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.

GENCODE reference annotation for the human and mouse genomes.

Abstract: The accurate identification and description of the genes in the human and mouse genomes is a fundamental requirement for high quality analysis of data informing both genome biology and clinical genomics. Over the last 15 years, the GENCODE consortium has been producing reference quality gene annotations to provide this foundational resource. The GENCODE consortium includes both experimental and computational biology groups who work together to improve and extend the GENCODE gene annotation. Specifically, we generate primary data, create bioinformatics tools and provide analysis to support the work of expert manual gene annotators and automated gene annotation pipelines. In addition, manual and computational annotation workflows use any and all publicly available data and analysis, along with the research literature to identify and characterise gene loci to the highest standard. GENCODE gene annotations are accessible via the Ensembl and UCSC Genome Browsers, the Ensembl FTP site, Ensembl Biomart, Ensembl Perl and REST APIs as well as https://www.gencodegenes.org.

CANDELS: The Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey

Abstract: The Cosmic Assembly Near-IR Deep Extragalactic Legacy Survey (CANDELS) is designed to document the first third of galactic evolution, from z approx. 8 - 1.5. It will image > 250,000 distant galaxies using three separate cameras on the Hubble Space Tele8cope, from the mid-UV to near-IR, and will find and measure Type Ia supernovae beyond z > 1.5 to test their accuracy as standard candles for cosmology. Five premier multi-wavelength sky regions are selected, each with extensive ancillary data. The use of five widely separated fields mitigates cosmic variance and yields statistically robust and complete samples of galaxies down to a stellar mass of 10(exp 9) solar mass to z approx. 2, reaching the knee of the UV luminosity function of galaxies to z approx. 8. The survey covers approximately 800 square arc minutes and is divided into two parts. The CANDELS/Deep survey (5(sigma) point-source limit H =27.7mag) covers approx. 125 square arcminutes within GOODS-N and GOODS-S. The CANDELS/Wide survey includes GOODS and three additional fields (EGS, COSMOS, and UDS) and covers the full area to a 50(sigma) point-source limit of H ? or approx. = 27.0 mag. Together with the Hubble Ultradeep Fields, the strategy creates a three-tiered "wedding cake" approach that has proven efficient for extragalactic surveys. Data from the survey are non-proprietary and are useful for a wide variety of science investigations. In this paper, we describe the basic motivations for the survey, the CANDELS team science goals and the resulting observational requirements, the field selection and geometry, and the observing design.

The Average Star Formation Histories of Galaxies in Dark Matter Halos from z = 0-8

Abstract: We present a robust method to constrain average galaxy star formation rates (SFRs), star formation histories (SFHs), and the intracluster light (ICL) as a function of halo mass. Our results are consistent with observed galaxy stellar mass functions, specific star formation rates (SSFRs), and cosmic star formation rates (CSFRs) from z = 0 to z = 8. We consider the effects of a wide range of uncertainties on our results, including those affecting stellar masses, SFRs, and the halo mass function at the heart of our analysis. As they are relevant to our method, we also present new calibrations of the dark matter halo mass function, halo mass accretion histories, and halo-subhalo merger rates out to z = 8. We also provide new compilations of CSFRs and SSFRs; more recent measurements are now consistent with the buildup of the cosmic stellar mass density at all redshifts. Implications of our work include: halos near 1012 M ☉ are the most efficient at forming stars at all redshifts, the baryon conversion efficiency of massive halos drops markedly after z ~ 2.5 (consistent with theories of cold-mode accretion), the ICL for massive galaxies is expected to be significant out to at least z ~ 1-1.5, and dwarf galaxies at low redshifts have higher stellar mass to halo mass ratios than previous expectations and form later than in most theoretical models. Finally, we provide new fitting formulae for SFHs that are more accurate than the standard declining tau model. Our approach places a wide variety of observations relating to the SFH of galaxies into a self-consistent framework based on the modern understanding of structure formation in ΛCDM. Constraints on the stellar mass-halo mass relationship and SFRs are available for download online.

Galaxy: A platform for interactive large-scale genome analysis

Abstract: Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

Evolution of genes and genomes on the Drosophila phylogeny.

Abstract: Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species.