We derive an expectation maximization algorithm for maximum-likelihood training of substitution rate matrices from multiple sequence alignments. The algorithm can be used to train hidden substitution models, where the structural context of a residue is treated as a hidden variable that can evolve over time. We used the algorithm to train hidden substitution matrices on protein alignments in the...

One of the most abundant and widely distributed groups of Helix-turn-helix (HTH) transcription factors is the metabolite-responsive GntR family of regulators (>8500 members in the Pfam database; Jan 2009). These proteins contain a DNA-binding HTH domain at the N terminus of the protein and an effector-binding and/or oligomerisation domain at the C terminus, where upon on binding an effector mol...

Policymakers have long hoped to find ways to buffer children from the ravages of poverty without excusing parents from the responsibility of providing for their offspring. For 60 years, the Aid to Families with Dependent Children (AFDC) program guaranteed cash assistance for poor single-parent families, allowing the mothers to remain home with their children. In 1993, federal and state governme...

Scholars have been slow to test welfare state theories on the extensive subnational variation in the United States during the recent period of retrenchment. We assess institutional politics theories, literature on race and social policy, and public opinion arguments relative to levels of support in states' Aid to Families Dependent Children programs from 1982 until its elimination in 1996. Pool...

The study of microbial pangenomes relies on the computation of gene families, i.e. the clustering of coding sequences into groups of essentially similar genes. There is no standard approach to obtain such gene families. Ideally, the gene family computations should be robust against errors in the annotation of genes in various genomes. In an attempt to achieve this robustness, we propose to clus...

What is the effect of the AFDC-Unemployed Parent (UP) program on two-parent families? This question has become particularly relevant following the passage of the Family Support Act (FSA) of 1988, effective October 1990, which extended the previously state-optional AFDC-Unemployed Parent program to all states. This study clarifies what is meant by "two-parent" family in the federal legislation a...

We document a negative association between nonmarital childbearing and the subsequent likelihood of first marriage in the United States, controlling for a variety of potentially confounding influences. Nonmarital childbearing does not appear to be driven by low expectations of future marriage. Rather, it tends to be an unexpected and unwanted event, whose effects on a woman's subsequent likelih...

While the number of solved 3D protein structures continues to grow rapidly, the structural rules that distinguish protein-protein interactions between different structural families are still not clear. Here, we classify and analyse the secondary structural features and promiscuity of a comprehensive non-redundant set of domain family binding sites (DFBSs) and hetero domain-domain interactions (...