Institution
University of California, Santa Cruz
Education•Santa 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, Stars, Redshift, Star formation
Papers published on a yearly basis
Papers
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TL;DR: It is found that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro, and it is demonstrated that the best predictions can significantly reduce the time spent on guide screening.
Abstract: The success of the CRISPR/Cas9 genome editing technique depends on the choice of the guide RNA sequence, which is facilitated by various websites. Despite the importance and popularity of these algorithms, it is unclear to which extent their predictions are in agreement with actual measurements. We conduct the first independent evaluation of CRISPR/Cas9 predictions. To this end, we collect data from eight SpCas9 off-target studies and compare them with the sites predicted by popular algorithms. We identify problems in one implementation but found that sequence-based off-target predictions are very reliable, identifying most off-targets with mutation rates superior to 0.1 %, while the number of false positives can be largely reduced with a cutoff on the off-target score. We also evaluate on-target efficiency prediction algorithms against available datasets. The correlation between the predictions and the guide activity varied considerably, especially for zebrafish. Together with novel data from our labs, we find that the optimal on-target efficiency prediction model strongly depends on whether the guide RNA is expressed from a U6 promoter or transcribed in vitro. We further demonstrate that the best predictions can significantly reduce the time spent on guide screening. To make these guidelines easily accessible to anyone planning a CRISPR genome editing experiment, we built a new website (
http://crispor.org
) that predicts off-targets and helps select and clone efficient guide sequences for more than 120 genomes using different Cas9 proteins and the eight efficiency scoring systems evaluated here.
1,256 citations
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TL;DR: It is found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivaries protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-st starch diets.
Abstract: Starch consumption is a prominent characteristic of agricultural societies and hunter-gatherers in arid environments. In contrast, rainforest and circum-arctic hunter-gatherers and some pastoralists consume much less starch. This behavioral variation raises the possibility that different selective pressures have acted on amylase, the enzyme responsible for starch hydrolysis. We found that copy number of the salivary amylase gene (AMY1) is correlated positively with salivary amylase protein level and that individuals from populations with high-starch diets have, on average, more AMY1 copies than those with traditionally low-starch diets. Comparisons with other loci in a subset of these populations suggest that the extent of AMY1 copy number differentiation is highly unusual. This example of positive selection on a copy number-variable gene is, to our knowledge, one of the first discovered in the human genome. Higher AMY1 copy numbers and protein levels probably improve the digestion of starchy foods and may buffer against the fitness-reducing effects of intestinal disease.
1,247 citations
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Ames Research Center1, University of California, Berkeley2, San Jose State University3, Las Cumbres Observatory Global Telescope Network4, Search for extraterrestrial intelligence5, Aarhus University6, University of Texas at Austin7, Lowell Observatory8, California Institute of Technology9, Harvard University10, Space Telescope Science Institute11, Lawrence Hall of Science12, Carnegie Institution for Science13, University of Florida14, University of California, Santa Cruz15, Massachusetts Institute of Technology16, Fermilab17, San Diego State University18, Southern Connecticut State University19, Marshall Space Flight Center20, University of Arizona21, University of Hertfordshire22, Centre National D'Etudes Spatiales23, Villanova University24
TL;DR: In this article, the Kepler mission released data for 156,453 stars observed from the beginning of the science observations on 2009 May 2 through September 16, and there are 1235 planetary candidates with transit-like signatures detected in this period.
Abstract: On 2011 February 1 the Kepler mission released data for 156,453 stars observed from the beginning of the science observations on 2009 May 2 through September 16. There are 1235 planetary candidates with transit-like signatures detected in this period. These are associated with 997 host stars. Distributions of the characteristics of the planetary candidates are separated into five class sizes: 68 candidates of approximately Earth-size (R_p < 1.25 R_⊕), 288 super-Earth-size (1.25 R_⊕ ≤ R_p < 2 R_⊕), 662 Neptune-size (2 R_⊕ ≤ R_p < 6 R_⊕), 165 Jupiter-size (6 R_⊕ ≤ R_p < 15 R_⊕), and 19 up to twice the size of Jupiter (15 R_⊕ ≤ R_p < 22 R_⊕). In the temperature range appropriate for the habitable zone, 54 candidates are found with sizes ranging from Earth-size to larger than that of Jupiter. Six are less than twice the size of the Earth. Over 74% of the planetary candidates are smaller than Neptune. The observed number versus size distribution of planetary candidates increases to a peak at two to three times the Earth-size and then declines inversely proportional to the area of the candidate. Our current best estimates of the intrinsic frequencies of planetary candidates, after correcting for geometric and sensitivity biases, are 5% for Earth-size candidates, 8% for super-Earth-size candidates, 18% for Neptune-size candidates, 2% for Jupiter-size candidates, and 0.1% for very large candidates; a total of 0.34 candidates per star. Multi-candidate, transiting systems are frequent; 17% of the host stars have multi-candidate systems, and 34% of all the candidates are part of multi-candidate systems.
1,241 citations
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TL;DR: In this paper, the authors show that if the companion is indeed a gas-giant planet, it is extremely unlikely to have formed at its present location, and suggest instead that the planet probably formed by gradual accretion of solids and capture of gas at a much larger distance from the star (∼5 AU), and that it subsequently migrated inwards through interactions with the remnants of the circumstellar disk.
Abstract: THE recent discovery1 and confirmation2 of a possible planetary companion orbiting the solar-type star 51 Pegasi represent a breakthrough in the search for extrasolar planetary systems. Analysis of systematic variations in the velocity of the star indicate that the mass of the companion is approximately that of Jupiter, and that it is travelling in a nearly circular orbit at a distance from the star of 0.05 AU (about seven stellar radii). Here we show that, if the companion is indeed a gas-giant planet, it is extremely unlikely to have formed at its present location. We suggest instead that the planet probably formed by gradual accretion of solids and capture of gas at a much larger distance from the star (∼5 AU), and that it subsequently migrated inwards through interactions with the remnants of the circumstellar disk. The planet's migration may have stopped in its present orbit as a result of tidal interactions with the star, or through truncation of the inner circumstellar disk by the stellar magnetosphere.
1,232 citations
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TL;DR: The University of California, Santa Cruz Genome Browser website provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users’ own annotation data.
Abstract: The University of California, Santa Cruz (UCSC) Genome Browser website (http://genome.ucsc.edu/) provides a large database of publicly available sequence and annotation data along with an integrated tool set for examining and comparing the genomes of organisms, aligning sequence to genomes, and displaying and sharing users' own annotation data. As of September 2009, genomic sequence and a basic set of annotation 'tracks' are provided for 47 organisms, including 14 mammals, 10 non-mammal vertebrates, 3 invertebrate deuterostomes, 13 insects, 6 worms and a yeast. New data highlights this year include an updated human genome browser, a 44-species multiple sequence alignment track, improved variation and phenotype tracks and 16 new genome-wide ENCODE tracks. New features include drag-and-zoom navigation, a Wiki track for user-added annotations, new custom track formats for large datasets (bigBed and bigWig), a new multiple alignment output tool, links to variation and protein structure tools, in silico PCR utility enhancements, and improved track configuration tools.
1,226 citations
Authors
Showing all 15733 results
Name | H-index | Papers | Citations |
---|---|---|---|
David J. Schlegel | 193 | 600 | 193972 |
David R. Williams | 178 | 2034 | 138789 |
John R. Yates | 177 | 1036 | 129029 |
David Haussler | 172 | 488 | 224960 |
Evan E. Eichler | 170 | 567 | 150409 |
Anton M. Koekemoer | 168 | 1127 | 106796 |
Mark Gerstein | 168 | 751 | 149578 |
Alexander S. Szalay | 166 | 936 | 145745 |
Charles M. Lieber | 165 | 521 | 132811 |
Jorge E. Cortes | 163 | 2784 | 124154 |
M. Razzano | 155 | 515 | 106357 |
Lars Hernquist | 148 | 598 | 88554 |
Aaron Dominguez | 147 | 1968 | 113224 |
Taeghwan Hyeon | 139 | 563 | 75814 |
Garth D. Illingworth | 137 | 505 | 61793 |