@article{law_redelings_kullman_2012, title={Comparative Genomics of Duplicate gamma-Glutamyl Transferase Genes in Teleosts: Medaka (Oryzias latipes), Stickleback (Gasterosteus aculeatus), Green Spotted Pufferfish (Tetraodon nigroviridis), Fugu (Takifugu rubripes), and Zebrafish (Danio rerio)}, volume={318B}, ISSN={["1552-5015"]}, DOI={10.1002/jez.b.21439}, abstractNote={Abstract}, number={1}, journal={JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION}, author={Law, Sheran Hiu Wan and Redelings, Benjamin David and Kullman, Seth William}, year={2012}, month={Jan}, pages={35–49} }
 @article{liang_weiss_redelings_suchard_2009, title={Improving phylogenetic analyses by incorporating additional information from genetic sequence databases}, volume={25}, ISSN={["1460-2059"]}, DOI={10.1093/bioinformatics/btp473}, abstractNote={Abstract}, number={19}, journal={BIOINFORMATICS}, author={Liang, Li-Jung and Weiss, Robert E. and Redelings, Benjamin and Suchard, Marc A.}, year={2009}, month={Oct}, pages={2530–2536} }
 @article{lamm_redelings_2009, title={Reconstructing ancestral ranges in historical biogeography: properties and prospects}, volume={47}, ISSN={["1759-6831"]}, DOI={10.1111/j.1759-6831.2009.00042.x}, abstractNote={Abstract  Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal–vicariance analysis, the dispersal–extinction–cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model‐based approaches to biogeographic analysis.}, number={5}, journal={JOURNAL OF SYSTEMATICS AND EVOLUTION}, author={Lamm, Kristin S. and Redelings, Benjamin D.}, year={2009}, month={Sep}, pages={369–382} }
 @article{choi_redelings_thorne_2008, title={Basing population genetic inferences and models of molecular evolution upon desired stationary distributions of DNA or protein sequences}, volume={363}, ISSN={["0962-8436"]}, DOI={10.1098/rstb.2008.0167}, abstractNote={Models of molecular evolution tend to be overly simplistic caricatures of biology that are prone to assigning high probabilities to biologically implausible DNA or protein sequences. Here, we explore how to construct time-reversible evolutionary models that yield stationary distributions of sequences that match given target distributions. By adopting comparatively realistic target distributions, evolutionary models can be improved. Instead of focusing on estimating parameters, we concentrate on the population genetic implications of these models. Specifically, we obtain estimates of the product of effective population size and relative fitness difference of alleles. The approach is illustrated with two applications to protein-coding DNA. In the first, a codon-based evolutionary model yields a stationary distribution of sequences, which, when the sequences are translated, matches a variable-length Markov model trained on human proteins. In the second, we introduce an insertion–deletion model that describes selectively neutral evolutionary changes to DNA. We then show how to modify the neutral model so that its stationary distribution at the amino acid level can match a profile hidden Markov model, such as the one associated with the Pfam database.}, number={1512}, journal={PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES}, author={Choi, Sang Chul and Redelings, Benjamin D. and Thorne, Jeffrey L.}, year={2008}, month={Dec}, pages={3931–3939} }
 @article{redelings_suchard_2007, title={Incorporating indel information into phylogeny estimation for rapidly emerging pathogens}, volume={7}, journal={BMC Evolutionary Biology}, author={Redelings, B. D. and Suchard, M. A.}, year={2007} }
 @article{suchard_redelings_2006, title={BAli-Phy: simultaneous Bayesian inference of alignment and phylogeny}, volume={22}, number={16}, journal={Bioinformatics}, author={Suchard, M. A. and Redelings, B. D.}, year={2006}, pages={2047–2048} }