It has long been known that the amino-acid sequence of a protein determines its 3-dimensional structure, but accurate ab initio prediction of structure from sequence remains elusive. We gain insight into local protein structure conformation by studying the relationship of dihedral angles in...

Simulation studies have been the main way in which properties of maximum likelihood estimation of evolutionary trees from aligned sequence data have been studied. Because trees are unusual parameters and because fitting is computationally intensive, such studies have a heavy computational cost....

We study the estimation of familial correlations from pedigree data without the assumption of multivariate normality, using asymptotic results to obtain standard errors and confidence intervals. Two extreme weights that can be given to pairs of observations from relatives in pedigrees are...

Infections with the human immunodeficiency virus type 1 (HIV-1) are treated with combinations of drugs. Unfortunately, HIV responds to the treatment by developing resistance mutations. Consequently, the genome of the viral target proteins is sequenced and inspected for resistance mutations as...

Gene expression over time can be viewed as a continuous process and therefore represented as a continuous curve or function. Functional data analysis (FDA) is a statistical methodology used to analyze functional data that has become increasingly popular in the analysis of time-course gene...

Specificity determining sites (SDSs) in alignments of protein sequences are sites at which subfamilies of the aligned sequences have been under differential selective pressure. Identifying SDSs is important because they are key in understanding the functional specificity of each subfamily....

Phylogenomic datasets often contain sequence alignments on different subsets of taxa for different genes. A major goal of phylogenetics is often to combine estimated gene trees from many loci into an overall estimate of a species tree. When data are missing for some combinations of genes and...

Hardy-Weinberg Equilibrium (HWE) is an important genetic property that populations should have whenever they are not observing adverse situations as complete lack of panmixia, excess of mutations, excess of selection pressure, etc. HWE for decades has been evaluated; both frequentist and Bayesian...

Simultaneously performing many hypothesis tests is a problem commonly encountered in high-dimensional biology. In this setting, a large set of p-values is calculated from many related features measured simultaneously. Classical statistics provides a criterion for defining what a “correct”...

Inference of gene networks is an important step in understanding cellular dynamics. In this work, a novel algorithm is proposed for inferring gene networks from gene expression data using linear ordinary differential equations. Under the proposed method, a combination of known statistical tools...