Plant Physiol. doi:10.1104/pp.108.128579
  • Janies, D., F. Habib, B. Alexandrov, A. Hill, D. (2008) Pol. Evolution of genomes, host shifts, and geographic spread of SARS-CoV and related coronaviruses. Cladistics.
    24: 111–130. http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2008.00199.x/full
  • Ott, M., J. Zola, S. Aluru, A. Johnson, D. Janies, A. Stamatakis. (2008) Large-scale Phylogenetic Analysis on Current HPC Architectures. Scientific Programming. 16:255-270.
  • Janies, D. and D. Pol. (2008) Phylogenetic analysis of emerging infectious diseases. In Tutorials in Mathematical Biosciences IV: Evolution and Ecology (Lecture Notes in Mathematics / Mathematical Biosciences Sub series) A. Friedman ed. http://www.springerlink.com/content/978-3-540-74328-6#section=246925&page=1
  • Janies, D., A. Hill, R. Guralnick, F. Habib, E. Waltari, W. Wheeler. (2007) Genomic Analysis and Geographic Visualization of the Spread of Avian Influenza (H5N1). Systematic Biology. 56:321-9. http://sysbio.oxfordjournals.org/content/56/2/321.full
  • Habib, F., A. Johnson, R. Bundschuh, D. Janies. (2007) Large scale genotype-phenotype correlation analysis based on phylogenetic trees. Bioinformatics. 23:785-788 http://bioinformatics.oxfordjournals.org/content/23/7/785.abstract
  • Janies, D., P. Goloboff, D. Pol, Large-scale phylogenetic analysis for the study of zoonosis and assessment of influenza surveillance. Scalable Computing: Practice and Experience. Volume 8, Number 2, pp. 143–146. 2007
  • Salzberg, S., C. Kingsford, G. Cattoli, D. Spiro, D. Janies, et al., (2007) Genome analysis links recent European and African H5N1 influenza viruses and shows them to be distinct from earlier outbreak strains. Emerging Infectious Diseases. 13:5
  • Zhang, X., M. Hasoksuz, D. Spiro, R. Halpin, S. Wang, A. Vlasova, D. Janies, L. Jones, E. Ghedin, L. Saif. (2007) Quasispecies of bovine enteric and respiratory coronaviruses based on complete genome sequences and genetic changes after tissue culture adaptation. Virology. 363:1-10
  • Vinh, L., A. Varon, D. Janies, W. Wheeler. (2007) Towards Phylogenomic Reconstruction. International Conference on Bioinformatics and Computational Biology. BIOCOMP'07. CSREA Press Vol. 1, page: 98-104.
  • Zhang X., M. Hasoksuz, D. Spiro, R. Halpin, S. Wang, S. Stollar, D. Janies, N. Hadya, Y. Tang, E. Ghedin, L. Saif. (2007) Complete genomic sequences, a key residue in the spike protein and deletions in non-structural protein 3b of US strains of the virulent and attenuated coronaviruses, transmissible gastroenteritis virus and porcine respiratory coronavirus. Virology. 358:424-35.