Tag: clusters

A high-throughput multispectral imaging system for museum specimens

The two-dimensional nature of many pinned Lepidoptera specimens allows us to omit some technical considerations, such as the variable incident angles that need to be carefully considered when imaging 3D objects, and our multi-spectral imaging rig with its custom designed platform can image both the dorsal and ventral sides of…

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What Is Stem Cell Research?

There are cells within our bodies that have a spectacular power. Known as stem cells, they build our bodies before we’re born and regenerate our tissues to keep us alive. For example, stem cells in the skin help us heal from cuts and other stem cells deep in the bone…

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Characterization, genome analysis and genetic tractability studies of a new nanocellulose producing Komagataeibacter intermedius isolate

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

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Ancient origin and constrained evolution of the division and cell wall gene cluster in Bacteria

Miyakawa, T., Matsuzawa, H., Matsuhashi, M. & Sugino, Y. Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112, 950–958 (1972). Article  CAS  PubMed  PubMed Central  Google Scholar  Ayala, J. A., Garrido, T., De Pedro,…

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Senior Research Scientist, Bioinformatician Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A Senior Research Scientist position is available immediately in Prof Chng Wee Joo’s groups for a highly motivated PhD graduate with experience in Bioinformatics (computational genomics). The focus of the lab is on deciphering transcriptional and genomic abnormalities in the context of blood cancer, including epigenetic and superenhancer deregulation, using single…

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Bioinformatics Analyst III Position In South San Francisco, CA

Job Description To discuss more about this job opportunity, please reach out to Chitrank Rastogi (LinkedIn URL – www.linkedin.com/in/chitrank-rastogi-55119a102/), email your updated resume at chitrank.rastogi@collabera.com or give me a call at (425) 523-1648. Thank you! Job Description:Job Roles & Responsibilities: The Genomic Research Center Computational Oncology group (GRC-CO) is seeking…

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Transcriptomic dysregulation across cerebral cortex in autism spectrum disorder

A recent study in Nature demonstrated transcriptomic dysregulation in the cerebral cortex in autism spectrum disorder (ASD). Study: Broad transcriptomic dysregulation occurs across the cerebral cortex in ASD. Image Credit: Ukrolenochka/Shutterstock Background The risk factors for ASD include a significant genetic component with hundreds of risk genes involved. Molecular profiling…

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Scikit-Learn Cheat Sheet (2022), Python for Data Science

The absolute basics for beginners learning Scikit-Learn in 2022 Photo from Unsplash by Tim Stief Scikit-learn is a free software machine learning library for the Python programming language. It features various classification, regression, clustering algorithms, and efficient tools for data mining and data analysis. It’s built on NumPy, SciPy, and Matplotlib. Sections:1….

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Sbatch How Submitted Location Using Jobid With Code Examples

Sbatch How Submitted Location Using Jobid With Code Examples With this piece, we’ll take a look at a few different examples of Sbatch How Submitted Location Using Jobid issues in the computer language. scontrol show job your_job_id_234533 We learned how to solve the Sbatch How Submitted Location Using Jobid by…

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Postdoctoral Scholar- Bioinformatics job with University of Florida

Postdoctoral Scholar- Bioinformatics Job No: 524142Work Type: Location: Main Campus (Gainesville, FL), AlachuaCategories: RealCatDepartment: 32030000 – PH-MEDICINAL CHEMISTRY Job Description Classification Title: Postdoctoral Associate Job Description: The Postdoctoral Scholar will work independently and collaboratively to develop a bioinformatics platform for discovering bioactive compounds directly from less-explored marine organisms. Additional duties…

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Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection

Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…

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

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

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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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Genomic signatures associated with maintenance of genome stability and venom turnover in two parasitoid wasps

Genomic features of two Anastatus wasps, A. japonicus and A. fulloi We employed PacBio high-fidelity (HiFi) long-read sequencing and Illumina short-read sequencing technologies to generate high-quality contigs for two Anastatus wasps, A. japonicus and A. fulloi (Supplementary Tables 1 and 2). These contigs were further scaffolded using Hi-C libraries to…

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Completed: Quarterly Cluster Maintenance Tuesday October 25 | crc.pitt.edu

Dear CRC User Community, We have completed our quarterly maintenance and have returned the clusters to production. The key changes to the CRC clusters are the following: Storage Systems updates – Improved performance of iX with cache upgrades SLURM Workload Manager –  Update to newest version (22.05) Due to incompatibility between…

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Immuno Cure secured maximum subsidy from HKSTP

Significant funding support for HIV Vaccine Clinical Trial HONG KONG SAR – Media OutReach – 17 October 2022 – Immuno Cure BioTech, a clinical stage biotechnology group based in the Hong Kong Science Park specialising in DNA vaccines and immunotherapies, announced today that Hong Kong Science and Technology Parks Corporation…

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Antarctic aldehyde dehydrogenase from Flavobacterium PL002 as a potent catalyst for acetaldehyde determination in wine

Sequence analysis of S2-ALDH BLAST screening of the Flavobacterium PL002 genome sequence42 led to identification of a coding region homologous to aldehyde dehydrogenase gene (1365 bp) coding for the hypothetical enzyme S2-ALDH of 454 amino acids, with calculated MW 49,062 (Supplementary Fig. 1S). Phylogenetic analysis of the S2-ALDH amino acid sequence in…

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University of Florida – Details – Postdoctoral Scholar

Postdoctoral Scholar- Bioinformatics Apply now Job no: 524142 Work type: Post Doc Associate Location: Main Campus (Gainesville, FL), Alachua Categories: Health Care Administration/Support, Medicine/Physicians Department:32030000 – PH-MEDICINAL CHEMISTRY Classification Title: Postdoctoral Associate Job Description: The Postdoctoral Scholar will work independently and collaboratively to develop a bioinformatics platform for discovering…

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Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations

Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of…

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Inferring and perturbing cell fate regulomes in human brain organoids

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

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Peripheral Neuroblastic Tumor Transcriptomes Point to Transitional Cell State

NEW YORK – With the help of single-cell RNA sequencing, investigators in China and Australia have untangled diverse tumor and microenvironment features for peripheral neuroblastic tumors (PNT), including a transitional tumor cell state that appears to coincide with more aggressive and difficult-to-treat forms of the pediatric neural crest cancers. “Historically,…

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The comprehensive detection of miRNA and circRNA in the regulation of intramuscular and subcutaneous adipose tissue of Laiwu pig

Zhou, G. et al. Global comparison of gene expression profiles between intramuscular and subcutaneous adipocytes of neonatal landrace pig using microarray. Meat. Sci. 86(2), 440–450 (2010). CAS  PubMed  Article  Google Scholar  Alfaia, C. M. et al. Current feeding strategies to improve pork intramuscular fat content and its nutritional quality. Adv….

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Low number of nCount_RNA in single-cell RNAseq clusters?

Low number of nCount_RNA in single-cell RNAseq clusters? 0 Hello, after standard Seurat workflow, I checked the metrics of each cluster in the object. Please see the attached picture. How may I explain, in some of clusters, such as cluster 9 which has low nCount_RNA and nFeature_RNA but with an…

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Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation

Martincorena, I. et al. Somatic mutant clones colonize the human esophagus with age. Science 362, 911–917 (2018). CAS  PubMed  PubMed Central  Google Scholar  Yizhak, K. et al. RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues. Science 364, eaaw0726 (2019). CAS  PubMed  PubMed Central  Google Scholar  Yokoyama, A….

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How to use Scikit-Learn in Python [Complete Tutorial]

In this tutorial, we will focus on Scikit-Learn library usage in Python. Scikit-Learn is simple, fast and useful library used in python machine learning. It provides simple and efficient tools used in data analysis and data mining. Its free, easy to use and accessible to everyone. It is reusable in…

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biopython – Parsing a gene bank file and outputting specific feature information to a csv using Bio Python

So I am trying to parse through a gene bank file, extract particular feature information and output that information to a csv file. The example gene bank file looks like this: SBxxxxxx.LargeContigs.gbk LOCUS scaffold_31 38809 bp DNA UNK 01-JAN-1980 DEFINITION scaffold_31. ACCESSION scaffold_31 VERSION scaffold_31 KEYWORDS . SOURCE . ORGANISM…

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Research Fellow, Bioinformatician – Cancer Science Institute job with NATIONAL UNIVERSITY OF SINGAPORE

Job Description A postdoctoral position is available immediately in Prof Chng Wee Joo’s groups for a highly motivated PhD graduate with experience in Bioinformatics (computational genomics). The focus of the lab is on deciphering transcriptional and genomic abnormalities in the context of blood cancer, including epigenetic and superenhancer deregulation, using single cell…

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Challenges of single-cell and single-nucleus RNA-sequencing from core needle biopsy specimens

Single-cell RNA sequencing (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) allow transcriptomic profiling of thousands of cells from a renal biopsy specimen at a single-cell resolution. Both methods are promising tools to unravel the underlying pathophysiology of glomerular diseases. KU Leuven researchers provide an overview of the technical challenges that should be…

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Running lammps on a cluster – LAMMPS Installation

Hello all,I have created a Linux cluster with ssh and NFS. I have installed lammps in the NFS folder. I have verified that the cluster works properly with openmpi and the communication is good. But when I run lammps, after reading the data file it gets stuck on the first…

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Bioinformatics Analysis of the Key Genes and Pathways in Multiple Myel

Introduction Multiple myeloma is a B-cell malignancy characterized by the malignant proliferation of clonal plasma cells in bone marrow,1 It is the second most common hematological malignancy after lymphoma.2 The age-standardised rate (ASR) of multiple myeloma incidence was 1·78 (95% UI 1·69-1·87) per 100 000 people globally and mortality was…

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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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NODULIN HOMEOBOX is required for heterochromatin homeostasis in Arabidopsis

NDX is a heterochromatin-associated factor To understand the genome-wide regulatory roles of NDX, we first analyzed its genomic distribution. For this, we performed chromatin immunoprecipitation sequencing (ChIP-seq) in 10-day old Arabidopsis seedlings expressing N-terminally and C-terminally tagged NDX fusion proteins (flag-NDX/ndx1-1(FRI)/flc-2 and NDX-GFP/ndx1-1(FRI)/flc-2, respectively) expressed from their endogenous promoter21,32. The…

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Assessment of genetic diversity and SNP marker development within peanut germplasm in Taiwan by RAD-seq

The cultivated peanut (Arachis hypogaea L.) is an important oil crop but has a narrow genetic diversity. Molecular markers can be used to probe the genetic diversity of various germplasm. In this study, the restriction site associated DNA (RAD) approach was utilized to sequence 31 accessions of Taiwanese peanut germplasm,…

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Acute phase of ischemia-reperfusion in rats

Introduction Stroke is one of the leading causes of death and disability worldwide, which causes substantial economic and social burdens.1 Ischemic stroke is caused by insufficient blood and oxygen supply to the brain,2 accounting for about 85% of the casualties of stroke patients.3 The concept of treatment for ischemic injury…

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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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Live-seq enables temporal transcriptomic recording of single cells

Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…

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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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Centre to Delhi and 6 states amid rise in Covid cases

As Covid cases are rising in some parts of the country, the Centre has asked Delhi and six states to ensure adequate testing, promote Covid-appropriate behaviour and increase the pace of vaccination to contain the surge. Union Health Secretary Rajesh Bhushan has written a letter to Delhi, Kerala, Karnataka,…

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JetBrains’ Big Data Tools 1.6 keeps track of Flink jobs

Big Data tools 1.6, a plug-in for accessing Zeppelin notebooks, can now also monitor Apache flink and integrate the Hive Metastore. jetbrains has updated the Big Data Tools. In version 1.6, the plug-in for the IDEs IntelliJ IDEA Ultimate, DataGrip, DataSpell and PyCharm Professional offers bug fixes and general improvements…

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(Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData

(Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData 0 I have a question regarding re-clustering after removing cells using SubsetData (R – Seurat package). I am in the process of analyzing a relatively large single-cell dataset (16 separate samples of ~5-10k cells each). In our first…

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Researchers assess the evolution and diversity of monkeypox virus genomes using phylogenomic analysis

In a recent study published in Travel Medicine and Infectious Disease, researchers phylogenomically analyzed the monkeypox virus (MPXV). Study: Phylogenomic analysis of the monkeypox virus (MPXV) 2022 outbreak: Emergence of a novel viral lineage? Image Credit: ART-ur/Shutterstock Background Since May 2022, there have been various reports of increasing MPVX infections…

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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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Postdoctoral Research Associate – Bioinformatics in Boston, MA for Northeastern University

Details Posted: 13-Jul-22 Location: Boston, Massachusetts Type: Full-time Salary: Open Postdoctoral Research Associate – Bioinformatics About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented…

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Postdoctoral Research Associate – Bioinformatics job with Northeastern University

Postdoctoral Research Associate – Bioinformatics About the Opportunity We are seeking a creative scientist with a background in computational biology and microbiology to work on a genomics analysis-based antibiotic discovery project. The successful applicant will join a team of talented researchers at the Antimicrobial Discovery Center. Several drug lead candidates…

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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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The evolutionary origin of host association in the Rickettsiales

Salje, J. Cells within cells: Rickettsiales and the obligate intracellular bacterial lifestyle. Nat. Rev. Microbiol. 19, 375–390 (2021). CAS  PubMed  Article  Google Scholar  Wang, S. & Luo, H. Dating Alphaproteobacteria evolution with eukaryotic fossils. Nat. Commun. 12, 3324 (2021). CAS  PubMed  PubMed Central  Article  Google Scholar  Strassert, J. F. H.,…

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GEDmatch | segment-ology

A Segment-ology TIDBIT Genetic Genealogy has two main parts: genetic – the Shared DNA Segments; and genealogy – the Most Recent Common Ancestor (MRCA) with a Match. In a perfect world we link a Match and his/her Shared DNA Segment to the MRCA who passed it down to both of…

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Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

Cell-type annotation scRNA-seq data were filtered to discard low-quality cells and doublets (Supplementary Fig. 1, Extended Data Fig. 1 and Methods). Supervised clustering (Reference Component Analysis v2 (RCA2)) at low resolution grouped cells into 11 major cell types (Extended Data Fig. 1). To identify epithelial cell subtypes, we initially analyzed…

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Immune Infiltration and N(6)-Methyladenosine ncRNA Isoform Detection in Acute Lung Injury

Acute lung injury (ALI) is a severe form of sepsis that is associated with a high rate of morbidity and death in critically ill individuals. The emergence of ALI is the result of several factors at work. Case mortality rates might range from 40% to 70%. Researchers have discovered that…

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scikit learn – python clustering package that can cluster based in distance matrix but also predict new row (without new clustering/distance matrix)

I am aware of various (sklearn) clustering algorithm that work with distance matrices – e.g. produced via a proximity matrix coming from a random forest (some clumsy reproducible code below). Is there any clustering algorithm (working with distance matrix), where the fitted cluster model (e.g. cluster_model below) can produce the…

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Genetic diversity of loquat (Eriobotrya japonica) revealed using RAD-Seq SNP markers & More Science News

Our research analyzed the genetic diversity of 95 cultivars and strains of loquat collected from everywhere in the world. On the premise of the evaluation of the inhabitants construction of 19 Chinese loquat cultivars and strains by RAD-Seq, Hubei Province in China has been recommended as the middle of origin…

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Hubble captures a galactic menagerie

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

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Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer

Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…

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Joint analysis of functionally related genes yields further candidates associated with Tetralogy of Fallot

Bailliard F, Anderson RH. Tetralogy of Fallot. Orphanet J Rare Dis. 2009;4:2. Article  Google Scholar  Jin SC, Homsy J, Zaidi S, Lu Q, Morton S, DePalma SR, et al. Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet. 2017;49:1593–601. CAS  Article  Google Scholar …

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LncRNA Sequencing Helps to Find Deep Links to Disease

Long non-coding RNAs (lncRNAs) are a class of RNAs that do not code for proteins and are typically greater than 200 nucleotides in length. Studies have shown that lncRNAs are quite complex in function and play an important role in various biological processes such as development, differentiation, proliferation, metastasis, apoptosis,…

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minimum number of protein sequences for a sequence logo

minimum number of protein sequences for a sequence logo 1 Hi, I’m interested in generating sequence logo of a series of defensin related proteins I’ve clustered using CD-Hit. There are aproximately 7600 sequences with about 2500 clusters, but many of them have few sequences per cluster. Which is the minimum…

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Frontiers | Divergence With Gene Flow and Contrasting Population Size Blur the Species Boundary in Cycas Sect. Asiorientales, as Inferred From Morphology and RAD-Seq Data

Introduction Incipient species are critical for evolutionary biologists to study speciation, but they also challenge taxonomy due to gene flow or ancestral polymorphism. The former and contrasting population size lead to larger intraspecific than interspecific variations, a phenomenon called the species-definition anomaly zone (Jiao and Yang, 2021). The latter results…

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Assistant Professor of Bioinformatics in Charlotte, NC for The University of North Carolina at Charlotte

Details Posted: 07-May-22 Location: Charlotte, North Carolina Salary: Open Categories: Academic/Faculty Medical – Research Position Number: 003980 Department: Coll of Computing&Informatics (Col) Employment Type: Permanent – Full-time Months Per Year: 9 Essential Duties and Responsibilities: The successful candidate will mentor and teach at both the undergraduate and graduate levels.  This…

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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…

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

Quantification of similarity between scRNA-seq datasets? : bioinformatics

I’m using a mouse model which has been used in a couple previous scRNA-seq studies, but I’ve added a novel treatment. I’m trying to determine the similarity between these previous studies and mine to determine how much our treatment affected the cell states. I am not looking to integrate the…

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DMRs, how common are they and how long?

DMRs, how common are they and how long? 1 Hi! Does anyone know how common differentially methylated regions (DMRs) (or just methylated regions) are? Say, in a 10,000bp region how many DMRs can one expect? Also, does anyone know about the distribution of the size/length of DMRs, i.e. how many…

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Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

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Mitogenome-wise codon usage pattern from comparative analysis of the first mitogenome of Blepharipa sp. (Muga uzifly) with other Oestroid flies

Outcome of DNA sequencing, assembly, and validation In this study, initially total DNA was isolated from the finely chopped, full-grown pupa of Blepharipa sp. The NanoDrop spectrophotometer (1294 ng/μl) and the Qubit fluorometer (732.8 ng/μl) both found that the concentration of total DNA in the sample at an optimum level for mitochondrial DNA enrichment. The Tape Station profile showed…

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All vs All blast not self hit? Orthogroup clustering and single copy genome?

Hey guys Self hit I have this actually a bit weird question about blast. I’ve been doing some work around single copy genome construction using Reciprocal best blast hit (RBBH) method. As I have something like 100+ annotated genome, I concatenated all annotated CDS into one fasta and makeblastdb with…

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Endometriosis-related functional modules and hub genes

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

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Genomic Analysis Reveals a New Dominant Lineage of SARS-CoV-2

Scientists and health officials throughout the world are raising the alarm about the emergence and spread of more COVID variants, subvariants and third generation subvariants with the worrying mutations, which have been linked to increased fusogenicity, illness severity, and death. Infectivity and transmissibility have also grown in these new BA.2 subvariants…

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CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology

Bartel, D. P. MicroRNAs: Target recognition and regulatory functions. Cell 136, 215–233 (2009). CAS  Article  Google Scholar  Bassett, A. R. et al. Understanding functional miRNA–target interactions in vivo by site-specific genome engineering. Nat. Commun. 5, 4640 (2014). ADS  CAS  Article  Google Scholar  Moore, M. J. et al. miRNA–target chimeras reveal…

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N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research

Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…

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How to link GCP VM disks allocated by dynamic pvc-HEXHEXHEX and `claim-username` again after irrevocably losing all kubernetes yaml? – Zero to JupyterHub on Kubernetes

TL;DR I destroyed my claim-usernames on a prod cluster deployed using current z2jh, and have a mob of nervous scientists scared they lost their data… how do I go about rebinding a hundred disk-HEXHEX GCP VM disks to the appropriate jupyterhub users? In the process of finally deploying / converting…

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Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

Sampling Six dioecious fig species (F. erecta, F. formosana, F. vaccinioides, F. abelii, F. pyriformis, and F. variolosa) and their pollinator wasp species were examined in this study. As mentioned in the Introduction, these fig species were considered to be well suited for this study because they are distributed in…

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Bioinformatics Pipeline Development Engineer II at Personalis, Inc

Personalis, Inc. is a leader in advanced cancer genomics for enabling the next generation of precision cancer therapies and diagnostics. The Personalis NeXT Platform® is designed to adapt to the complex and evolving understanding of cancer, providing its biopharmaceutical customers and clinicians with information on all of the approximately 20,000 human genes,…

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Genetic characteristics involving the PD-1/PD-L1/L2 and CD73/A2aR axes and the immunosuppressive microenvironment in DLBCL

Key messages What is already known on this topic Targeting immunosuppressive pathways have emerged as promising strategies for cancer treatment. The genetic characteristics of PD-1/PD-L1/L2 (programmed cell death protein 1/programmed cell death ligand 1/ligand 2) and CD73/A2aR (A2a adenosine receptor) and the effect of these two signalings on dysfunctional CD8+…

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Single-Cell Technology Measures Epigenetic States and Gene Expression in One Go

Advances in single-cell technologies have not only made it possible to analyze multiple molecular families in individual cells, they have also enabled scientists to parse through limitations in data analysis arising from the intercellular diversity of measured parameters. Although single-cell sequencing is now widely available, techniques to detect epigenetic markers…

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rna seq – How will Seurat handle pre-normalized and pre-scaled data?

I don’t do transcriptome analysis, it ain’t my thing, however I do understand statistical analysis as well as the underlying issue regarding the public availability of molecular data … I agree with the OP its not ideal. However, yes the OP can continue with ‘clustering’, personally I definitely prefer it…

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Database for scATAC-seq datasets similar to ENCODE? : bioinformatics

Does anyone know of any public scATAC-seq databases? Up until now I’ve been using the scATAC.Explorer library in R to get my scATAC datasets, but there doesn’t seem to be a fragment file associated with any of the experiments. I’d like to plot some gene activity matrices/coverage plots. Alternatively, if…

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deeptools plotHeatMap – Convert bed files to gene list?

I might suggest limiting your search to genes: gtf2bed < Mus_musculus.GRCm38.102.gtf | grep -w “gene” > sorted-mm10.genes.bed But that’s up to you. Otherwise, I think you may also get transcripts/exons, which may be more than you want. Again, up to you. If hnf4a-ko-downreg-clusters.bed is the file containing peaks, as described…

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2D and 3D Human Induced Pluripotent Stem Cell-Based Models to Dissect Primary Cilium Involvement during Neocortical Development

We present detailed protocols for the generation and characterization of 2D and 3D human induced pluripotent stem cell (hIPSC)-based models of neocortical development as well as complementary methodologies enabling qualitative and quantitative analysis of primary cilium (PC) biogenesis and function. The overall goal of the procedure we detail here is…

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One-step induction of photoreceptor-like cells from human iPSCs by delivering transcription factors

Introduction of CRX and NEUROD1 using piggyBac vector into iPSCs and differentiation to induced photoreceptor-like cells (iPRCs) (A) Design of polycistronic piggyBac vector for CRX and NEUROD1 mediated conversion under control of the tetracycline operator rtTA and neomycin resistance gene. Dox: doxycycline, rtTA: reverse tetracycline transactivator, neo: neomycin resistance gene….

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LAMMPS Patch Release 24 March 2022

LAMMPS Patch 24 March 2022 Release Overview What is LAMMPS used for? LAMMPS is a classical molecular dynamics (MD) code that models ensembles of particles in a liquid, solid, or gaseous state. It can model atomic, polymeric, biological, solid-state (metals, ceramics, oxides), granular, coarse-grained, or macroscopic systems using a variety of…

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Clustalo failing to complete multiple sequence alignments

Clustalo failing to complete multiple sequence alignments 0 Hi, I have been using clustalo in the terminal to create multiple sequence alignments for the past few weeks, but every time I try lately it fails. I’ve tried on two computers, with different files. I’ve tried looking up the errors but…

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Genomic sequencing aids the global tuberculosis fight

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

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H100 Transformer Engine Supercharges AI Training, Delivering Up to 6x Higher Performance Without Losing Accuracy

The largest AI models can require months to train on today’s computing platforms. That’s too slow for businesses. AI, high performance computing and data analytics are growing in complexity with some models, like large language ones, reaching trillions of parameters. The NVIDIA Hopper architecture is built from the ground up…

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DataViz question for DEG and scRNA-seq

DataViz question for DEG and scRNA-seq 1 Maybe a dumb question, but I recently came across a single-cell paper that showed “volcano” plots for all clusters in one image by filtering for all genes that were FDR <0.05, the x-axis being represented by different colors characterizing different clusters, the y-axis…

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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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Genetic diversity of common carp (Cyprinus carpio L.) strains breed in Poland based on microsatellite, AFLP, and mtDNA genotype data.

Abstract Abstract The common carp (Cyprinus carpio L.) has a long-standing history in Polish pond aquaculture, which has given rise to a great number of local breeds, strains and hatchery populations. They are well adapted to their local conditions, play an important role for fisherman’s livelihoods and…

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Google Researchers Use Machine Learning Approach To Annotate Protein Domains

Source: www.nature.com/articles/s41587-021-01179-w.epdf Proteins play an important part in the construction and function of all living organisms. Each protein is made up of a chain of amino acid building blocks. Much like an image might have numerous things, a protein can have multiple components, known as protein domains. Researchers have been…

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Transcriptional kinetics and molecular functions of long noncoding RNAs

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

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Role of mobile genetic elements in the global dissemination of the carbapenem resistance gene blaNDM

Wu, W. et al. NDM metallo-β-lactamases and their bacterial producers in health care settings. Clin. Microbiol. Rev. 32, e00115–18 (2019). Yong, D. et al. Characterization of a new metallo-β-lactamase gene, bla NDM-1, and a novel erythromycin esterase gene carried on a unique genetic structure in Klebsiella pneumoniae sequence type 14…

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Identification of Hub Genes Associated with COPD Through Integrated Bi

Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…

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Research Associate job with KINGS COLLEGE LONDON

Job description A Postdoctoral Research Associate (PDRA) – Computational biology position is available in the Centre for Gene Therapy and Regenerative Medicine, King’s College London. This is an exciting opportunity to join an interdisciplinary team of scientists working on a Wellcome Trust funded research programme aimed at studying the mammalian…

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Change of protein-protein-interaction free energy upon ligand binding (procedure and controls) – User discussions

GROMACS version: 2021.1GROMACS modification: No Dear Gromacs and simulation community, in the course of my master’s thesis, I want to determine the protein-protein-binding free energy between two GTPases using PMF calculations via umbrella sampling. Especially I am interested in the contribution of the bound nucleotides (one per protein) which are…

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Top 50 H20 interview questions and answers

H20 interview questions and answers 1) What is AutoML in H2O? H2O’s Automatic Machine Learning (AutoML) H2O is a fully open-source, distributed in-memory machine learning platform with linear scalability. … H2O AutoML can be used for automating the machine learning workflow, which includes automatic training and tuning of many models…

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In vitro Assessment of Cardiac Reprogramming by Measuring Cardiac Specific Calcium Flux with a GCaMP3 Reporter

We describe here, the establishment and application of an Tg(Myh6-cre)1Jmk/J /Gt(ROSA)26Sortm38(CAG-GCaMP3)Hze/J (referred to as αMHC-Cre/Rosa26A-Flox-Stop-Flox-GCaMP3 below) mouse reporter line for cardiac reprogramming assessment. Neonatal cardiac fibroblasts (NCFs) isolated from the mouse strain are converted into induced cardiomyocytes (iCMs), allowing for convenient and efficient evaluation of reprogramming efficiency and functional maturation…

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AutoKinship at GEDmatch by Genetic Affairs

Genetic Affairs has created a new version of AutoKinship at GEDmatch. The new AutoKinship report adds new features, allows for more kits to be included in the analysis, and integrates multiple reports together: AutoCluster – the autoclusters we all know and love AutoSegment – clusters based on segments AutoTree –…

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r – How to subset (or filter?) taxa in a phyloseq object, within a grouping?

I am attempting to subset (or filter?) taxa that have relative abundance >= 35%,and belong in >= 70% of samples within a grouping (in my case it is the number of ‘clusters’ in my data). Is there a simple line of code on how to do this? I have started…

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Fatty infiltration after rotator cuff tear

Introduction Rotator cuff tear (RCT) is a common shoulder disorder causing shoulder pain and disability. The prevalence of full-thickness RCT is 20.7% in the general population, and increased with age.1 Rotator cuff play essential roles in shoulder function and the treatment of proximal humeral fractures.2,3 It is important to repair…

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Genomic analysis on Galaxy using Azure CycleCloud

Cloud computing and digital transformation have been powerful enablers for genomics. Genomics is expected to be an exabase-scale big data domain by 2025, posing data acquisition and storage challenges on par with other major generators of big data. Embracing digital transformation offers a practically limitless ability to meet the genomic…

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NetApp provides data infrastructure for EMBL

The European Molecular Biology Laboratory (EMBL) is running a data lake across two datacentre sites, based on NetApp storage, to support scientific research. Modern scientific research is heavily dependent on big data analysis and increasingly relies on artificial intelligence (AI)-based methods. EMBL’s research groups develop their own AI models,…

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r – Reorder and split the ggplot heatmap based on the clusters in one of the columns

I generated a heatmap with ggplot, and order the samples by using hclust, However, I still need more reordering to get all the similar values corespondent with one of the samples in the ordered cluster. Here I generate a samples data to explain better. set.seed(99) M <- data.frame(names = paste0(“g”,…

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Vertical stratification of the air microbiome in the lower troposphere

Significance Large-scale meteorological and biological data demonstrate the vertical stratification of airborne biomass. The previously described diel cycle of airborne microorganisms is shown to disappear at height. Atmospheric turbulence and stratification are shown to be defining factors for the scale and boundaries, dynamics, and natural variability of airborne biomass, resulting…

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