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Institution

University of California, Santa Cruz

EducationSanta Cruz, California, United States
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.
Topics: Galaxy, Population, Star formation, Redshift, Planet


Papers
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Journal ArticleDOI
19 Jun 2003-Nature
TL;DR: In this article, the authors reported evidence for a very energetic supernova (a hypernova), temporally and spatially coincident with a gamma-ray burst at redshift z=0.1685.
Abstract: Over the past five years evidence has mounted that long-duration (greater than 2s) gamma-ray bursts (GRBs), the most brilliant of all astronomical explosions, signal the collapse of massive stars in our Universe. This evidence, originally based on the probable association of one unusual GRB with a supernova, now includes the association of GRBs with regions of massive star-formation in distant galaxies, tantalizing evidence of supernova-like light-curve 'bumps' in the optical afterglows of several bursts, and lines of freshly synthesized elements in the spectra of a few X-ray afterglows. These observations support, but do not yet conclusively validate, models based upon the deaths of massive stars, presumably associated with core collapse. Here we report evidence for a very energetic supernova (a hypernova), temporally and spatially coincident with a GRB at redshift z=0.1685. The timing of the supernova indicates that it exploded within a few days of the GRB, strongly suggesting that core-collapse events can give rise to GRBs. Amongst the GRB central engine models proposed to-date, the properties of this supernova thus favour the collapsar model.

1,415 citations

Journal ArticleDOI
TL;DR: This paper analyzed the adjustment dynamics of real exchange rates through impulse response analysis and found that the dynamic response pattern suggests that the shock response is initially amplified before dissipating and that such non-monotonic dynamics can contribute to more than one-third of the observed persistence of the real exchange rate.

1,390 citations

Journal ArticleDOI
TL;DR: In this paper, the authors used the photometric parallax method to estimate the distances to ~48 million stars detected by the Sloan Digital Sky Survey (SDSS) and map their three-dimensional number density distribution in the Galaxy.
Abstract: Using the photometric parallax method we estimate the distances to ~48 million stars detected by the Sloan Digital Sky Survey (SDSS) and map their three-dimensional number density distribution in the Galaxy. The currently available data sample the distance range from 100 pc to 20 kpc and cover 6500 deg2 of sky, mostly at high Galactic latitudes (|b| > 25). These stellar number density maps allow an investigation of the Galactic structure with no a priori assumptions about the functional form of its components. The data show strong evidence for a Galaxy consisting of an oblate halo, a disk component, and a number of localized overdensities. The number density distribution of stars as traced by M dwarfs in the solar neighborhood (D < 2 kpc) is well fit by two exponential disks (the thin and thick disk) with scale heights and lengths, bias corrected for an assumed 35% binary fraction, of H1 = 300 pc and L1 = 2600 pc, and H2 = 900 pc and L2 = 3600 pc, and local thick-to-thin disk density normalization ρthick(R☉)/ρthin(R☉) = 12% . We use the stars near main-sequence turnoff to measure the shape of the Galactic halo. We find a strong preference for oblate halo models, with best-fit axis ratio c/a = 0.64, ρH ∝ r−2.8 power-law profile, and the local halo-to-thin disk normalization of 0.5%. Based on a series of Monte Carlo simulations, we estimate the errors of derived model parameters not to be larger than ~20% for the disk scales and ~10% for the density normalization, with largest contributions to error coming from the uncertainty in calibration of the photometric parallax relation and poorly constrained binary fraction. While generally consistent with the above model, the measured density distribution shows a number of statistically significant localized deviations. In addition to known features, such as the Monoceros stream, we detect two overdensities in the thick disk region at cylindrical galactocentric radii and heights (R,Z) ~ (6.5,1.5) kpc and (R,Z) ~ (9.5,0.8) kpc and a remarkable density enhancement in the halo covering over 1000 deg2 of sky toward the constellation of Virgo, at distances of ~6-20 kpc. Compared to counts in a region symmetric with respect to the l = 0° line and with the same Galactic latitude, the Virgo overdensity is responsible for a factor of 2 number density excess and may be a nearby tidal stream or a low-surface brightness dwarf galaxy merging with the Milky Way. The u − g color distribution of stars associated with it implies metallicity lower than that of thick disk stars and consistent with the halo metallicity distribution. After removal of the resolved overdensities, the remaining data are consistent with a smooth density distribution; we detect no evidence of further unresolved clumpy substructure at scales ranging from ~50 pc in the disk to ~1-2 kpc in the halo.

1,375 citations

Journal ArticleDOI
TL;DR: This work incorporates several different evidence sources into the gene finder AUGUSTUS, a widely used and essential tool for analyzing newly sequenced genomes and correctly predicts at least one splice form exactly correct in 57% of human genes.
Abstract: Motivation: Computational annotation of protein coding genes in genomic DNA is a widely used and essential tool for analyzing newly sequenced genomes. However, current methods suffer from inaccuracy and do poorly with certain types of genes. Including additional sources of evidence of the existence and structure of genes can improve the quality of gene predictions. For many eukaryotic genomes, expressed sequence tags (ESTs) are available as evidence for genes. Related genomes that have been sequenced, annotated, and aligned to the target genome provide evidence of existence and structure of genes. Results: We incorporate several different evidence sources into the gene finder AUGUSTUS. The sources of evidence are gene and transcript annotations from related species syntenically mapped to the target genome using TransMap, evolutionary conservation of DNA, mRNA and ESTs of the target species, and retroposed genes. The predictions include alternative splice variants where evidence supports it. Using only ESTs we were able to correctly predict at least one splice form exactly correct in 57% of human genes. Also using evidence from other species and human mRNAs, this number rises to 77%. Syntenic mapping is well-suited to annotate genomes closely related to genomes that are already annotated or for which extensive transcript evidence is available. Native cDNA evidence is most helpful when the alignments are used as compound information rather than independent positionwise information. Availability: AUGUSTUS is open source and available at http://augustus.gobics.de. The gene predictions for human can be browsed and downloaded at the UCSC Genome Browser (http://genome.ucsc.edu) Contact: mstanke@gwdg.de Supplementary information: Supplementary data are available at Bioinformatics online.

1,364 citations

Journal ArticleDOI
Feng Yue1, Feng Yue2, Yong Cheng3, Alessandra Breschi, Jeff Vierstra4, Weisheng Wu2, Weisheng Wu5, Tyrone Ryba6, Tyrone Ryba7, Richard Sandstrom4, Zhihai Ma3, Carrie A. Davis8, Benjamin D. Pope6, Yin Shen1, Dmitri D. Pervouchine, Sarah Djebali, Robert E. Thurman4, Rajinder Kaul4, Eric Rynes4, Anthony Kirilusha9, Georgi K. Marinov9, Brian A. Williams9, Diane Trout9, Henry Amrhein9, Katherine I. Fisher-Aylor9, Igor Antoshechkin9, Gilberto DeSalvo9, Lei Hoon See8, Meagan Fastuca8, Jorg Drenkow8, Chris Zaleski8, Alexander Dobin8, Pablo Prieto, Julien Lagarde, Giovanni Bussotti, Andrea Tanzer10, Olgert Denas11, Kanwei Li11, M. A. Bender4, M. A. Bender12, Miaohua Zhang12, Rachel Byron12, Mark Groudine12, Mark Groudine4, David McCleary1, Long Pham1, Zhen Ye1, Samantha Kuan1, Lee Edsall1, Yi-Chieh Wu13, Matthew D. Rasmussen13, Mukul S. Bansal13, Manolis Kellis14, Manolis Kellis13, Cheryl A. Keller2, Christapher S. Morrissey2, Tejaswini Mishra2, Deepti Jain2, Nergiz Dogan2, Robert S. Harris2, Philip Cayting3, Trupti Kawli3, Alan P. Boyle3, Alan P. Boyle5, Ghia Euskirchen3, Anshul Kundaje3, Shin Lin3, Yiing Lin3, Camden Jansen15, Venkat S. Malladi3, Melissa S. Cline16, Drew T. Erickson3, Vanessa M. Kirkup16, Katrina Learned16, Cricket A. Sloan3, Kate R. Rosenbloom16, Beatriz Lacerda de Sousa17, Kathryn Beal, Miguel Pignatelli, Paul Flicek, Jin Lian18, Tamer Kahveci19, Dongwon Lee20, W. James Kent16, Miguel Santos17, Javier Herrero21, Cedric Notredame, Audra K. Johnson4, Shinny Vong4, Kristen Lee4, Daniel Bates4, Fidencio Neri4, Morgan Diegel4, Theresa K. Canfield4, Peter J. Sabo4, Matthew S. Wilken4, Thomas A. Reh4, Erika Giste4, Anthony Shafer4, Tanya Kutyavin4, Eric Haugen4, Douglas Dunn4, Alex Reynolds4, Shane Neph4, Richard Humbert4, R. Scott Hansen4, Marella F. T. R. de Bruijn22, Licia Selleri23, Alexander Y. Rudensky24, Steven Z. Josefowicz24, Robert M. Samstein24, Evan E. Eichler4, Stuart H. Orkin25, Dana N. Levasseur26, Thalia Papayannopoulou4, Kai Hsin Chang4, Arthur I. Skoultchi27, Srikanta Gosh27, Christine M. Disteche4, Piper M. Treuting4, Yanli Wang2, Mitchell J. Weiss, Gerd A. Blobel28, Xiaoyi Cao1, Sheng Zhong1, Ting Wang29, Peter J. Good30, Rebecca F. Lowdon29, Rebecca F. Lowdon30, Leslie B. Adams31, Leslie B. Adams30, Xiao Qiao Zhou30, Michael J. Pazin30, Elise A. Feingold30, Barbara J. Wold9, James Taylor11, Ali Mortazavi15, Sherman M. Weissman18, John A. Stamatoyannopoulos4, Michael Snyder3, Roderic Guigó, Thomas R. Gingeras8, David M. Gilbert6, Ross C. Hardison2, Michael A. Beer20, Bing Ren1 
20 Nov 2014-Nature
TL;DR: The mouse ENCODE Consortium has mapped transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types as mentioned in this paper.
Abstract: 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 transcription, DNase I hypersensitivity, transcription factor binding, chromatin modifications and replication domains throughout the mouse genome in diverse cell and tissue types By comparing with the human genome, we not only confirm substantial conservation in the newly annotated potential functional sequences, but also find a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization Our results illuminate the wide range of evolutionary forces acting on genes and their regulatory regions, and provide a general resource for research into mammalian biology and mechanisms of human diseases

1,335 citations


Authors

Showing all 15733 results

NameH-indexPapersCitations
David J. Schlegel193600193972
David R. Williams1782034138789
John R. Yates1771036129029
David Haussler172488224960
Evan E. Eichler170567150409
Anton M. Koekemoer1681127106796
Mark Gerstein168751149578
Alexander S. Szalay166936145745
Charles M. Lieber165521132811
Jorge E. Cortes1632784124154
M. Razzano155515106357
Lars Hernquist14859888554
Aaron Dominguez1471968113224
Taeghwan Hyeon13956375814
Garth D. Illingworth13750561793
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Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202351
2022328
20212,157
20202,353
20192,209
20182,157