• Marino M.E., Mironovich M.A., Ineck N.E., Citino S.B., Emerson J.A., Maggs D.J., Coghill L.M., Dubovi E.J., Turner R.C., Carter R.T., Lewin A.C. Full Viral Genome Sequencing and Phylogenomic Analysis of Feline Herpesvirus Type 1 (FHV-1) in Cheetahs (Acinonyx jubatus). Viruses. 13(11).
  
• Khalyfa, A., Qiao, Z., Raju, M., Shyu, C.-R.,Coghill, L.M., Ericsson, A., Gozal, D. Monocarboxylate Transporter-2 ExpressionRestricts Tumor Growth in a Murine Model of Lung Cancer : A Multi-Omic Analysis.. Int. J. Mol. Sci. 22 (10616).
  
• Calderon, R.B., Jeong, C.Y., Ku, H.-H., Coghill, L.M., Ju, Y.J., Kim, N., Ham, J.H. Changes in the Microbial Community in Soybean Plots Treated with Biochar and Poultry Litter.. Agronomy 11:1428
  

• Lewin, Andrew C., Coghill, Lyndon M., Mironovich, Melanie, Liu, Chin-Chi, Carter, Renee T., Ledbetter, Eric C. Phylogenomic Analysis of Global Isolates of Canid Alphaherpesvirus 1. Viruses 12:1421 1-16.
  
• Cohen, AS, Cox, CR, Masucci M, Le, TP, Cowan, TM, Coghill, Lyndon M., Holmlund, TB, Elvevåg, B. Digital phenotyping using multimodal data. Current Behavioral Neuroscience Reports 1-9.
  
• Lewin, Andrew C., Coghill, Lyndon M. and Kousoulas, Konstantin G. Genomic analysis for virulence determinants in Feline herpesvirus type-1 isolates. Virus genes 56 (1), 49-57.
  

• Thaljeh, Lana F., Rothschild, Ainsley J., Naderi, Misagh., Coghill, Lyndon M., Brown, Jeremy M. and Brylinksi, Michal. Hinge region in DNA packaging terminase pUL15 of herpes simplex virus: A potential allosteric target for antiviral drugs. Biomolecules. 9:10:603.
  
• ^Rider, Paul J.F., ^Coghill, Lyndon M., ^Misah Naderi, Michal Brylinksi, Jeremy M. Brown, and K.G. Kousoulas. Phylogenetics and Molecular Evolution of a Conserved Alphaherpesvirus Protein, Glycoprotein K (gK), Reveal Molecular Signatures Important for Viral Entry, Assembly, and Egress. Scientific Reports. 9:14625.
  

• Höhna, Sebastian, Coghill, Lyndon M., Mount, Genevieve G., Thomson, Robert C., and Brown, Jeremy M. P3: Phylogenetic Posterior Prediction in RevBayes. Molecular Biology Evolution. 35:4: 1028–1034.
  

• Fujimoto, Kayo, Coghill, Lyndon M., Weier, Christopher A., Hwang, Lu-Yu, Kim, Ju Yeong, Schneider, John A., Metzker, Michael L., and Brown, Jeremy M. Lack of Support for Socially Connected HIV-1 Transmission Among Young Adult Black Men Who Have Sex with Men. AIDS Research Human Retroviruses. 33:9: 935–940.
  

• Hinchliff, Cody E., Smith, Stephen A., Allman, James F., Burleigh, J. Gordon, Chaudhary, Ruchi, Coghill, Lyndon M., Crandall, Keith A., Deng, Jiabin, Drew, Bryan T., Gazis, Romina, Gude, Karl, Hibbett, David S., Katz, Laura A., Laughinghouse, H. Dail, McTavish, Emily Jane, Midford, Peter E., Owen, Christopher L., Ree, Richard H., Rees, Jonathan A., Soltis, Douglas E., Williams, Tiffani, and Cranston, Karen A. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. Proceedings of the National Academy of Science of the United States of America. 112:41 12764–12769.
  

• Coghill, Lyndon M., Darrin Hulsey, C., Chaves-Campos, Johel, Leon, Francisco J., and Johnson, Steven G. Next generation phylogeography of cave and surface Astyanax mexicanus. Molecular Phylogenetics and Evolution. 79: 368–374.
  
• Lorenz, Otto Thomas, Smith, Patrick, and Coghill, Lyndon M. Condition and morphometric changes in tilapia (Oreochromis sp.) after an eradication attempt in Southern Louisiana. Neobiota. 20: 49–59.
  

• Coghill, Lyndon M. Statistical and Comparative Phylogeography of Mexican Freshwater Taxa in Extreme Aquatic Environments. PhD Dissertation, University of New Orleans.
  
• Coghill, Lyndon M., Hulsey, C. Darrin, Chaves-Campos, Johel, Leon, Francisco J., and Johnson, Steven G. Phylogeography and conservation genetics of a distinct lineage of sunfish in the Cuatro Cienegas valley of Mexico. PLoS One. 8:10: e77013.
  

• Chaves-Campos, Johel, Coghill, Lyndon M., Al-Salamah, Manalle A., De Witt, Thomas J., and Johnson, Steven G. Field heritabilities and lack of correlation of snail shell form and anti-predator function estimated using Bayesian and maximum likelihood methods. Evolutionary Ecology Research. 14: 743–755.
  
• Chaves-Campos, Johel, Coghill, Lyndon M., León, Francisco J., and Johnson, Steven G. The effect of aquatic plant abundance on shell crushing resistance in a freshwater snail. PLoS One. :9: e44374.
  

• Coghill, Lyndon M., Chaves-Campos, Johel, and Garcia-Vazquez, Arturo. Gopherus Berlandieri Geographic Distribution in Mexico. Herpetological Review 2011. 42:3: 388.
  
• Coghill, Lyndon M., Chaves-Campos, Johel, Espinoza, Flor E., Lance, Stacey L, Glenn, Travis C, and Johnson, Steven G. Microsatellite markers isolated from the Mexican banded spring snail Mexipyrgus churinceanus. Conservation Genetic Resources* 3:1: 29–31.
  

A software pipeline implemented to conduct tests of model fit using posterior predictive testing, based on both data- and inference-based test statistics in phylogenetics. This new implementation makes a large spectrum of models available for use through a user-friendly and flexible interface.

RevBayes is a software package designed to conduct Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language.

Phyloboost is a python pipeline and web application that allows the reconstruction, augmentation, and visualizaton of similarity-cluster-based tree sets constructed from an input dataset of sequences.

The Open Tree of Life is an online phylogenetic tree of life, funded by the National Science Foundation. The first draft, including 2.3 million species, was released in September 2015. The Interactive graph allows the user to zoom in to taxonomic classifications, phylogenetic trees, and information about a node.