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Approximate MAP inference in graphical models is an important and challenging problem for many domains including computer vision , computational biology and natural language understanding. Current state-of-the-art approaches employ convex relaxations of these problems as surrogate objectives, but only provide weak running time guarantees. In this paper, we(More)
Although, much progress has been made in our understanding of DC ontogeny and function, the transcriptional regulation of DC lineage commitment and functional specialization in vivo is poorly understood. We performed a comprehensive comparative analysis of CD8+, CD103+, CD11b+, and plasmacytoid DC subsets and the recently identified Macrophage DC precursors(More)
Next-generation sequencing technologies produce a large number of noisy reads from the DNA in a sample. Metagenomics and population sequencing aim to recover the genomic sequences of the species in the sample, which could be of high diversity. Methods geared towards single sequence reconstruction are not sensitive enough when applied in this setting. We(More)
Predictive analysis using publicly available yeast functional genomics and proteomics data suggests that many more proteins may be involved in biogenesis of ribonucleoproteins than are currently known. Using a microarray that monitors abundance and processing of noncoding RNAs, we analyzed 468 yeast strains carrying mutations in protein-coding genes, most(More)
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on modelling the block structure as well as the transitions or co-occurrence of the alleles in these blocks as a way to(More)
We propose a multi-view depthmap estimation approach aimed at adaptively ascertaining the pixel level data associations between a reference image and all the elements of a source image set. Namely, we address the question, what aggregation subset of the source image set should we use to estimate the depth of a particular pixel in the reference im-age? We(More)
MOTIVATION We consider models useful for learning an evolutionary or phylogenetic tree from data consisting of DNA sequences corresponding to the leaves of the tree. In particular, we consider a general probabilistic model described in Siepel and Haussler that we call the phylogenetic-HMM model which generalizes the classical probabilistic models of Neyman(More)
The differentiation of hematopoietic stem cells into cells of the immune system has been studied extensively in mammals, but the transcriptional circuitry that controls it is still only partially understood. Here, the Immunological Genome Project gene-expression profiles across mouse immune lineages allowed us to systematically analyze these circuits. To(More)
There is considerable heterogeneity in immunological parameters between individuals, but its sources are largely unknown. To assess the relative contribution of heritable versus non-heritable factors, we have performed a systems-level analysis of 210 healthy twins between 8 and 82 years of age. We measured 204 different parameters, including cell population(More)