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Institution

University of California, San Francisco

EducationSan Francisco, California, United States
About: University of California, San Francisco is a(n) education organization based out in San Francisco, California, United States. It is known for research contribution in the topic(s): Population & Health care. The organization has 83381 authors who have published 186236 publication(s) receiving 12068420 citation(s). The organization is also known as: UCSF & UC San Francisco.

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Topics: Population, Health care, Cancer ...read more
Authors

Showing all 83381 results

NameH-indexPapersCitations
Robert Langer2812324326306
Meir J. Stampfer2771414283776
Gordon H. Guyatt2311620228631
Eugene Braunwald2301711264576
John Q. Trojanowski2261467213948
Fred H. Gage216967185732
Robert J. Lefkowitz214860147995
Peter Libby211932182724
Edward Giovannucci2061671179875
Rob Knight2011061253207
Irving L. Weissman2011141172504
Eugene V. Koonin1991063175111
Peter J. Barnes1941530166618
Virginia M.-Y. Lee194993148820
Gordon B. Mills1871273186451
Papers
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Open accessJournal ArticleDOI: 10.1002/JCC.20084
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.

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  • Figure 3. Three structures in Chimera associated with sequences in an alignment shown by Multalign Viewer. The sequences with color swatches behind their names are associated with the pectate lyase structures 1jta,45 1bn8,46 and 2pec47 (shown in yellow, magenta, and cyan, respectively). The structures were superimposed using the sequence alignment; the fits were refined by iteratively removing bad residue pairings. The sequences are colored by secondary structure (strand and helix regions are pink and gold, respectively) and selected structure regions are green (indicated on the structures with a green outline). Chimera’s zone selection method was used to select all residues within 3.6 Å of the active-site metal ion in one of the structures.
    Figure 3. Three structures in Chimera associated with sequences in an alignment shown by Multalign Viewer. The sequences with color swatches behind their names are associated with the pectate lyase structures 1jta,45 1bn8,46 and 2pec47 (shown in yellow, magenta, and cyan, respectively). The structures were superimposed using the sequence alignment; the fits were refined by iteratively removing bad residue pairings. The sequences are colored by secondary structure (strand and helix regions are pink and gold, respectively) and selected structure regions are green (indicated on the structures with a green outline). Chimera’s zone selection method was used to select all residues within 3.6 Å of the active-site metal ion in one of the structures.
  • Figure 4. The ViewDock interface lists docked molecules; clicking on a line displays just the corresponding molecule and shows its information in the lower part of the panel. Ribose monophosphate is shown docked to H-Ras (121p48). Carbon atoms are light gray, oxygen atoms are red, nitrogen atoms are blue, and phosphorus atoms are cyan. Hydrogens are not shown. Potential hydrogen bonds are indicated with yellow lines.
    Figure 4. The ViewDock interface lists docked molecules; clicking on a line displays just the corresponding molecule and shows its information in the lower part of the panel. Ribose monophosphate is shown docked to H-Ras (121p48). Carbon atoms are light gray, oxygen atoms are red, nitrogen atoms are blue, and phosphorus atoms are cyan. Hydrogens are not shown. Potential hydrogen bonds are indicated with yellow lines.
  • Figure 5. Density map for rice dwarf virus P8 capsid protein shown as a mesh (left). The map was obtained by electron cryo-microscopy and has 6.8-Å resolution.49 Computationally identified alpha helices are shown as cylinders50 and the connecting turns have been hand traced using Chimera’s Volume Path Tracer. On the right is a crystal structure of the distantly related bluetongue virus capsid protein (1bvp51).
    Figure 5. Density map for rice dwarf virus P8 capsid protein shown as a mesh (left). The map was obtained by electron cryo-microscopy and has 6.8-Å resolution.49 Computationally identified alpha helices are shown as cylinders50 and the connecting turns have been hand traced using Chimera’s Volume Path Tracer. On the right is a crystal structure of the distantly related bluetongue virus capsid protein (1bvp51).
  • Figure 6. Fluorescently labeled Drosophila chromosome imaged by wide-field deconvolution microscopy (M. Lowenstein and J. Sedat, UCSF, unpublished data). Three fluorophores were used to label specific segments of chromosome 2L. Two homologous copies of the chromosome are shown. The cyan isosurface is the nuclear envelope. The individual fluorescent spots have been marked with the Volume Path Tracer extension and paths connecting the markers are shown as smooth tubes. Traced structures from many cells can be clustered to study structural patterns of chromosome organization in the nucleus.
    Figure 6. Fluorescently labeled Drosophila chromosome imaged by wide-field deconvolution microscopy (M. Lowenstein and J. Sedat, UCSF, unpublished data). Three fluorophores were used to label specific segments of chromosome 2L. Two homologous copies of the chromosome are shown. The cyan isosurface is the nuclear envelope. The individual fluorescent spots have been marked with the Volume Path Tracer extension and paths connecting the markers are shown as smooth tubes. Traced structures from many cells can be clustered to study structural patterns of chromosome organization in the nucleus.
Topics: Unix (50%), OS X (50%)

28,452 Citations


Open accessJournal ArticleDOI: 10.1016/S0092-8674(00)81683-9
Douglas Hanahan1, Robert A. Weinberg2Institutions (2)
07 Jan 2000-Cell
Abstract: We wish to thank Terry Schoop of Biomed Arts Associates, San Francisco, for preparation of the figures, Cori Bargmann and Zena Werb for insightful comments on the manuscript, and Normita Santore for editorial assistance. In addition, we are indebted to Joe Harford and Richard Klausner, who allowed us to adapt and expand their depiction of the cell signaling network, and we appreciate suggestions on signaling pathways from Randy Watnick, Brian Elenbas, Bill Lundberg, Dave Morgan, and Henry Bourne. R. A. W. is a Ludwig Foundation and American Cancer Society Professor of Biology. His work has been supported by the Department of the Army and the National Institutes of Health. D. H. acknowledges the support and encouragement of the National Cancer Institute. Editorial policy has rendered the citations illustrative but not comprehensive.

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26,950 Citations


Journal ArticleDOI: 10.1016/0006-2952(61)90145-9
Abstract: A photometric method for determining acetylcholinesterase activity of tissue extracts, homogenates, cell suspensions, etc., has been described. The enzyme activity is measured by following the increase of yellow color produced from thiocholine when it reacts with dithiobisnitrobenzoate ion. It is based on coupling of these reactions: The latter reaction is rapid and the assay is sensitive (i.e. a 10 μ1 sample of blood is adequate). The use of a recorder has been most helpful, but is not essential. The method has been used to study the enzyme in human erythrocytes and homogenates of rat brain, kidney, lungs, liver and muscle tissue. Kinetic constants determined by this system for erythrocyte eholinesterase are presented. The data obtained with acetylthiocholine as substrate are similar to those with acetylcholine.

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Topics: Aryl-acylamidase activity (54%), Thiocholine (53%), Acetylthiocholine (53%) ...read more

20,867 Citations


Journal ArticleDOI: 10.1021/BI00591A005
27 Nov 1979-Biochemistry
Abstract: Intact ribonucleic acid (RNA) has been prepared from tissues rich in ribonuclease such as the rat pancreas by efficient homogenization in a 4 M solution of the potent protein denaturant guanidinium thiocyanate plus 0.1 M 2-mercaptoethanol to break protein disulfide bonds. The RNA was isolated free of protein by ethanol precipitation or by sedimentation through cesium chloride. Rat pancreas RNA obtained by these means has been used as a source for the purification of alpha-amylase messenger ribonucleic acid.

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19,784 Citations


Journal ArticleDOI: 10.1001/JAMA.283.15.2008
Donna F. Stroup1, Jesse A. Berlin2, Sally C. Morton3, Ingram Olkin4  +7 moreInstitutions (8)
19 Apr 2000-JAMA
Abstract: ObjectiveBecause of the pressure for timely, informed decisions in public health and clinical practice and the explosion of information in the scientific literature, research results must be synthesized. Meta-analyses are increasingly used to address this problem, and they often evaluate observational studies. A workshop was held in Atlanta, Ga, in April 1997, to examine the reporting of meta-analyses of observational studies and to make recommendations to aid authors, reviewers, editors, and readers.ParticipantsTwenty-seven participants were selected by a steering committee, based on expertise in clinical practice, trials, statistics, epidemiology, social sciences, and biomedical editing. Deliberations of the workshop were open to other interested scientists. Funding for this activity was provided by the Centers for Disease Control and Prevention.EvidenceWe conducted a systematic review of the published literature on the conduct and reporting of meta-analyses in observational studies using MEDLINE, Educational Research Information Center (ERIC), PsycLIT, and the Current Index to Statistics. We also examined reference lists of the 32 studies retrieved and contacted experts in the field. Participants were assigned to small-group discussions on the subjects of bias, searching and abstracting, heterogeneity, study categorization, and statistical methods.Consensus ProcessFrom the material presented at the workshop, the authors developed a checklist summarizing recommendations for reporting meta-analyses of observational studies. The checklist and supporting evidence were circulated to all conference attendees and additional experts. All suggestions for revisions were addressed.ConclusionsThe proposed checklist contains specifications for reporting of meta-analyses of observational studies in epidemiology, including background, search strategy, methods, results, discussion, and conclusion. Use of the checklist should improve the usefulness of meta-analyses for authors, reviewers, editors, readers, and decision makers. An evaluation plan is suggested and research areas are explored.

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Topics: Observational study (56%), Checklist (54%), Scientific literature (53%)

15,106 Citations


Performance
Metrics
No. of papers from the Institution in previous years
YearPapers
202291
202111,514
202010,574
20199,343
20188,319
20178,733

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Institution's top 5 most impactful journals

PLOS ONE

2K papers, 80K citations

Journal of Biological Chemistry

1.9K papers, 187.9K citations

bioRxiv

1.8K papers, 9.1K citations

Nature

1.5K papers, 609.6K citations

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