Tag: RNA

Integration of RNA seq data aligned to different reference genome versions 0 Hi all, I would like to integrate a bulk RNA seq and an scRNA seq dataset. The data was already provided as count matrices, but unfortunately, the bulk RNA seq data was aligned to hg38 whereas the scRNA…

Low featurecounts assignment rate 0 Hi all, I am currently running QC, trimming, and alignment steps on bulkseq RNA mouse samples (lung from diabetic vs. wildtype). For each sample, I received R1 & R2 reads. The alignment runs alright, but once I put the sorted BAM files into FeatureCounts I…

The Vlachos Lab and the Spatial Technologies Unit (www.spatialtechnology.org) are currently looking for talented postdoctoral researchers to lead large-scale spatial/single cell initiatives within our research program as well as to devise novel computational methods that will enable us to bring these two novel technologies closer to translation. The researcher will…

Abstract In virtually all eukaryotes, the mitochondrial genome (mitochondrial DNA, mtDNA) encodes proteins necessary for oxidative phosphorylation (OXPHOS) and the RNA machinery required for their synthesis inside the mitochondria. Appropriate regulation of mtDNA copy number and expression is essential for ensuring the correct stoichiometric formation of OXPHOS complexes assembled from…

Broadcast Date: April 14, 2023Time: 8:00 am PT, 11:00 am ET, 17:00 CET In recent years, single-cell RNA sequencing has transformed our understanding of cellular heterogeneity within highly complex tissues and organs, revealing thus far undiscovered cell types and states and characterizing perturbations in disease. However, despite the advances in single-cell technologies,…

Uncover the mysteries of RNA dysregulation in cancer Our understanding of the complex biology of cancers is currently limited by the sequencing technology that we have available. For example, a study previously published in Science Advances showed that short-read based RNA-seq approaches only capture a faction of RNA isoforms that…

Gene Editing Tool Market Allied Market Research Analyst have added a new research study on Title Gene Editing Tool Market, Global Outlook and Forecast 2023-2030 with detailed information & Key Players Such as Thermo Fischer Scientific Inc., Horizon Discovery Group plc, Merck KGaA, Genscript Biotech Corporation, Sangamo Therapeutics Inc., Lonza…

Researchers from Germany, Portugal, and Canada reporting in Nature Ecology and Evolution outline gut microbial community shifts in two wild seabird species subjected to microplastics in the environment. The team turned to 16S ribosomal RNA sequences to profile the microbiome communities within cloaca and proventriculus organ samples from dozens of…

Introduction Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma, accounting for 30% of non-Hodgkin’s lymphoma. Approximately 150,000 new cases are diagnosed annually worldwideCitation1. DLBCL is characterized by heterogeneity, aggressiveness, and frequent relapse or resistance to chemotherapyCitation2. Due to the heterogeneity of DLBCL, the immunological, pathological, molecular, and genetic…

Role: Oncology Bioinformatics Genomic Data Analyst Location: SFO, CA ( 3-4 days Onsite) Type: 10-12 months+ We are seeking a highly experienced Genomic Data Analyst to support computational research within our Oncology Bioinformatics department focused on Reverse Translation efforts in Cancer Immunology. This role will focus on applying statistical and…

Kirchberger PC, Schmidt ML, Ochman H. The ingenuity of bacterial genomes. Annu Rev Microbiol. 2020;74:815–34. Article  CAS  PubMed  Google Scholar  Rodríguez-Gijón A, Nuy JK, Mehrshad M, Buck M, Schulz F, Woyke T, et al. A genomic perspective across Earth’s microbiomes reveals that genome size in Archaea and Bacteria is linked…

The enteric adenovirus types F40 and 41 (EAdVs) have lately been implicated in the development of acute hepatitis in children and are a major contributor to diarrhea and diarrhea-related mortality in children below the age of 5. EAdVs show a clear preference for the gastrointestinal tract, but other adenovirus types…

Ross, J., Jiang, H., Kanost, M. R. & Wang, Y. Serine proteases and their homologs in the Drosophila melanogaster genome: An initial analysis of sequence conservation and phylogenetic relationships. Gene 304, 117–131 (2003). Article  CAS  PubMed  Google Scholar  Rawlings, N. D. & Barrett, A. J. Evolutionary families of peptidases. Biochem….

Exogenous expression of the transcription factors Pdx1, Neurog3, and MafA in human fibroblasts We first sought to examine whether the transcription factors Neurog3, Pdx1, and MafA could induce expression of the INSULIN (INS) gene in human fibroblasts as readout of the capacity of these cells to be transformed toward a…

LONDON–(BUSINESS WIRE)–Mar 28, 2023– Silence Therapeutics plc, Nasdaq: SLN (“Silence” or “the Company”), an experienced and innovative biotechnology company committed to transforming people’s lives by silencing diseases through precision engineered medicines, today announced it will be acquiring back exclusive worldwide rights to two siRNA drug targets under the collaboration agreement…

ReportLinker The whole exome sequencing market is expected to register a CAGR of 22.1% over the forecast period. The outbreak of the COVID-19 pandemic pushed the pharmaceutical industry into action, with a race to develop therapeutic and preventive interventions. New York, March 20, 2023 (GLOBE NEWSWIRE) — Reportlinker.com announces the…

            Speaker: Zakayo Kazibwe, genetics, development and cell biology graduate student in Bassham Lab Title: “Exploring the association between nucleotide homeostasis and TOR-mediated autophagy responses in rRNA turnover-defective Arabidopsis mutants”   Abstract: To maintain cell viability, organisms degrade aberrant, nonfunctional or old cell components and…

When to merge multiple fastq files into one for RNAseq analysis? 1 I’m a little confused on the files I am trying to analyze and so I just wanted to doublecheck on here before proceeding if that’s okay: For each RNA-seq sample (paired end sequencing), the sequencing core gave back…

Research reported in this study complies with all relevant ethical regulations, and our animal study protocol has been approved by the Animal Experimental Board of Finland (license number ESAVI/28687/2020. Phage panning Sherpabody phage display library (size ~1011 cfu) was obtained from Next Biomed Therapies Oy. To develop sherpabodies specific for SARS-CoV-2…

The specific assay and tissue types for each dataset are indicated with network clustering based on hardware. See Supplementary Data 1 and 2 for the Matrix driving this visualization. Note the hardware used to analyze plant response to spaceflight often defines the types of tissue that are available and so…

Payroll Title:BIOINFORMATICS PROGR 1 Department:MEDICINE/Cardiology Hiring Pay Scale$25.67 – $33.00 / Hour Worksite:Campus Appointment Type:Career Appointment Percent:100% Union:Uncovered Total Openings:1 Work Schedule:Days, 8 hrs/day, Mon – Fri #122294 Bioinformatics Programmer IFiling Deadline: Fri 4/7/2023 Apply Now UC San Diego values equity, diversity, and inclusion. If you are interested in…

TbRAP1 interacts with the active VSG RNA in vivo RAP1 homologs have been identified from kinetoplastids to mammals21. None of the known RAP1 homologs has been reported to have any RNA binding activity. We previously found that TbRAP1 does not bind the telomeric repeat-containing RNA (TERRA) in RNA IP experiments22,23,24….

An analysis of 400 pancreatic cancer tumor samples has linked a protein that controls RNA processing to the formation of metastases, suggesting that it may be possible to delay the spread of the cancer. Evaluations of pancreatic cancer genomes have uncovered four genes that drive the initial formation of the…

1. Introduction Cancer is one of the main causes of death around the world, with the most significant being lung, liver, stomach, colon, and breast cancers. As a major concern, the dissemination of metastases is responsible for more than 90% of deaths by cancer. Tumor cells spread by lymphatic and…

TileDB database first to implement an open data model and API specification, enabling rapid cloud-optimized analysis of large single-cell datasets CAMBRIDGE, Mass., March 28, 2023–(BUSINESS WIRE)–TileDB, the database for any complex data and compute, today announced the launch of TileDB–SOMA, the first collection of software libraries that implement the open-source…

The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group established in 2016, with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient samples. Led by director, Simon Gayther, PhD, the primary goals of the CBFG are to…

Details Posted: 28-Mar-23 Location: La Jolla, California Salary: Open UCSD Layoff from Career Appointment: Apply by 03/28/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 04/07/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position…

When patients begin to experience chest pain or shortness of breath while exercising, doctors may struggle to correctly diagnose if the problem is caused by coronary artery disease. Classic symptoms of heart disease such as chest pain and shortness of breath are nonspecific and may stem from other medical issues…

Naik RR, Singamaneni S. Introduction: bioinspired and biomimetic materials. Chem Rev. 2017;117(20):12581–3. Article  CAS  PubMed  Google Scholar  Huang G, Li F, Zhao X, Ma Y, Li Y, Lin M, et al. Functional and biomimetic materials for engineering of the three-dimensional cell microenvironment. Chem Rev. 2017;117(20):12764–850. Article  CAS  PubMed  PubMed Central …

NEW YORK – Riding the wave of recent technological advancements in long-read sequencing, single-cell RNA isoform analysis has not only become feasible but is snowballing into a thriving field. The approach, based on the ability of long-read platforms to capture full-length transcriptomes, allows scientists to take a closer looker at…

C. elegans strains All strains were cultured under standard conditions78 and were always incubated at 20 °C during the experiments. The strains used were N2 (Bristol; WT): DREAM: MT8839 lin-52(n771) III, MT10430 lin-35(n745) I, MT15107 lin-53(n3368) I/hT2 [bli-4(e937) let-?(q782) qIs48] (I;III), MT8879 dpl-1(n2994) II, MT11147 dpl-1(n3643) II, JJ1549 efl-1(se1) V, BJS634…

Structure-based identification of a small-molecule PAF1 complex (PAF1C) inhibitor that impairs PAF1 chromatin localization and releases RNA Pol II. (A) Schematic representation of the structure-based identification of small-molecule disruptors of PAF1 and CTR9 interactions using in silico screen followed by RNA Pol II ChIP-seq screening. iPAF1C binding residues of CTR9…

Schematic of the experimental workflow employed in this study. A sample of gDNA extracted from each strain of each species was split in order to prepare parallel sequencing libraries for both long-read (PacBio RSII) and short-read (Illumina MiSeq) sequencing. Biological replicates for transcriptomics, proteomics, and metabolomics were generated from a…

Hi, I am performing RNA-seq analysis on 12 samples. After mapping the reads with Hisat2, I want to count the number of reads using feaureCounts, but I reencountered a problem in reading the gff file downloaded from TAIR. (I also tried downloading it from Ensmbl, but no difference). featureCounts -p…

Time change in expression vs time change in phenotype 0 Hello everyone; We have a prospective study for which at two time points (t1,t2) we collected blood samples and some quantitative traits Q. Using DESeq2, we can ask if the blood gene expression E at t1 or t2 is associated…

Nextflow rnaseq finishing early 0 Hi I’m running the RNA-seq pipeline from nextflow and I have been running it without problems until this dataset it just stops prematurely saying it has finished when it doesn’t even aligns the reads with salmon. Any ideas what may be going on? I have…

differential gene analysis 0 hello! i am working on differential gene expression of cell free RNA… In this process i have created the count matrix then calculated the log of count per matrix further calculated the Z_score and calculate the variance using log and created the boxplots…so these 2 boxplots…

Cancer Breast cancer (BC) is a prevalent form of cancer among women globally. Recent studies suggest that circular RNA (circRNA) plays a significant role in BC progression, but the biological functions and underlying mechanisms remain unexplored. According to a recent study published in the Journal of Translational Medicine, the interaction…

Job Description Bioinformatics Scientist R0135789 University of Nevada, Reno – Main Campus The University of Nevada, Reno (UNR) appreciates your interest in employment at our growing institution. We want your application process to go smoothly and quickly. Final applications must be submitted prior to the close of the recruitment. If…

OraSure’s Colli-Pee® First-Void Urine Collection and Preservation Device and nRichDX Revolution Sample Prep System for cfDNA Extraction IRVINE, Calif., March 27, 2023 /PRNewswire/ — nRichDX and OraSure Technologies, Inc., have advanced a commercial collaboration to validate and co-promote their products for researchers developing liquid biopsy applications using first-void urine samples. Notably,…

Link products to their genes 0 Hello everyone, In my gff/gtf files, I have complete product names (proteins) for the up/down-regulated genes, and my edfeR-generated csv file contains only the gene_IDs and their statistics. After checking both gff/gtf files, I found that they only contain complete product names but not…

In the past few years, our company absorbed and digested advanced technologies both at home and abroad. Meanwhile, our company staffs a team of experts devoted to the development of Bioinformatics Companies , Otu , Competing Endogenous Rna , Sincerely hope we are growing up together with our customers all…

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease. At present, the mechanism of non-coding RNA in renal injury in SLE patients is still unclear. A total of 64 DEcircRNAs, 75 DEmiRNAs, and 249 DEmRNAs were identified. We integrated 10 circRNAs, 10 miRNAs, and 88 target mRNAs into a circRNA-miRNA-mRNA…

Massive parallel sequencing uncovers actionable FGFR2-PPHLN1 fusion and ARAF mutations in intrahepatic cholangiocarcinoma – Fingerprint — Icahn School of Medicine at Mount Sinai Sort by Weight Alphabetically Physics & Astronomy sequencing 80% mutations 69% fusion 47% cancer 41% oncogenes 26% prognosis 21% harbors 18% inhibitors 17% liver 16% ducts 14%…

Dispersal is a key process in ecology and evolutionary biology, as it shapes biodiversity patterns over space and time. Mounting evidence is showing that attitude to disperse is unevenly distributed among individuals within animal populations, and that individual personality can have pivotal roles in the shaping of this attitude. Here,…

1. Introduction Neuroendocrine tumors (NETs) are a heterogeneous group of tumors originating from neuroendocrine cells and harbor malignant potential [1,2]. The incidence of NETs is becoming more common worldwide, and their characteristics and behavior can vary widely [1,2]. The incidence of gastrointestinal NETs depends on the primary tumor site, with…

Abstract Large-scale short hairpin RNA (shRNA) screens on well-characterized human cancer cell lines have been widely used to identify novel cancer dependencies. However, the off-target effects of shRNA reagents pose a significant challenge in the analysis of these screens. To mitigate these off-target effects, various approaches have been proposed that…

DOI: 10.18129/B9.bioc.scRNAseq   This is the development version of scRNAseq; for the stable release version, see scRNAseq. Collection of Public Single-Cell RNA-Seq Datasets Bioconductor version: Development (3.17) Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata. Author: Davide Risso [aut, cph],…

Trajectory analysis using Monocle3 with Seurat sub-clustering 0 Hi all, I am analyzing single cell RNA-seq data using Seurat and trying to do trajectory analysis using Monocle3. My analysis pipeline is below. # QC, NormalizeData, FindVariableFeatures for each sample independetly SelectIntegrationFeatures > FindIntegrationAnchors > IntegrateData > > ScaleData > RunPCA…

News:The Canadian Bioinformatics Workshops are back for summer 2023 0 After a hiatus in 2022, the Canadian Bioinformatics Workshops are back! We will be offering the following workshops in 2023: Infectious Disease Genomic Epidemiology: April 18-21, virtual Pathway and Network Analysis: June 5-7, Toronto Introduction to R: June 26-27, Toronto…

Error parsing strand (?) from GFF line 0 I am trying to assemble RNA transcripts using stringtie and facing the following error. Error parsing strand (?) from GFF line: NC_037304.1 RefSeq gene 58315 59481 . ? . ID=gene-DA397_mgp34;Dbxref=GeneID:36335702;Name=nad1;exception=trans-splicing;gbkey=Gene;gene=nad1;gene_biotype=protein_coding;locus_tag=DA397_mgp34;part=2 my comand is : stringtie -p 8 -G Genome/arab_thaliana.gtf -o Assemble/NR1.gtf –l…

News:Next-Generation Sequencing Data Analysis: A Practical Introduction (May 3-5, 2023 in Munich, Germany) 0 📣Attention all biologists! 🧬 Are you interested in expanding your knowledge in Next-Generation Sequencing (NGS) and bioinformatics? 🧐 Look no further! We are excited to announce our upcoming hands-on workshop on NGS Data Analysis from May…

Kallisto bustools for scRNA-seq 0 Hi, I followed several tutorials about single cell rna-seq analysis for paired end. However, I need to quantify single ends scRNA-seq dataset. I have used for paired ends. Does anyone know how to use kallisto scrna-seq for single ends? I am open to other suggestions….

Tool:BioLabImage – Mac program for DNA/RNA/protein gel/blot, cells/colonies image analysis 0 BioLabImage is a tool for the analysis of DNA/RNA/protein gel/blot images as wells as cells/colonies images. The app provides automatic measurement of relative fold-change of the selected bands on the gel/blot images. The user can automatically count the bacteria/yeast…

Part of NVIDIA AI Foundations, New BioNeMo Cloud Service Accelerates Life Sciences Research, Drug Discovery and Protein Engineering; Amgen and a Dozen Startups Among Early Access Customers GTC—NVIDIA today announced an expanded set of generative AI cloud services for customizing AI foundation models to accelerate the creation of new proteins…

Multiple proteins are required to maintain the fidelity of transcription in yeast Using genetically engineered yeast strains21,36,37 and massively parallel sequencing technology34,35, we and others previously demonstrated that the non-essential subunits Rpb9 and TFIIS enhance the fidelity of transcription of RNAPII in living cells16,21,26,34,35,36,37,38,39. In addition, we showed that the…

TreeFrog Therapeutics is leaping ahead in cell therapies through resources such as new technologies and investor partnerships. For more than a decade, manufacturers have been exploring new ways to improve the efficiency of cell therapy production to make it more cost-effective and accessible to those in need. Many companies have…

PRESS RELEASE Published March 24, 2023 Reports and Insights freshly added a report titled “Central Labs Market: Opportunity Analysis and Future Assessment 2023-2031” in its database of market research reports which offers its readers a detailed and profound analysis on the fresh growth opportunities, trends and growth drivers that are…

Falkowski, P. G., Barber, R. T. & Smetacek, V. Biogeochemical controls and feedbacks on ocean primary production. Science (1979) 281, 200–206 (1998). CAS  Google Scholar  Nemergut, D. R. et al. Patterns and processes of microbial community assembly. Microbiol. Mol. Biol. Rev. 77, 342–356 (2013). Article  PubMed  PubMed Central  Google Scholar …

A fully supported postdoc position is immediately available at the Italian Institute of Technology (IIT) in Genova-Italy. The successful candidate will  work in a multi-disciplinary team and will analyze in-house produced multi-omic data aiming to understand the role of non-coding RNAs in mediating 3D chromatin architecture in embryonic stem cells…

Apply HERE: www.seek.com.au/job/66338853?type=standout#sol=7aa1e7675337a8352fbe779962671540ecd67524 Company description: Peter MacCallum Cancer Centre Job description: Outstanding candidates are encouraged to apply for positions now open at Peter MacCallum Cancer Centre – a place where our normal days are extraordinary; as are the people we care for. Peter Mac is one of a handful of…

Dublin, March 21, 2023 (GLOBE NEWSWIRE) — The “Transfection Reagents and Equipment Market by Product, by Method, by Application, by End User, and by Region – Global Forecast to 2022-2033” report has been added to ResearchAndMarkets.com‘s offering. The transfection reagents and equipment market size are estimated to be USD 1,147.2…

China has approved its first Covid-19 vaccine based on mRNA technology, months after the country lifted strict pandemic measures. The vaccine was developed by CSPC Pharmaceutical Group, a homegrown firm based in the northern Chinese city of Shijiazhuang, it said in a Wednesday statement to the Hong Kong stock exchange….

Description: The German Center for Neurodegenerative Diseases (DZNE) is a world-leading internationally oriented research center, committed to discovering new approaches to prevent and treat neurodegenerative diseases. To this end, researchers at ten DZNE sites across Germany pursue a translational and interdisciplinary strategy comprising five interconnected areas: fundamental research, clinical research,…

PRESS RELEASE Published March 24, 2023 mRNA Extraction and Purification Market to Record an Exponential CAGR by 2030 – Exclusive Report by InsightAce Analytic InsightAce Analytic Pvt. Ltd. has announced the publication of a market research report titled “Global mRNA Extraction and Purification Market– By Product (Kits/Reagents, Instruments) End-user (Academics…

In order to ensure the prevention and control of methicillin-resistant Staphylococcus aureus (MRSA) infection, rapid and accurate detection of pathogens and their resistance phenotypes is a must. Therefore, this study aimed to develop a fast and precise nucleic acid detection platform for identifying S. aureus and MRSA. We initially constructed…

An inside view on a platform that could help take RNA therapeutics to the next level of delivery Arthur T Suckow | 03/21/2023 | 5 min read It was during my PhD in Pharmacology at UC San Diego that I found my desire to launch a biotech company. Amazed by…

Multifactorial Design for DESEQ2 1 @b4de4377 Last seen 3 days ago Netherlands Hello community, I’m interested in conducting a DEG analysis to obtain differentially expressed genes based on treatment per cell line. In other words, determine the effect of condition per cell line and extract DEGs based on treatment. Overview…

Genetic redundancy in translational components is costly under nutrient poor conditions, but beneficial under nutrient rich conditions. Credit: Max Planck Society When viewed from an engineer’s perspective, biology is often messy and imperfect. For example, redundancy is a common feature of biological systems, with the job of one biological component…

Anti-Epithelial cell adhesion molecule (EpCAM) Aptamer(Cat#: CTApt-100) This product is an aptamer which binds to the Cancer stem cell marker epithelial cell adhesion molecule with an affinity of 54.5 nM . Specifications Target Category Protein Target Cancer stem cell marker…

Once more, we’re talking about the origins of SARS-CoV-2, the virus that causes COVID-19. First the US Department of Energy’s review gave more emphasis to the laboratory leak hypothesis than previously, although the confidence for this conclusion was low. Second, and more importantly, is the release and analysis this week…

Basillica di Santa Croce. Tomba di Galileo Galilei. Preamble Data challenging any scientific consensus that has been woven into a political fabric is frequently met with irrational hostility. In these circumstances it is prudent to make your hypothesis as easily reproducible as possible. When lives are at stake, waiting 6-12…

Abstract Common genetic variants confer substantial risk for chronic lung diseases, including pulmonary fibrosis (PF). Defining the genetic control of gene expression in a cell-type-specific and context-dependent manner is critical for understanding the mechanisms through which genetic variation influences complex traits and disease pathobiology. To this end, we performed single-cell…

Confused on strandedness, what are antisense transcripts? 1 Hello, I am trying to wrap my head around anti-sense transcripts. When looking at refseq’s annotations on IGV you can see a (-) or a (+) for each transcript. From reading this paper www.ncbi.nlm.nih.gov/pmc/articles/PMC3664467/#sec-2title I understand that transcription from the antisense strand…

FOR IMMEDIATE RELEASE Research from Johns Hopkins Kimmel Cancer Center experts revealed a type of RNA, previously considered to be “junk,”  that may help doctors distinguish and treat a subgroup of patients with medulloblastoma. Medulloblastoma is the most common malignant brain tumor in children, accounting for about 20% of all…

Tell me about making a transcriptome model of a specific tissue. 0 Student here, working on a project and wondering if I’m getting it right. I’m trying to make a model of a specific tissue in a model organism, in order to compare diseased tissue to it. I found about…

How to fix FreeBayes error “unable to find FASTA index entry for bed files” 0 I’m trying to use freebayes to call variants through the following parameters using RNA-Seq data: $freebayes –fasta-reference $ref \ –region $BED \ $bam \ ${outdir}/${sample}.freebayes.vcf and my bed files like this: chr1:11868-12227 chr1:12612-12721 chr1:12974-13052 chr1:13220-14501…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::11/03/2020 18:15:02 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline (PGAP) Annotation Method::Best-placed reference protein set; GeneMarkS-2+ Annotation Software revision::4.13 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::2,578 CDSs (total)::2,494 Genes (coding)::2,447 CDSs (with protein)::2,447 Genes (RNA)::84 rRNAs::7, 6, 6 (5S, 16S, 23S) complete rRNAs::7, 6, 6…

Böhm S, Fabian H, Welfle H (1982) Universal structural features of prokaryotic and eukaryotic ribosomal 5 S RNA derived from comparative analysis of their sequences. Acta Biol Med Ger 41:1–16 PubMed  Google Scholar  Dams E, Vandenberghe A, De Wachter R (1983) Sequences of the 5 S RNAs ofAzotobacter vinelandii, Pseudomonas…

Shuang Feng and James L. Manley Department of Biological Sciences, Columbia University, New York, New York 10027, USA Corresponding author: jlm2{at}columbia.edu Abstract Nucleoli are the major cellular compartments for the synthesis of rRNA and assembly of ribosomes, the macromolecular complexes responsible for protein synthesis. Given the abundance of ribosomes, there…

Mutations in genes that form the desmosome are the most common cause of the cardiac disease arrhythmogenic cardiomyopathy (ACM), which affects one in 2000 to 5000 people worldwide. Researchers from the group of Eva van Rooij now discovered how a mutation in the desmosomal gene plakophilin-2 leads to ACM. They…

Penev, Petar I.; Claudia Alvarez-Carreno; Eric Smith; Anton S. Petrov and Loren Dean Williams We have developed the program TwinCons, to detect noisy signals of deep ancestry of proteins or nucleic acids. As input, the program uses a composite alignment containing pre-defined groups, and mathematically determines a ‘cost’ of transforming…

The 18-genome data package To investigate the genome inversion landscape of Asian rice from a population structure perspective, we first combined a set of 16 previously published high-quality genomes32,33,34 that represent the K = 15 population structure of O. sativa, plus the largest Xian/indica (XI) admixed subpopulation (XI-adm: Minghui 63 (MH63)) to…

PRESS RELEASE Published March 24, 2023 InsightAce Analytic Pvt. Ltd. announces the release of a market assessment report on the “Global Single-Cell Bioinformatics Software and Services Market By Product (Bioinformatics Software and Bioinformatics Services), Application (Oncology, Immunology, Neurology, Non-invasive Prenatal Diagnosis (NIPD), Microbiology, and Other Applications), End-user (Research and Academic Institutes,…

how to know what adapter sequences to trim for RNA-seq? 0 Hello, I’m very new to RNA-seq analysis and am currently stuck on the trimming step. The libraries I am trying to analyze were built using the NEXTFLEX Rapid Directional RNA-seq kit with their Unique Dual Index Barcodes (perkinelmer-appliedgenomics.com/wp-content/uploads/2022/02/NOVA-51292X-NEXTFLEX-RNA-Seq-2-0-UDI-Barcodes-V22-02-new.pdf). They…

Emergence of structure when scaling language models to 15 billion parameters. (A) Predicted contact probabilities (bottom right) and actual contact precision (top left) for PDB 3LYW. A contact is a positive prediction if it is within the top L most likely contacts for a sequence of length L. (B to…

RevGel-seq sample preparation workflow Experiments were performed with the RevGel-seq protocol, capable of analyzing 10,000 input cells per sample with the specially designed gelation device (Fig. S3). The individual steps shown in Fig. 1A, from cell-barcoded bead coupling to library preparation for sequencing, are more fully described below: Cell labeling Cells…

doi: 10.1093/bioinformatics/btad150. Online ahead of print. Affiliations Expand Affiliations 1 The Roslin Institute and R(D)SVS, University of Edinburgh, Edinburgh, EH25 9RG. 2 Wobble Genomics, University of Edinburgh, Edinburgh, EH25 9RG. Item in Clipboard Sébastien Guizard et al. Bioinformatics. 2023. Show details Display options Display options Format AbstractPubMedPMID doi: 10.1093/bioinformatics/btad150. Online ahead…

Scientists from the University of Hamburg, Germany, have developed a novel methodology, DiNiro, for unraveling differential regulatory disease mechanisms from single-cell RNA-seq data. Computational tools for analyzing differential gene expression profiles and differential pathway expression have been previously developed. DiNiro is the first known method based on single-cell data for…

Stock photo of a microchip in a syringe Missouri state legislators are trying to regulate the fabricated scene inside this stock photo. A subset of Missouri legislators care deeply about freedom. For instance: The God-given right to NOT accept a life-saving vaccination and still attend public school or go to…

Fungi, ain’t a kingdom most of us will know much about. The only thing I can guess at is that in bacteria there has resurgence in methods for de novo assembly specifically aimed at reducing the total number of contigs in an assembly. The ‘new wave’ is summarised in this…

Experimental animals and DOX treatment All animal experiments performed on live animals were approved by Fudan University’s Committee on the Ethics of Animal Experiments and adhered to relevant guidelines including the ARRIVE guidelines for animal experiments in the study. Adult male C57BL/6 mice (8–10 weeks old; 23–26 g; Department of Laboratory…

More than twelve billion doses of mRNA vaccines have been administered globally since the start of the COVID pandemic, saving millions of lives. But RNA-based therapies for other diseases have so far proven more challenging to develop. The full-body immune response caused by mRNA vaccines is fantastic for fighting off…

Credit: Pixabay/CC0 Public Domain Why do some people with a genetic mutation associated with leukemia remain healthy, while others with the same mutation develop the blood cancer? In a new study published in Blood, scientists from the USC Stem Cell laboratory of Rong Lu discovered a mechanism that linked a…

Ruminants have a semi-invasive placenta, which possess highly vascularized placentomes formed by maternal endometrial caruncles and fetal placental cotyledons and required for fetal development to term. The synepitheliochorial placenta of cattle contains at least two trophoblast cell populations, including uninucleate (UNC) and binucleate (BNC) cells that are most abundant in…

Fagagna, F. et al. A DNA damage checkpoint response in telomere-initiated senescence. Nature 426, 194–198 (2003). Article  Google Scholar  Takai, H., Smogorzewska, A. & de Lange, T. DNA damage foci at dysfunctional telomeres. Curr. Biol. 13, 1549–1556 (2003). Article  CAS  PubMed  Google Scholar  Olovnikov, A. M. A theory of marginotomy:…

RNA Sequencing and Vg pan -transcriptome build 0 Hello! I am new to building a pan-transcriptome utilizing assemblies produced by the Human Pangenome Reference Consortium from year 1 data, 47 samples. I planned to use all of the Fasta files for my reference genomes… I then planned to add vcf…

Onsite role   Scientific Associate – Bioinformatics   We are seeking a highly motivated bioinformatics scientist to perform quality control and analysis of next-generation sequencing data (e.g., RNA-sequencing and cell-free DNA-sequencing) from clinical trial samples. The successful candidate will work collaboratively with computational biologists, drive quality control of sequencing data,…

Research Software Engineer (Bioinformatics/Genomics/Neuroscience) US-NJ-Princeton Job ID: 2023-16265Type: Full-Time# of Openings: 1Category: Engineering Princeton University Overview Do you want to help enable and advance groundbreaking neuroscience research through software development? Do you have a background in research but love to write code? Are you looking to apply your scientific programming…

UCSD Layoff from Career Appointment: Apply by 03/28/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 04/07/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will remain open until a successful candidate has been…