Citation Link
Tamar E Carter, Araya Gebresilassie, Shantoy Hansel, Lambodhar Damodaran, Callum Montgomery, Victoria Bonnell, Karen Lopez, Daniel Janies, Solomon Yared. "Analysis of the Knockdown Resistance Locus (kdr) in Anopheles stephensi, An. arabiensis, and Culex pipiens sl for Insight Into the Evolution of Target-site Pyrethroid Resistance in Eastern Ethiopia." The American journal of tropical medicine and hygiene (2022).https://doi.org/10.4269/ajtmh.20-1357 Link
Ford, Anthony, Daniel Kepple, Jonathan Williams, Gabrielle Kolesar, Colby T. Ford, Abnet Abebe, Lemu Golassa, Daniel A. Janies, Delenasaw Yewhalaw, and Eugenia Lo. "Gene Polymorphisms Among Plasmodium vivax Geographical Isolates and the Potential as New Biomarkers for Gametocyte Detection." Frontiers in Cellular and Infection Microbiology (2022): 1438. https://doi.org/10.3389/fcimb.2021.789417 Link
Gezahegn Solomon Alemayehu, Kayla Blackburn, Karen Lopez, Cheikh Cambel Dieng, Eugenia Lo, Daniel Janies, Lemu Golassa. "Detection of high prevalence of Plasmodium falciparum histidine-rich protein 2/3 gene deletions in Assosa zone, Ethiopia: implication for malaria diagnosis" Malaria Journal 20 , No.1 (2021):1-11.https://doi.org/10.1186/s12936-021-03629-x Link
Gezahegn Solomon Alemayehu, Alebachew Messele, Kayla Blackburn, Karen Lopez, Eugenia Lo, Daniel Janies, Lemu Golassa. "Genetic variation of Plasmodium falciparum histidine-rich protein 2 and 3 in Assosa zone, Ethiopia: its impact on the performance of malaria rapid diagnostic tests" Malaria Journal 20 , No.1 (2021):1-13.https://doi.org/10.1186/s12936-021-03928-3 Link
Gezahegn Solomon Alemayehu, Karen Lopez, Cheikh Dieng, Eugenia Lo, Daniel Janies, and Lemu Golassa, Performance of PfHRP2 and PfPLDH Rapid Diagnostics Test for Diagnosis of Plasmodium falciparum in Assosa Zone, Northwest Ethiopia. The American Journal of Tropical Medicine and Hygiene 2020. http://www.ajtmh.org/content/journals/10.4269/ajtmh.20-0485 Link
Tamar E Carter, Solomon Yared, Dejene Getachew, Joseph Spear, Sae Hee Choi, Jeanne N Samake, Peter Mumba, Dereje Dengela, Gedeon Yohannes, Sheleme Chibsa, Matthew Murphy, Gunawardena Dissanayake, Cecilia Flately, Karen Lopez, Daniel Janies, Sarah Zohdy, Seth R Irish, Meshesha Balkew. "Genetic diversity of Anopheles stephensi in Ethiopia provides insight into patterns of spread" Parasites & vectors 14, No.602 (2021):1-12.https://doi.org/10.1186/s13071-021-05097-3 Link
Tamar E Carter, Solomon Yared, Dejene Getachew, Joseph Spear, Sae Hee Choi, Jeanne N Samake, Peter Mumba, Dereje Dengela, Gedeon Yohannes, Sheleme Chibsa, Matthew Murphy, Gunawardena Dissanayake, Cecilia Flately, Karen Lopez, Daniel Janies, Sarah Zohdy, Seth R Irish, Meshesha Balkew. "Tracking of Anopheles stephensi in Ethiopia using mitochondrial DNA reveals pattern of spread." bioRxiv (2021).https://doi.org/10.1101/2021.04.07.437873 Link
Shi Chen, Rajib Paul, Daniel Janies, Keith Murphy, Tinghao Feng, Jean-Claude Thill." Exploring feasibility of multivariate deep learning models in predicting covid-19 epidemic" Frontiers in public health 9 (2021).https://doi.org/10.3389/fpubh.2021.661615 Link
Shi Chen, Lina Zhou, Yunya Song, Qian Xu, Ping Wang, Kanlun Wang, Yaorong Ge, Daniel Janies." A novel machine learning framework for comparison of viral COVID-19–Related Sina Weibo and Twitter Posts: Workflow Development and Content Analysis"Journal of medical Internet research 23, No.1 (2021).https://doi.org/10.2196/24889 Link
Shi Chen, Lina Zhou, Yunya Song, Qian Xu, Ping Wang, Kanlun Wang, Yaorong Ge, Daniel Janies." Comparison of Viral COVID-19 Sina Weibo and Twitter Contents: a Novel Feature Extraction and Analytical Workflow." Journal of Medical Internet Research (2021). Link
Cheikh Cambel Dieng, Colby T Ford, Anita Lerch, Dickson Doniou, Jennifer Huynh, Kovidh Vegesna, Jun-tao Guo, Daniel Janies, Linda Amoah, Yaw Afrane, Eugenia Lo. "Protein Interaction Analysis of Plasmodium falciparum Circumsporozoite Protein Variants With Human Immunoproteins Explains RTS,S Vaccine Efficacy" Plasmodium falciparum (2021).http://dx.doi.org/10.2139/ssrn.4000573 Link
Colby T Ford, Gezahegn Solomon Alemayehu, Kayla Blackburn, Karen Lopez, Cheikh Cambel Dieng, Lemu Golassa, Eugenia Lo, Daniel Janies." Modeling Plasmodium falciparum Diagnostic Test Sensitivity using Machine Learning with Histidine-Rich Protein 2 Variants" Frontiers in Tropical Diseases (2021).https://doi.org/10.3389/fitd.2021.707313 Link
Colby T Ford, Denis Jacob Machado, Daniel A Janies. "Predictions of the SARS-CoV-2 Omicron variant (B. 1.1. 529) spike protein receptor-binding domain structure and neutralizing antibody interactions." bioRxiv (2021).https://doi.org/10.1101/2021.12.03.471024 Link
Colby T Ford, Rachel Scott, Denis Jacob Machado, Daniel Janies. "Sequencing data of North American SARS-CoV-2 isolates shows widespread complex variants" medRxiv (2021).https://doi.org/10.1101/2021.01.27.21250648 Link
Daniel Kepple, Alfred Hubbard, Musab M Ali, Beka R Abargero, Karen Lopez, Kareen Pestana, Daniel A Janies, Guiyun Yan, Muzamil Mahdi Hamid, Delenasaw Yewhalaw, Eugenia Lo. "Plasmodium vivax From Duffy-Negative and Duffy-Positive Individuals Share Similar Gene Pools in East Africa" The Journal of Infectious Diseases 224, No.8 (2021): 1422-1431.https://doi.org/10.1093/infdis/jiab063 Link
Denis Jacob Machado, Rachel Scott, Sayal Guirales, Daniel A Janies. "Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2" Cladistics 37, No.5 (2021). https://doi.org/10.1111/cla.12454 Link
Denis Jacob Machado, Richard Allen White, Janice Kofsky, Daniel A Janies. "Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions" Antimicrobial Stewardship and Healthcare Epidemiology 1, (2021) https://doi.org/10.1017/ash.2021.222 Link
Shaun Truelove, Claire P. Smith, Michelle Qin, Luke C. Mullany, Rebecca K. Borchering, Justin Lessler, Katriona Shea, Emily Howerton, Lucie Contamin, John Levander, Jessica Salerno, Harry Hochheiser, Matt Kinsey, Kate Tallaksen, Shelby Wilson, Lauren Shin, Kaitlin Rainwater-Lovett, Joseph C. Lemaitre, Juan Dent, Joshua Kaminsky, Elizabeth C. Lee, Javier Perez-Saez, Alison Hill, Dean Karlen, Matteo Chinazzi, Jessica T. Davis, Kunpeng Mu, Xinyue Xiong, Ana Pastore y Piontti, Alessandro Vespignani, Ajitesh Srivastava, Przemyslaw Porebski, Srinivasan Venkatramanan, Aniruddha Adiga, Bryan Lewis, Brian Klahn, Joseph Outten, James Schlitt, Patrick Corbett, Pyrros Alexander Telionis, Lijing Wang, Akhil Sai Peddireddy, Benjamin Hurt, Jiangzhuo Chen, Anil Vullikanti, Madhav Marathe, Stefan Hoops, Parantapa Bhattacharya, Dustin Machi, Shi Chen, Rajib Paul, Daniel Janies, Jean-Claude Thill, Marta Galanti, Teresa Yamana, Sen Pei, Jeffrey Shaman, Nicholas G. Reich, Jessica M. Healy, Rachel B. Slayton, Matthew Biggerstaff, Michael A. Johansson, Michael C. Runge, and Cécile Viboud,"Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination." medRxiv , no.2 (2021).https://doi.org/10.1101/2021.08.28.21262748 Link
TE Carter, A Gebresilassie, S Hansel, L Damodaran, C Montgomery, V Bonnell, K Lopez, D Janies, S Yared. "Comparison of the knockdown resistance locus (kdr) inAnopheles stephensi,An. arabiensis, andCulex pipiens s.l.suggests differing mechanisms of pyrethroid resistance in east Ethiopia." bioRxiv (2020).https://doi.org/10.1101/2020.05.13.093898 Link
Shi Chen, Yakubu Owolabi, Ang Li, Eugenia Lo, Patrick Robinson, Daniel Janies, Chihoon Lee, Michael Dulin." Patch dynamics modeling framework from pathogens’ perspective: Unified and standardized approach for complicated epidemic systems" PloS one 15, No.10 (2020).https://doi.org/10.1371/journal.pone.0238186 Link
Colby T Ford, Daniel Janies." Ensemble machine learning modeling for the prediction of artemisinin resistance in malaria" F1000Reseach 9 (2020).https://doi.org/10.12688/f1000research.21539.5 Link
Sayal Guirales, Denis Jacob Machado, Adriano de Bernardi Schneider, Daniel Janies." FLAVi-Web: A Web Annotator for Viral Genomes of Flaviviridae with a Revised Phylogeny of the Family"The FASEB Journal 34, No.S1 (2020):1.https://doi.org/10.1096/fasebj.2020.34.s1.09730 Link
Daniel A Janies, Larry R McEdward." Heterotopy, pelagic direct development, and new body plans in velatid asteroids" Echinoderms Through Time (2020):319-324. https//doi.org/10.1201/9781003077831-73 Link
Vladimir Mashanov, Jennifer Akiona, Maleana Khoury, Jacob Ferrier, Robert Reid, Denis Jacob Machado, Olga Zueva, Daniel Janies." Active Notch signaling is required for arm regeneration in a brittle star" PloS one 15, No.5 (2020).https://doi.org/10.1371/journal.pone.0232981 Link
Katriona Shea, Rebecca K Borchering, William JM Probert, Emily Howerton, Tiffany L Bogich, Shouli Li, Willem G van Panhuis, Cecile Viboud, Ricardo Aguás, Artur Belov, Sanjana H Bhargava, Sean Cavany, Joshua C Chang, Cynthia Chen, Jinghui Chen, Shi Chen, YangQuan Chen, Lauren M Childs, Carson C Chow, Isabel Crooker, Sara Y Del Valle, Guido España, Geoffrey Fairchild, Richard C Gerkin, Timothy C Germann, Quanquan Gu, Xiangyang Guan, Lihong Guo, Gregory R Hart, Thomas J Hladish, Nathaniel Hupert, Daniel Janies, Cliff C Kerr, Daniel J Klein, Eili Klein, Gary Lin, Carrie Manore, Lauren Ancel Meyers, John Mittler, Kunpeng Mu, Rafael C Núñez, Rachel Oidtman, Remy Pasco, Ana Pastore y Piontti, Rajib Paul, Carl AB Pearson, Dianela R Perdomo, T Alex Perkins, Kelly Pierce, Alexander N Pillai, Rosalyn Cherie Rael, Katherine Rosenfeld, Chrysm Watson Ross, Julie A Spencer, Arlin B Stoltzfus, Kok Ben Toh, Shashaank Vattikuti, Alessandro Vespignani, Lingxiao Wang, Lisa White, Pan Xu, Yupeng Yang, Osman N Yogurtcu, Weitong Zhang, Yanting Zhao, Difan Zou, Matthew Ferrari, David Pannell, Michael Tildesley, Jack Seifarth, Elyse Johnson, Matthew Biggerstaff, Michael Johansson, Rachel B Slayton, John Levander, Jeff Stazer, Jessica Salerno, Michael C Runge." COVID-19 reopening strategies at the county level in the face of uncertainty: Multiple Models for Outbreak Decision Support" medRxiv (2020).https://doi.org/10.1101/2020.11.03.20225409 Link
Solomon Yared, Araya Gebressielasie, Lambodhar Damodaran, Victoria Bonnell, Karen Lopez, Daniel Janies, Tamar E Carter." Insecticide resistance in Anopheles stephensi in Somali Region, eastern Ethiopia" Malaria Journal 19, No1 (2020):1-7.https://doi.org/10.1186/s12936-020-03252-2 Link
Adriano de Bernadi Schneider, Denis Jacob Machado, Sayal Guirales, and Daniel A. Janies, FLAVi: An Enhanced Annotator for Viral Genomes of Flaviviridae. Viruses 2020, 12, 892. https://www.mdpi.com/1999-4915/12/8/892 Link
Shi Chen, Patrick Robinson, Daniel Janies, and Michael Dulin, Four Challenges Associated with Current Mathematical Modeling Paradigm of Infectious Diseases and Call for a Shift. Open Forum Infectious Diseases, ofaa333, https://doi.org/10.1093/ofid/ofaa333 Link
Colby T. Ford, Gabriel Lopez Zenarosa, Kevin B. Smith, David C. Brown, John Williams, and Daniel Janies, Genetic capitalism and stabilizing selection of antimicrobial resistance genotypes in Escherichia coli, Cladistics, https://onlinelibrary.wiley.com/doi/abs/10.1111/cla.12421 Link
Jia Wen, Colby T. Ford, Daniel Janies, Xinghua Shi, A Parallelized Strategy for Epistasis Analysis Based on Empirical Bayesian Elastic Net Models, Bioinformatics, btaa216, https://doi.org/10.1093/bioinformatics/btaa216 Link
Jih-Pai Lin, Mong-Hsun Tsai, Andreas Kroh, Aaron Trautman, Denis Jacob Machado, Lo-Yu Chang, Robert Reid, Kuan-Ting Lin, Omri Bronstein, Shyh-Jye Lee, Daniel Janies. The first complete mitochondrial genome of the sand dollar Sinaechinocyamus mai (Echinoidea: Clypeasteroida). Genomics. 2019 Oct 17. pii: S0888-7543(19)30185-5. doi: 10.1016/j.ygeno.2019.10.007. Link
Vladimir Mashanov, Jennnifer Akiona, Maleana Khoury, Jacob Ferrier, Robert Reid, Denis Jacob Machado, Olga Zueva, Daniel Janies. 2019. Active Notch Signaling is Required for Arm Regeneration in a Brittle Star. bioRxiv 2019.12.13.875401. Link
Colby T. Ford, Daniel Janies. Ensemble Machine Learning Modeling for the Prediction of Artemisinin Resistance in Malaria. F1000Research 2020, 9:62 Link
Meshesha Balkew, Peter Mumba, Dereje Dengela, Gedeon Yohannes, Dejene Getachew, Solomon Yared, Sheleme Chibsa, Matthew Murphy, Kristen George, Karen Lopez, Daniel Janies, Sae Hee Choi, Joseph Spear, Seth R Irish, Tamar E Carter, 2020. Geographical distribution of Anopheles stephensi in eastern Ethiopia. Parasites Vectors 13, 35. Link
Adriano de Bernardi Schneider, Denis Jacob Machado, Daniel Janies. 2019. Enhanced genome annotation strategy provides novel insights on the phylogeny of Flaviviridae. bioRxiv 674333. Link
Thomas A. Ebert, Daniel Janies. 2019. Modeling the life cycle of echinoderm larvae clones. University of Miami - Rosenstiel School of Marine and Atmospheric Science. Link
Daniel Janies, Yoalli Quetzalli Hernández-Díaz, Francisco Alonso Solís-Marín, Karen Lopez, Boyan Alexandrov, Madeline Galac, Joan Herrera, Janessa Cobb, Thomas A. Ebert, and Isidro Bosch. 2019. Discovery of Adults Linked to Cloning Oceanic Starfish Larvae (Oreaster, Asteroidea: Echinodermata). The Biological Bulletin. Link
Shi Chen, Ari Whiteman, Ang Li, Tyler Rapp, Eric Delmelle, Gang Chen, Cheryl L. Brown, Patrick Robinson, Maren J. Coffman, Daniel Janies, Michael Dulin. 2019. An operational machine learning approach to predict mosquito abundance based on socioeconomic and landscape patterns. Landscape Ecology. Link
Eugenia Lo, Jessica B. Hostetler, Delenasaw Yewhalaw, Richard D. Pearson, Muzamil M. A. Hamid, Karthigayan Gunalan, Daniel Kepple, Anthony Ford, Daniel A. Janies, Julian C. Rayner, Louis H. Miller, Guiyun Yan. 2019. Frequent expansion of Plasmodium vivax Duffy Binding Protein in Ethiopia and its epidemiological significance. PLOS Neglected Tropical Diseases 13(9): e0007222. Link
Lambodhar Damodaran, Adriano de Bernardi Schneider, Shi Chen, Daniel A Janies. 2019. Evolution of endemic and sylvatic lineages of dengue virus. Cladistics. Link
Adriano de Bernardi Schneider, Roman Ochsenreiter, Reilly Hostager, Ivo L. Hofacker, Daniel Janies and Michael T. Wolfinger. 2019. Updated Phylogeny of Chikungunya Virus Suggests Lineage-Specific RNA Architecture. Viruses. Link
Daniel Janies. 2019. Phylogenetic concepts and tools applied to epidemiologic investigations of infectious diseases. ASM Microbiology Spectrum. 7(4). Link
Trevisan B, Alcantara DMC, Machado DJ, Marques FPL, Lahr DJG. 2019. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ 7:e7543 Link
Adriano de Bernardi Schneider, Colby T Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V Çatalyürek, Joel O Wertheim, Daniel Janies, StrainHub: A phylogenetic tool to construct pathogen transmission networks, Bioinformatics, btz646, in press Link
Chen, S., Whiteman, A., Li, A., Rapp, T., Delmelle, E., Chen, G., Brown, C.L., Robinson, P., Coffman, M.J., Janies, D., and Dulin, M. 2019. An operational machine learning approach to predict mosquito abundance based on socioeconomic and landscape patterns. Landscape Ecology, in press
Janessa C. Cobb, John M. Lawrence, Joan C. Herrera, Karen Lopez and Daniel Janies. (2019) A new species of Astropecten (Echinodermata: Asteroidea: Paxillosida: Astropectinidae) and a comparison of the Astropecten species from the Gulf of Mexico and the East Florida Shelf. Accepted, Zootaxa. Link
Tamar Carter, Solomon Yared, Shantoy Hansel, Karen Lopez, Daniel Janies. (2019). Sequence-based identification of Anopheles species in eastern Ethiopia. Malaria Journal. Link
Tyler J. Carrier, Kennedy Wolfe, Karen Lopez, Mailie Gall, Daniel A. Janies, Maria Byrne, Adam M. Reitzel. 2018. Diet-induced shifts in the crown-of-thorns (Acanthaster sp.) larval microbiome. Marine Biology. Link
Ezeoke, I., Galac, M., Lin, Y., Liem, A., Roth, P., Kilianski, A., Gibbons, H., Bloch, D., Kornblum, D., Del Rosso, P., Janies, D., Weiss, D. (2018). Tracking a serial killer: Integrating phylogenetic relationships, epidemiology, and geography for two invasive meningococcal disease outbreaks. PLoS ONE. 13(11). Link
Eugenia Lo, Mariangela Bonizzoni, Elizabeth Hemming-Schroeder, Anthony Ford, Daniel A. Janies, Anthony A. James, Yaw Afrane, Harrisone Etemesi, Guofa Zhou, Andrew Githeko, and Guiyun Yan. Selection and Utility of Single Nucleotide Polymorphism Markers to Reveal Fine-Scale Population Structure in Human Malaria Parasite Plasmodium falciparum. Front. Ecol. Evol., 26 September 2018 Link
Jacob Machado, D., Janies, D., Brouwer, C., Grant, T., 2018. A New Strategy to Infer Circularity Applied to Four New Complete Frog Mitogenomes. Ecology and Evolution. 8:4011–4018 Link
Carlos E. Santibáñez-López, Ricardo Kriebel, Jesús A. Ballesteros, Nathaniel Rush, Zachary Witter, John Williams, Daniel A. Janies, Prashant P. Sharma. 2018. Integration of phylogenomics and molecular modeling reveals lineage-specific diversification of toxins in scorpions. PeerJ doi: 10.7717/peerj.5902 Link
Carter, T.E., Yared, S., Gebresilassie, A., Bonnell, V., Damodaran, L., Lopez, K., Ibrahim, M., Mohammed, S., Janies, D. 2018. First detection of Anopheles stephensi [Liston, 1901 (Diptera: Culicidae)] in Ethiopia using molecular and morphological approaches. Link
Carrier, T.J., Wolfe, K., Lopez, K., Gall, M., Janies, D., Byrne, M., and Reitzel, A.M. 2018. Diet-induced shifts in the crown-of-thorns (Acanthaster sp.) larval microbiome. Marine Biology. Accepted.
Macrander, J., Panda, J., Janies, D., Daly, M., Reitzel, A.M. 2018. Venomix: A Simple Bioinformatic Pipeline for Identifying and Characterizing Toxin Gene Candidates from Transcriptomic Data. PeerJ. Link
Campioni, F., Cao, G., Kastanis, G., Janies, D., Bergamini, A., Rodrigues, D., Stones, R., Brown, E., Allard, M., and Falcao, J. 2018. Changing of the Genomic Pattern of Salmonella Enteritidis Strains Isolated in Brazil Over a 48 year-period revealed by Whole Genome SNP Analyses. Scientific Reports. 8:10478; DOI:10.1038/s41598-018-28844-6.
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. A., Ford, C., Damodaran, L., & Witter, Z. (2017). Spread of Middle East Respiratory Coronavirus: Genetic versus Epidemiological Data. Online Journal of Public Health Informatics, 9(1), e004. (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.