Category: SED

Using AWS for Bioinformatics

Using AWS for Bioinformatics 3 Does anyone have experience using Amazons AWS for their bioinformatics work? I have experience using traditional HPC clusters that I can install Anaconda/Mamba on and then conda install any packages I need for my workflows. The AWS is slightly confusing because while I have installed…

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Mappability calculation based on 150 bp reads after mapping with bwa

Mappability calculation based on 150 bp reads after mapping with bwa 0 Hi, I am trying to apply some filters on whole exome sequencing data. Firstly I did the mapping using bwa and then I followed the proposed pipeline from GATK for Calling variants on cohorts of samples using the…

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GTEX eQTLs’ extraction

GTEX eQTLs’ extraction 0 Hello everyone, I am a still a student and I am new to this forum, but I would need help regarding GTEX and how to work with it. I was given a task, which includes finding and extracting eQTLs for specific genes from the GTEX portal…

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Proteome-pI 2.0 – Proteome Isoelectric Point Database

www.isoelectricpointdb2.org – Proteome Isoelectric Point Database 2.0 Proteome-pI 2.0 is an updated version of an online database containing the information about predicted isoelectric points. The isoelectric point, the pH at which a particular molecule carries no net electrical charge, is an important parameter for many analytical biochemistry and proteomics techniques,…

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Full length sequences from hhblits

Full length sequences from hhblits 1 It depends exactly what version of the database you use, but all the hits will usually have UniProt numbers in them. The first hit from one of my uniclust searches is A0A0P1IPI8_9RHOB, and from bfd it is A0A1F1QC50_9PSED. Both of those can be found…

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Calculating Allele Balance in GATK4

Calculating Allele Balance in GATK4 0 Hi All, I know GATK3 has option to compute Allele Balance and populate ABHet and ABHom fields. I do not see this option in GATK4. I used to run this command in GATK3: java ${JAVAOPTS} -jar /usr/local/genome/GATK-3.6-0/GenomeAnalysisTK.jar -T VariantAnnotator -A AlleleBalance -I AF1.vcf.gz -R…

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Calculation of gene coverage from BAM file

If you want more statistics than just counts of reads that overlap gene annotations, perhaps the following answer will help. Starting with a generic BAM file, it can be converted to BED via bam2bed. The 13th column (QUAL) can be converted from its printable characters back to an average Phred…

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Plink v2.0 does not produce a Z-compressed file (.zst)

Plink v2.0 does not produce a Z-compressed file (.zst) 0 Good morning, I would like to convert a merged VCF in a Plink compressed format (.pgen, .psam and .pvar files), so I run plink2 –vcf MyMerged.vcf.gz –make-pgen –zst-level 3 –out MySamples It basically works, as it produces such files: ls…

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Unrecognized values used for CHROM, Replacing with 0.

VCFTools error: Unrecognized values used for CHROM, Replacing with 0. 1 Hi all! I was trying to run VCFtools on .vcf output file from dDocent program (ddocent.wordpress.com/) and I get this error: Unrecognized values used for CHROM: E81_L257 –  Replacing with 0. I was wondering if anyone encountered that and…

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PhD Scholarship in bioinformatics applied to ancient and sedimentary DNA

DTU Health Tech is looking for a qualified candidate for a vacant PhD position in bioinformatics. In this position, you will develop algorithms and computational methods to deal with the analysis of large datasets from modern and ancient sources. More specifically, these algorithms will be aimed at analyzing relationships between…

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Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator

1. Pérez, J., Moraleda-Muñoz, A., Marcos-Torres, F. J. & Muñoz-Dorado, J. Bacterial predation: 75 years and counting!. Environ. Microbiol. 18, 766–779 (2016). PubMed  Article  PubMed Central  Google Scholar  2. Linares-Otoya, L. et al. Diversity and antimicrobial potential of predatory bacteria from the Peruvian coastline. Mar. Drugs. 15, E308. doi.org/10.3390/md15100308 (2017)….

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MGI Unveils Performance Upgrades for its Sequencing Platforms* and Customized ATOPlex Platform at the 16th International Conference on Genomics

QINGDAO, China, Nov. 1, 2021 /PRNewswire/ — MGI Tech Co., Ltd. (MGI), a global life science leader and innovator, introduced a series of performance upgrades for its gene sequencing platforms* and a new multiplex PCR platform at the 16th International Conference on Genomics (ICG-16) held in Qingdao, China. As one of…

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‘Dust specks’ are genome building blocks

Scientists have discovered that tiny ‘microchromosomes’ in birds and reptiles, initially thought to be specks of dust on the microscope slide, are linked to a spineless animal ancestor that lived 684 million years ago. They prove to be the building blocks of all animal genomes, but underwent “dizzying rearrangement” in…

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Bioinformatics Analyst – Molecular Biology, Full-time, Days Job Opening in Chicago, IL at Northwestern Memorial Healthcare

Company Description At Northwestern Medicine, every patient interaction makes a difference in cultivating a positive workplace. This patient-first approach is what sets us apart as a leader in the healthcare industry. As an integral part of our team, you’ll have the opportunity to join our quest for better healthcare, no…

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How Gene Editing Can Support Sustainable Agriculture

By Ingrid Fung When the CRISPR-Cas9 system was discovered in 2012, its precision and relative simplicity of use captured the imaginations of popular media, investors, and scientists alike. It was expected that CRISPR-Cas9 would make genome editing economically viable for a vast array of commercial applications. Suddenly, gene editing was…

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Quantum computing in the enterprise: Four factors to consider

Image: Getty/ gremlin Quantum computing is still in its infancy, yet the technology is tipped to transform entire industries, whether by revolutionising healthcare through new drug discovery and DNA sequencing, or by assisting humans in their search for extra-terrestrial life on as-yet-undiscovered planets. Special Report The CIO’s guide to Quantum…

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Illumina hiring Bioinformatics Scientist in United States

Introduction Illumina’s Bioinformatics group are looking for an enthusiastic and highly numerate bioinformatician to join their team based in San Diego, CA to support the development of new Illumina products and help maintain on-market solutions. Members of the team work in close collaboration with wet lab scientists to support assay…

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CRISPR-Cas Can Help Reduce Climate Change

By Monika Paulė, PhD Monika Paulė, PhDCo-Founder and CEO, CasZyme Many industries and fields of science are investigating innovative technologies to mitigate the effects of climate change—effects that are already evident as an alarming collection of environmental, social, and economic problems. CRISPR-Cas gene editing has been successfully applied in human…

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Towson University: Checking Out What Is In TU’s DNA

Professor Kelly Elkins, TU Human Remains Identification Lab provide answers, experience In early October, it was announced that an independent group of cold-case investigatorsclaimed to have found the identity of the Zodiac Killer, one of America’s most notoriousserial killers and a case that has gone unsolved for more than 50…

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Microbialtec Provides One-stop Bacillus Genome Editing Services to Support Researches in the Field of Microbial Genome Editing

Microbialtec announced the release of one-stop bacillus genome editing service to process professional studies in the field of microbial genome editing. New York, USA – November 1, 2021 – Microbialtec, the division of Creative Biogene, is a high-tech service provider specialized in the microbiological field, focusing on developing cutting-edge technologies…

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DESeq2 ratio of ratios and p-value

Hello, I am new to DeSeq2 and I am trying to use a multi-factor design to answer this question: Is captured/input in condition 1 different from captured/input in condition 2 ? I used a combination of the DeSeq2 manual and DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) to…

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New method refines CRISPR base editing

1 November 2021 Splitting and reconstituting the enzyme used in the base editing method of genome editing may make more controlled changes possible.  Base editing differs from the CRISPR/Cas9 method because instead of cutting and replacing a section of DNA, an enzyme called DNA deaminase chemically changes a target base. However, unregulated DNA…

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“Genetic Goldmine” Uncovered for Plant Survival in One of the Harshest Environments on Earth

Evolutionary genomics approach identifies genes that enable plants to live in the Atacama Desert, offering clues for engineering more resilient crops to face climate change. An international team of researchers has identified genes associated with plant survival in one of the harshest environments on Earth: the Atacama Desert in Chile….

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Tracing the impact of a long-lost relative on modern bread wheat — ScienceDaily

Genetic detective work has uncovered an obscure ancestor of modern bread wheat, in a finding similar to uncovering a famous long-lost relative through DNA analysis in humans. In a study which appears in Nature Biotechnology researchers sequenced the DNA from 242 unique accessions of Aegilops tauschii gathered over decades from…

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Ombre Raises $3 Mln in Seed Funding After Rebranding to Continue Its Mission to Facilitate Microbiome Self-Care

Ombre, a San Francisco-based healthtech startup previously known as Quantbiome, has raised $3 million in seed funding to provide users with a means to evaluate their microbiome at home to improve their general health. Led by PivotNorth Capital, with participation from Trail Mix Ventures, Shanda Group, Unilever Ventures, Social Starts’…

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UK BioBank study links gene variants to health

1 November 2021 Analysis of DNA sequences from over 450,000 participants in the UK BioBank has helped connect hundreds of genes to health outcomes. Researchers in New York tested the association of around 2.8 million genetic variants in the protein-coding parts of the genome to 3994 different health-related traits – an enormous scale…

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Bioconductor – sparrow

DOI: 10.18129/B9.bioc.sparrow     Take command of set enrichment analyses through a unified interface Bioconductor version: Release (3.14) Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of…

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Bioconductor – courses and conferences

About press copyright contact us creators advertise developers terms privacy policy & safety how youtube works test new features press copyright contact us creators online – flexible short courses. This course is the ideal introduction to english garden history. It provides an overview of five centuries of development, from baroque…

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a bioconductor R package for fully unsupervised deconvolution of complex tissues.

Authors Lulu Chen, Chiung-Ting Wu, Niya Wang, David M Herrington, Robert Clarke, Yue Wang Published in Bioinformatics (Oxford, England). Volume 36. Issue 12. Pages 3927-3929. Jun 01, 2020. Abstract We develop a fully unsupervised deconvolution method to dissect complex tissues into molecularly distinctive tissue or cell subtypes based on bulk…

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Very low read counts for PD1 when using STAR aligner compared to BWA

Very low read counts for PD1 when using STAR aligner compared to BWA 0 HI all, I am processing RNA-seq data. Initially, the company used BWA and GRCh37/hg19 as an aligner. I subsequently realigned them using STAR and GRCh38/hg38. Counts are generated using feature counts for both. Although most of…

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CONVERT PSF to TOP grimaces

namd-l: Re: CONVERT PSF to TOP grimaces I might be a little biased since I wrote TopoGromacs for my own needs, but I think it’s a fine way to generate the .top file GROMACS expects. This defines the system topology and parameters, which are combined with a .mdp file into…

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Virtual Double-System Single-Box for Absolute Dissociation Free Energy Calculations in GROMACS

We describe a step-by-step protocol for the computation of absolute dissociation free energy with GROMACS code and PLUMED library, which exploits a combination of advanced sampling techniques and nonequilibrium alchemical methodologies. The computational protocol has been automated through an open source Python middleware (HPC_Drug) which allows one to set up…

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Intra-individual state-dependent comparison of plasma mitochondrial DNA copy number and IL-6 levels in patients with bipolar disorder

Background: Patients with bipolar disorder (BD) have increased plasma IL-6 levels, which are higher in depressed BD (dBD) than remitted BD (rBD). However, the mechanism that differentiates the cytokine levels between dBD and rBD is not understood. First, we determined whether brain-derived mtDNA can be detected in plasma using neuron-specific…

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FASTAFS: file system virtualisation of random access compressed FASTA files | BMC Bioinformatics

FASTA File System (FASTAFS) file format consists of four blocks: (1) File Header (2) Per-Sequence-Data (3) Per-Sequence-Header and (4) File Metadata, to efficiently store sequence and metadata (Fig. 1). During conversion, the metadata flag sets the archives status to incomplete. Each block of compressed sequence data is followed by the CRAM…

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Counting hexamers in fasta sequence and identify its structure (and interruptions)

I have a lot of fasta files, each one with thousand of reads containing the hexameric motif “CCCTCT”. The hexameric motif is highly continuous in most cases but interruptions may occur. I need to count the hexameric motif keeping the read ID and identify their structure (CCCTCT)n. These interruptions are…

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Bioinformatics Single-Cell RNA Analysis – Software Trainer

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

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In python how to create dataframe with 2 different values from a column

In python how to create dataframe with 2 different values from a column 1 In python, I need help with a code that lets me view two atoms for a column from a pdb file. I used the following new = df [‘atom_name’] == [ ‘NH1’ , ‘NH2’ ] But…

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Improving ligand-ranking of AutoDock Vina by changing the empirical parameters

doi: 10.1002/jcc.26779. Online ahead of print. T Ngoc Han Pham  1 , Trung Hai Nguyen  2   3 , Nguyen Minh Tam  3   4 , Thien Y Vu  1 , Nhat Truong Pham  5 , Nguyen Truong Huy  1 , Binh Khanh Mai  6 , Nguyen Thanh Tung  7   8 , Minh Quan Pham  8  …

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Postdoctoral Fellow – Computational Biology, Biostatistics and Bioinformatics

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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Scientific Bioinformatics Analyst job with General Bioinformatics

An important position in our bioinformatics analysis team where your passion for delivering excellent, high quality outcomes for science is foremost in your role. Combining scientific insight with bioinformatics analysis you will complete analyses to support genomics studies in non-model organisms. The Opportunity A fantastic opportunity for an early stage…

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This Week in San Diego Jobs: November 1, 2021

Nov 01, 2021 – Heather Dewis Whether you need a new job or you’re looking for a challenge, life sciences, tech, and lifestyle companies are hiring. Here are five opportunities for the week of November 1, 2021: 1. Director, Global Regulatory CMC Cell Therapy – Bristol Myers Squibb Bristol Myers…

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Bioinformatics Programmer – software / qa / dba / etc

QR Code Link to This Post MilliporeSigma is hiring a Bioinformatics Programmer at their Rockville, MD location A career with MilliporeSigma is an ongoing journey of discovery: our 58,000 people are shaping how the world lives, works and plays through next generation advancements in Healthcare, Life Science and Electronics. For more…

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Use PS4 Controller on Your PC

If you have always played on a console ever since you were a kid and have now switched to a gaming PC but would still like to use your good old PS4 controller instead of mouse and keyboard, Windows 10 will let you do that without having to install any…

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The purpose of scaling to a negative binomial distribution in single cell RNA-seq

The purpose of scaling to a negative binomial distribution in single cell RNA-seq 1 Hi, I’m still a bit new to computational analysis of single cell data, but I’m doing my best to understand why things are done. As I understand it, when people cluster their data, typically they do…

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How to correctly calculate Alternative Allele Frequency (AAF) from Samtools mpileup

I have a hard time to figure it out how correctly calculate the Alternative Allele Frequency (AAF) from Samtools mpileup. I received the code which using samtools 1.8 mpileup (following code) get the following format: …. samtools mpileup -l … capture_targets.bed -t DP,AD,ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -d100000000 –output-BP –output-MQ –output-QNAME … Later in…

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Is there ever a good reason to use a log transformation instead of Box-Cox?

I often deal with non-normal data distributions, and for some downstream application it is needed to transform the data to at least resemble a normal distribution. It seems that the logarithm transformation (LT) is most often used in the literature, followed by sqrt(Y) and sometimes 1/sqrt(Y). Questions are often asked…

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Human Exome Variant Reference

Human Exome Variant Reference 3 Hi, I want to compare the variants for my WES analysis result using Illumina/hap.py. However I cant find the reference variants for the whole exome. I know that files (vcf, bed) in GiaB are usually used as reference variants, but I don’t know which file…

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Extracting specific regions from bam file as FASTA format

Extracting specific regions from bam file as FASTA format 0 Hello, first time asking, so sorry in advance for beginner’s mistakes. I have an indexed bam file, and I want to extract the FASTA format of all the reads that appear within the defined region (or partially appear) for example:…

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troubleshooting benchmarking small variants: hap.py and rtg

Hi! I tried to do what other posts reported and I have a problem that I do not fully understand why … 1) I downloaded the fastq files from Garvan (ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/NA12878/Garvan_NA12878_HG001_HiSeq_Exome/) with the bed file. I had to convert the bed file to hg38 (my_regions) … as I understand it…

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How to bechmark a human dataset ? (is it needed)

How to bechmark a human dataset ? (is it needed) 1 Hi I’m working on exome dataset I generated variant calls from different combination of aligners vs variant callers. Can i benchmark my exome dataset with Genome-in-bottle (HG001, HG002,HG003, HG004 & HG005) to find the Truth positives (TP) and False…

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Using R in Conda

(DISCLAIMER: some of the steps described here explicitly go against the official conda installation & usage instructions; beginners should follow the official guides instead before trying any of these steps, and fully understand what these steps are doing before trying them out) Thanks for the detailed notes. I have never…

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The Biostar Herald for Monday, November 01, 2021

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, GenoMax, and was…

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Gene expression (RNA-seq) clustering

Unsupervised class discovery is a data mining method to identify unknown possible groups (clusters) of items solely based on intrinsic features and no external variables. Basically clustering includes four steps: 1 Data preparation and Feature selection, 2 Dissimilarity matrix calculation, 3 applying clustering algorithms, 4 Assessing cluster assignment I use…

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bedtools getfasta does not give a proper fasta output

bedtools getfasta does not give a proper fasta output 2 I have a problem with the output from bedtools getfasta, it used to work before. My bed-file looks like this – C1_64090263 131 164 C1_64090263-1:33 V1_87574936:0 – 33 0 And I am using the command –bedtools getfasta -fi in.fa -bed…

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Research Fellow (Postdoc) in Computational Radiation Biology and Oncology at UCL

Job:Research Fellow (Postdoc) in Computational Radiation Biology and Oncology at UCL 0 The Computational Radiation Biology and Oncology Lab, led by Dr Jamie Dean, is seeking a Research Fellow with a background in theoretical/mathematical/computational modelling and data analysis (as demonstrated by publication/s) to join the Computational Radiation Biology and Oncology…

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Construction of the reference genome database (GCA_000001405.15_GRCh38) with snpeff

Construction of the reference genome database (GCA_000001405.15_GRCh38) with snpeff 1 Dear colleagues I used the reference genome GRCh38 version GCA_000001405.15_GRCh38 / seqs_for_alignment_pipelines.ucsc_ids downloaded from ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ This version was used for alignment and variant calling, however, I wanted to annotate genetic variants by snpeff v5. I did not find this version…

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Gromacs: gmx::StandardInputStream Class Reference

#include <gromacs/utility/filestream.h> This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] This browser is not able to show SVG: try Firefox, Chrome, Safari, or Opera instead. [legend] Text input stream implementation for reading from stdin. Implementations for the TextInputStream methods throw FileIOError on…

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Bioconductor – GeneSummary

DOI: 10.18129/B9.bioc.GeneSummary     RefSeq Gene Summaries Bioconductor version: Release (3.14) This package provides long description of genes collected from the RefSeq database. The text in “COMMENT” section started with “Summary” is extracted as the description of the gene. The long text descriptions can be used for analysis such as…

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Research advances emerging DNA sequencing technology

New Jersey, United States, – The report on the High-precision lens market comes from extensive research carried out by a team of industry experts. The report briefly covers the products or services in the market and their application. The report also provides information on the technological advancements in the High…

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Gene Sequencing Type ‘Transcriptomics’ Determines When Dragonflies, Damselflies First Emerged

1 days ago Researchers, which include a University of Tsukuba member, have applied in a recently published research a gene sequencing type called transcriptomics to reconstruct the insect order Odana’s phylogeny. CloseA ScienceDirect report said, through calibration of this sequencing with the use of the fossil record, researchers were able…

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Scientists completed DNA sequencing of human remains unearthed in Xinjiang and finally solved the mystery of origin

An archaeological study on hundreds of natural preserved remains unearthed from the Tarim Basin in China was also featured on the homepages of the official websites of well-known academic journals “Nature” and “Science”. The official website of “Nature” put this research on the headlines. This research has solved the problem…

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Enhancers: Conserved in Activity, Not in Sequence

About 700 million years ago, sponges branched off from all other animals on the tree of life. Despite this evolutionary distance, sponges share a form of gene regulation with much more complex species. The mechanisms are so similar, in fact, that a genetic element called an enhancer from the sea…

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DeepMind’s AI solved a 50-year-old protein-related challenge

Source:DeepMind DeepMind is a research company owned by Google that specialises in using Artificial Intelligence for positive impacts in the world. According to recent reports, DeepMind is successfully continuing to do its job in finding answers to impossible questions and to solve challenges with Artificial Intelligence. DeepMind has recently solved…

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Recreating QC of 1000 Genomes project

Recreating QC of 1000 Genomes project – removing non overlapping SNPs 0 Hi everyone, I am attempting to recreate the the quality control analysis performed in the 1000 genomes project (tcag.ca/documents/tools/omni25_qcReport.pdf). I am fairly new to performing QC on a dataset, and am currently stuck on section 5.1 of the…

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Science News | Scientists Find Medications That Reverse Alzheimer’s Disease

Washington [US], October 31 (ANI): Researchers have managed to reverse the symptoms of Alzheimer’s disease in mice by administering drugs currently used to treat hypertension and inflammation in humans. Alzheimer’s disease is the most common cause of dementia in Western societies and it is estimated that 24 million people worldwide…

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The integrity and assay performance of tissue mitochondrial DNA is considerably affected by choice of isolation method

Available online 30 October 2021 doi.org/10.1016/j.mito.2021.10.005Get rights and content Highlights • The procedure chosen for isolation of mtDNA from solid tissues has a considerable effect on the integrity of the product, as routine isolation methods yield mtDNA with numerous single-stranded nicks per mtDNA strand. • Modifications that benefit mtDNA integrity…

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Bioconductor – TRESS

DOI: 10.18129/B9.bioc.TRESS     Toolbox for mRNA epigenetics sequencing analysis Bioconductor version: Release (3.14) This package is devoted to analyzing MeRIP-seq data. Current functionality is for detection of transcriptome-wide m6A methylation regions. The method is based on hierarchical negative binomial models. Author: Zhenxing Guo [aut, cre], Hao Wu [ctb] Maintainer:…

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Post Doctorate Fellow Job at Tata Memorial Centre – Bioinformatics

The Tata Memorial Centre is a Comprehensive Cancer Centre with a mission to achieve the highest standards in patients care, cancer prevention, cancer research and professional development for oncology and allied disciplines. TMC is an autonomous Grant-In-Aid Institute of the Department of Atomic Energy, Government of India. TMC is affiliated…

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Counting the kingdoms | Otago Daily Times Online News

As our understanding has deepened, life has branched out, writes marine science professor Abby Smith. When I was in school we learned that life was classified into four kingdoms: animals, plants, other stuff (remember Paramecium?) and really tiny stuff (bacteria). We felt pretty smug because we knew that mushrooms are…

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The MOTS-c K14Q polymorphism in the mtDNA is associated with muscle fiber composition and muscular performance

Available online 30 October 2021, 130048 doi.org/10.1016/j.bbagen.2021.130048Get rights and content Highlights • There is an East Asian-specific m.1382A>C polymorphism in the mtDNA that changes the 14th amino acid of MOTS-c (i.e., K14Q). • The C allele carriers of the MOTS-c m.1382A>C polymorphism exhibited a higher percentage of myosin heavy chain-IIx…

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bbduk flags ‘tossbrokenreads’ and ‘nullifybrokenquality’

bbduk flags ‘tossbrokenreads’ and ‘nullifybrokenquality’ 2 I seek help understanding these 2 flags for BBDUK of BBMAP = ‘tossbrokenreads‘ and ‘nullifybrokenquality‘ I see these flags mentioned in the STDERR of my bbduk.sh step using BBMap version 38-60 while decontaminating Illumina SE 100nt raw reads via “Adapter and Quality Trimming” –…

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map file for BEAGLE imputation

Forum:map file for BEAGLE imputation 0 Hello Community, I am having an issue with BEAGLE V5.2 throwing an error stating all my loci have the same genetic position when they most certainly do not. I have posted the error and a sample of the top of the map file I…

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python – Why Kaggle doesn’t suppot imshow() ? Or how to display image using open-cv in kaggle

I’m using kaggle last week.when i tried to open picture using the command cv2.imshow(“preview”,path) but i got error that is : /tmp/ipykernel_36/628293590.py in <module> 1 img=cv2.imread(path,0) —-> 2 cv2.imshow(‘img’,img) 3 cv2.waitKey(0) 4 cv2.destroyAllWindows() error: OpenCV(4.5.3) /tmp/pip-req-build-fvfwe_ss/opencv/modules/highgui/src/window.cpp:1274: error: (-2:Unspecified error) The function is not implemented. Rebuild the library with Windows, GTK+…

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retrieving dN and dS in BiomaRt

Hi! I want to retrieve values of dn and ds for human/mouse gene comparisons in Ensembl using BiomaRt (R application), but now in the list of attributes ensembl <- useEnsembl(biomart=”ensembl”) ensembl <- useDataset(‘hsapiens_gene_ensembl’, mart=ensembl) att = listAttributes(ensembl) It is not appear the dN or dS attributes related that appeared in…

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Mammoth Biosciences hiring Scientist, Bioinformatics in Brisbane, CA, US

About Mammoth Biosciences The CRISPR-based platform for disease detection. Mammoth’s vision is to provide a CRISPR-based platform on which an infinite number of tests can be built by both ourselves and our partners – democratizing access to an endless variety of tests for bio sensing in healthcare, as well as…

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machine learning – The productivity of Colab: to load directly from the Net(e.g. Kaggle) databases or to upload them on the colab directory and then extract them?

Recently I tried to search for the fastest approach to work with large data files in colab. Because I use colab as an environment for machine learning and thus have used files from the physical hard drive on the computer. However, I began to wonder if it would be better…

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Result page 3 for Botany Lecturer Jobs in Chennai, Tamil Nadu (Oct 2021) – 362 Active Botany Lecturer Openings in Chennai, Tamil Nadu

Job Description Position: Medical Coder -Work from Home   Ct: HR Kamatchi – 8870660998 Job Description:Medical Coding is the process of conversion of text information related to healthcare services into numeric Diagnosis (Medical Problems) and Procedure (Treatments) Codes using ICD-10 CM and CPT code books.   Requirement:   knowledge in…

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Job: Senior Bioinformatics Scientist – (28180-JOB) at Illumina Singapore Pte Ltd Singapore

Job Description Basic Function and Scope of the Position: As a Sr. Bioinformatics Scientist, your primary responsibility is to enable the data analysis and processing and successfully delivery of data within a cloud system to meet project based KPIs for to client(s) in Singapore, as part of large and strategic…

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Cell identity and nucleo-mitochondrial genetic context modulate OXPHOS performance and determine somatic heteroplasmy dynamics

Sammendrag Heteroplasmy, multiple variants of mitochondrial DNA (mtDNA) in the same cytoplasm, may be naturally generated by mutations but is counteracted by a genetic mtDNA bottleneck during oocyte development. Engineered heteroplasmic mice with nonpathological mtDNA variants reveal a nonrandom tissue-specific mtDNA segregation pattern, with few tissues that do not show…

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main-armv6-default][science/cp2k-data] Failed for cp2k-data-7.1.0 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/cp2k-data-7.1.0.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building science/cp2k-data build started at Fri Oct 29…

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Reg relax_multip

Hello users, Can somebody enlighten me on the actual use of the relax_multip keyword?  As per the manual, the keyword Do not enforce the occupation of alpha and beta MOs due to the initially defined multiplicity, but rather follow the Aufbau principle.  So while performing UKS based simulations, does it mean…

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Recruitment of Research Associate/Senior Research Associate at IDEAYA Biosciences, San Francisco

About IDEAYA Biosciences: Biotechnology company IDEAYA Biosciences (NASDAQ: IDYA) develops synthetic lethality-focused precision medicine for cancer patients using DNA sequencing and other molecular diagnostics. The company is publicly traded. Small molecule drug discovery is integrated with biomarker identification and validation to identify patient populations most likely to benefit from the…

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AI-based technology rapidly identifies genetic causes of rare disorders with high accuracy

An artificial intelligence (AI)-based technology rapidly diagnoses rare disorders in critically ill children with high accuracy, according to a report by scientists from University of Utah Health and Fabric Genomics, collaborators on a study led by Rady Children’s Hospital in San Diego. The benchmark finding, published in Genomic Medicine, foreshadows…

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Transforming cancer treatment with precision medicine | Business Weekly | Technology News | Business news

We are entering a new era of precision medicine, where technological advances may revolutionise the field of cancer treatment by making sure every patient receives the right individualised therapy at the right time — and the impact on patients will be enormous, writes Barnaby Balmforth, CEO of Biofidelity.  Over the past…

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PM Modi at G20 summit

Prime Minister Narendra Modi talked about the COVID-19 vaccine production goals set by India for the next year during his address at the G-20 Summit session in Rome on October 30. He also talked about the importance of getting Indian vaccines recognized by the WHO at the earliest. During his…

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Researchers develop eToeholds for safe, effective RNA and cellular therapies

RNAs are best known as the molecules that translate information encoded in genes into proteins with their myriad of activities. However, because of their structural complexity and relative stability, RNA also has attracted great attention as a valuable biomaterial that can be used to create new types of therapies, synthetic…

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DCAF1-targeting microRNA-3175 activates Nrf2 signaling and inhibits dexamethasone-induced oxidative injury in human osteoblasts

This article was originally published here Cell Death Dis. 2021 Oct 29;12(11):1024. doi: 10.1038/s41419-021-04300-8. ABSTRACT Activation of nuclear-factor-E2-related factor 2 (Nrf2) signaling can protect human osteoblasts from dexamethasone-induced oxidative injury. DDB1 and CUL4 associated factor 1 (DCAF1) is a novel ubiquitin E3 ligase for Nrf2 protein degradation. We identified a…

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main-armv6-default][biology/p5-BioPerl] Failed for p5-BioPerl-1.007007_1 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: sunp…@freebsd.org Log URL: beefy8.nyi.freebsd.org/data/main-armv6-default/pebf5105f9a4d_s23024f004a/logs/p5-BioPerl-1.007007_1.log Build URL: beefy8.nyi.freebsd.org/build.html?mastername=main-armv6-default&build=pebf5105f9a4d_s23024f004a Log: =>> Building biology/p5-BioPerl build started at Fri Oct 29…

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CS Genetics hiring Bioinformatics Scientist in Cambridge, MA, US

About CS Genetics CS Genetics is a developer of tools and techniques for genomics. Job Description Our Company CS Genetics is developing pathbreaking new technology for genomics, based on foundational scientific insights and sophisticated conceptual innovations in sequencing techniques. Our work will accelerate basic biologic research and enable lifesaving new…

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On fixing priorities for vaccinating children

Which high-risk sub-group and age sub-group to start with has to be determined by reviewing hospitalisation and mortality data from India: Chandrakant Lahariya In August, the Indian drug regulator (DCGI) granted an emergency use approval for Zydus Cadila’s DNA vaccine for use in adults and children aged 12 years and…

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Assistant Scientist – Bioinformatics job with University of Miami

Job location: Miami, FL Employment Type: Full-time Posted data: 2021-10-25 Req: R100051885 Current Employees:If you are a current Staff, Faculty or Temporary employee at the University of Miami, please click here to log in to Workday to use the internal application process. To learn how to apply for a faculty…

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New approach to control the hierarchical assembly of protein pathways with DNA

Northwestern investigators have identified a novel approach to control the hierarchical assembly of protein pathways with DNA, according to a study published the Proceedings of the National Academy of Sciences (PNAS). The approach may facilitate the construction of synthetic protein materials, which can be used for a variety of medical…

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Animals are throwing away DNA during reproduction, and we don’t know why

To do their lab work, Laura Ross and her team must conduct an itty-bitty surgery. First, they dissect out the reproductive tissues of the black-winged fungus gnat, a diminutive black fly about one-sixteenth to one-eighth of an inch long. Then they home in on particular cells in that tissue: the…

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Genome assembly for identifying SNPs

Genome assembly for identifying SNPs 0 Hello there, I’m a little confused on how to proceed – I want to identify if there are SNPs in my small RNA dataset. If I align using the top level genome assembly (Ensembl) with 0 mismatches, can I use SNP calling tools directly…

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replacing ensembl ID with the gene symbol?

Im a noob with a very unclear idea of what I am doing, but I’m doing my best. The other day, the ncbi webpage for downloading genomes and GTF files was down. As a result, I had to do my analysis on this RNA seq data using the ensembl files,…

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Converting Ensembl gene id to Gene symbol

Converting Ensembl gene id to Gene symbol 0 Hi all, As mentioned earlier in this post, I tried to convert the Ensembl gene ids to the Gene symbol. I didn’t receive any error by the code below but the nrow of ens_to_symbol_biomart is 55605 and the length of ens is…

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Can someone explain PLINK allele REF/ALT management strategy?

Can someone explain PLINK allele REF/ALT management strategy? 0 Sometimes when merging two plink files, the Reference (REF) and Alternative (ALT) alleles may be reversed, e.g. REF G ALT A versus REF A ALT G. The main reason for that is the default action of PLINK. You see, when using…

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Missing some predictions based on dbNSFP v4.2a

Missing some predictions based on dbNSFP v4.2a 0 Hello everybody, I used dbNSFP v4.2a database for functional prediction and variant annotation. As mentioned in the download site sites.google.com/site/jpopgen/dbNSFP, this version compiles prediction scores from several prediction algorithms (SIFT, SIFT4G, Polyphen2-HDIV, Polyphen2-HVAR. ….), and other information, including allele frequencies observed in…

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How to generate a 2D PCA plot from bulk RNA-seq data (log2 CPM) using the PCAtools?

How to generate a 2D PCA plot from bulk RNA-seq data (log2 CPM) using the PCAtools? 1 Hi all, I have bulk RNA-seq data with 12 samples – WT (x4), ‘A’ KO (x4), and ‘B’ KO (x4). I want to generate a 2D PCA plot (biplot) like below figure to…

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Research Associate job with Indiana University Bloomington

The Indiana University Bloomington Center for Genomics and Bioinformatics (CGB), cgb.indiana.edu/, seeks a Research Associate to serve in the genomics lab. The expected start date is January 3, 2022. Duties include the performance and documentation of bench experiments, organization and maintenance of lab space, and other lab assignments. Must have…

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