Tag: STAR

a rising star in plant biology

Abdelmohsen, K., Panda, A.C., Munk, R., Grammatikakis, I., Dudekula, D.B., De, S., Kim, J., Noh, J.H., Kim, K.M., Martindale, J.L. et al., 2017. Identification of HuR target circular RNAs uncovers suppression of PABPN1 translation by CircPABPN1. RNA Biol. 14, 361-369 Aktas,…

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CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment

CircRNA extraction from bulk RNA seq datasets using CIRCexplorer2 with STAR alignment 0 Hello there, I newbie in bioinformatics, I tried to extract circular RNA from bulk RNA sequencing datasets using CIRCexplorer2 with STAR alignment tools. I followed below tutorial. circexplorer2.readthedocs.io/en/latest/tutorial/assembly/ But the problem occured until assembly part. Here they…

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Creating reference genome that includes HIV genome

Creating reference genome that includes HIV genome 1 Hi all, In this paper (www.ncbi.nlm.nih.gov/pmc/articles/PMC9831945/) the authors use a reference genome that includes the HIV genome. Seen in this sentence of the paper: “Adapters and low-quality bases were trimmed using Cutadapt v1.18 software 11 before alignment with the human reference genome(hg38andHIV-1:…

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Marvel Just Released Epic Infinity Saga Posters For MCU Phase 3 Movies

Following a recent trend of MCU-inspired variant covers, Marvel unveiled six new covers for what is quickly seeming to become a collectible set. Recently, Marvel revealed a WandaVision-inspired variant by David Nakayama for Steve Orlando and Sara Pichelli’s Scarlet Witch ongoing series. Prior to that, in 2021, mini-sets depicting moments…

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Scholarships and Career Opportunities: Postdoctoral researcher in bioinformatics

 Lund University was founded in 1666 and is repeatedly ranked among the world’s top 100 universities. The University has around 46 000 students and more than 8 000 staff based in Lund, Helsingborg and Malmö. We are united in our efforts to understand, explain and improve our world and the…

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STAR is running but .sam file size does not increase after hours mapping

STAR is running but .sam file size does not increase after hours mapping 0 Hi there, I’m using STAR with a small genome. My samples are paired. The commands are: For genome indexes STAR –runThreadN 20 –runMode genomeGenerate –genomeDir /path/to/folder/Analyses/STAR/ –genomeFastaFiles /path/to/genome_reference/genome.fna –readFilesCommand zcat path/to/folder/with/giz_samples/R1.fq.gz R2.fq.gz –sjdbGTFfile path/to/genome_reference/genome.gff –genomeSAindexNbases 11…

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Phylogenetic and AlphaFold predicted structure analyses provide insights for A1 aspartic protease family classification in Arabidopsis

Introduction Proteases regulate various biological processes including protein synthesis and maturation, activity modification, degradation and turnover. Depending on their catalytic mechanisms, these proteases are primarily classified into cysteine, metallo-, serine, threonine and aspartic protease family (Beers et al., 2004). The latter protease family is known as acid protease family because they…

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EDIT stock, BEAM stock win bullish views in Cantor gene editing coverage (NASDAQ:EDIT)

Natali_Mis Editas Medicine (NASDAQ:EDIT), Intellia Therapeutics (NASDAQ:NTLA), and Beam Therapeutics (NASDAQ:BEAM) were among clinical-stage biotechs to receive Overweight ratings at Cantor Fitzgerald as the firm launched its coverage on several gene editing companies. The analyst Rick Bienkowski sees multiple catalysts for gene editing companies at a time when the subsector…

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A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea

A paralog of Pcc1 is widely distributed among archaea The recent discovery of a fifth subunit of KEOPS in metazoa raised the possibility that a corresponding subunit could exist in archaea. In search for such a subunit, we noticed in the model archaeon Thermococcus kodakarensis KOD1 the existence of two…

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‘Saturday Night Live’ Spoofs Mousy ‘Merrick Garland’ As Whip-Crackin’ Lawman

Attorney General Merrick Garland (Mikey Day) was jabbed hard on the cold open of “Saturday Night Live” as a squeaky-voiced, mousy lawman who is well aware he looks and acts like he was “born in a library.” Nevertheless, he announces chillingly at a faux press conference: “I am the law.”…

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The Global Bioinformatics Market size is expected to reach $19.9 billion by 2028, rising at a market growth of 12.5% CAGR during the forecast period

ReportLinker In order to serve several fields of scientific study, including biomedicine, bioinformatics—a mix of biology and information technology—links biological data with methods for information storage, dissemination, and analysis. New York, Jan. 27, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “Global Bioinformatics Market Size, Share &…

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Data Cornering – Page 28 of 28

Here is how to create a jitter chart in Power BI with averages by categories and using only Power BI and DAX capabilities.… Here is how to add GIF animation to the plot in R and draw extra attention. You can take a static ggplot2 plot… If you see the…

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I want to start using ggplot – ggplot2

library(cluster) library(factoextra) #> Loading required package: ggplot2 #> Welcome! Want to learn more? See two factoextra-related books at goo.gl/ve3WBa library(ggplot2) x <- data.frame( aaddr = c( “800 Coddingtown Ctr”, “900 Coddingtown Ctr”, “1363 N Mcdowell Blvd”, “8270 Petaluma Hill Rd”, “311 Rohnert Park Expy W”, “100 Santa Rosa Plz” ),…

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Sarah Dash Net worth January 2023, Height, Weight, Age, Bio

Quick Facts Name Sarah Dash Age 77 Years Old Nick Name Sarah Birth Name Sarah Dash Birth Date 1945-08-18 Gender Female Profession American Singer Nationality American Birth Nation America Place Of Birth Trenton, New Jersey, U.S. Ethnicity African-American Race Black Religion Christian Horoscope Leo Father Abraham Dash Mother Mary Elizabeth…

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Whole-transcriptome profiling across different developmental stages of Aedes albopictus (Diptera: Culicidae) provides insights into chitin-related non-coding RNA and competing endogenous RNA networks | Parasites & Vectors

Benelli G, Wilke A, Beier JC. Aedes albopictus (Asian Tiger Mosquito). Trends Parasitol. 2020;36:942–3. Article  Google Scholar  Bhatt S, Gething PW, Brady OJ, Messina JP, Farlow AW, Moyes CL, et al. The global distribution and burden of dengue. Nature. 2013;496:504–7. Article  CAS  Google Scholar  Bonizzoni M, Gasperi G, Chen X,…

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Healthcare Hires of Note – MedCity News

This edition of Healthcare Hires of Note is presented by SnapNurse SnapNurse, which matches quality nurses and medical professionals with employment opportunities nationwide, has named Jeff Grant as its new CEO. Grant will focus on catalyzing growth of SnapNurse’s tech platform, which makes it easy to place and onboard qualified healthcare clinicians. The platform powers…

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Which RUVr batch corrected output is better to calculate TPM?

Which RUVr batch corrected output is better to calculate TPM? 0 I have downloaded several samples from 5 studies (5 batches). Example of my count table: S_rep1_batch1 S_rep2_batch1 S_rep1_batch2 S_rep2_batch2 S_rep3_batch2 . . . Gene1 34 54 65 76 67 Gene2 87 77 90 35 19 Gene3 47 67 70…

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Bio, Net Worth, Death, Cause of Death, Age, Husband, Family, Nationality, Ethnicity, Height, Weight, Parents, Facts, Wiki, Career, Albums

Quick Facts American singer-actress Sarah Dash was well-known for her work with the band LaBelle and as a studio musician for groups like The Rolling Stones. She became well-known as a solo performer because to records like the Top 10 disco track “Sinner Man.” As a member of Patti LaBelle…

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BULK mRNA-seq with UMIs. Do I need to normalize by gene length?

Hi, I am analyzed some BULK mRNA-seq data that included UMIs during the sequencing. I don’t have much experience analyzing bulk RNA-seq, and it is my first time dealing with UMIs there. I have more experience in single-cell RNA-seq, and I thought that the concept of UMIs will translate directly…

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nf-core/circrna: a portable workflow for the quantification, miRNA target prediction and differential expression analysis of circular RNAs | BMC Bioinformatics

Sanger HL, Klotz G, Riesner D, Gross HJ, Kleinschmidt AK. Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures. Proc Natl Acad Sci. 1976;73(11):3852–6. doi.org/10.1073/pnas.73.11.3852. Article  CAS  Google Scholar  Arnberg AC, Van Ommen G-JB, Grivell LA, Van Bruggen EFJ, Borst P. Some yeast mitochondrial RNAs…

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Hundreds of local high schoolers get a glimpse at life as a scientist during STEM Day at Brown

Ultimately, the faculty wanted the young students to see scientists as approachable people and build an appreciation for the fact that they could become scientists as well, Rubenstein added. “I grew up in an area that, in some sense, was a STEM desert,” she said. “I’m very much committed to…

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Seven technologies to watch in 2023

From protein sequencing to electron microscopy, and from archaeology to astronomy, here are seven technologies that are likely to shake up science in the year ahead. Single-molecule protein sequencing The proteome represents the complete set of proteins made by a cell or organism, and can be deeply informative about health…

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Philly’s firewood suppliers have a tough job, but they love to do it

Sweat streams down Andrew Mays’ face as he hefts a freshly sawed segment of oak onto the back of his firewood processor, stored at his parents’ rural Hammonton house. He guides the log — taller than he is and almost as broad — into a cage-covered chamber, then slices it…

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The metazoan landscape of mitochondrial DNA gene order and content is shaped by selection and affects mitochondrial transcription

Boore, J. L. Animal mitochondrial genomes. Nucleic Acids Res. 27, 1767–1780 (1999). Article  CAS  Google Scholar  Calvo, S. E., Clauser, K. R. & Mootha, V. K. MitoCarta2. 0: an updated inventory of mammalian mitochondrial proteins. Nucleic Acids Res. 44, D1251–D1257 (2016). Article  CAS  Google Scholar  Andrews, R. M. et al….

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Error in GDC download in TCGAbiolinks

Hello all, could you please help me, I can’t download data from TCGA. library(TCGAbiolinks) stadquery <- GDCquery(project = “TCGA-STAD”, data.category = “Transcriptome Profiling”, data.type = “Gene Expression Quantification”, workflow.type = “STAR – Counts”, legacy = F, experimental.strategy = “RNA-Seq”) GDCdownload(query = stadquery, method = “api”) Unfortunately when I run GDCdownload…

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Help for RNA sequencing analysis with DESEQ2

Help for RNA sequencing analysis with DESEQ2 0 @80066fff Last seen 1 day ago Canada Hello everyone, I’m currently trying to perform DESEQ2 with my own RNA sequencing results. I performed whole transcriptome RNA sequencing and the subsequent analysis I performed via galaxy. I performed first fastp on the samples,…

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A minimally invasive fin scratching protocol for fast genotyping and early selection of zebrafish embryos

Aleström, P. et al. Zebrafish: Housing and husbandry recommendations. Lab. Anim. 54, 213–224 (2020). Article  Google Scholar  Hubrecht, R. C. & Carter, E. The 3Rs and humane experimental technique: Implementing change. Animal (Basel) 9, E754 (2019). Google Scholar  Russell, W. M. S. & Burch, R. L. The Principles of Humane…

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Rick & Morty Full-On Stole Futurama’s Grossest Joke

Even though the series Rick and Morty hates copying other animated series’ work, it straight up stole the grossest joke in the history of Futurama. Despite Rick’s total disdain for outright copying another animated series (with ‘putting one’s own spin on it’ apparently being the only suitable exception), Rick and…

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A new approach to treating resistant hypertension

Many patients have resistant hypertension, which isuncontrolled byavailable drugs and behavioural interventions. Hence, new treatment approaches are needed. The endothelin pathway (an antihypertensive mechanism) is thought to contribute to hypertension, and currently no medications target this pathway. On the heels of positive preliminary evidence, investigators conducted an industry-supported, randomised, phase…

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DNA vaccination: A challenging cancer therapeutic strategy

Immunotherapies have gained much attention nowadays in the treatment of cancer. Among them, therapeutic DNA cancer vaccines are now considered a very promising strategy to activate the immune system against cancer tumour. DNA-mediated immunisation began in the 1990s. DNA vaccines have been developed to treat a variety of pathologies, including…

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Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs

Ellis, E. C. et al. Anthropogenic transformation of the biomes, 1700 to 2000. Glob. Ecol. Biogeogr. 19(5), 589–606 (2010). Google Scholar  Soleimani, T., Hermesch, S. & Gilbert, H. Economic and environmental assessments of combined genetics and nutrition optimization strategies to improve the efficiency of sustainable pork production. J. Anim. Sci….

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Research Fellow (Bioinformatician) job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description The National University of Singapore invites applications for a motivated Bioinformatician in the Department of Ophthalmology, Yong Loo Lin School of Medicine. The individual will join a multi-disciplinary team, comprising clinician scientists, animal model experts, and stem cell and molecular biologists. As a Bioinformatician, you will be leading…

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The Efficiency of Gene Activation Using CRISPR/dCas9-Based Transactivation Systems Depends on the System Run Time

Zhang H., Qin C., An C., Zheng X., Wen S., Chen W., Liu X., Lv Z., Yang P., Xu W., Gao W., Wu Y. 2021. Application of the CRISPR/Cas9-based gene editing technique in basic research, diagnosis, and therapy of cancer. Mol. Cancer. 20 (1), 126. doi.org/10.1186/s12943-021-01431-6 Article  CAS  Google Scholar …

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Research Fellow, Bioinformatics job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description We are seeking for a full-time bioinformatician in the cancer biology laboratory of Dr. Shruti Bhatt in the Department of Pharmacy at the National University of Singapore.  Check out Bhatt lab research focus, via this link:   pharmacy.nus.edu.sg/team/asst-prof-shruti-bhatt/ We are looking for candidates who share our excitement to…

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Genetic genealogy ‘game changer’ offers hope for near-unsolvable Ontario cold cases

“Now that we have the killer’s DNA, we just need a name to go with it.” “Forensic testing was done and DNA was identified, but it does not link to any known offenders in the national DNA data bank.” “While the offender is not on the national DNA data bank,…

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Improving Stem Cell Cultivation in Bioreactors

Cultivating quality cells is a key requirement for innovative approaches in regenerative medicine. Stirred-tank bioreactors are promising cultivation systems for the cultivation and differentiation of human induced pluripotent stem cells (hiPSCs), as they have the capacity to produce high cell numbers, allowing scale-up, and cutting-edge opportunities for improving the control…

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Inovio Pharmaceuticals Stock Up By 28% In The Last 21 Sessions

(VIANEWS) – Shares of Inovio Pharmaceuticals (NASDAQ: INO) rose by a staggering 28.66% in 21 sessions from $1.64 at 2022-10-20, to $2.11 at 14:28 EST on Friday, after two sequential sessions in a row of losses. NASDAQ is falling 0.39% to $11,101.66, after two successive sessions in a row of…

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Bioinformatician – Urgent Role at Artificial Intelligence Expert

We are searching for a hardworking Bioinformatician to join our all-star team at Artificial Intelligence Expert in Cluj-Napoca.Growing your career as a Full Time Bioinformatician is an amazing opportunity to develop exceptional skills.If you are strong in adaptability, project management and have the right initiative for the job, then apply…

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Single-cell transcriptome analysis reveals cellular heterogeneity in mouse intra- and extra articular ligaments

Amiel, D., Frank, C., Harwood, F., Fronek, J. & Akeson, W. Tendons and ligaments: a morphological and biochemical comparison. J. Orthop. Res. 1, 257–265 (1984). PubMed  CAS  Google Scholar  Lipps, D. B., Wojtys, E. M. & Ashton-Miller, J. A. Anterior cruciate ligament fatigue failures in knees subjected to repeated simulated…

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logits to softmax pytorch

A tag already exists with the provided branch name. Join the PyTorch developer community to contribute, learn, and get your questions answered. Space – falling faster than light? We are converting the layers using ReLu and other neural networks. Learn more, including about available controls: Cookies Policy. In addition, the…

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Merging csv files with specific headers

Hello all, I have a directory with csv files (tab delimited). Each file have different sections (4 headers): miRDeep2 score novel miRNAs reported by miRDeep2 novel miRNAs, estimated false positives novel miRNAs, estimated true positives known miRNAs in species known miRNAs in data known miRNAs detected by miRDeep2 estimated signal-to-noise…

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Dual roles of mTORC1-dependent activation of the ubiquitin-proteasome system in muscle proteostasis

Sustained skeletal muscle mTORC1 activity upregulates the ubiquitin proteasome system To understand the molecular mechanisms causing atrophy in muscles with high mTORC1 activation, we first analyzed the transcriptome of the fast-type extensor digitorum longus (EDL) muscle in 3-month-old TSCmKO mice6. A short-term (3 day) treatment with rapamycin was used to…

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Cas9 targeted nanopore sequencing with enhanced variant calling improves CYP2D6-CYP2D7 hybrid allele genotyping

Please use this url to cite or link to this publication: hdl.handle.net/1854/LU-8771189 MLA Rubben, Kaat, et al. “Cas9 Targeted Nanopore Sequencing with Enhanced Variant Calling Improves CYP2D6-CYP2D7 Hybrid Allele Genotyping.” PLOS Genetics, edited by Guanzheng Luo, 2022, doi:10.1371/journal.pgen.1010176. APA Rubben, K., Tilleman, L., Deserranno, K., Tytgat, O., Deforce, D., &…

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Inovio Pharmaceuticals Stock Is 9% Up Today

(VIANEWS) – Shares of Inovio Pharmaceuticals (NASDAQ: INO) rose 9.15% to $1.79 at 16:14 EST on Friday, after four sequential sessions in a row of losses. NASDAQ is jumping 1.89% to $10,815.92, after two consecutive sessions in a row of losses. This seems, up until now, an all-around positive trend…

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Rawan Dash Bio, Age, YouTube, Net Worth, Single, Height, Instagram : Biography Celeb

Rawan Dash is a popular and talented Emirati social media star. Rawan Dash is popular for her self-titled Youtube channel where she shares beauty, lifestyle, and mukbang videos among others. Early Life Rawan Dash was born on 16 October 1997 and her age is currently 24 years old. She hails…

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Gengis Khan: Profile & Match Listing

Profile & Match Listing • Facts & Stats • PWI Ratings • Opponents & Partners • Win/Loss Record • Star Ratings • Win Types • Relations • PPV   Name: Isaias Rodriguez Preferred Name: Gengis Khan Date Of Birth: Oct 3rd 1941 Place of Birth: Guadalajara, Jalisco,…

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[100% Discount] Image Recognition for Beginners using CNN in R Studio

You’re looking for a complete Convolutional Neural Network (CNN) course that teaches you everything you need to create an Image Recognition model in R, right? You’ve found the right Convolutional Neural Networks course! After completing this course you will be able to: Identify the Image Recognition problems which can be solved using CNN Models….

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AI Training Dataset Market Study 2022-2030 by Current

The most recent report published by Market Research Inc. indicates that the AI Training Dataset Market is likely to accelerate significantly in the next few years. Specialists have studied market drivers, restraints, risks and prospects in the global market. The AI Training Dataset Market report shows the likely direction of…

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24 groundbreaking events that happened during the Queen’s reign

When Queen Elizabeth was crowned in 1953, she promised to rule for her whole life. It was a commitment that never waivered and saw her on the throne for more than 70 years, over which time the world changed significantly. During her reign, the Queen saw some of the most…

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Evolution of stickleback spines through independent cis-regulatory changes at HOXDB

Darwin, C. On the Origin of Species by Means of Natural Selection (John Murray, 1859). Owen, R. On the Archetype and Homologies of the Vertebrate Skeleton (Richard and John E. Taylor, 1848). Stern, D. L. & Orgogozo, V. Is genetic evolution predictable? Science 323, 746–751 (2009). CAS  PubMed  PubMed Central …

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Gengis Don & The Empire / Fullmoon Groove : Brooklyn Roads

Gengis Don & The Empire collide two musical worlds and leave their funky fingerprints on the music as the audience joins along a journey through the Hip Hop universe. Blast off in 3, 2, 1…described as the love child of Jazz & Boom Bap, Gengis Don has a sound of his own….

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Study Claims Sun Will Devour Mercury, Venus And Earth, And Explains How

Recent research suggests that the Sun has reached middle age. The Sun is the source of life on Earth. It emits light and heat, or solar energy, which allows different species to reproduce on Earth. But what happens when a giant star runs out of all its fuel? It is…

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The number of unique SNPs and indels in Clinvar

The number of unique SNPs and indels in Clinvar 1 Is it provided by clinvar or an easy way to get the number of unique SNPs and indels in Clinvar? I have found the unique variation record in here. But this also included structural variation such as CNVs. ClinVar submissions…

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Patrick Murphy Bulk RNA-Seq – HackMD

Patrick Murphy Bulk RNA-Seq – HackMD        owned this note   Published Linked with GitHub — title: ‘Patrick Murphy Bulk RNA-Seq’ disqus: hackmd — Patrick Murphy bulk RNA-Seq Analysis === ## Table of Contents [TOC] ## 1. Introduction This is a bulk RNA-Seq project, which includes human data….

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Bioinformatics Analyst in Minneapolis, MN for University of Minnesota, Twin Cities

Details Posted: 13-Aug-22 Location: Minneapolis, Minnesota Salary: 43944.32 – 123022.07 Categories: Research Support – Laboratory/Non-Laboratory Staff/Administrative Additional Information: 2 openings available. The Research Informatics Solutions (RIS) group within the University of Minnesota Supercomputing Institute (MSI) is hiring two full-time Bioinformatics Analysts to support research at the University of Minnesota. Analysts…

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In vivo transomic analyses of glucose-responsive metabolism in skeletal muscle reveal core differences between the healthy and obese states

Animals and sample preparation Animal experiments were performed as previously described12. C57BL/6J WT mice or ob/ob mice at ten weeks of age were purchased from Japan SLC Inc. (Shizuoka, Japan). The phenotypic data of the mice are summarized in Table S1. Animal experiments were approved by the animal ethics committee…

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Senior Research Fellow, Quantitative Research Scientist – CHILD job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description An exciting position is available with the NUS Yong Loo Lin School of Medicine’s Centre for Holistic Initiatives for Learning and Development (CHILD) for an enthusiastic, collaborative senior research fellow (research scientist) with strong quantitative skills. The scientist will work within highly transdisciplinary teams across multiple projects aiming…

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A*STAR Research hiring #SGUnitedJobs Bioinformatics Specialist, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is focused…

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

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A*STAR RESEARCH ENTITIES hiring #SGUnitedJobs Bioinformatics Specialist, Laboratory of Computational Cancer Genomics, GIS in Singapore, Singapore

Why do cancer treatments work in some patients, but not in others? How can we use genomics data to discover new drug targets? We seek an energetic and team-oriented Data Scientist with expertise in software development (especially web-based data visualisation) to join a multi-disciplinary effort to discover new biomarkers and…

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A*STAR RESEARCH ENTITIES hiring #SGUnitedJobs Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS in Singapore, Singapore

The Laboratory of Cancer Epigenetic Regulation, helmed by GIS Executive Director Patrick Tan, is seeking a Bioinformatician to join a new multi-institutional effort targeting the genetic basis of cancer to create novel therapies and diagnostics. Led by an award-winning thought leader in the field of Asian gastrointestinal cancer research with…

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Difference in number of DEGs from Deseq2 and limma-voom

Difference in number of DEGs from Deseq2 and limma-voom 0 Hello, I have RNA-seq data from two different treatment groups (F and NF ) at 2 different time points (T1 and T2). The mapping was done with STAR aligner and the quantification was done with FeatureCounts. I run differential expression…

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Tramadol Therapy and CYP2D6 Genotype – Medical Genetics Summaries

Introduction Tramadol (brand names ConZip, Ultram, UltramER, Odolo) is an analgesic used to treat moderate to severe pain. It is used for a variety of pain conditions, including post-operative pain, cancer pain, and musculoskeletal pain. Tramadol is a centrally acting opioid analgesic with mu-opioid binding activity as well as weak…

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Science News Roundup: Ancient DNA solves mystery over origin of medieval Black Death; U.S. issues new warnings on ‘forever chemicals’ in drinking water and more

Following is a summary of current science news briefs. Isolated Greenland polar bear population adapts to climate change An isolated population of polar bears in Greenland has made a clever adaptation to the decline in the sea ice they depend upon as a platform for hunting seals, offering…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

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….

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73 Boys Enrolled for DMD Therapy Pamrevlumab’s Second Phase 3 Trial

FibroGen has completed patient enrollment for its Phase 3 trial evaluating pamrevlumab in combination with corticosteroids as a potential treatment for children with Duchenne muscular dystrophy (DMD). The LELANTOS-2 study (NCT04632940) has enrolled 73 boys with DMD, ages 6 to 12, who maintain their ability to walk. The trial, the second…

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Imaging Replicative Domains in Ultrastructurally Preserved Chromatin by Electron Tomography

This protocol presents a technique for high-resolution mapping of replication sites in structurally preserved chromatin in situ that employs a combination of pre-embedding EdU-streptavidin-Nanogold labeling and ChromEMT. We present a protocol for the electron microscopic visualization of the replicative domains in the cell by the EdU labeling of the newly…

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genetic epidemiology postdoc

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…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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Multiplexed genome regulation in vivo with hyper-efficient Cas12a

. 2022 Apr;24(4):590-600. doi: 10.1038/s41556-022-00870-7. Epub 2022 Apr 12. Lucie Y Guo #  1   2 , Jing Bian #  3 , Alexander E Davis  4 , Pingting Liu  4 , Hannah R Kempton  3 , Xiaowei Zhang  3 , Augustine Chemparathy  3 , Baokun Gu  3 , Xueqiu Lin  3 , Draven A Rane  3 , Xiaoshu Xu  3 , Ryan M…

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On a reference pan-genome model (Part II)

12 July 2019 I wrote a blog post on a potential reference pan-genome model. I had more thoughts in my mind. I didn’t write about them because they are immature. Nonetheless, a few readers raised questions related to my immature thoughts, so I decide to add this “Part II” as…

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New NSCC Singapore Collaborations to Develop HPC-Enabled Bioinformatics Capabilities

Singapore, April 22, 2022 — Two collaborations were signed today between APBioNET and NSCC as well as between AMBIS and NSCC to strengthen cooperation to develop and upskill the field of bioinformatics in Singapore. The proposed activities include developing high-performance computing (HPC) capability and talent development for bioinformatics, education and…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications.

Liau Y et al. Pharmacogenomics. 2019 Sep; 20(14):1033-1047 doi.org/10.2217/pgs-2019-0080PMID: 31559921 Show Details AbstractAuthors Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the…

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HTSeq Counts no longer available

HTSeq Counts no longer available 1 @vm-21340 Last seen 8 hours ago Brazil I’m working with breast cancer expression data from the TCGA-BRCA project. All my scripts were written to retrieve HTSeq counts from GDC, but they seem to have been removed from the GDC Data Portal. When using GDCquery,…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

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Accurate assembly of multi-end RNA-seq data with Scallop2

Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). Article  Google Scholar  Guttman, M. et al. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28,…

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Untangling SNP Variations within CYP2D6 Gene in Croatian Roma

CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups…

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New Image Shows Mysterious ‘Odd Radius Circles’ in Space

Mystery of space would be about to be deciphered 0:53 (CNN) — There’s a mysterious new kind of object in space, and after capturing their best image to date, astronomers are one step closer to understanding these strange celestial balls. They are known as odd radius circles (ORC). Though thinking…

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AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS  PubMed  PubMed Central  Google Scholar  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

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rna seq – RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. Objective Our ultimate goal with this genotypic data is to search for variants (both SNPs and indels)…

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Results From Genome Sequencing and Clinical Genotyping.docx

Objective: Hmong individuals represent a unique East Asian subpopulation in whom limited information concerning pharmacogenetic variation exists. The objectives of this study were to comprehensively characterize the highly polymorphic CYP2D6 gene in Hmong, estimate allele and phenotype frequencies and to compare results between two testing platforms. Methods: DNA from 48…

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Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS  CAS  Article  PubMed  PubMed Central  Google Scholar  WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…

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Low transcript quantification with Salmon using GRCm39 annotations

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS  Google Scholar  Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS  PubMed  Google…

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Next Generation Sequencing (NGS) Leader Nick McCooke Joins Genomics Company RevoluGen as Strategic Advisor

LONDON, March 10, 2022–(BUSINESS WIRE)–UK genomics company, RevoluGen Ltd. (RevoluGen or the Company), today announces that Nick McCooke, widely recognised leader in the next generation sequencing (NGS) field, has been appointed as Strategic Advisor. This press release features multimedia. View the full release here: www.businesswire.com/news/home/20220310005076/en/ Nick McCooke, NGS Expert and…

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Top 17 b cell lymphoma treatment in 2022

Below are the best information and knowledge on the subject b cell lymphoma treatment compiled and compiled by our own team tuhoangkaido: 1. Treating B-Cell Non-Hodgkin Lymphoma 2. Treatments for B-Cell Lymphoma 3. Diffuse Large B-Cell Lymphoma: Treatment Options 4. B-cell Lymphoma 5. B-cell Lymphoma: Types, Symptoms & Prognosis 6….

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Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Download Galaxy Genome [Space Sim] Mod Varies with device for android apk & iphone ios 4.4 and up Galaxy Genome is an open world sci-fi space simulator. You can upgrade your ship and customize each component as you hunt, explore, fight, mine, smuggle, trade and survive in a brutal galaxy….

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Research Roundup: New Insights into Alzheimer’s, ALS and FTD

BSIP/UIG Via Getty Images One particular gene variant, APOE4, is associated with an increased risk of Alzheimer’s disease. But why that is the case, what the mechanism of action is, has eluded researchers. At least one pathway has been determined, and it has possible repercussions in developing therapies against the…

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How to extract fasta sequences from assembled transcripts generated by Stringtie

How to extract fasta sequences from assembled transcripts generated by Stringtie 4 Hi all, I used STAR and stringtie for mapping reads to reference genome and assembly. As you know, the generated assembled transcripts by stringtie are in gtf format. Now, I want to have fasta sequence of assembled transcript….

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HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd

Bioinformatics Scientist 2 Hours: 37.5 hours per week Salary: Competitive Ref No: HRJOB7442 Business Unit: Diagnostic Services Location: Craigavon or Manchester Open To: Internal and External Applicants The Company Almac Diagnostic Services is a leading stratified medicine business, specialising in biomarker-driven clinical trials. We are incredibly proud to be involved…

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Aaron Rodgers apologises to Shailene Woodley amid break-up rumours

NFL Player Aaron Rodgers has recently spoken in length about his relationship with actor Shailene Woodley, addressing how criticism of his COVID-19 vaccination status has affected his loved ones. According to The Hollywood Reporter, both stars confirmed their engagement last year, although some media outlets recently reported that the…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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Difference of results with the same input [RNAseq analysis]

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

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What Is The Difference Between Dgp And Ddgtp?

DIG stands for Deputy Inspector General. It is a one- star rank in the Indian Police Service. This is a senior rank than Senior Superintendent of Police (SSP) or Deputy Commissioner of Police (DCP). An officer holding this position works under the Inspector General of Police (IG) or Joint Commissioner…

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ATF7ip Targets Transposable Elements for H3K9me3 Deposition to Modify CD8+ T Cell Effector and Memory Responses

Key Points ATF7ip is a critical regulator of CD8+ T cell effector and memory responses. Deletion of ATF7ip in CD8+ T cells results in enhanced Il2 and Il7r expression. ATF7ip targets transposable elements to modulate Il7r and Il2 expression. Abstract CD8+ T cells are critical for the immune response to…

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