Tag: UCSF

Introduction Aminoglycoside antibiotics (AGs) are some of the most commonly prescribed antibacterials, despite their well-known capacity to cause toxic side effects to the kidneys and inner ear (Huth et al., 2011). Although their use in the industrialized world is usually limited to severe infections, they remain very popular in the…

Hope S. Rugo, MD, FASCO, director of Breast Oncology and Clinical Trials Education and professor of medicine in the Division of Hematology and Oncology at the University of California San Francisco (UCSF) Helen Diller Family Comprehensive Cancer Center, discusses the methods, design, and key findings from the phase 3 CAPItello-291…

How do I calculate differential expression for RNA-seq values with the “limma” package and the “ebayes” function? 0 So for context, I have a set of TPM values (which I converted to log2(TPM+1) for multiple genes for different samples, and I need to calculate the differential expression for RNA-seq values….

R. Kate (Katie) Kelley, MD, professor, Clinical Medicine, the Department of Medicine, Hematology and Oncology, the University of California, San Francisco (UCSF), affiliated faculty member, the Cancer Immunotherapy Program, UCSF, discusses unmet needs and treatment challenges within the current standard-of-care for patients with cholangiocarcinoma. Treatment advancements with the addition of…

Hampoelz, B., Andres-Pons, A., Kastritis, P. & Beck, M. Structure and assembly of the nuclear pore complex. Annu. Rev. Biophys. 48, 515–536 (2019). Article  CAS  PubMed  Google Scholar  Lin, D. H. & Hoelz, A. The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725–783 (2019). Article …

NLRP3 expression and purification Both wild-type NLRP3 and CAPS mutants were cloned in the mammalian expression vector pcDNA3.1HisB. Plasmid was purified using Qiagen Giga Prep up to 2000 ng/μl and subsequently transfected into Expi293 with Expifectamine per manufacturer instructions. Expression was allowed to proceed for 3 days before harvesting. Cells were…

Details Posted: 25-May-23 Location: San Francisco, California Type: Full-time Salary: Open Categories: Staff/Administrative Note: This is 1 year contract that offers full benefits (including medical, dental, vision along with retirement & pension plans). Under direct supervision, will analyze clinical datasets (with an emphasis on structured and unstructured data in electronic…

Indee Labs announces an exclusive marketing and distribution deal with Sunko Instruments in China for Hydropore Research Use Only. BERKELEY, Calif., May 25, 2023 /PRNewswire/ — Indee Labs is a biotechnology company developing the Hydropore™ for non-viral intracellular delivery. Sunko Instruments is a professional distributor of scientific and laboratory instruments in…

Liberles, S. D. & Buck, L. B. A second class of chemosensory receptors in the olfactory epithelium. Nature 442, 645–650 (2006). Article  ADS  CAS  PubMed  Google Scholar  Buck, L. & Axel, R. A novel multigene family may encode odorant receptors: a molecular basis for odor recognition. Cell 65, 175–187 (1991)….

R. Kate (Katie) Kelley, MD The selective FGFR2 inhibitor RLY-4008 has generated higher response rates compared with historical data for prior pan-FGFR inhibitors in patients with cholangiocarcinoma harboring FGFR2 fusions or alterations who have not been exposed to a prior FGFR inhibitor, according to R. Kate (Katie) Kelley, MD. Data…

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see arrayQuality. Assessing array quality on spotted arrays Bioconductor version: 2.11 Functions for performing print-run and array level quality assessment. Author: Agnes Paquet and Jean Yee Hwa Yang <yeehwa at stat.berkeley.edu> Maintainer: Agnes Paquet…

[chimerax-users] How to describe methods Tom Goddard goddard at sonic.net Tue May 9 14:25:27 PDT 2023 Hi Jim, As Elaine says, ChimeraX is using ColabFold, which is an optimized version of AlphaFold. So you should cite ColabFold (and AlphaFold and ChimeraX). Also your description of the template use is a…

Steering Committee on Quality Improvement and Management, Subcommittee on Febrile Seizures American Academy of Pediatrics. Febrile seizures clinical practice guideline for the long-term management of the child with simple febrile seizures. Pediatrics. 2008;121:1281–6. Camfield P, Camfield C. Febrile seizures and genetic epilepsy with febrile seizures plus (GEFS+). Epileptic Disord. 2015;17:124–33….

Category:ScienceLab/Area:Stem Cell Core Description: The Stem Cell Core is a state-of-the-art facility providing comprehensive pluripotent stem cell related services (standard and customized), training and consultations. Our focus includes reprogramming of somatic cells into iPSCs, differentiation of iPSCs into various cell lineages and genome editing in iPSCs. Our mission is to…

[chimerax-users] unifold Roger Leng rleng at ualberta.ca Fri May 5 10:58:35 PDT 2023 Many thanks, Elaine. I agree with your point. I find Alphafold is very close to “exactly” detecting two or three protein interactions. I used an example ” p53-MDM2 interaction” (structure and experiments) to test Alphafold Program. Also,…

Shkoporov, A. N. & Hill, C. Bacteriophages of the human gut: the “known unknown” of the microbiome. Cell Host Microbe 25, 195–209 (2019). Article  CAS  PubMed  Google Scholar  Dutilh, B. E. et al. A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes. Nat. Commun. 5, 4498…

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our condensed consolidated financial statements and the related notes and other financial information included elsewhere in this Quarterly Report on Form 10-Q and our Annual Report on Form 10-K for the…

Centers for Disease Control and Prevention. Past Seasons Vaccine Effectiveness Estimates, www.cdc.gov/flu/vaccines-work/past-seasons-estimates.html (2022). Accessed 10 March 2022. Centers for Disease Control and Prevention. Pandemic influenza—past pandemics, www.cdc.gov/flu/pandemic-resources/basics/past-pandemics.html (2022). Accessed 10 March 2022. Erbelding, E. J. et al. A universal influenza vaccine: the strategic plan for the National Institute of Allergy…

A research initiative co-led by Nobel laureate and CRISPR pioneer Jennifer Doudna, PhD, has been awarded $70 million to address health and climate challenges by combining the genome editing technology with genome-resolved metagenomics through the microbiome. TED’s Audacious Project, a collaborative funding effort designed to help solve grand-scale social impact…

Vincent, F., Sheyn, U., Porat, Z., Schatz, D. & Vardi, A. Visualizing active viral infection reveals diverse cell fates in synchronized algal bloom demise. Proc. Natl Acad. Sci. USA 118, e2021586118 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Suttle, C. A. Marine viruses — major players in the global…

The Audacious Project, an initiative housed at TED, encourages the world’s greatest changemakers to dream bigger. A new initiative led by Jennifer Doudna and Jill Banfield at the Innovative Genomics Institute and announced today at the TED Conference in Vancouver is a big dream that uses the smallest tools: microbes. The research initiative, “Engineering…

Aer Therapeutics, a joint University College Dublin (UCD) and University of California, San Francisco (UCSF) biopharmaceutical spin-out company developing novel inhaled treatments for muco-obstructive lung diseases, has announced the closing of a $36 million Series A financing round.Funding was received from a syndicate of premier life science industry investors, including…

van Giesen, L., Kilian, P. B., Allard, C. A. H. & Bellono, N. W. Molecular basis of chemotactile sensation in octopus. Cell 183, 594–604.e14 (2020). Article  PubMed  PubMed Central  Google Scholar  Noviello, C. M. et al. Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 184, 2121–2134 (2021)….

Lower respiratory tract infection (LRTI), which includes conditions such as pneumonia, has long been the leading cause of death from communicable agents and a leading cause of death in children worldwide. But despite its prevalence, LRTI is tricky for doctors to treat effectively because the current diagnostic approach often fails…

Sample preparation The genes encoding ISDra2 TnpB (TnpB from D. radiodurans ISDra2; residues 1 to 408) and the 247-nt ωRNA were synthesized by Eurofin Genomics and cloned into the modified pETDuet vector (Novagen). The N-terminally MBP-tagged TnpB and ωRNA were co-expressed in Escherichia coli Rosetta2 (DE3). The E. coli cells were cultured…

Research reported in this study complies with all relevant ethical regulations, and our animal study protocol has been approved by the Animal Experimental Board of Finland (license number ESAVI/28687/2020. Phage panning Sherpabody phage display library (size ~1011 cfu) was obtained from Next Biomed Therapies Oy. To develop sherpabodies specific for SARS-CoV-2…

The Molecular Dynamics (MD) is one of the techniques incorporated into bioinformatics, specifically by structural bioinformatics. With that, it is possible to obtain kinetic and thermodynamic characteristics of biomolecular structures. For example, macromolecular stability, identification of allosteric sites, elucidation of mechanisms of enzymatic activity, molecular recognition and properties of complexes…

Details Posted: 18-Mar-23 Location: San Francisco, California Type: Full-time Salary: Open The Krogan lab at the Quantitative Biosciences Institute (QBI) at UCSF is looking for a seasoned, experienced, analytical Senior Bioinformatics Programmer with a broad understanding of computational algorithms, systems and their application to omics and related systems-level biological data…

Bray, F. et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 68, 394–424 (2018). Article  PubMed  Google Scholar  Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers…

NeurologyFull Time65411BRJob SummaryA bright, hardworking individual with very strong communication and organizational skills is sought by the Hollenbach Lab in the Department of Neurology at the University of California at San Francisco, to serve as a staff bioinformatician providing support for ongoing research projects related to the immunogenetics of disease,…

During the forecast period, the global Gene Synthesis Market is expected to grow at a steady rate of 19.2%. The market is expected to be worth US$ 779.4 million in 2023. The estimate is that by 2033, it will have surpassed US$ 4.5 billion. The current biotechnology system relies heavily…

Statistics and reproducibility Huc purification and PAGE analysis Huc was purified from M. smegmatis cells on eight separate occasions throughout the course of the study. The yield of purified Huc (mg per litre of culture) varied by a factor of five between purifications. The relative abundance of the Huc oligomer…

A mystery disease wound its way through the Mission this January, wreaking runny noses and headaches upon its victims. But when doctors had patients test for likely diseases — Covid-19, flu, Respiratory Syncytial Virus (RSV) — results turned up negative for all three.  What was…

Summary What are we trying to achieve?We are trying to create accurate models of our final protein products. These models will help us verify that our sequences are correct, since we know of similar structures from literature, and these models will help us run many protein interactions simulations to infer…

Bruce Cree, MD, PhD, MAS, FAAN Findings of an ad hoc analysis of data from the phase 3 SUNBEAM (NCT02294058) and RADIANCE (NCT02047734) clinical trials, as well as the open-label extension DAYBREAK (NCT02576717), suggest that regardless of age, patients with relapsing multiple sclerosis (MS) who were treated with ozanimod (Zeposia;…

Researchers at Gladstone Institutes have conducted an analysis of numerous human and chimpanzee HARs and found that a number of the modifications that occurred during human evolution had opposing effects on each other. Many alterations to the genomes of early humans had opposing effects, likely due to a delicate balance…

Bryan Dechairo, PhD, Sherlock Biosciences president and CEO Sherlock Biosciences has gained U.S. rights to a patent for diagnostic use of a CRISPR system based on the smaller Cas12 enzyme as single RNA-guided endonuclease. Sherlock—whose co-founders include CRISPR pioneer Feng Zhang, PhD, of the Broad Institute—says its exclusive U.S. rights to…

CHAPEL HILL – When people living with HIV take antiviral therapy (ART), their viral loads are driven so low that a standard blood test cannot detect the virus. However, once ART is stopped, detectable HIV re-emerges with new cells getting infected. This is called “rebound” virus, and the cells that…

Job Title: Postdoctoral Scholar in the Franklin Huang Lab Location: San Francisco, CA, USA The Franklin Huang Lab at UCSF (franklinhuanglab.ucsf.edu) is seeking a highly motivated and talented postdoctoral researcher to join our team. The successful candidate will work on cutting-edge research projects in the field of cancer biology and…

Proportion of AlphaFold2 models that can be brought into CATH Identification of domains in AF2 protein models We applied an in-house Hidden-Markov Model-based protocol CATH-Resolve-Hits (CRH)26 to assign domain regions in all sequences from the 21 model organisms modelled by AlphaFold2 (AF2) (see “Methods” for description and Fig. 1). CRH identifies…

Credit: Pixabay/CC0 Public Domain Medical innovations typically take 17 years from the time a lightbulb goes off in a scientist’s head until the first person benefits. But every once in a while, an idea is so powerful and so profound its effects are felt much faster. That’s been the case…

Hampton, H. G., Watson, B. N. J. & Fineran, P. C. The arms race between bacteria and their phage foes. Nature 577, 327–336 (2020). Article  CAS  Google Scholar  Makarova, K. S. et al. Evolution and classification of the CRISPR-Cas systems. Nat. Rev. Microbiol. 9, 467–477 (2011). Article  CAS  Google Scholar …

Ray-Soni, A., Bellecourt, M. J. & Landick, R. Mechanisms of bacterial transcription termination: all good things must end. Annu. Rev. Biochem. 85, 319–347 (2016). Article  CAS  Google Scholar  Proudfoot, N. J. Transcriptional termination in mammals: stopping the RNA polymerase II juggernaut. Science 352, aad9926 (2016). Arimbasseri, A. G. & Maraia,…

[chimerax-users] ChimeraX Alphafold Multiple jobs Tom Goddard goddard at sonic.net Fri Dec 16 12:37:56 PST 2022 Hi Rayees, ChimeraX can only run one AlphaFold prediction at a time. I tried various tricks to run two predictions at a time and they did not work. I tried starting two copies of…

By By Cara Murez HealthDay Reporter, HealthDay Reporter (HealthDay) MONDAY, Sept. 26, 2022 (HealthDay News) — Scientists have been looking to the microbiome, and its numerous gut bacteria, as an area of research with plenty of potential for finding connections to various diseases. Now, scientists have found evidence of significant…

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

Qualification Details. Objective/methods: This report investigates by histology, immunohistochemistry and in situ hybridization the histological and . Philip Lupo, Ph.D. Dr. Lupo is a co-principal investigator in the Systems Epidemiology of Cancer Training Program and an associate professor in the Section of Hematology-Oncology in the Department of Pediatrics. . «Genetic…

Zhang, X., Bai, XC & Chen, ZJ Structures and mechanisms of the cGAS-STING innate immunity pathway. Immunity 5343–53 (2020). CAS PubMed Google Scholar Article Ishikawa, H. & Barber, GN STING is an endoplasmic reticulum adapter that facilitates innate immune signaling. Nature 455674–678 (2008). ADS CAS PubMed PubMed Central Article Google…

Based on their genetics, some people don’t need as much sleep as others, which could also influence their risk for disease, the Atlanta Journal-Constitution writes. Researchers from the University of California, San Francisco, have been studying people who only need four to six hours of sleep, less than the commonly…

Overview This is a hands-on workshop that covers how to use ggplot2 for common visualizations using the R programming language. It is not an introductory R programming workshop. See prerequisities below. Objectives In this workshop you will see how to use ggplot2 for: describing single variables and plotting simple…

Date: 11th February 2022 The immune system is a critical biological network of processes that protects an organism from disease, and depends on the ability to distinguish self from non-self, a role driven by antigens.  In humans, T cells respond to antigen stimulation together with the production of cytokines however,…

Scientists at Gladstone Institutes and UC San Francisco (UCSF) say they have co-opted the CRISPR-Cas9 system to forcibly activate genes—rather than edit them—in human immune cells. The method, known as CRISPRa, lets them discover genes that play a role in immune cell biology more thoroughly and rapidly than previously possible,…

SAN FRANCISCO, CA—February 4, 2022—CRISPR genome editing has served as a powerful tool for deleting or altering DNA sequences and studying the resulting effect. Now, researchers at Gladstone Institutes and UC San Francisco (UCSF) have co-opted the CRISPR-Cas9 system to forcibly activate genes—rather than edit them—in human immune cells. The…

Visualizing biological macromolecules is a critical skill for students and professionals in the biological sciences. In this protocol, we demonstrate how to model the active site of the enzyme glucokinase using four freely available programs for molecular modeling. This tutorial highlights several steps of the protocol for each program, which…

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see HEEBOdata. HEEBO set and HEEBO controls. Bioconductor version: 2.9 R objects describing the HEEBO oligo set. Author: Agnes Paquet Maintainer: Agnes Paquet <apaquet at medsfgh.ucsf.edu> Citation (from within R, enter citation(“HEEBOdata”)): Installation To…

Web Resources Virtualab Home AgricultureBioinformaticsBiophysicsCancerCareerCellBiologyDevelopmentEcologyEducationFunGeneticsGenomicsHealthLabMicrobiologyMolecularMoleculeNeurosciencesPaleontologyPlantPolicySociety Instructionsupplierprotocol… Career Links AACC Onlin – American Association of Clinical Chemistry career center. Academia : Job listings in academia, major US universities, and positions in Australia, Canada, and Europe. Academic Employment Network: US academic positions. Academic network : Jobs in higher education. Academic, Physician…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see marray. Exploratory analysis for two-color spotted microarray data Bioconductor version: 2.13 Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking. Author: Yee Hwa (Jean) Yang…

Job Code and Payroll Title009403 BIOINFORMATICS PROGR 1 Job SummaryA smart hardworking individual with very strong communication and organizational skills is sought by the UCSF MS EPIC Study to serve as a Junior Biostatistics Analyst. Under direct supervision, individual will apply professional bioinformatics concepts and computational procedures to complete projects related…

Listing Results R bioconductor courses Bioconductor Introduction To R / Bioconductor Harvard Bioconductor.org All Courses 016-05-16 Just NowIntroduction to R / Bioconductor. Buffalo, NY. 2016-05-16 ~ 2016-05-17. Instructors. Martin Morgan; Lori Shepherd; Description. This is a two-day course introducing R and Bioconductor for the analysis and comprehension of high-throughput genomic…

How to download data for visualising and analysing in RINalyzer in Cytoscape. 1 I am new to this plugin in Cytoscape. I want to visualise RIN from pdb and analyze the network. According to the tutorial we can download daat from RIN data websever. But when I am trying to…

CRISPR systems that rely on inactivated Cas enzymes—that is, dead Cas (dCas) enzymes—never looked more alive. They harness the targeting power associated with CRISPR—but not the double-strand cuts. As such, they give researchers new ways to interrogate and manipulate gene function. Possibilities include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa)…

    This package is for version 2.9 of Bioconductor; for the stable, up-to-date release version, see aCGH. Classes and functions for Array Comparative Genomic Hybridization data. Bioconductor version: 2.9 Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for…

As far as I can find, there is only one tutorial about loading Seurat objects into WGCNA (ucdavis-bioinformatics-training.github.io/2019-single-cell-RNA-sequencing-Workshop-UCD_UCSF/scrnaseq_analysis/scRNA_Workshop-PART6.html). I am really new to programming so it’s probably just my inexperience, but I am not sure how to load my Seurat object into a format that works with WGCNA’s tutorials (horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/Tutorials/)….