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The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into both shared and species-specific transcriptional and cellular regulatory programs in the mouse, the Mouse ENCODE Consortium has mapped(More)
Figure S1. Sample relationships using diverse epigenome marks colored according to Reference Epigenome Mapping Center (REMC). Multi-Dimensional Scaling (MDS) Analysis of all 111 reference epigenomes for histone modification marks when available (see Fig. 2). Signal confidence scores for each histone mark are computed in relevant chromatin states (see(More)
The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative(More)
INTRODUCTION: The notion that species boundaries can be porous to introgression is increasingly accepted. Yet the broader role of introgression in evolution remains contentious and poorly documented, partly because of the challenges involved in accurately identifying introgression in the very groups where it is most likely to occur. Recently diverged(More)
Variation in vectorial capacity for human malaria among Anopheles mosquito species is determined by many factors, including behavior, immunity, and life history. To investigate the genomic basis of vectorial capacity and explore new avenues for vector control, we sequenced the genomes of 16 anopheline mosquito species from diverse locations spanning ~100(More)
Accurate gene tree reconstruction is a fundamental problem in phylogenetics, with many important applications. However, sequence data alone often lack enough information to confidently support one gene tree topology over many competing alternatives. Here, we present a novel framework for combining sequence data and species tree information, and we describe(More)
Alan P. Boyle1,*, Carlos L. Araya1,*, Cathleen Brdlik1, Philip Cayting1, Chao Cheng5, Yong Cheng1, Kathryn Gardner6, LaDeana Hillier8, Judith Janette6, Lixia Jiang1, Dionna Kasper6, Trupti Kawli1, Pouya Kheradpour3, Anshul Kundaje2,3, Jingyi Jessica Li9,10, Lijia Ma4, Wei Niu6, E. Jay Rehm4, Joel Rozowsky5, Matthew Slattery4, Rebecca Spokony4, Robert(More)
Dengue virus (DENV) is the leading cause of arboviral diseases in humans worldwide. The envelope (E) protein of DENV is the major target of neutralizing antibodies (Abs). Previous studies have shown that a significant proportion of anti-E Abs in human serum after DENV infection recognize the highly conserved fusion loop (FL) of E protein. The role of(More)
MOTIVATION Phylogenetic tree reconciliation is a widely used method for reconstructing the evolutionary histories of gene families and species, hosts and parasites and other dependent pairs of entities. Reconciliation is typically performed using maximum parsimony, in which each evolutionary event type is assigned a cost and the objective is to find a(More)
Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene(More)