Citation Link
Carter, T., Kebede, S. Lopez, K., Bonnell, V., Damodaran, L., Aseffa, A., Janies, D. in press. Glucose-6-phosphate dehydrogenase deficiency (G6PD) genetic variants in malaria patients in southwestern Ethiopia.  American Journal of Tropical Medicine & Hygiene.
Linchangco, G., Foltz, D., Reid, R., Williams, J., Nodzak, C., Kerr, A., Miller, A., Hunter, R., Wilson, N., Nielsen, W., Mah, C., Rouse, G., Wray, G., Janies, D. 2017. The phylogeny of extant starfish (Asteroidea: Echinodermata) including Xyloplax, based on comparative transcriptomics.  Molecular Phylogenetics and Evolution. Volume 115, October 2017, Pages 161-170
Clouse, R.M., Branstetter, M.G., Buenavente, P.A.C., Crowley, L.M., Czekanski-Moir, J., General, D.E.M., Giribet, G., Harvey, M.S., Janies, D.A., Mohagan, A.B., Sharma, P.P. & Wheeler, W.C. 2017. First molecular phylogeny of two arachnid orders (Schizomida and Uropygi) supports a tropical Pangean origin and mid-Cretaceous diversification. Journal of Biogeography. Link
Janies, D.,  Ford, C.,  Damodaran, L., Witter. Z.  2016. Spread of Middle East Respiratory Coronavirus: Genetic versus Epidemiological Data.  International Society for Disease Surveillance Conference December 6-9th in Atlanta, GA Link
de Bernardi Schneider, A., Malone,  R., Guo, J.T., Homan, J., Linchangco, G., Witter, Z., Vinesett, D., Damodaran, L., Janies. D. 2017. Molecular evolution of Zika virus as it crossed the Pacific to the Americas.  Cladistics 33: 1-20.   Link
Julien Herrmann, Zachary L. Witter, Nakul Patel, Jonathan Kho,  Daniel A. Janies,  Ümit V. Çatalyürek. 2016. Visual analytics on the spread of pathogens.  BCB'16, October 2-5, 2016, Seattle, WA, USA.
Galac, M., Bosch, I., Janies, D. 2016. Bacterial communities of oceanic sea star (Asteroidea: Echinodermata) larvae.  Marine Biology.  July 2016, 163:162. Link
Nathalie Oulhen, Andreas Heylan, Tyler Carrier, Vanesa Zazueta, Tara Fresques, Jessica Laird, Thomas Onorato, Daniel Janies, Gary Wessel.  2016.  Regeneration in bipinnaria larvae of the bat star Patiria miniata induces rapid and broad new gene expression. Mechanisms of Development. 142:10-21.
Robert W Malone, Jane Homan, Michael V Callahan, Jill Glasspool-Malone, Lambodhar Damodaran, Adriano De Bernardi Schneider, Rebecca Zimler, James Talton, Ronald R Cobb, Ivan Ruzic, Julie Smith-Gagen, James Wilson, Daniel Janies 2016.  Zika Virus: Medical Countermeasure Development Challenges. PLoS Negl Trop Dis 10(3): e0004530. doi: 10.1371/journal.pntd.0004530
Daniel A. Janies, Zach Witter, Gregorio V. Linchangco, David W. Foltz, Allison K. Miller, Alexander M. Kerr, Jeremy Jay, Robert W. Reid, and Gregory A. Wray 2016. EchinoDB, an application for comparative transcriptomics of deeply-sampled clades of echinoderms. BMC Bioinformatics.  DOI: 10.1186/s12859-016-0883-2 Link
Clouse RM, Linchangco Jr GV, Kerr AM, Reid RW, Janies DA 2015. Phylotranscriptomic analysis uncovers a wealth of tissue inhibitor of metalloproteinases variants in echinoderms. Royal Society Open Science. 2: 150377. Link
Daniel Janies, Zachary Witter, Christian Gibson, Thomas Kraft, Izzet F. Senturk, Ümit Çatalyürek. 2015. Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application. MEDINFO-2015. Link
Christopher Jones; Meet Zandawala; Dean Semmens; Sarah Anderson; Graeme Hanson; Daniel Janies; Maurice Elphick. 2015. Identification of a neuropeptide precursor protein that gives rise to a "cocktail" of peptides that bind Cu(II) and generate metal-linked dimers. BBA - General Subjects.  In Press.
Ana B Christensen; Joseph L Herman; Maurice R Elphick; Kord M Kober; Daniel Janies; Gregorio Linchangco; Dean C Semmens; Xavier Bailly; Serge N Vinogradov; David Hoogewijs. 2015.  Phylogeny of Echinoderm hemoglobins, PLoS One.
Stephen W. Attwood, Motomu Ibaraki, Yasuhide Saitoh, Naoko Nihei, Daniel A Janies. 2015. Comparative Phylogenetic Studies on Schistosoma japonicum and its Snail Intermediate Host Oncomelania hupensis: Origins, Dispersal and Coevolution. PLOS Neglected Tropical Diseases. DOI:10.1371/journal.pntd.0003935
Danielle M. Grace-Lema, Solomon Yared, Andrew Quitadamo, Daniel A. Janies, Ward C. Wheeler, Meshesha Balkew, Asrat Hailu, Alon Warburg, Ronald M. Clouse. 2015  A molecular phylogeny of sand flies (Diptera : Psychodidae : Phlebotominae), using recent Ethiopian collections and a broad selection of public sequence data. Systematic Entomology. DOI: 10.1111/syen.12135
Hoffman M, Luo Y, Monday SR, Ottensen A, Gonza-les-Escalona N, Timme R, Muruvanda R, Wang C, Kastanis G, Keys C, Janies D, Senturk I, Catalyurek UV, Hammack TS, Chu A, Myers R, Haendiges J, Wolfgang WJ, Schoonmaker-Bopp D, Evans P, Meng J, Strain E, Allard MW, Brown EW. 2016. Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak linked to Tuna from an Indian Facility. Journal of Infectious Diseases.  213:502-508
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. Cladistics. Article first published online: 21 JAN 2015 DOI: 10.1111/cla.12107.  Link
Samuel K. Handelman, Jacob M. Aaronson, Michal Sweryn, Igor Voronkin, Jesse J. Kwiek, Wolfgang Sadee, Joseph S. Verducci, and Daniel A. Janies. Cladograms with Path to Event (ClaPTE): A novel algorithm to detect associations between genotypes of phenotypes using phylogenies. Computers in Biology and Medicine. Published Online: December 23, 2014. Link
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 63(3). Link
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.  Link
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. Link
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. Link
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. Link
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
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.  Link
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.  Link
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
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. Link
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 ONE6(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. Link
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 Link
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. Link
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 Link
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 Link
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 Link
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. Link
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. Link
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. Link
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. Link
Ott, M., J. Zola, S. Aluru, A. Johnson, D. Janies, A. Stamatakis. (2008) Large-scale Phylogenetic Analysis on Current HPC Architectures. Scientific Programming. 4:25 PM5-270.
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. Link
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. Link
Habib, F., A. Johnson, R. Bundschuh, D. Janies. (2007) Large scale genotype-phenotype correlation analysis based on phylogenetic trees. Bioinformatics. 23:785-788  Link
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.
Kurc, T., D. Janies, A. Johnson, S. Langella, S. Oster, S. Hastings, F. Habib, T. Camerlengo, D. Ervin, U. Catalyurek, J. Saltz. (2006) An XML-based System for Synthesis of Data from Disparate Databases.  Journal of the American Medical Informatics Association. 13:289-301.
Wheeler, W.C., L. Aagesen, C.P. Arango,  J. Faivovich, T. Grant, C. D'Haese,  D. Janies, W.L. Smith,  A. Varón,  G. Giribet. (2006) Dynamic homology and phylogenetic systematics: a unified approach using POY. American Museum of Natural History, New York.  365 pp. ISBN 0-913424-58-7.
Wang, Q., M. Han, J. Funk, G. Bowman, D. Janies, L.J. Saif. (2005) Genetic diversity and recombination of porcine sapoviruses. Journal of Clinical Microbiology. 43: 5963-72.
Hastings, S., S. Langella, S. Oster, T. Kurc, T. Pan, U. Catalyurek, D. Janies, Saltz, J. (2005) Grid-based Management of Biomedical Data using an XML-based Distributed Data Management System. Symposium on Applied Computing. Santa Fe. March 13-17, 2005. 
Clouse, R., D. Janies, A. Kerr. (2005) Resurrection of Bohadschia bivittata from B. marmorata (Holothuroidea: Holothuriidae) based on behavioral, morphological, and mitochondrial DNA evidence. Zoology. 108:27-39.
Kerr, A., D. Janies, R. Clouse, J. Kuszak, J. Kim. (2005) Molecular phylogeny of coral-reef sea cucumbers (Holothuroidea: Aspidochirotida) based on 16S mtrDNA sequence. Marine Biotechnology. 7:53-60.
Janies, DA. (2004)  "Evolution of asterozoan echinoderms and their development." Echinoderms: München: 586-587. Balkema International Publishers, T. Heinzeller and J.H. Nebelsick (eds): Leiden, Netherlands. 
Wheeler, W., Janies, D., DeLaet, J., (2004) Parallel computing and sequence alignment. McGraw-Hill 2004 Yearbook of Science & Technology.
Janies, D. (2003) Reversibility in life cycle and larval evolution among echinoderms.  Cladistics 19:154.
Janies, D. (2003) Bioinformatics. Access science @ McGraw Hill. Link
Janies, D. and W. Wheeler. (2002) Theory and practice of parallel direct optimization, in Techniques in Molecular Systematics and Evolution.  R. Desalle, G. Giribet, and W. Wheeler (eds). Birkhauser Verlag, Basel. pp. 115-23.
Janies, D and W. Wheeler. (2001)  Efficiency of parallel direct optimization. Cladistics. 17: S71-S82. 
Janies, D. (2001) Phylogenetic relationships of extant echinoderm classes. Canadian Journal of Zoology. 79:1232-1250.
Frost, D., R. Etheridge, D. Janies, and T. Titus. (2001) Total evidence, sequence alignment, evolution of polychrotid lizards, and a reclassification of the Iguania (Squamata: Iguanania). American Museum of Natural History, Novitates. 3343. 38 pp.
Frost, D., D. Janies, P. le Fras Mouton, T. Titus. (2001) A molecular perspective on the phylogeny of the girdled lizards (Cordylidae, Squamata). American Museum of Natural History, Novitates. 3310. 
Giribet, G., D. Janies, and W. Wheeler. (2001) Introduction. Cladistics. 17: S1-S2.
Phillips, A. D. Janies, and W. Wheeler. (2000)  Multiple sequence alignment in phylogenetic analysis. Molecular Phylogenetics and Evolution. 16:317-30.
Blake, D., D. Janies, and R. Mooi. (2000) Evolution of Starfishes: Morphology, Molecules, Development, and Paleobiology. American Zoologist. 40: 311-315.
Janies, D. and R. Desalle. (1999) Development, Evolution, and Corroboration.  Anatomical Record (The New Anatomist). 257: 6-14. 
Janies D. and R.  Mooi. (1999) Xyloplax is an asteroid. in Echinoderm Research 1998, M. Candia Carnevali and F. Bonasoro (eds).  Balkema, Rotterdam. pp. 311-316.
McEdward, L. and D. Janies. (1997) Relationships among development, ecology, and morphology in the evolution of echinoderm larvae and life cycles.  Biological Journal of the Linnean Society. 60: 381-400.
Janies, D. A. and L. R. McEdward. (1994) Heterotopy, pelagic direct development, and new body plans in velatid asteroids, in: Echinoderms Through Time, B. David , A. Guille , J.P. Féral, and M. Roux (eds). Balkema, Rotterdam, Netherlands.  319-324.
Janies, D. A. and L. R. McEdward. (1994) A hypothesis for the evolution of the concentricycloid water-vascular system, in: Reproduction and Development of Marine Invertebrates, W.H. Wilson Jr., S.A. Stricker, and G.L. Shinn (eds) Johns Hopkins Press, Baltimore.  246-257.
Janies, D. A. and L. R. McEdward. (1993) Highly derived coelomic and water-vascular morphogenesis in a starfish with pelagic direct development.  Biological Bulletin.  185: 56-76.
McEdward, L. R. and D. A. Janies. (1993) What is a larva?  Life cycle evolution in asteroids.  Biological Bulletin.  184: 255-268.