@article{xie_wehner_wollenberg_purugganan_conkling_2003, title={Intron and polypeptide evolution of conserved NPA to NPA motif regions in plant aquaporins}, volume={128}, number={4}, journal={Journal of the American Society for Horticultural Science}, author={Xie, J. H. and Wehner, T. C. and Wollenberg, K. and Purugganan, M. D. and Conkling, M. A.}, year={2003}, pages={591–597} }
 @article{wollenberg_swaffield_2001, title={Evolution of proteasomal ATPases}, volume={18}, ISSN={["1537-1719"]}, DOI={10.1093/oxfordjournals.molbev.a003897}, abstractNote={In eukaryotic cells, the majority of proteins are degraded via the ATP-dependent ubiquitin/26S proteasome pathway. The proteasome is the proteolytic component of the pathway. It is a very large complex with a mass of around 2.5 MDa, consisting of at least 62 proteins encoded by 31 genes. The eukaryotic proteasome has evolved from a simpler archaebacterial form, similar in structure but containing only three different peptides. One of these peptides is an ATPase belonging to the AAA (Triple-A) family of ATPASES: Gene duplication and diversification has resulted in six paralogous ATPases being present in the eukaryotic proteasome. While sequence analysis studies clearly show that the six eukaryotic proteasomal ATPases have evolved from the single archaebacterial proteasomal ATPase, the deep node structures of the phylogenetic constructions lack resolution. Incorporating physical data to provide support for alternative phylogenetic hypotheses, we have constructed a model of a possible evolutionary history of the proteasomal ATPASES:}, number={6}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Wollenberg, K and Swaffield, JC}, year={2001}, month={Jun}, pages={962–974} }
 @article{atchley_lokot_wollenberg_dress_ragg_2001, title={Phylogenetic analyses of amino acid variation in the serpin proteins}, volume={18}, ISSN={["1537-1719"]}, DOI={10.1093/oxfordjournals.molbev.a003936}, abstractNote={Phylogenetic analyses of 110 serpin protein sequences revealed clades consistent with independent phylogenetic analyses based on exon-intron structure and diagnostic amino acid sites. Trees were estimated by maximum likelihood, neighbor joining, and partial split decomposition using both the BLOSUM 62 and Jones-Taylor-Thornton substitution matrices. Neighbor-joining trees gave results closest to those based on independent analyses using genomic and chromosomal data. The maximum-likelihood trees derived using the quartet puzzling algorithm were very conservative, producing many small clades that separated groups of proteins that other results suggest were related. Independent analyses based on exon-intron structure suggested that a neighbor-joining tree was more accurate than maximum-likelihood trees obtained using the quartet puzzling algorithm.}, number={8}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Atchley, WR and Lokot, T and Wollenberg, K and Dress, A and Ragg, H}, year={2001}, month={Aug}, pages={1502–1511} }
 @article{atchley_wollenberg_fitch_terhalle_dress_2000, title={Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis}, volume={17}, ISSN={["0737-4038"]}, DOI={10.1093/oxfordjournals.molbev.a026229}, abstractNote={An information theoretic approach is used to examine the magnitude and origin of associations among amino acid sites in the basic helix-loop-helix (bHLH) family of transcription factors. Entropy and mutual information values are used to summarize the variability and covariability of amino acids comprising the bHLH domain for 242 sequences. When these quantitative measures are integrated with crystal structure data and summarized using helical wheels, they provide important insights into the evolution of three-dimensional structure in these proteins. We show that amino acid sites in the bHLH domain known to pack against each other have very low entropy values, indicating little residue diversity at these contact sites. Noncontact sites, on the other hand, exhibit significantly larger entropy values, as well as statistically significant levels of mutual information or association among sites. High levels of mutual information indicate significant amounts of intercorrelation among amino acid residues at these various sites. Using computer simulations based on a parametric bootstrap procedure, we are able to partition the observed covariation among various amino acid sites into that arising from phylogenetic (common ancestry) and stochastic causes and those resulting from structural and functional constraints. These results show that a significant amount of the observed covariation among amino acid sites is due to structural/functional constraints, over and above the covariation arising from phylogenetic constraints. These quantitative analyses provide a highly integrated evolutionary picture of the multidimensional dynamics of sequence diversity and protein structure.}, number={1}, journal={MOLECULAR BIOLOGY AND EVOLUTION}, author={Atchley, WR and Wollenberg, KR and Fitch, WM and Terhalle, W and Dress, AW}, year={2000}, month={Jan}, pages={164–178} }
 @article{wollenberg_atchley_2000, title={Separation of phylogenetic and functional associations in biological sequences by using the parametric bootstrap}, volume={97}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.070154797}, abstractNote={Quantitative analyses of biological sequences generally proceed under the assumption that individual DNA or protein sequence elements vary independently. However, this assumption is not biologically realistic because sequence elements often vary in a concerted manner resulting from common ancestry and structural or functional constraints. We calculated intersite associations among aligned protein sequences by using mutual information. To discriminate associations resulting from common ancestry from those resulting from structural or functional constraints, we used a parametric bootstrap algorithm to construct replicate data sets. These data are expected to have intersite associations resulting solely from phylogeny. By comparing the distribution of our association statistic for the replicate data against that calculated for empirical data, we were able to assign a probability that two sites covaried resulting from structural or functional constraint rather than phylogeny. We tested our method by using an alignment of 237 basic helix–loop–helix (bHLH) protein domains. Comparison of our results against a solved three-dimensional structure confirmed the identification of several sites important to function and structure of the bHLH domain. This analytical procedure has broad utility as a first step in the identification of sites that are important to biological macromolecular structure and function when a solved structure is unavailable. Sign up for PNAS alerts. Get alerts for new articles, or get an alert when an article is cited. Manage alerts}, number={7}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Wollenberg, KR and Atchley, WR}, year={2000}, month={Mar}, pages={3288–3291} }
 @article{wollenberg_avise_1998, title={Sampling properties of genealogical pathways underlying population pedigrees}, volume={52}, DOI={10.2307/2411228}, number={4}, journal={Evolution}, author={Wollenberg, K. and Avise, J. C.}, year={1998}, pages={957–966} }