Tag: FAIR

Experts urge caution over biotech that can wipe out insect pests

Credit: Unsplash/CC0 Public Domain Dozens of scientists, experts and campaigners called for a ban on the release of genetically-edited organisms into the wild, in a statement Friday warning of potentially severe risks to the world’s pollinators. The appeal was launched at crunch biodiversity talks in Montreal, where delegates from almost…

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Unexpected finding in mucus clearance system may inform future pulmonary disease treatment

Generation and validation of MUC5B/AC-KO cultures. (A) Overview of the MUC5B/MUC5AC gene-targeting approach via lentivirus-mediated delivery of sgRNA and CRISPR-Cas9. Transduced and sorted cells were differentiated at air-liquid interface (ALI). Once fully differentiated, the mucus gel was collected by apically washing cultures. HEK293T, human embryonic kidney–293T; FACS, fluorescence-activated cell sorting;…

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A strategy to thermally stabilize microneedle vaccine technology

Credit: Thanh Nguyen/University of Connecticut Researchers in the Department of Biomedical Engineering—a shared department between the UConn Schools of Dental Medicine, Medicine, and Engineering—unlocked a new strategy using sugar molecules to thermally stabilize their existing microneedle vaccine technology, eliminating the need for cold-chain storage. Associate Professor Thanh Duc Nguyen from…

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Comment: Unable to convert "NULL" to either zero or NA

Fair enough, I just glanced over your screenshot, because that magrittr pipe is intimidatingly long, and you had already ascertained that *this is because some values in these columns are “NULL”. All the other times with other data frames the empty values are always “NA” and I can use na.rm=T…

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Ontology Development Kit Looks to Harmonize, Streamline Management of Biomedical Semantics

CHICAGO – Nearly seven years after it first appeared online as a beta release, the Ontology Development Kit (ODK) has matured into an open-source software package used by the developers and keepers of dozens of biomedical ontologies. The ODK is meant to implement the principles of the Open Biological and…

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IMUNON, INC. MANAGEMENT’S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS. (form 10-Q)

The following discussion and analysis of our financial condition and results of operations This discussion contains forward-looking statements that involve risks and uncertainties. Our actual results may differ materially from those discussed in forward-looking statements. Factors that might cause a difference include, but are not limited to, those discussed above…

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New study finds that CRISPR/Cas9 leads to unexpected genomic changes

Credit: Unsplash/CC0 Public Domain The widely used gene scissor (CRISPR/Cas) can modify the genetic content in cells to study the molecular roles of genes and has gained great clinical relevance in gene therapy to treat genetic diseases. A new study performed by Claudia Kutter’s research group at the Department of…

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Postdoctoral Scientist – Dr. Casero Lab – Bioinformatics

Principal Investigator, David Casero, PhD is looking for a Postdoctoral Scientist to join the team! The depth and breadth of the information generated by modern high-throughput technologies has promoted the integration of data-mining computational methods into everyday basic and clinical research. These so-called omics technologies can detect and quantify a…

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3D protein structure predictions made by AI could boost cancer research and drug discovery

The space of characteristic structural elements in AF2 structural models for 21 species. Visualization of t-SNE dimensionality reduction analysis, in which structures with similar structural elements are placed closer together and the 20 most common superfamilies are colored. The axes corresponding to the t-SNE dimension 1 and t-SNE dimension 2…

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Senior Bioinformatics Scientist at Invitae

Invitae is a biotechnology company focused on providing tools and services for clinical research applications of genomics. Our mission is to unlock the power of precision medicine in improving patient care by providing a technology platform to advance genomics and facilitate collaborative research. Invitae is seeking senior Bioinformaticians to join…

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Myriad Genetics to Submit Hereditary Cancer Risk Variants to ClinVar in 2023

NEW YORK – Myriad Genetics will begin submitting variants detected by its hereditary cancer risk test, including variants in BRCA1 and BRCA2 genes, to the public database ClinVar starting in the spring of 2023. The Salt Lake City-based company is infamous, derided, and even boycotted in certain circles in the…

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Multi-level cellular and functional annotation of single-cell transcriptomes using scPipeline

Software Figure preparation: CorelDRAW x8 (Corel); Bioinformatic analyses: R v 4.0.3 (R Foundation for Statistical Computing). Computational resources Analyses were run on a desktop computer with an Intel Core i9-10900L CPU (3.70 GHz, 10 cores, 20 threads) with 120 GB RAM running Windows 10 Pro (v21H2). Data preprocessing scRNA-seq data sets…

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Single change in genetic code promotes development of inflammation, high blood pressure and resulting kidney damage

Credit: Circulation Research (2022). DOI: 10.1161/CIRCRESAHA.121.320625 Researchers at Vanderbilt University Medical Center have found that the change in a single letter of the genetic code promotes, in a mouse model, the development of inflammation, high blood pressure and resulting kidney damage. Their findings, featured Oct. 14 on the cover of…

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South Sudan Key Message Update: Conflict and flooding continue to drive Crisis (IPC Phase 3) or worse outcomes, September 2022 – South Sudan

Attachments Key Messages: Crisis (IPC Phase 3) outcomes, with an increasing number of areas in Emergency (IPC Phase 4), are widespread across South Sudan due to the impacts of conflict, flooding, and macroeconomic challenges. In September, the availability and consumption of the first-season harvest in bimodal areas of southern South…

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4basebio Plc – Half-year Report

4basebio PLC(“4basebio”, the “Company” or the “Group”) Half-year Reportfor the six months ended 30 June 2022 4basebio PLC (AIM: 4BB), the specialist life sciences group focused on exploiting intellectual property in the field of cell and gene therapies and DNA vaccines, announces its unaudited half-year results for the six months…

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PhD position: Virus bioinformatics – Academic Positions

The Computational Biology Group at the Department of Biosystems Science and Engineering of ETH Zurich in Basel works at the interface of mathematics, statistics, and computer science with biology and medicine. We develop statistical and evolutionary models and efficient algorithms for high-throughput molecular profiling data, with applications in oncology and…

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Project Scientist – Knott Lab – Bioinformatics & Functional Genomics

Are you passionate about applying genomics, computer science, and probability theory to study cancer progression? The Knott laboratory at Cedars-Sinai Medical Center is searching for a Project Scientist with a strong background in tumor biology and the immune microenvironment to lead single cell-based omics studies of immunotherapy clinical trials being…

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Unsure how to run FastQC on interactive node : bioinformatics

Hi all. My goal has long been to get involved in biology-problems — especially in the biomedical realm, but I haven’t had a direct path to doing so because I don’t love “doing” biology itself. For instance, I did a BS and MS in applied math with a healthy dose…

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Aged neurons generated directly from skin more accurately model Parkinson’s disease

Induced dopaminergic neurons directly reprogrammed from the skin cells of a patient with idiopathic Parkinson’s Disease. Credit: Janelle Drouin-Ouellet, University of Montreal, Canada The possibility to make virtually all cell types of the human body from induced pluripotent stem cells (iPSCs), which are embryonic-like cells generated from a patient’s skin,…

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Postdoctoral Scientist – Bioinformatics and Integrative Genomics Research Cluster at Cedars-Sinai

Responsibilities Requisition # 20002022A At Cedars-Sinai, postdoctoral scientists and other junior researchers fulfill a critical role in expanding the horizons of medical knowledge through biomedical research. By hosting more than 100 postdocs, who conduct vital research and receive advanced training with expert faculty mentors, Cedars-Sinai supports the ongoing medical education process that continues…

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The scent that could save California’s avocados

Weevil grub that made its way into an avocado seed to feed, rendering the fruit inedible. Credit: Mark Hoddle/UCR UC Riverside scientists are on the hunt for a chemical that disrupts “evil” weevils’ mating and could prevent them from destroying California’s supply of avocados. Avocado weevils—small beetles with long snouts—drill…

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Laboratory Officer/ Research Technician at European Molecular Biology Laboratory (EMBL)

About the team/job The Developmental Biology Unit at EMBL Heidelberg is seeking to recruit a research staff member to work in the Rapti group with responsibilities of Laboratory officer/ Research Technician. Research in the Rapti group focuses on the cellular and molecular mechanisms of nervous system development, glia-neuron morphogenesis and…

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Data Management Coordinator – Germany Jobs IT Engineering Academic Remote NGO Charity Work

About the team/jobThe Data Science Centre, launched in February 2022 to promote cutting-edge research and services in Data Science across all of EMBL, is looking for a bioinformatician, computational biologist or computer scientist as a Data Management Coordinator. The Data Science Centre will ensure that biological research data at our…

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InnoCare Releases 2022 Mid-Year Results and Business Highlights

BEIJING–(BUSINESS WIRE)–InnoCare Pharma (HKEX: 09969), a leading biopharmaceutical company focusing on cancer and autoimmune diseases, today announced 2022 mid-year results which ended on June 30, 2022. Dr. Jasmine Cui, Co-founder, Chairwoman and CEO of InnoCare said: “The announcement of 2022 mid-year results coincides with our seventh anniversary. In the challenging…

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Can safeguards for digital genomic data from biodiversity be ensured

Developing countries feel digital sequence information provides a loophole through which developed countries can circumvent the Convention of Biodiversity Negotiations on how to regulate the use of digital sequence information (DSI) of genetic resources could further delay the finalisation of the Post-2020 Global Biodiversity Framework under the UN Convention on Biological Diversity (CBD)….

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Job Application for C++ Software Developer in Bioinformatics and Big Data at NIH-NCBI

Overview Black Canyon Consulting (BCC) in partnership with Medical Science and Computing (MSC) is searching for a C++ Software Developer in Bioinformatics and Big Data to support the National Center for Biotechnology Information (NCBI).  This opportunity is full time and onsite at the NCBI in Bethesda, MD and/or remote work. NCBI,…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in WORLDWIDE

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. This opportunity is…

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Research Bioinformatician IV – Bioinformatics (Statistics)

Responsibilities Requisition # HRC0992682 The newly formed Precision Biomarkers Laboratories (PBL) at Cedars-Sinai is seeking a highly skilled bioinformatics professional with an expertise in statistical methods and data applications. This role will be responsible for developing robust statistical measures to evaluate, analyze, and integrate proteomics data for continuous quality control…

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Clinical Scientist (State Registered in Bioinformatics) in Manchester

Main duties of the job To employ all the competences required of a State Registered Clinical Scientist to provide bioinformatics support to diagnose genetic disease. To provide clinical liaison and a high level of scientific knowledge, skill and expertise. To collaborate with other members of the department to achieve an…

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Bioinformatics Scientist Job In Dovel Technologies, LLC At

Overview: We are currently searching for a Bioinformatics Scientist to provide support to the National Institutes of Health (NIH). This opportunity is a full-time position with MSC, and it is on-site in Gaithersburg, MD. Duties & Responsibilities: Work independently and collaboratively to develop or optimize procedures that improve the throughput…

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Drosophila embryonic development at single-cell resolution

A new atlas that maps the continuum of embryo development in fruit flies has gone beyond, thanks to machine learning. Credit: Isabel Romero Calvo/EMBL Scientists have constructed the most complete and detailed single-cell map of embryo development in any animal to date, using the fruit fly as a model organism….

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A jab at the vaccine story

India’s Vaccine Growth Story: From Cowpox to Vaccine Maitri is divided into nine chapters with an epilogue Topics BOOK REVIEW | Literature | Vaccine India’s Vaccine Growth Story: From Cowpox to Vaccine Maitri TO READ THE FULL STORY, SUBSCRIBE NOW NOW AT JUST RS 249 A MONTH. Key…

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How to Find Standard Deviation in R?

Being a statistical language, R offers standard function sd(’ ‘) to find the standard deviation of the values. So what is the standard deviation? ‘Standard deviation is the measure of the dispersion of the values’. The higher the standard deviation, the wider the spread of values. The lower the standard…

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Research Bioinformatician II – Li Lab – Computational Biomedicine

Everyone’s unique health journey is informed by data. Join us as we translate today’s discoveries into tomorrow’s medicine! Cedars-Sinai is home to some of the most advanced biomedical research and training programs in the world, which attracts renowned physician-scientists seeking an unparalleled environment for fostering invention and teamwork. The Department…

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Sequencing Driven Metagenomics Market Size, Share, Regional Growth Analysis, Upcoming Trends, R&D Status with Current and Future Industry Figures Research Report 2028

The comprehensive Sequencing Driven Metagenomics market survey report covers an array of factors that have an influence on the market and Sequencing Driven Metagenomics industry which includes industry insight and critical success factors (CSFs), market segmentation and value chain analysis, industry dynamics, drivers, restraints, key opportunities, technology and application outlook,…

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Group Leader – Structural or Molecular Systems Biology at European Molecular Biology Laboratory (EMBL)

About the team/job The Structural and Computational Biology (SCB) Unit at EMBL Heidelberg pursues an ambitious and cross-disciplinary research program in integrated structural and computational systems biology, bridging between temporal and spatial scales. The SCB Unit seeks to recruit a highly motivated group leader in the area of structural or…

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Why The Fight Over DNA Is Central To Biodiversity Conservation

Nairobi (Kenya): In 2020, when the Covid-19 pandemic was at its peak and vaccine manufacturers rushed to find a one, a research director at the US vaccine company Inovio Pharmaceuticals Inc said that it took them only “three hours” to design a vaccine, once they were able to download the…

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Turncoat T cells are at the core of multiple sclerosis and other inflammatory central nervous system disorders

scRNAseq replicates. CD45.1+ P14 cells were adoptively transferred into adult CD45.2+ GP or GFAP:GP mice 24h before i.c. infection with rLCMV-GP33. At least six weeks later, mice were treated with antiCD8a depleting antibody or isotype control. One week after depletion, mice were treated with TAM i.p. for four consecutive days…

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Unexpected behaviour during hybrid Monte-Carlo simulations (ReaxFF) – LAMMPS Beginners

T.Dem June 25, 2022, 5:41pm #1 Dear LAMMPS users, I am trying to run Monte Carlo simulations using reaxff to study the oxygen coverage on a Pt nanoparticle. I defined my oxygen reservoir using the chemical potential definition for a perfect gas. Initially, the system is very small (350 atoms)…

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Hubble captures a galactic menagerie

Credit: ESA/Hubble & NASA, H. Ebeling; Acknowledgment: L. Shatz The NASA/ESA Hubble Space Telescope captured this massive galaxy cluster, called Abell 1351, with its Wide Field Camera 3 and Advanced Camera for Surveys. Abell 1351 lies in the constellation Ursa Major in the northern hemisphere. This image is filled with…

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Researchers use nanotechnology to destroy and prevent relapse of solid tumor cancers

Generation and characterization of DCNV-rAd-Ag. a, Generation of DCNVs derived from adenovirus-infected mature dendritic cells. (1) The genes of tumor-specific antigen were genetically engineered into the adenovirus vector. (2) Recombinant adenovirus infected the immature DC2.4 cells to express the modified antigen on the cell surface and stimulate it. (3) Differentiation,…

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Cas12c provides antiviral immunity without the need to cut DNA

Graphical abstract. Credit: Molecular Cell (2022). DOI: 10.1016/j.molcel.2022.04.020 A trio of researchers at the University of California, Berkeley, has found that the protein Cas12c can provide antiviral immunity for bacteria without the need to cut DNA. In their paper published in the journal Molecular Cell, Carolyn Huang, Benjamin Adler and…

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New gene-edited tomatoes boost vitamin D levels

An international team of scientists primarily based out of the John Innes Centre in the United Kingdom has used gene-editing to create a vitamin D-enriched tomato. Using CRISPR-Cas9, they switched off an enzyme in tomatoes that ordinarily prevents the molecular forerunner of vitamin D3 (called 7-dehydrocholesterol, or 7-DHC) from accumulating…

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First genomic sequencing of monkeypox from Switzerland is now available

The virus can be identified with a PCR test, especially from affected lesions and other samples. Credit: Geneva University Hospitals (HUG) The Geneva Centre for Emerging Viral Diseases shares the first sequencing results of the monkeypox genome from Switzerland. This important step will enable further analysis and comparison with genome…

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How a genetic mutation affects the body’s immune system response to viruses, development of blood cancers

Graphical abstract. Credit: Cell Reports (2022). DOI: 10.1016/j.celrep.2022.110856 The body’s innate immune system, active from birth, is the first line of defense against viruses and other pathogens that cause disease. Using vaccination as an example, after receiving a vaccine, pain, redness, or swelling may occur at the injection site. This…

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CENTURY THERAPEUTICS, INC. Management’s discussion and analysis of financial condition and results of operations (form 10-Q)

The following discussion and analysis should be read in conjunction with our financial statements and accompanying notes included in this Quarterly Report on Form 10-Q and the financial statements and accompanying notes thereto for the fiscal year ended December 31, 2021 and the related Management’s Discussion and Analysis of Financial…

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Molecular mechanism of ZDHHC18-mediated palmitoylation of cGAS in innate immunity inhibition

Detection of double-stranded DNA by cGAS triggers innate immune responses. ZDHHC18-mediated palmitoylation of cGAS sheds light on a novel posttranslational modification that leads to the fine-tuning of cGAS-mediated innate immune responses. Credit: The EMBO Journal (2022). DOI: 10.15252/embj.2021109272 Cyclic GMP-AMP synthase (cGAS), a double-stranded DNA (dsDNA) sensing protein, plays an…

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Cogent Biosciences Reports Recent Business Highlights and First Quarter 2022 Financial Results

Cogent Biosciences, Inc. Initial bezuclastinib APEX data to be presented at the European Hematology Association (EHA) 2022 Annual Congress Building a portfolio of discovery stage programs, creating potential best-in-class small molecule kinase inhibitors for genetically defined oncology indications and rare diseases Ended 1Q 2022 with $191.0 million in cash, sufficient…

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Production Bioinformatics Manager, Clinical Informatics (Operations)

Invitae is dedicated to bringing comprehensive genetic information into mainstream medicine to improve healthcare for billions of people. The Clinical Informatics team is driven to make a difference for the patients we serve. We are leading the transformation of the genetics industry by making genetic testing affordable and accessible for…

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Team develops method to increase gene editing efficiency while minimizing DNA deletion sizes

Targeting E. coli DNA pol I to DSBs increased the ratio of 1-bp deletions versus >1-bp deletions and TIS versus non-TIS. (A) Counteracting DNA resection (e.g. MRE11) by pol I fused to Cas9. The expected result is suppression of the MMEJ and SSA DNA repair pathways, which require DNA resection. (B)…

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Unlocked enzyme structure shows how strigolactone hormone controls plant growth

Using a permanently unlocked form of the plant enzyme MAX3, UC Davis researchers are exploring the mechanism by which the plant hormone strigoractone regulates a massive network of genes controlling plant growth and architecture. Credit: Nitzan Shabek/UC Davis As sessile organisms, plants have to continually adapt their growth and architecture…

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Job Hunting? New Jersey Is Hiring Thousands for Its Brand New Marijuana Industry

nattrass / Getty Images/iStockphoto Recreational marijuana sales are now officially legal in New Jersey, and the industry is staffing up to meet demand. The Garden State already has nearly 3,150 full-time jobs supporting $189 million in statewide sales, NJ.com reported, citing comments from Bruce Barcott, senior editor and executive producer…

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Skill-Based Hiring Could Address Technical Staffing Shortages

A Harvard Business Review study found that, to meet the demand for experienced tech staff to drive digital transformation efforts, many companies have adopted skill-based hiring (vs. hiring based on degrees). Such an approach complements automation efforts that try to make efficient use of a staff’s time. In the mid-2010s,…

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Euro-BioImaging Bio-Hub – FAIR Image Data Steward at European Molecular Biology Laboratory (EMBL)

About the team/job Euro-BioImaging ERIC (www.eurobioimaging.eu) is a leading pan-European research infrastructure that provides the research community open access to cutting-edge imaging services. The Euro-BioImaging Bio-Hub hosted by European Molecular Biology Laboratory (EMBL) is looking for a highly motivated FAIR Image Data Steward to develop general guidelines and technically support…

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Bioinformatics Data Engineer in Boston, MA for Dana-Farber Cancer Institute

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-26005 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute (DFCI) brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people…

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DCGI emergency use nod for Covaxin, Corbevax and ZyCoV-D across age groups

The Drug Controller General of India (DCGI) on Tuesday granted emergency use approvals to COVID-19 vaccines Covaxin, Corbevax and ZyCoV-D. While the emergency use authorisation (EUA) was granted to Bharat Biotech’s Covaxin for the age group of 6-12 years, Biological E’s Corbevax bagged the nod…

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Research team follows nearly 8,000 paths towards better cell factories

Saccharomyces cerevisiae, SEM image. Credit: Mogana Das Murtey and Patchamuthu Ramasamy/CC BY-SA 3.0 Microorganisms that efficiently convert plant biomass into renewable biofuels and biochemicals play a major role in the sustainable society of the future. However, the efficiency of these microbial cell factories is inhibited by several compounds that are…

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Unit Manager – Bioinformatics and Genomic Epidemiology

MPHI is a Michigan-based and nationally engaged, non-profit public health institute.  We are a team of teams, process and content experts, dedicated to building A world where tomorrow is healthier than today!   Title:                              Unit Manager – Bioinformatics and Genomic Epidemiology                                        $66,100 – $97,200 / Posted Thru:  4-28-22   Location: …

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14 Postdoctoral Fellowship at Umea University, Sweden

Umea University, Sweden invites online Application for various Postdoctoral Fellowship in their different Departments. We are providing a list of Postdoc Fellowship positions available at Umea University, Sweden. Eligible candidate may Apply as soon as possible.   (01) Postdoctoral Fellowship Position Postdoc Fellowship Position summary/title: Postdoctoral fellow – Molecular epidemiology…

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Do preteens really need an HPV vaccine?

by Dr. Rebekah Fenton and Dr. Rebecca Perkins Gardasil vaccine and box. Image: Wikipedia Q: Why is it important for my 10-year-old to get the HPV vaccine? A: If you are the parent of a preteen who is between the ages of 9 and 12, it’s time to make sure…

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[Solved] ggplot with 2 y axes on each side and different

Sometimes a client wants two y scales. Giving them the “flawed” speech is often pointless. But I do like the ggplot2 insistence on doing things the right way. I am sure that ggplot is in fact educating the average user about proper visualization techniques. Starting with ggplot2 2.2.0 you can…

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Fix error handling in pcm030_fabric_probe

[PATCH] ASoC: fsl: Fix error handling in pcm030_fabric_probe * [PATCH] ASoC: fsl: Fix error handling in pcm030_fabric_probe @ 2022-03-01 7:53 Miaoqian Lin 2022-03-02 13:44 ` Mark Brown 0 siblings, 1 reply; 7+ messages in thread From: Miaoqian Lin @ 2022-03-01 7:53 UTC (permalink / raw) To: Liam Girdwood, Mark Brown,…

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UCSC and Amazon Web Services work to accelerate genomics research

The UC Santa Cruz Genomics Institute is collaborating with Amazon Web Services (AWS) to allow researchers to quickly and efficiently execute bioinformatics pipelines on AWS’s global cloud infrastructure. AWS and UCSC are committed to accelerating genomics research by integrating the Dockstore project, a leading repository for scientific and biomedical workflows…

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FAIR trees: phylogenetics in Galaxy workshop Tickets, Wed 15 Jun 2022 at 09:00

Currently, phylogenetic analysis using sequence data involves many steps using various bioinformatic tools. This translates into a steep and long learning curve for researchers with little bioinformatic knowledge since the majority of these tools run on the command line. Galaxy is an open-source, free platform for FAIR data analysis that…

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A new technique to unravel gene regulation

Zebrafish notochord nuclei at 15-somite stage. Grey: nuclear DNA (DAPI). Color: histone H3K9me3. Credit: Phong Nguyen, Franka Rang & Kim de Luca. How is the activity of genes regulated by the packaging of DNA? To answer this question, a technique to measure both gene expression and DNA packaging at the…

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Study shows strong influence of external environment on fungal communities in the primate gut

Illustration of bacteria in the human gut. Credit: Darryl Leja, National Human Genome Research Institute, National Institutes of Health Researchers are starting to understand the importance of gut fungi in mammals and the ways different environmental factors can shape these fungal communities, which play a crucial role in regulating immune…

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What is ClustalW? Tutorial of How to Use ClustalW

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

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Bioinformatics Scientist – GWAS – Invitae

Invitae is a rapidly growing, purposeful company. Our mission is to empower doctors and patients with genetic information to help them make informed medical decisions at all stages of life. The Integrated Risk Assessment Platform plays a meaningful role in rapidly growing our understanding of genomic health and personalized medicine….

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Two drugs show promise in rejuvenating lung epithelial progenitor cells damaged by COPD

Overview of the transcriptomics-guided drug discovery strategy.(A) Schematic outline of the drug screening strategy. (B) Heatmap shows the gene expression pattern of the druggable genes (www.dgidb.org) identified both in CS-exposed mice and patient with COPD databases. (C) Reactome pathway enrichment analysis of genes differentially expressed from patients with COPD (8)…

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Genomic sequencing aids the global tuberculosis fight

Total number of isolates for each drug by sensitivity. Each drug is represented by a colored circle weighted by the prevalence of phenotypic resistance to that drug. The center of each circle shows the intersection between values on the x-axis and y-axis. Group 1 = associated with resistance. Group 2…

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Team develops new process for evaluating impacts of gene edits that alter rather than ‘knock out’ DNA code

CRISPR-associated protein Cas9 (white) from Staphylococcus aureus based on Protein Database ID 5AXW. Credit: Thomas Splettstoesser (Wikipedia, CC BY-SA 4.0) A new study from scientists at ChristianaCare’s Gene Editing Institute is advancing the safety and efficacy of using CRISPR gene editing in patient treatments by demonstrating how to identify and…

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A-Prot: protein structure modeling using MSA transformer | BMC Bioinformatics

Benchmarking contact prediction First, we benchmarked the long-range contact prediction performance of A-Prot using the FM and FM/TBM targets of CASP13 [24]. The benchmark results show that the performance of our model outperforms that of the existing methods (Table 1). We compared the precision of our model’s top L/5, L/2,…

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An R package for comprehensive data analysis of peptide- and protein-centric bottom-up proteomics data

Overview of protti functions. protti can be used on the output of any software package for quantitative analysis of bottom-up proteomics experiments and provides a flexible set of functions for quality control, as well as data pre-processing, data analysis and data interpretation. Credit: Bioinformatics Advances (2021). DOI: 10.1093/bioadv/vbab041 A recent…

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Crystallography, cryo-EM and AlphaFold shed light on key human antibacterial proteins

Figure 1. Model of the human UMOD/FimH interaction, assembled by combining the structural information described in the study. A, The high-mannose sugar chain (green) of the decoy modules branching out from a filament of UMOD (shades of blue) is bound by the FimH sugar-binding domain at the tip of bacterial…

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Family History Fair Held In M.V.

By CRAIG HIGGINS The Progress Local storyteller and personal historian Charlene Paul teaches a class at the Moapa Valley Family History Fair on Saturday, Feb. 26. PHOTO BY CRAIG HIGGINS/The Progress Local residents had an opportunity to make a connection with their ancestors on Saturday, Feb. 26, at the annual…

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Research Biologist Computational Bioinformatics Geneticist Research Associate Job in PEORIA, IL

Summary The Agricultural Research Service (ARS) is the United States Department of Agriculture’s chief scientific research agency and one of the world’s premiere scientific organizations. ARS Postdoctoral Research Associates are hired to supplement a lead scientist’s research on agricultural problems of high national priority affecting American agriculture. **ANNOUNCEMENT IS OPEN…

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Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis

INTRODUCTION Next-generation sequencing (NGS) has revolutionized many areas of biological research (1, 2), providing ever-more data at an ever-decreasing cost. One such area is microbiome research, the study of microbes in their theater of activity using metagenomic sequencing (3). Here, deep short-read sequencing, and improving performance of long-read sequencing, are…

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Admissible Machine Learning w/E LeDell, Chief Machine Learning Scientist, H2O.ai

Erin Ledell is Chief Machine Learning Scientist at H2O.ai, the company that produces the open source, distributed machine learning platform, H2O. At H2O.ai, she leads the development of the H2O AutoML algorithm. She is also the founder of WiMLDS and co-founder of R-Ladies Global. Talk will cover: Admissible Machine Learning…

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UH Manoa Campus Events Calendar

Scientific Workflows and Gateways February 18, 2:00pm – 4:00pm Mānoa Campus, In Person at 103 Keller Hall, UH Manoa or Online via Zoom Workshop Description Sciences are becoming more data intensive and thus managing, handling and exploring data are becoming more prevalent issues in research. Using these data sets…

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h2o AutoML vs h2o XGBoost – model metrics

The problem here is that you are comparing training metrics for XGBoost to CV metrics for AutoML models. The code you posted for the manual XGBoost models provides training metrics. Instead, you will need to grab the CV metrics if you want to make a fair comparison to the performance…

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Bioinformatics Scientist Job Opening in Seattle, WA at Alpine Immune Sciences

Job Posting for Bioinformatics Scientist at Alpine Immune Sciences Alpine Immune Sciences is applying our platform discovery technology to bring innovative new therapies to people living with serious or life-threatening illnesses or conditions, such as cancer and autoimmune/inflammatory diseases. Exciting challenges lie ahead—guided by our core values, we’ll…

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r – Where does ggplot set the order of the color scheme?

I think this is a reproducible example of what you’re seeing. In the diamonds dataset, the mean price of “Good” diamonds is actually higher than the mean for “Very Good” diamonds. library(dplyr) diamonds %>% group_by(cut) %>% summarize(mean_price = mean(price)) # A tibble: 5 x 2 cut mean_price <ord> <dbl> 1…

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Scientists identify promising transmission chain breakers in the fight against malaria

Credit: CC0 public domain Blocking important proteins found in Anopheles gambiensis, the leading carrier of malaria transmission to humans in Africa, blocks malaria parasite transmission and parasite humans, according to researchers at Johns Hopkins Malaria Research. You can prevent infection to. Johns Hopkins Bloomberg Institute for Public Health School. and…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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Increasingly efficient production of human pluripotent stem cells

Reliable production of high-quality iPS cells enables their increasingly efficient utilization in biomedical applications. Credit: Ras Trokovic, University of Helsinki Researchers at the University of Helsinki have developed a new, faster and more reliable technique for reverting human cells to the stem cell state. Pluripotent stem cells are a key…

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Multi-organoid system to simulate human liver-islet axis in normal and type 2 diabetes

Schematic of hiPSCs derived multi-organoid-on-chip system to model human liver-pancreatic islet axis in vitro. Credit: Tao Tingting Type 2 diabetes (T2DM) is a systematic multi-organ metabolic disease, which is characterized by dynamic interplay among different organs. Pancreatic islet-liver axis is closely associated with normal glucose regulation and homeostasis maintenance. The…

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High school student learning ML with a short-term goal of placing top on Kaggle? : learnmachinelearning

I’m an 11th grade student who’s fairly interested in machine learning and the AI industry. I have coding experience but haven’t learned ML yet. My short term goal is to place high on a Kaggle competition because there aren’t that many tangible goals I can place as a high school…

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Functioning induced liver cells from skin tissue

Figure 1. Urea metabolism is impaired in patient-derived human-induced pluripotent stem cells (hiPSCs) differentiated into hepatocytes (hiPSC-Heps). (A) Scheme showing the urea cycle detoxifying ammonia (NH4+) into nontoxic urea in five consecutive urea cycle enzyme (UCE)–mediated reactions in mitochondria in hepatocytes. (B) Urea secretion in four control hiPSC-Hep lines (Ctrl_1-4)…

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Genetic strategies reverse pesticide resistance

Nature Communications i>In a new empirical study published in, a gene drive designed to bias heredity, called an allelic drive, was applied without pesticide treatment to create natural-level insects that were balanced with pesticide susceptibility. Population that has been shown to be recoverable. Credits: Bier Lab, University of California, San…

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PyTorch’s Cult Following

PyTorch’s popularity spread only three years after its launch: the open-source ML library posted a 194% user growth in the first half of 2019. Since then PyTorch has not looked back. According to the survey by Stackoverflow, while TensorFlow is the most in-demand library, PyTorch is more preferred. Data from…

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Genome research: Finding the invisible

Fig. 1: Ladder-seq uses mRNA length information to aid transcriptome reconstruction. Credit: DOI: 10.1038/s41587-021-01136-7 LMU researchers have developed a method to extract more information from sequencing data. This will afford deeper insights into biology. Higher organisms store their genetic material in the nuclei of cells as deoxyribonucleic acid (DNA). In…

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The membrane structure of inner ear protein prestin is revealed

Force spectroscopy of prestin, the motor protein in the inner ear. Credit: Kanazawa University As mammals, we have very sensitive hearing, thanks to a process known as cochlear amplification. This amplification is down to sensory cells in the inner ear called outer hair cells (OHCs), and it is thought to…

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Researchers identify new bacteria and viruses on human skin

Data representing the diverse range of microbes found in the human skin microbiome. Credit: Karen Arnott/EMBL Researchers at EMBL’s European Bioinformatics Institute (EMBL-EBI), the National Institutes of Health (NIH) National Human Genome Research Institute (NHGRI), the NIH National Institute of Arthritis and Musculoskeletal and Skin Diseases, and colleagues have identified…

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Postdoctoral Scientist – Knott Lab – Bioinformatics & Functional Genomics

Requisition # HRC0544032C Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient…

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Researchers identify new bacteria and viruses in human skin

Data representing a variety of microorganisms found in the human skin microflora. Credits: Karen Arnott / EMBL Researchers and colleagues at EMBL’s European Bioinformatics Institute (EMBL-EBI), National Institutes of Health (NIH) National Institute for Human Genome (NHGRI), NIH National Institute for Arthritis, Musculoskeletal and Skin Diseases are new bacteria and…

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The direction of your DNA may be as important as which parent it came from

Fig. 1: H19 gene expression was derepressed on the paternally inherited inverted-ICR allele in fetal livers but not in placentas. a Breeding scheme. In order to distinguish parental origin of the alleles by using SNPs between inbred mouse strains, inverted-ICR heterozygous male mice (WT/INV; C57BL/6J [B6] background) were mated with…

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First time genome editing made possible on cells lining blood vessel walls

Credit: Pixabay/CC0 Public Domain The lab of Youyang Zhao, Ph.D., from Stanley Manne Children’s Research Institute at Ann & Robert H. Lurie Children’s Hospital of Chicago developed a unique nanoparticle to deliver genome editing technology, including CRISPR/Cas9, to endothelial cells, which are cells that line blood vessel walls. This is…

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Introduction to Generative Adversarial Networks with PyTorch

Introduction to Generative Adversarial Networks with PyTorch. A comprehensive course on GANs including state of the art methods, recent techniques, and step-by-step hands-on projects What you’ll learn How Generative Adversarial Networks work internally How to implement state of the art GANs techniques and methods using PyTorch How to improve the…

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The Hot Topic In Probabilistic Programming

One of the biggest challenges of this decade is solving uncertainty, ethical and explainable problems in the thousands of machine learning models we interact with daily. Meta, formerly Facebook, announced the release of their supplement to aid this developing sphere. Bean Machine, Meta’s probabilistic programming system, is a PyTorch-based model…

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Brem Looks at Multiple Treatments for Patients With DLBCL

During a Targeted OncologyTM Case-Based Roundtable event, Elizabeth A. Brem, MD, an assistant professor in Division of Hematology/Oncology, Department of Medicine at UC Irvine Health in Los Angeles, CA, moderated a discussion about a 43-year-old woman with diffuse large B-cell lymphoma. Targeted Oncology™: What therapeutic options would you consider at…

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