University of California, Santa Cruz

About: University of California, Santa Cruz is a education organization based out in Santa Cruz, California, United States. It is known for research contribution in the topics: Galaxy & Population. The organization has 15541 authors who have published 44120 publications receiving 2759983 citations. The organization is also known as: UCSC & UC, Santa Cruz.

Defining functional DNA elements in the human genome

Abstract: With the completion of the human genome sequence, attention turned to identifying and annotating its functional DNA elements. As a complement to genetic and comparative genomics approaches, the Encyclopedia of DNA Elements Project was launched to contribute maps of RNA transcripts, transcriptional regulator binding sites, and chromatin states in many cell types. The resulting genome-wide data reveal sites of biochemical activity with high positional resolution and cell type specificity that facilitate studies of gene regulation and interpretation of noncoding variants associated with human disease. However, the biochemically active regions cover a much larger fraction of the genome than do evolutionarily conserved regions, raising the question of whether nonconserved but biochemically active regions are truly functional. Here, we review the strengths and limitations of biochemical, evolutionary, and genetic approaches for defining functional DNA segments, potential sources for the observed differences in estimated genomic coverage, and the biological implications of these discrepancies. We also analyze the relationship between signal intensity, genomic coverage, and evolutionary conservation. Our results reinforce the principle that each approach provides complementary information and that we need to use combinations of all three to elucidate genome function in human biology and disease.

UBIQUITOUS OUTFLOWS IN DEEP2 SPECTRA OF STAR-FORMING GALAXIES AT z = 1.4

Abstract: Galactic winds are a prime suspect for the metal enrichment of the intergalactic medium (IGM) and may have a strong influence on the chemical evolution of galaxies and the nature of QSO absorption-line systems. We use a sample of 1406 galaxy spectra at z ~ 1.4 from the DEEP2 redshift survey to show that blueshifted Mg IYI ?? 2796, 2803 absorption is ubiquitous in star-forming galaxies at this epoch. This is the first detection of frequent outflowing galactic winds at z ~ 1. The presence and depth of absorption are independent of active galactic nuclei spectral signatures or galaxy morphology; major mergers are not a prerequisite for driving a galactic wind from massive galaxies. Outflows are found in co-added spectra of galaxies spanning a range of 30 times in stellar mass and 10 times in star formation rate (SFR), calibrated from K-band and from the Multiband Imaging Photometer for Spitzer IR fluxes. The outflows have column densities of order NH ~ 1020 cm-2 and characteristic velocities of ~?300-500?km?s?1, with absorption seen out to 1000?km?s?1 in the most massive, highest SFR galaxies. The velocities suggest that the outflowing gas can escape into the IGM and that massive galaxies can produce cosmologically and chemically significant outflows. Both the Mg II equivalent width and the outflow velocity are larger for galaxies of higher stellar mass and SFR, with V wind ~ SFR0.3, similar to the scaling in low redshift IR-luminous galaxies. The high frequency of outflows in the star-forming galaxy population at z ~ 1 indicates that galactic winds occur in the progenitors of massive spirals as well as those of ellipticals. The increase of outflow velocity with mass and SFR constrains theoretical models of galaxy evolution that include feedback from galactic winds, and may favor momentum-driven models for the wind physics.

The occurrence and mass distribution of close-in super-Earths, Neptunes, and Jupiters.

Abstract: The questions of how planets form and how common Earth-like planets are can be addressed by measuring the distribution of exoplanet masses and orbital periods. We report the occurrence rate of close-in planets (with orbital periods less than 50 days), based on precise Doppler measurements of 166 Sun-like stars. We measured increasing planet occurrence with decreasing planet mass (M). Extrapolation of a power-law mass distribution fitted to our measurements, df/dlogM = 0.39 M^(−0.48), predicts that 23% of stars harbor a close-in Earth-mass planet (ranging from 0.5 to 2.0 Earth masses). Theoretical models of planet formation predict a deficit of planets in the domain from 5 to 30 Earth masses and with orbital periods less than 50 days. This region of parameter space is in fact well populated, implying that such models need substantial revision.

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

Abstract: Background - The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly of such data into high-quality, finished genome sequences remains challenging. Many genome assembly tools are available, but they differ greatly in terms of their performance (speed, scalability, hardware requirements, acceptance of newer read technologies) and in their final output (composition of assembled sequence). More importantly, it remains largely unclear how to best assess the quality of assembled genome sequences. The Assemblathon competitions are intended to assess current state-of-the-art methods in genome assembly. Results - In Assemblathon 2, we provided a variety of sequence data to be assembled for three vertebrate species (a bird, a fish, and snake). This resulted in a total of 43 submitted assemblies from 21 participating teams. We evaluated these assemblies using a combination of optical map data, Fosmid sequences, and several statistical methods. From over 100 different metrics, we chose ten key measures by which to assess the overall quality of the assemblies. Conclusions - Many current genome assemblers produced useful assemblies, containing a significant representation of their genes, regulatory sequences, and overall genome structure. However, the high degree of variability between the entries suggests that there is still much room for improvement in the field of genome assembly and that approaches which work well in assembling the genome of one species may not necessarily work well for another.

Static and space-time visual saliency detection by self-resemblance.

Abstract: We present a novel unified framework for both static and space-time saliency detection. Our method is a bottom-up approach and computes so-called local regression kernels (i.e., local descriptors) from the given image (or a video), which measure the likeness of a pixel (or voxel) to its surroundings. Visual saliency is then computed using the said "self-resemblance" measure. The framework results in a saliency map where each pixel (or voxel) indicates the statistical likelihood of saliency of a feature matrix given its surrounding feature matrices. As a similarity measure, matrix cosine similarity (a generalization of cosine similarity) is employed. State of the art performance is demonstrated on commonly used human eye fixation data (static scenes (N. Bruce & J. Tsotsos, 2006) and dynamic scenes (L. Itti & P. Baldi, 2006)) and some psychological patterns.