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UC San Diego’s Bioengineering Team Uses TSCC at SDSC for Bioinformatics Tool
Jan. 19, 2024 — Over 18 million people worldwide are annually diagnosed with cancer, with each case hiding many mutations in its genome. Understanding these mutations furthers cancer research, while also providing a deeper understanding to create possible cures, therapies and prevention strategies. The Triton Shared Computer Cluster at the…
Assessment of Post-Chronic Social Defeat Treatment in Mice: Social Threat-Safety Test, Scoring, and Analysis
Begin by relocating all chronic, socially defeated or CSD-treated and control mice into new cages, mirroring the conditions they first arrived in and letting them rest overnight. The following morning, sanitize the three-chambered arena using a 5%ethanol solution and set it up beneath the camera, ensuring a light condition of…
The Biostar Herald for Tuesday, December 19, 2023
The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…
Sequencing 101: Structural variation – PacBio
Over the last 50 years, many monumental achievements in genetics and biology have unfolded before our eyes. From the invention of DNA sequencing technologies to the completion of the human genome project and the emergence of genomic medicine, we have made many intellectual and technological leaps in our understanding of…
Detecting small- and medium-length copy number variants by whole-genome sequencing
Gains and losses of genetic material can be almost any size: a single base pair or an entire chromosome spanning tens of millions. As genomic analysis technologies have evolved, researchers have separated these often medically relevant variants into bins based on their size and the methods used to detect them….
DESeq2 interaction term + sva
Hello, I am performing DGE analysis using DESeq2. I have two groups to compare: CTRL and SA, and I have performed a group comparison using DESeq2 and there’s no issue with that. However, I have males and females in each group, and I’m curious to see if there’s an interaction…
SOCS3 inhibiting JAK-STAT pathway enhances oncolytic adenovirus efficacy by potentiating viral replication and T-cell activation
Kaufman HL, Kohlhapp FJ, Zloza A. Oncolytic viruses: a new class of immunotherapy drugs. Nat Rev Drug Discov. 2015;14:642–62. Article CAS PubMed PubMed Central Google Scholar Kessler T, Wick W. Oncolytic virotherapy: potentially a game-changing tumor treatment. Cancer Cell. 2021;39:753–5. Article CAS PubMed Google Scholar Koch J, Schober SJ, Hindupur…
Study uncovers vast genomic diversity in Aboriginal Australian communities
In a recent study published in the journal Nature, researchers investigated the previously underrepresented genomic diversity of four Aboriginal Australian communities. They used population-scale whole-genome (WGS) long-read sequencing. Study findings revealed unique alleles comprised of insertion-deletion variants, variable copy number regions, and structural variants, 62% of which are novel to…
Beyond the exome: utility of long-read whole genome sequencing in exome-negative autosomal recessive diseases | Genome Medicine
Our cohort comprises 34 families in which a presumably autosomal recessive disease defied molecular diagnosis by clinical exome sequencing (short-read sequencing-based) and reanalysis performed on the index individual for each family (Fig. 1). The index patient in each family was subjected to an average of 10 × depth lrWGS except for Family F8602…
Construction of a risk stratification model integrating ctDNA to predict response and survival in neoadjuvant-treated breast cancer | BMC Medicine
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article PubMed Google Scholar Giaquinto AN, Sung H, Miller KD, Kramer JL, Newman LA,…
DNA Contamination of COVID Vaccines Explored in Journal of American Physicians and Surgeons
DNA Contamination of COVID Vaccines Explored in Journal of American Physicians and Surgeons TUCSON, Ariz., Dec. 11, 2023 (GLOBE NEWSWIRE) — The current controversy over the alleged DNA contamination of COVID-19 vaccines involves complex issues, and also shows the difficulties in arriving at truth in today’s polarized and politicized atmosphere,…
STWOA Success | News, Sports, Jobs
Southwestern’s Tavio Hoose works on top of St. Francis’ Zachary Caldwell during the 190-pound final at the Southern Tier Wrestling Officials Association Tournament on Saturday at Jamestown Community College’s Physical Education Complex. Hoose won 8-1. Photo courtesy of Shelly Phillips The Southern Tier Wrestling Officials Association Kickoff Classic featured plenty…
vcfdist: accurately benchmarking phased small variant calls in human genomes
The affine gap design space for selecting variant representations As demonstrated in Fig. 1, the main issue with a difference-based format such as VCF is that often there are multiple reasonable sets of variant calls that can be used to represent the same final sequence relative to a reference FASTA. Since…
Whole-genome long-read sequencing downsampling and its effect on variant-calling precision and recall
William T. Harvey1, Peter Ebert2,3,4, Jana Ebler2,4, Peter A. Audano5, Katherine M. Munson1, Kendra Hoekzema1, David Porubsky1, Christine R. Beck5,6, Tobias Marschall2,4, Kiran Garimella7 and Evan E. Eichler1,8 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195-5065, USA; 2Institute for Medical Biometry and Bioinformatics, Medical Faculty,…
Integrative taxonomy of Metastrongylus spp. in wild boars from Brazil | Parasites & Vectors
Study areas The samples were collected from wild boars hunted in rural properties from the municipalities of São Simão, Monte Azul, Paraíso, Colina, Matão, Bebedouro e Monte Alto (São Paulo), Ipiranga (Paraná), and Santo Antônio das Missões (Rio Grande do Sul) (Fig. 1). Fig. 1 Sampling collection sites of wild boars…
Treat Yourself With the 2024 Nissan Murano
If you are in the mood to reward yourself, then the 2024 Nissan Murano is for you. After 20 years on the market, the Nissan Murano continues to impress drivers with its upscale appointments and sleek styling. Despite ample competition in its segment, the Murano holds its own, offering a…
Help! RStudio starts to a blank screen after update; clean install worked, but not after time machine backup. – RStudio IDE
Error Information: Description of issue – After updating to OS Sonoma, RStudio is a blank window. I only see the name of the toolbar. There are no options in the toolbar either, it says empty. R app works fine. Attempted steps taken to fix –Reinstalled appsReinstalled OS system sonoma (didn’t…
Extracting only soft/hard clipped reads from a bam file
Extracting only soft/hard clipped reads from a bam file 4 Hello all! I am working on some data but need a little bit of help with a bit of an unusual task. We are looking at where lentiviral DNA has inserted itself in our host genome, and to do this…
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file 0 Do vg filter out some variants during the construction of the pan-genome, and if so, what are the criteria for filtering? The number of variations in the pan-genome is reduced compared…
Help finding the correct file version for dbSNP VCF ID replacement
Tried to use dbSNP version 156 using bcftools to replace the ID field in a reference VCF which originally contains a different position ID format. It seems the bcftools command did not work because a numeric chromosome column format in the #CHROM field which might not be compatible with bcftools…
Exome and genome sequencing to unravel the precise breakpoints of partial trisomy 6q and partial Monosomy 2q | BMC Pediatrics
Here, we report a proband with characteristic features of the clinical syndrome, including downward-slanting palpebral fissures; delayed development of bilateral optic nerve hypoplasia; facial deformity with a small mouth, thin lips, micrognathia, and blepharophimosis; short neck; abnormal deciduous teeth; and malformations of the thorax and short ribs. The proband showed…
Structural Variant Detection Tools Struggle with Whole Exome Sequencing (WES) Data
Whole exome sequencing (WES) is a targeted sequencing technique that sequences only the protein-coding regions of the genome. As WES is significantly cheaper than whole genome sequencing (WGS) while still providing meaningful information, WES has become a respected tool in identifying small genetic variants underlying diseases. It is also used,…
Most large structural variants in cancer genomes can be detected without long reads
JaBbA v1 outperforms previous CN algorithms We enhanced our previous JaBbA (v0.1; ref. 4) model with several methodological innovations to increase robustness to read depth waviness, improve algorithm convergence and enforce junction balance for allele-specific as well as total CN (Extended Data Fig. 1a–d and Methods). We also rigorously defined…
Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine
Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article PubMed Google Scholar Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…
Leveraging GPT-4 for Rapid Data Processing and Machine Learning on Kaggle Datasets | by Purvil Patel | Nov, 2023
In the age of data, having the skills to process, analyze, and derive insights from vast amounts of information is crucial. However, the process can often be time-consuming, especially with the variety and complexity of datasets available. This article delves into the journey of harnessing the power of GPT-4’s code…
An accident waiting to happen? Exposing the potential of urogenital schistosomiasis transmission in the Lake Albert region, Uganda | Parasites & Vectors
WHO. Schistosomiasis (Bilharzia. Schistosomiasis. 2023. www.who.int/health-topics/schistosomiasis#tab=tab_1. Accessed 26 Sept 2023. WHO. Control of neglected tropical diseases. 2023. www.who.int/teams/control-of-neglected-tropical-diseases/schistosomiasis/epidemiology. Accessed 27 Sept 2023. Aula OP, McManus DP, Jones MK, Gordon CA. Schistosomiasis with a focus on Africa. Trop Med Infect Dis. 2021;6:109. Article PubMed PubMed Central Google Scholar Brown DS. Freshwater…
Structural Variants in gnomAD v4
Today, we are thrilled to announce the release of genome-wide structural variants (SVs) for 63,046 unrelated samples with genome sequencing (GS) data. All site-level information for 1,199,117 high-quality SVs discovered in these samples is browsable in the gnomAD browser (gnomAD SV v4) and downloadable from the gnomAD downloads page. For…
What does the future hold?
In this interview, Adanma Ayanambakkam, MD, discusses the current state of treatment of advanced bladder cancer, including the need for predictive and prognostic markers for immune therapy as well as the potential showed by circulating tumor DNA (ctDNA). Ayanambakkam is an assistant professor of medicine in the section of hematology/oncology…
papain family cysteine protease containing protein, maker-scaffold1702_size30647-snap-gene-0.14 (gene) Tigriopus kingsejongensis
Associated RNAi Experiments Homology BLAST of papain family cysteine protease containing protein vs. L. salmonis genes Match: EMLSAG00000006045 (supercontig:LSalAtl2s:LSalAtl2s327:400616:404607:-1 gene:EMLSAG00000006045 transcript:EMLSAT00000006045 description:”augustus_masked-LSalAtl2s327-processed-gene-4.0″) HSP 1 Score: 590.497 bits (1521), Expect = 0.000e+0Identity = 283/525 (53.90%), Postives = 368/525 (70.10%), Query Frame = 0 Query: 49 GHVARPLGKSPPNFVRDPPPRTTPPAQWLWNNVNETNFLTVSRNQHLPTYCGSCWAHAATSSLSDRIKIARQGAWPDINLAPQVLISCGPGDGCHGGEAGDANAYMHAQGITDETCSIYRARGQDNGLPCSKLEICSTCE—SKCYQPQHFFTYRVDEFHDVEGESNGEQEANMMAEIHHRGPISCGIAVTQALV-NYTGGLFHDKTGAQEIDHDISVVGYGVDEGTQEKYWLIRNSWGTYWGEQGFFRLIRGVNNLGIESGTCSWATPADTWSDAARE—RAAILSNEITLQKP——LWKQLWTVVADFVDNTRDTDLFRRLKLMQKGCKKLSSPRVPVVNIRPRPQDYVSTADLPEALDWRSVNGTNFLSWSVNQHLPVYCGSCWAQAGLSSLADRFTIADRKRFANLALSVQYILNCQAGGSCHGGDAFPLYAFIQKQGVPDVTCQPYEALDEGPLTDCSKPSKLVCKDCTWPPPEPGQEGNCWAKEKFHRYYVDEYNGVEGADNMKKEILERGPVT 560 GH+ R G+…
BDQ resistance and molecular characterization of RR-TB
Enyu Tong,1,* Ying Zhou,1,* Zhengwei Liu,2 Yelei Zhu,2 Mingwu Zhang,2 Kunyang Wu,2 Junhang Pan,2 Jianmin Jiang1– 3 1School of Public Health, Hangzhou Normal University, Hangzhou, 311100, People’s Republic of China; 2Tuberculosis Control Department, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, People’s Republic of China; 3Key Laboratory of…
Increased binding of anti-dsDNA antibodies to short oligonucleotides modified with topoisomerase I reveals a potential new enzyme function independent from DNA relaxation | BMC Research Notes
Lee MP, Brown SD, Chen A, Hsieh TS. DNA topoisomerase I is essential in Drosophila melanogaster. Proc Natl Acad Sci U S A. 1993;90(14):6656–60. doi.org/10.1073/pnas.90.14.6656. [published Online First: Epub Date]|. Article CAS PubMed PubMed Central Google Scholar Morham SG, Kluckman KD, Voulomanos N, Smithies O. Targeted disruption of the mouse…
Electronic Genome Mapping – Nabsys
Electronic Genome Mapping Setting a new standard in structural variant analysis Nabsys, the pioneer of electronic genome mapping (EGM), uses solid-state nanodetectors to survey long DNA molecules to construct high-density maps with long-range information to detect structural variants (SVs). Unlike other DNA mapping technologies that rely on the use of…
vg call problem request
vg call problem request 0 Hello, recently I’m genotyping some SVs using illumila data, however, I have met some problems that I can not figure it out. The questions are as follows: For some large DEL SVs, for example, SV length > 1kb, the variants will be filtered in the…
How to correct for known and surrogate variables in DESeq2?
Dear all, We have RNA-seq data of 9 High force versus 9 Low force scallop adductors along with known covariates like Height, Length, Width, Weight (I have cut() them )and Strain. So in DESeq2 I could correct for these covariates as follows: #We only chose Height, Weight and Strain as…
Efficacy and safety of zuranolone co-initiated with an antidepressant in adults with major depressive disorder: results from the phase 3 CORAL study
Malhi GS, Mann JJ. Depression. Lancet. 2018;392:2299–312. Article PubMed Google Scholar Bromet E, Andrade LH, Hwang I, Sampson NA, Alonso J, de Girolamo G, et al. Cross-national epidemiology of DSM-IV major depressive episode. BMC Med. 2011;9:90. Article PubMed PubMed Central Google Scholar Collaborators, COVID-19 Mental Disorders Collaborators. Global prevalence and…
Identification and cultivation of anaerobic bacterial scavengers of dead cells
Bar-On YM, Phillips R, Milo R. The biomass distribution on Earth. Proc Natl Acad Sci USA. 2018;115:6506–11. Article CAS PubMed PubMed Central Google Scholar Ogawa H, Amagai Y, Koike I, Kaiser K, Benner R. Production of refractory dissolved organic matter by bacteria. Science. 2001;292:917–20. Article CAS PubMed Google Scholar Liang…
Combination of RNAseq and RADseq to Identify Physiological and Adaptive Responses to Acidification in the Eastern Oyster (Crassostrea virginica)
Aguilera F, McDougall C, Degnan BM (2017) Co-option and de novo gene evolution underlie molluscan shell diversity. Mol Biol Evol 34(4):779–792 CAS PubMed PubMed Central Google Scholar Alexa A, Rahnenfuhrer J (2020) topGO: Enrichment analysis for gene ontology. R package version 2.40.0 Google Scholar Arivalagan J, Yarra T, Marie B,…
Rational probe design for efficient rRNA depletion and improved metatranscriptomic analysis of human microbiomes
doi: 10.1186/s12866-023-03037-y. Asako Tan # 1 , Senthil Murugapiran # 2 , Alaya Mikalauskas # 3 , Jeff Koble 4 , Drew Kennedy 4 , Fred Hyde 1 , Victor Ruotti 1 , Emily Law 2 , Jordan Jensen 2 , Gary P Schroth 4 , Jean M Macklaim 3 , Scott Kuersten 5 , Brice LeFrançois 6 , Daryl M Gohl 7 8 …
Macrophage polarization and metabolism in atherosclerosis
Organization WH the top 10 causes of death. www.who.int/news-room/fact-sheets/detail/the-top-10-causes-of-death, 2019. Rana JS, Khan SS, Lloyd-Jones DM, Sidney S. Changes in mortality in Top 10 causes of death from 2011 to 2018. J Gen Intern Med. 2021;36:2517–8. Article PubMed Google Scholar Libby P. The changing landscape of atherosclerosis. Nature. 2021;592:524–33. Article …
Health Canada’s startling admission confirms secret DNA contamination discovered in COVID-19 vaccines
Health Canada, responsible for authorizing and regulating the novel mRNA injections, admitted that they have confirmed the presence of at least one plasmid…
vg call coverage/suppport
vg call coverage/suppport 0 Hello, I am using vg 1.48.0 to try and calculate SV frequencies from short-read poolseq data mapped to a pangenome using giraffe. I was wondering about how the read depth for the reference vs alternate allele is calculated in vg call – is it the (total…
Cdd Post-Doc Bioinformatic (M/W) | Universities and Institutes of France
14 Oct 2023 Job Information Organisation/Company CNRS Department Institut de Recherche sur le Cancer et le Vieillissement, Nice Research Field Biological sciences » Biology Researcher Profile Recognised Researcher (R2) Country France Application Deadline 3 Nov 2023 – 23:59 (UTC) Type of Contract Temporary Job Status Full-time Hours Per Week 35…
Prospects of Whole Genome Sequencing in Animal Breeding
Prospects of Whole Genome Sequencing in Animal Breeding The development of high-throughput sequencing technologies has revolutionized animal genetics and genomics. The widespread use of whole-genome sequencing (WGS) allows detection of a full range of common and rare genetic variants of different types across almost the entire genome which facilitates rare…
Scan report for “s1.fastqc.com” – Online Nmap scanner
Fast Scan (nmap -F …)Nmap scan (nmap …)Ping Scan (nmap -sP …)Port scan (nmap -sV -p 21,22,25,80,110,143,443,445 …)Scan OS information and Traceroute (nmap -A …)OS Detection (nmap -O …)CVE-2021-41773 Path Traversal (nmap –script=http-vuln-cve-2021-41773 -p 80,443,631,7080,8080,8443,8088,5800,3872,8180,8000 …) $ Forward-confirmed Reverse DNS (nmap -sn -Pn –script fcrdns …) $ Firewall Detection (nmap…
Bioconductor – RSVSim
DOI: 10.18129/B9.bioc.RSVSim RSVSim: an R/Bioconductor package for the simulation of structural variations Bioconductor version: Release (3.11) RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed…
Whole-genome sequencing analysis of suicide deaths integrating brain-regulatory eQTLs data to identify risk loci and genes
Li QS, Shabalin AA, DiBlasi E, Gopal S, Canuso CM, FinnGen ISGC, et al. Genome-wide association study meta-analysis of suicide death and suicidal behavior. Mol. Psychiatry 2023;28:891–900. McGuffin P, Marusic A, Farmer A. What can psychiatric genetics offer suicidology? Crisis. 2001;22:61–65. Article CAS PubMed Google Scholar Pedersen NL, Fiske A….
Influence of variant-specific mutations, temperature and pH on conformations of a large set of SARS-CoV-2 spike trimer vaccine antigen candidates
Protein production Soluble spike constructs were purified from supernatants of transiently or stably transfected CHO cells; a summary of all constructs tested in this study is provided in Supplementary Table 1. Purified proteins separated by SDS-PAGE and stained with Coomassie Blue are shown in Supplementary Fig. 1. All variants show high…
Training NeMo Framework Models – NVIDIA Docs
You must prepare several datasets for the NeMo framework to use, depending on the type of model you are using. The Pile: NVIDIA provides utilities to download and prepare the Pile dataset. This dataset comprises 22 smaller datasets, blended by using the mix described in the paper The Pile:…
Predicting tumour content of liquid biopsies from cell-free DNA | BMC Bioinformatics
Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med. 2012;4(136):136ra68. Article PubMed Google Scholar Newman AM, Bratman SV, To J, Wynne JF, Eclov NCW, Modlin LA, et al….
Recommendations for extending contigs from denovo assembly to identify SV insertion sites on chromosome
I performed WGS of a new transgenic mouse model generated by random integration of a 10.316Kb transgene with the goal of locating the insertion site/s and calculating copy-number. The PromethION flowcell produced an output of 54.86Gb with 2.37 Million reads generated and I received this data in the form of…
Semiconductor Probe Card Market Size, Share, Analysis, Demand, and Forecast 2023 to 2030 | Shenzhen Fastprint Circuit Technology Co Ltd, FormFactor, Technoprobe S.p.A
The Market Research Report 2023-2030 is an in-depth analysis of the Global Semiconductor Probe Card Market. Based on historic growth analysis and the current scenario of the Semiconductor Probe Card Marketplace, the report intends to offer actionable insights into Global market growth projections. Authenticated data presented in the report is…
Brain microvascular endothelial cells and blood-brain barrier dysfunction in psychotic disorders
Murray CJL, Vos T, Lozano R, Naghavi M, Flaxman AD, Michaud C, et al. Disability-adjusted life years (DALYs) for 291 diseases and injuries in 21 regions, 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010. Lancet. 2012;380:2197–223. Article PubMed Google Scholar Martin J, Taylor MJ, Lichtenstein P….
Mass spectrometry for expediting biologics to patients
A key element of development for new molecular format biological products is to leverage the appropriate analytical tools to enhance product and process understanding throughout the development lifecycle. Here, Ian Anderson, Mostafa Zarei and Qifeng Zhang at Lonza highlight the benefits of using mass spectrometry technologies to accelerate and de-risk product…
How to create structural variants ground truth for alignment of two long-read genome assemblies?
Hello everyone, I’m a student in the area of genomics. I have two genome assemblies from long reads (from haploid genomes). One is the reference of the organism (K. phaffii, a yeast), which represents the wild type. The other (the query) is an assembly of an K. phaffii strain, which…
How to run delly with multi-threading mode?
How to run delly with multi-threading mode? 1 Hi, I am wondering how to run delly with multi-threading mode? Actually there is a guideline on the manually page, which indicates to use openMP API to do this. But the manually guideline is too simple to follow for me. This is…
NIH Center for Alzheimer’s and Related Dementias publication shows comprehensive, high accuracy sequencing approach, using new Oxford Nanopore sequencing chemistry
In a new publication in Nature Methods, a team contributing to the National Institutes of Health (NIH) Center for Alzheimer’s and Related Dementias (CARD) share an end-to-end pipeline that produces state-of-the-art single nucleotide polymorphism (SNP), structural variant and methylation calls, while being cost-effective and scalable for large projects OXFORD, England,…
Two of leopards trapped near Tirumala temple released
Tirupati : Andhra Pradesh forest department has released one of the four leopards captured on pedestrian walkway to the Tirumala temple into the forest and shifted another to Visakhapatnam Zoo after it was confirmed that they were not responsible for the death of a six-year-old girl last month. The forest…
Mitochondrially mediated RNA interference, a retrograde signaling system affecting nuclear gene expression
Andersson DI, Jerlstrom-Hultqvist J, Nasvall J (2015) Evolution of new functions de novo and from preexisting genes. Cold Spring Harb Perspect Biol 7:a017996 Article PubMed PubMed Central Google Scholar Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Auyeung VC, Ulitsky I, McGeary SE, Bartel…
how to remove description from header?
how to remove description from header? 2 I have a header like this- >sp|A0A0H2Z7X0|TPBB_PSEAB Diguanylate cyclase TpbB OS=Pseudomonas aeruginosa (strain UCBPP-PA14) OX=208963 GN=tpbB PE=1 SV=1 MNRRRRYTGSNPSLRRVLYRAHLGVALVAVFTAGLAVTLVGLLTLRAYADPNQQLIARSI SYTVEAAVVFGDAQAAEESLALIASSEEVSSAIVYDRQGQPLASWHRESTGPLHLLEQQL And I want my header like this >A0A0H2Z7X0 MNRRRRYTGSNPSLRRVLYRAHLGVALVAVFTAGLAVTLVGLLTLRAYADPNQQLIARSI SYTVEAAVVFGDAQAAEESLALIASSEEVSSAIVYDRQGQPLASWHRESTGPLHLLEQQL Thank you! fasta • 43 views • link updated 1 hour ago by…
Roche hiring Principal Scientist I Bioinformatics in Mississauga, Ontario, Canada
The PositionRoche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to support…
Powered by PacBio: Selected publications for August 2023
Want to know what PacBio users have been up to? In this summary, get the latest on some of the hottest scientific publications to incorporate PacBio sequencing methods. Selections from the month of August 2023 include papers on human genomics, Mendelian genetics, and rare disease research. Read the bullet points,…
How to Use Kaggle for Computer Vision
Kaggle is a data science and machine learning platform, primarily known for hosting a wide range of datasets and competitions. It is one of the most popular platforms for data scientists and machine learning enthusiasts with the availability of free resources and publicly available datasets This comprehensive guide will cover…
ISCN annotation for SV/CN VCF files
Forum:ISCN annotation for SV/CN VCF files 0 Hi I’m trying to annotate the output of a VCF file that contains SV and CNV calls from long read sequencing. The conventional tools work well enough, but I can find anything that will annotate with the ISCN annotation for the whole VCF…
Solanum americanum genome-assisted discovery of immune receptors that detect potato late blight pathogen effectors
Genome assembly and gene model prediction of S. americanum S. americanum is a globally distributed Solanaceae species that is resistant to many pathogens, including P. infestans and Ralstonia solanacearum25,29,33. Four S. americanum accessions SP1102, SP2271, SP2273 and SP2275 were selected for sequencing based on their variation in resistance to late…
ENA submission organelle trans_table conflict
I am validating a flatfile of an annotated chloroplast genome scaffold. It includes /organism=”Cannabis sativa” and /organelle=”plastid:chloroplast”. This means the CDS should be translated according to the bacterial translation table and I therefore included the /transl_table=11 qualifier in my CDS annotations. See head of of the flatfile below (some info…
$100 Million In Funding Closed To Fix AI Infrastructure For Developers
Modular recently announced that it has raised $100 million in a new round of funding led by General Catalyst and filled by existing investors GV (Google Ventures), SV Angel, Greylock, and Factory. This second funding round follows the company’s first $30 million round from last year and will enable the…
Modular Raises $100 Million to Expand AI Development Platform
Modular, a startup focused on creating a platform for developing and optimizing AI systems, has raised $100 million in a funding round. The funding was led by General Catalyst, with participation from GV (Google Ventures), SV Angel, Greylock, and Factory. This brings the total amount raised by Modular to $130…
An IgM-like inhalable ACE2 fusion protein broadly neutralizes SARS-CoV-2 variants
Protein expression hACE2-hIgG1 was constructed by fusing the extracellular domain of human ACE2 (amino acid 19–615) (UniProt Q9BYF1) to the human IgG1 hinge and Fc (UniProt P01857). H374N and H378N mutations were introduced to inactivate the Zinc metallo-enzyme activity17. HH-120 was constructed by fusing hACE2-hIgG1 with an IgM tailpiece (PTLYNVSLVMSDTAGTCY)33….
The role of chromosome 20p11.2 deletions
In a recent study posted to the medRxiv* preprint server, a group of researchers identified large deletions in individuals with unexplained hyperinsulinism (HI), thereby elucidating the potential dysregulation of Forkhead box protein A2 (FOXA2) expression and its implications for syndromic HI. Study: Chromosome 20p11.2 deletions cause congenital hyperinsulinism via the likely…
Annotation of DELLY variants
Annotation of DELLY variants 0 I ran snpEff for the SV annotation by using this delly results, and found INS/ INV can not be detected by snpeff software. How should I modify the raw input vcf? delly snpeff • 23 views • link updated 1 hour ago by Ram 40k…
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph
The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph 0 My objective is to identify the structural variations (SVs) located on chromosome NC_058090.1. The reason for solely focusing on a single chromosome is due to…
Comparing SV calls produced by VG call on a Minigraph-Cactus produced Pangenome Graph vs. a linear reference
Comparing SV calls produced by VG call on a Minigraph-Cactus produced Pangenome Graph vs. a linear reference 0 I’m presently working on generating structural variant (SV) calls using vg call. I constructed the graph using whole genome assemblies using Minigraph-Cactus (MC), and aligned short-read data using vg giraffe. I would…
Genotype diversity of brucellosis agents isolated from humans and animals in Greece based on whole-genome sequencing | BMC Infectious Diseases
Pappas G, Papadimitriou P, Akritidis N, Christou L, Tsianos EV. The new global map of human brucellosis. Lancet Infect Dis. 2006;6(2):91–9. Article PubMed Google Scholar Pappas G. The changing Brucella ecology: novel reservoirs, new threats. Int J Antimicrob Agents. 2010;36(Suppl 1):8–11. Article Google Scholar Wyatt HV. Lessons from the history…
Efficiency of mitochondrial genes and nuclear Alu elements in detecting human DNA in blood meals of Anopheles stephensi mosquitoes: a time-course study | Parasites & Vectors
WHO. World malaria report 2022. 2022. www.who.int/teams/global-malaria-programme/reports/world-malaria-report-2022. Accessed 27 March 2023 Takken W, Verhulst NO. Host preferences of blood-feeding mosquitoes. Annu Rev Entomol. 2013;58:433–53. Article CAS PubMed Google Scholar Santos CS, Pie MR, da Rocha TC, Navarro-Silva MA. Molecular identification of blood meals in mosquitoes (Diptera, Culicidae) in urban and…
Principal Scientist II Bioinformatics – Hiring Now at F. Hoffmann-La Roche Ltd in Mississauga, ON
We are searching for a persistent Principal Scientist II Bioinformatics to join our energetic team at F. Hoffmann-La Roche Ltd in Mississauga, ON.Growing your career as a Full Time Principal Scientist II Bioinformatics is an incredible opportunity to develop key skills.If you are strong in leadership, critical thinking and have…
Detecting CNV’s (copy number variation) in haploid yeast cells
Detecting CNV’s (copy number variation) in haploid yeast cells 0 Hey all, I have whole-genome-sequencing data from 22 yeast strains grown in lab evolution experiments. I want to compute copy number variation to see whether a specific gene/chromosome was duplicated throughout the experiment. I am struggling to find a good,…
Modular Inc. in Talks with Investors for $600 Million Funding Round
Artificial intelligence startup Modular Inc. is reportedly engaged in discussions with investors, including General Catalyst, for a significant funding round that could value the company at approximately $600 million. This comes at a time when AI has become a prominent trend in the technology industry. Modular’s software provides an alternative…
Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples
doi: 10.1186/s13104-023-06451-7. Affiliations Expand Affiliations 1 Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia. 2 School of Pharmacy and Medical Sciences, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia. 3 Menzies Health Institute Queensland, Griffith University, Parklands Drive, Southport, QLD, 4215, Australia. a.cox@griffith.edu.au. 4 School of…
Comparison of four DNA extraction methods for 16s rRNA microbiota profiling of human faecal samples | BMC Research Notes
Huang Z, Liu K, Ma W, Li D, Mo T, Liu Q. The gut microbiome in human health and disease-where are we and where are we going? A bibliometric analysis. Front Microbiol. 2022;13:1018594. Article PubMed PubMed Central Google Scholar Bukin YS, Galachyants YP, Morozov IV, Bukin SV, Zakharenko AS, Zemskaya…
Infection of sheep by Echinococcus multilocularis in Gansu, China: evidence from mitochondrial and nuclear DNA analysis | Infectious Diseases of Poverty
Craig PS, Hegglin D, Lightowlers MW, Torgerson PR, Wang Q. Echinococcosis: control and prevention. Adv Parasitol. 2017;96:55–158. Article CAS PubMed Google Scholar Deplazes P, Dinkel A, Mathis A. Molecular tools for studies on the transmission biology of Echinococcus multilocularis. Parasitology. 2003;127(Suppl):S53–61. Article CAS PubMed Google Scholar Deplazes P, Rinaldi L,…
Structural Variant detection and comparison
Course: STRUCTURAL VARIANT DETECTION AND COMPARISON Dates: 11-13 December 2023 | Online Course website: www.physalia-courses.org/courses-workshops/svs/ We are delighted to invite you to the upcoming Biostars course on “Structural Variant Detection and Comparison.” This exciting course aims to introduce biologists and bioinformaticians to the fascinating field of Structural Variant (SV) detection…
The potential for zoonotic malaria transmission in five areas of Indonesia inhabited by non-human primates | Parasites & Vectors
Jeyaprakasam NK, Liew JWK, Low VL, Wan-Sulaiman WY, Vythilingam I. Plasmodium knowlesi infecting humans in Southeast Asia: what’s next? PLoS Negl Trop Dis. 2020;14:e0008900. doi.org/10.1371/journal.pntd.0008900. Article PubMed PubMed Central Google Scholar Lee KS, Vythilingam I. Plasmodium knowlesi: emergent human malaria in Southeast Asia. In: Parasites and their vectors. Vienna: Springer…
Transcriptomic risk scores for attention deficit/hyperactivity disorder
Song P, Zha M, Yang Q, Zhang Y, Li X, Rudan I. The prevalence of adult attention-deficit hyperactivity disorder: A global systematic review and meta-analysis. J Glob Health. 2021;11:1–9. Article Google Scholar Faraone SV, Asherson P, Banaschewski T, Biederman J, Buitelaar JK, Ramos-Quiroga JA, et al. Attention-deficit/hyperactivity disorder. Nat Rev…
Partial thyroid hormone-binding globulin deficiency
Introduction Thyroxine-binding globulin (TBG) is the main binding protein of the thyroid hormone in the human body. It combines around 75% of thyroxine (T4) and 70% of triiodofoxygen (T3).1 Thyroxine-binding globulin deficiency is a rare thyroid disease, mostly caused by a gene mutation, and is generally acquired through X-linked recessive…
Working Group Guideline for Gene-Drug Interactions Between CYP2D6, CYP3A4, and CYP1A2 With Antipsychotics
Background Within the field of pharmacogenomics (PGx), there has been significant interest in its application to psychotropic medications, which include various antidepressants and antipsychotics. Particularly, CYP2D6 and CYP2C19 are implicated to some degree in the metabolism of 80% of psychiatric labels.1 Image credit: tadamichi – stock.adobe.com Despite this, research has…
SV calling using giraffe/vg
SV calling using giraffe/vg 0 It’s not very clear to me how exactly VG or Giraffe carries out SV calling (if it truly does). The tutorials mention how we can do genotyping using existing SV calls, but I was wondering if VG or Giraffe can actually identify novel SVs in…
I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox)
I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox) 0 Hi I tried to upload vcf of SV from HiFi CNV and pbsv into Franklin (by genoox). For inherited disease family case, I used 1 file of merged vcf for SNV from Deeptrio,…
Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites | BMC Medicine
Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, et al. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan. China JAMA. 2020;323(11):1061–9. Article CAS PubMed Google Scholar Zhao Y, Zhao Z, Wang Y, Zhou Y, Ma Y, Zuo W. Single-cell RNA expression…
A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis | Parasites & Vectors
Adam RD. Biology of Giardia lamblia. Clin Microbiol Rev. 2001;14:447–75. Article CAS PubMed PubMed Central Google Scholar Solaymani-Mohammadi S, Singer SM. Giardia duodenalis: the double-edged sword of immune responses in giardiasis. Exp Parasitol. 2010;126:292–7. Article CAS PubMed PubMed Central Google Scholar Solaymani-Mohammadi S. Mucosal defense against Giardia at the intestinal…
Reduced polymorphism of Plasmodium vivax early transcribed membrane protein (PvETRAMP) 11.2 | Parasites & Vectors
WHO. World malaria report 2020. 20 years of global progress and challenges. 2020. www.who.int/publications/i/item/9789240015791. Datoo MS, Natama HM, Somé A, Bellamy D, Traoré O, Rouamba T, et al. Efficacy and immunogenicity of R21/Matrix-M vaccine against clinical malaria after 2 years’ follow-up in children in Burkina Faso: a phase 1/2b randomised…
Detection of Circulating Tumor DNA in Plasma Using Targeted Sequencing
Sorrells RB (1974) Synovioanalysis (“liquid biopsy”). J Ark Med Soc 71(1):59 CAS PubMed Google Scholar Siena S, Sartore-Bianchi A, Garcia-Carbonero R, Karthaus M, Smith D, Tabernero J, Van Cutsem E, Guan X, Boedigheimer M, Ang A, Twomey B, Bach BA, Jung AS, Bardelli A (2018) Dynamic molecular analysis and clinical…
Factors affecting the size of a structural variant
Factors affecting the size of a structural variant 1 Dear Biostars, Does anyone have a good journal article discussing the factors that determine the length of a structural variant in humans? I ask because I have done a genomewide SV burden analysis in a case-control cohort and have found two…
what is gene synthesis used for
As the resulting plasmid contains the original prefix and suffix sequences, it can be used to join with more BioBricks parts. The development of the Golden Gate assembly methods and its variants has allowed researchers to design tool-kits to speed up the synthetic biology workflow. By using the BsaI restriction…
IJMS | Free Full-Text | RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines
MDPI and ACS Style Zoroddu, S.; Sanna, L.; Bordoni, V.; Weidong, L.; Murineddu, G.; Pinna, G.A.; Forcales, S.V.; Sala, A.; Kelvin, D.J.; Bagella, L. RNAseq Analysis of Novel 1,3,4-Oxadiazole Chalcogen Analogues Reveals Anti-Tubulin Properties on Cancer Cell Lines. Int. J. Mol. Sci. 2023, 24, 11263. doi.org/10.3390/ijms241411263 AMA Style Zoroddu S,…
Lollipop plots for structural variation coordinates
Lollipop plots for structural variation coordinates 0 Hi! I’m a research intern with a (relatively) amateur skill level at industry-standard bioinformatics techniques. Currently, I have a bunch of files (mostly .bed’s and derivatives of .vcf’s) containing specific coordinates for the locations of structural variations in a specific chromosome. I’m trying…
Principal Scientist I Bioinformatics job with F. Hoffmann-La Roche AG
The Position Roche Sequencing Solutions (RSS), a business within Roche Diagnostics, focused on developing a disruptive Next-Generation Sequencing (NGS) platform along with a portfolio of reagents, assays and informatics solutions for multiple disease areas. We are looking for a Principal Bioinformatics Scientist in the NGS Algorithms and Applications team to…
Evaluation of RFLP and RAPD markers in a comparison of Brassica napus breeding lines
Demeke T, Adams RP, Chibbar, R (1992) Potential taxonomic use of random amplified polymorphic DNA (RAPD): a case study in Brassica. Theor Appl Genet 84:990–994 Google Scholar Echt CS, Erdahl LA, McCoy TJ (1992) Genetic segregation of random amplified polymorphic DNA in diploid cultivated alfalfa. Genome 35:84–87 Google Scholar Efron…
Whole genome and RNA sequencing analyses for 254 Taiwanese hepatocellular carcinomas | Biomarker Research
Clinical data The demographic data of the 254 HCC patients are presented in Table S1. We found that treatment received by HCC patients were associated with patient survival, as shown in Fig. S1. Somatic mutations The mutational landscape is shown in Fig. 1. The top 10 most common mutated genes were…
FORMAT column with GT for somatic SV VCFs
FORMAT column with GT for somatic SV VCFs 0 Hi, I have done tumor-only somatic structural variant (SV) calling with Manta. This results in several VCFs with candidate variants. However, some of these do not contain GT in FORMAT (GitHub issue). In tumor-only mode I do not get somaticSV.vcf.gz as…
Dealing with failure of cBioPortal’s cBioDataPack() function to recognize a valid studyId?
Hi all, I attempted to download a list of multi assay experiments using cBioDataPack a moment ago. after cbio <- cBioPortal() studies <- getStudies(cbio, buildReport = TRUE) PedPanCanStudyIds<-studies[grepl(‘Ped’, studies$name, ignore.case=TRUE) & grepl(‘Pan’, studies$name, ignore.case=TRUE), ]$studyId I ran PedPanCanMaeList<-list(); setwd(oD) PedPanCanMaeList[[PedPanCanStudyIds[1]]]<-cBioDataPack(PedPanCanStudyIds[1]); saveRDS(PedPanCanMaeList[[ PedPanCanStudyIds[1] ]], file=paste0(‘./cBioPortal/’, PedPanCanStudyIds[1], ‘.Rds’) ) PedPanCanMaeList[[PedPanCanStudyIds[2]]]<-cBioDataPack(PedPanCanStudyIds[2]); saveRDS(PedPanCanMaeList[[ PedPanCanStudyIds[2]…