#RNASeq Data Analysis

[cbirt]

Exploring bulk RNA-seq data has become a cornerstone for uncovering crucial insights into gene expression patterns and their relationship to phenotypes in biomedical research. One of the key tools in this domain is DESeq2, a powerful R package that has revolutionized differential expression analysis. However, a recent trend towards Python-based bioinformatics tools has highlighted the need for a native Python package to perform differential expression analysis (DEA) with generalized linear models on bulk RNA-seq data. In lieu of this, researchers from Owkin France introduced PyDESeq2, a novel Python implementation of the DESeq2 workflow. PyDESeq2 not only reproduces similar results to its R counterpart but also brings lots of additional benefits to the table.

PyDESeq2’s re-implementation yields results that align closely with DESeq2. It achieves higher model likelihood, a testament to its robustness in modeling raw counts using a negative binomial distribution. Notably, PyDESeq2 demonstrates substantial speed improvements on large datasets, as demonstrated in experiments conducted on The Cancer Genome Atlas (TCGA) data.

Python’s popularity in the data science community is undeniable, and PyDESeq2 capitalizes on this by seamlessly interfacing with modern Python-based data science tools. Leveraging well-maintained and efficient scientific computing packages like NumPy and sciPy, PyDESeq2 provides a familiar environment for researchers, facilitating a smoother workflow.

Continue Reading

[evoldir]

Fwd: Job: BostonU.ResSupport.EvolGenomics

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Job: BostonU.ResSupport.EvolGenomics > Date: 6 October 2024 at 05:12:17 BST > To: rdmpage@gmail.com > > > > > Seeking Research Support Specialist in Evolutionary Genomics > > Location: Mullen Lab, Boston University, Boston, MA > > Start Date: Position available immediately, but preferred start by > January 2025 > > Job Description: > The Mullen Evolutionary Genomics Lab at Boston University seeks > applications for a Research Support Specialist. Research in the Mullen > Lab is aimed at understanding the origin and maintenance of diversity > across levels of biological organization. Current projects in the lab > focus on testing mimicry theory, understanding the structure, function, > and evolution of cis-regulatory elements influencing color pattern > development in butterflies, and investigating the causes and consequences > of synanthropic life-history evolution in the webbing clothes moth. > > The primary objectives of this role will include direct supervision of > Mullen Lab graduate students in bioinformatic techniques and wet lab > experiments. If interested, there is also potential for the successful > candidate to work on independent data analysis of a whole genome > sequencing dataset aimed at understanding the role of cis-regulatory > elements in a butterfly mimicry complex. The successful applicant > will have demonstrated success in project management, analysis of next > generation sequencing data, population genomic analyses, bioinformatics, > and a strong interest in mentorship. The ideal candidate will have > demonstrated experience analyzing whole genome sequencing data, RNAseq, > and ATACseq data. Candidates with either a MSc or PhD and appropriate > experience are encouraged to apply. > > The Mullen Lab embraces open and equitable access to opportunities for > scientific learning and development, regardless of race, ethnicity, gender > and gender expression, age, disability, nationality, sexual orientation, > citizenship status, veteran status, religious/non-religious beliefs, > socio-economic class, or any other differences that have been the basis > for oppression, misunderstanding or bias. > > Position Details: > The initial appointment will be for one year, with the possibility > of extending for an additional 2 years contingent on satisfactory > performance. Staff benefits include health insurance (Blue Cross Blue > Shield Massachusetts), flexible spending accounts (FSAs) for supplemental > medical costs, and a 403(b) retirement plan. Starting salary is $67,500 > USD with potential for merit-based raises each year. > > The candidate will additionally receive professional mentoring from the > PI, and can expect a professional development stipend of $2,500. The > successful applicant will be based in the Biology Department at Boston > University and will be expected to be present in person at least 75% > of the time. > > To Apply: > Qualified candidates should submit a short cover letter, curriculum > vitae, and contact information for three references to smullen@bu.edu and > haich@bu.edu with “Research Support Specialist App” in the subject > line. The closing date for applications is November 1, 2024. > > > Hannah E. Aichelman M.Sc Ph.D. > she/her/hers > > Postdoctoral Associate, Mullen & Davies Labs > Boston University > > https://ift.tt/wFBhg8r > > Hannah Aichelman

[gis56]

"Enhancing Precision Medicine with RNA-seq"

Next-generation sequencing (NGS)-based RNA sequencing, commonly known as RNA-seq, has revolutionized transcriptomic analysis by enabling comprehensive and high-throughput examination of gene expression profiles. This advanced technology involves the sequencing of RNA molecules extracted from biological samples, providing valuable insights into RNA transcripts, splice variants, and gene fusion events across various conditions and tissues. RNA-seq facilitates the discovery of novel transcripts and regulatory elements, elucidates biological pathways, and aids in biomarker identification for diseases such as cancer. Key methods include strand-specific RNA-seq, single-cell RNA-seq (scRNA-seq), and bulk RNA-seq, each tailored to specific research needs. Advances in NGS platforms, bioinformatics tools, and data analysis algorithms have enhanced the sensitivity, accuracy, and scalability of RNA-seq applications. The growing adoption of RNA-seq in biomedical research, personalized medicine, and agricultural genomics underscores its pivotal role in advancing our understanding of gene regulation and molecular mechanisms. Challenges include data integration, standardization of protocols, and computational demands, which ongoing research aims to address for broader utilization and interpretation of RNA-seq data.

#RNAseq #NextGenSequencing #Transcriptomics #NGS #BiomedicalResearch #PrecisionMedicine #SingleCellRNAseq #Bioinformatics #Genomics #BiomarkerDiscovery #CancerResearch #DataScience #ResearchAndDevelopment #GeneExpression #HealthTech

[leedsomics]

Dynamic Single Cell Transcriptomics Defines Kidney FGF23/KL Bioactivity and Novel Segment-Specific Inflammatory Targets

FGF23 via its coreceptor Klotho (KL) provides critical control of phosphate metabolism, which is altered in rare and very common syndromes, however the spatial-temporal mechanisms dictating renal FGF23 functions remain poorly understood. Thus, developing approaches to modify specific FGF23-dictated pathways has proven problematic. Herein, wild type mice were injected with rFGF23 for 1, 4 and 12h and renal FGF23 bioactivity was determined at single cell resolution. Computational analysis identified distinct epithelial, endothelial, stromal, and immune cell clusters, with differential expressional analysis uniquely tracking FGF23 bioactivity at each time point. FGF23 actions were sex independent but critically relied upon constitutive KL expression mapped within proximal tubule (S1-S3) and distal tubule (DCT/CNT) cell sub-populations. Temporal KL-dependent FGF23 responses drove unique and transient cellular identities, including genes in key MAPK- and vitamin D-metabolic pathways via early- (AP-1-related) and late-phase (EIF2 signaling) transcriptional regulons. Combining ATACseq/RNAseq data from a cell line stably expressing KL with the in vivo scRNAseq pinpointed genomic accessibility changes in MAPK-dependent genes, including the identification of FGF23-dependent EGR1 distal enhancers. Finally, we isolated unexpected crosstalk between FGF23-mediated MAPK signaling and pro-inflammatory TNF receptor activation via NF-{kappa}B, which blocked FGF23 bioactivity in vitro and in vivo. Collectively, our findings have uncovered novel pathways at the single cell level that likely influence FGF23-dependent disease mechanisms. http://dlvr.it/T7Xb9d

[larryhbernsteinme]

QIAGEN - International Leader in NGS and RNA Sequencing

QIAGEN – International Leader in NGS and RNA Sequencing

QIAGEN – International Leader in NGS and RNA Sequencing

Reporter: Aviva Lev-Ari, PhD, RN

  The reader is encouraged to review all the products of QIAGEN on the company web site.

miRCURY Exosome Kits  

For enrichment of exosomes and other extracellular vesicles from serum/plasma or cell/urine/CSF samples

Excellent recovery of exosomes and other extracellular vesicles

Easy and…

[jobrxiv]

Bioinformatician Thomas Jefferson University Application Deadline: 2023-02-09 Job Summary A Bioinformatician position is immediately available in the laboratory of Dr. Fadia Ibrahim in the Department of Biochemistry and Molecular Biology, at Thomas Jefferson University. Our research program is focused on studying the molecular mechanism of a novel RNA decay process that we discovered recently and named "ribothrypsis" (Nature SMB 2018), and investigating the role of RNA dysregulation in neurodegenerative diseases including amyotrophic lateral sclerosis. We use a combination of molecular biology, biochemistry, and novel high-throughput RNA sequencing methods. This position seeks a highly motivated computational biologist to provide bioinformatics support for ongoing studies, setup, develop and implement bioinformatics tools and pipelines, and manage all aspects of data analysis and processing of complex short- and long-sequencing reads. Required Qualifications: ·       Ph.D. or MS. in computational biology, bioinformatics, Biomedical      engineering, or related ... See the full job description on jobRxiv: https://jobrxiv.org/job/thomas-jefferson-university-27778-bioinformatician/?feed_id=24770 #ScienceJobs #hiring #research #Bioinformatician, #NGS, #RNASeq, #Genomics, #PhD or #MS

[cuzunla]

Araştırma Planı-ŞUBAT

1. "MULTI OMICS ON CANCER" LİTERATÜR TARAMASI

Kullanılabilir methodların listelenmesi ve uygulanması

Teknik öğrenmek için https://www.ebi.ac.uk/training/on-demand Aim to Learn

https://www.ebi.ac.uk/training/online/courses/introductory-bioinformatics-pathway/what-is/

https://www.ebi.ac.uk/training/online/courses/functional-genomics-i-introduction-and-design/#vf-tabs__section--contents

https://www.ebi.ac.uk/training/online/courses/functional-genomics-ii-common-technologies-and-data-analysis-methods/learn-more/

https://www.ebi.ac.uk/training/online/courses/functional-genomics-iii-submitting-data/

https://www.ebi.ac.uk/training/online/courses/expression-atlas-quick-tour/what-is/

https://www.ebi.ac.uk/training/online/courses/a-guide-to/molecular-sequence-features-and-analysis/sequence-similarity-search-for-biomolecular-sequences/

2.RNASeq datası olan Phosphoproteomics Databaselerinin bulunması

[cbirt]

RNA sequencing is currently a useful tool for studying the dynamic transcriptional mechanisms that control the operation of eukaryotic cells. Nevertheless, complicated experimental designs with various biological variables and multiple analysis time points cannot be automatically analyzed by the tools that are currently on the market for the analysis of raw sequencing data. Multiple programs are combined into a single framework by the MultiRNAflow suite by researchers from the University of Lorraine, France, enabling supervised and exploratory statistical analysis of temporal data for various biological situations. Nuclear DNA genes in eukaryotic cells are translated into messenger RNA molecules prior to being translated into proteins that maintain normal cellular activities. Stochastic events that impact transcription during cell dormancy cause a transcriptional noise within the cell. Thousands of genes are triggered upon changes to the cellular environment (such as receptor activation or cellular stress), which causes a dynamic, transient transcriptional response that enables the cells to adjust to the initial environmental disturbance. 

Continue Reading

[evoldir]

Fwd: Course: Online.NGSDataAnalysis.Oct21-25

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Course: Online.NGSDataAnalysis.Oct21-25 > Date: 12 September 2024 at 06:59:12 BST > To: rdmpage@gmail.com > > > > Dear all, > > We are excited to announce the Autumn School in Bioinformatics (Online), > taking place from 21-25 October. > > Course website: ( > https://ift.tt/ucf8Q9L ) > > This course focuses on understanding and working with Next Generation > Sequencing (NGS) data, including quality assessment, genome assembly, > RNAseq, differential gene expression, phylogenomics and more. The > course includes hands-on sessions using Illumina, Nanopore, and PacBio > data. Participants will also learn how to make their analysis workflows > fully reproducible using Docker and pipeline workflow managers. > > Only 5 seats available! > > For the full list of our courses and workshops, please visit: ( > https://ift.tt/ucf8Q9L ) > > Best regards, Carlo > > > Carlo Pecoraro, Ph.D > Physalia-courses DIRECTOR > info@physalia-courses.org > mobile: +49 17645230846 > > > "info@physalia-courses.org"

[leedsomics]

Single cell transcriptomics of the Drosophila embryonic salivary gland reveals not only induction but also exclusion of expression as key morphogenetic control steps

How tissue shape and therefore function is encoded by the genome remains in many cases unresolved. The tubes of the salivary glands in the Drosophila embryo start from simple epithelial placodes, specified through the homeotic factors Scr/Hth/Exd. Previous work indicated that early morphogenetic changes are prepatterned by transcriptional changes, but an exhaustive transcriptional blueprint driving physical changes was lacking. We performed single-cell-RNAseq-analysis of FACS-isolated early placodal cells, making up less than 0.4% of cells within the embryo. Differential expression analysis in comparison to epidermal cells analysed in parallel generated a repertoire of genes highly upregulated within placodal cells prior to morphogenetic changes. Furthermore, clustering and pseudo-time analysis of single-cell-sequencing data identified dynamic expression changes along the morphogenetic timeline. Our dataset provides a comprehensive resource for future studies of a simple but highly conserved morphogenetic process of tube morphogenesis. Unexpectedly, we identified a subset of genes that, although initially expressed in the very early placode, then became selectively excluded from the placode but not the surrounding epidermis, including hth, grainyhead and tollo/toll-8. We show that maintaining tollo expression severely compromised the tube morphogenesis. tollo is likely switched off to not interfere with key Tolls/LRRs that are expressed and function in the placode. http://dlvr.it/T6glCl

[dr-afsaeed]

16 Postdoc Positions, Masaryk University, Czech Republic

16 Postdoc Positions, Masaryk University, Czech Republic

16 Postdoc Positions, Masaryk University, Czech Republic (1) Postdoctoral Position: Summary Of Postdoc Position: The successful candidate will lead the analysis of data from multiomics profiles spanning from targeted (16S rRNA seq) and whole-metagenomic profiles, transcriptomic profiles (RNAseq, miRNA seq), tumour cancer panel profiles (DNAseq) and metabolomic profiles in association with…

[biotechtimes]

NIPGR Project Recruitment 2021 – Biotech / Biochem / Bioinfo Jobs

New Post has been published on https://biotechtimes.org/2021/03/11/nipgr-project-recruitment-2021-biotech-biochem-bioinfo-jobs/

NIPGR Project Recruitment 2021 – Biotech / Biochem / Bioinfo Jobs

NIPGR Project Recruitment 2021

NIPGR Project Recruitment 2021 – Life Sciences JRF / SRF / PA Jobs. National Institute of Plant Genome Research has announced project positions for candidates having a Biotech / Biochem / Bioinfo background. Interested candidates can check out the details below:

National Institute of Plant Genome Research Aruna Asaf Ali Marg, P.O. Box No. 10531, New Delhi-110067

Candidates are invited to appear for an online interview before a selection committee for filling up the purely temporary position in the following projects of Dr. Senjuti Sinharoy, Scientist, NIPGR. The details of the position are as under:

SERB- ECRA project entitled “Understanding the role of nodule specific PIN-LIKES (PILS) protein in peanut root nodule development”,

Post-I: Junior Research Fellow

No. of Post: 01 (one post)

Emoluments: as per DST/DBT norms and as sanctioned in the project

Qualification: Candidates selected through National Eligibility Tests as mentioned in the DST Office Memorandum number SR/S9/Z-08/2018 dated January 30, 2019, and having Master’s degree in Biotechnology/ Microbiology/ Life Sciences with at least 60 % (or equivalent) marks can apply.

Experience of basic Microbiology, isolation of microbe, ribotyping of microbe and PGPR related experience are desirable. Person with prior in-depth knowledge about rhizobium-legume symbiosis will be given preference.

DBT project entitled “Determination the role of (Cysteine- Rich Secretory Proteins, Antigen 5, and Pathogenesis-Related 1 Proteins (CAP) during Arachis- Bradyrhizobium symbiosis”.

Post-II: Project Associate-I

No. of Post: 01 (one post)

Upper Age Limit: 35 years

Emoluments: as per DST/DBT norms and as sanctioned in the project.

Qualification: Candidates having M.Sc. /M. Tech./M.C.A degree (Bioinformatics/ Computational Biology/ Computer Application/ Statistics/ Mathematics/ Genomics) with at least 55% (or equivalent) can apply. The candidate is required to have knowledge in HTML/CSS scripting, MySQL, fluency in Linux.

Prior work experience in R programming language, machine learning, RNAseq data analysis and along with ability of phenomics/transcriptomics-based database development is preferred.

Post-III: Senior Research Fellow

No. of Post: 01 (one post)

Emoluments: as per DST/DBT norms and as sanctioned in the project

Qualification: Candidates selected through National Eligibility Tests as mentioned in the DST Office Memorandum number SR/S9/Z-08/2018 dated January 30, 2019, and having Master’s degree in Biochemistry/ Biotechnology/ Microbiology /Life Sciences with at least 60 % (or equivalent) marks can apply.

Experience of basic molecular biology-related work such as plasmid isolation, RNA isolation, qRT-PCR analysis, Western blot are necessary. Person having experience in recombinant protein purification are desirable. Person with prior in-depth knowledge about rhizobium-legume symbiosis will be given preference.

How to Apply

Eligible candidates for the above positions may send the completed application in the given format with a cover letter showing interest and specifying the position along with attested copies of the certificates (from Class X onwards) and proof of research experience AS A CONSOLIDATED SINGLE PDF COPY to ssinharoy@nipgr.ac.in. The applications should be sent on or before March 15, 2021. Candidates need to fill up the necessary information in the given google form.

Candidates who will send multiple separate attachments and will not fill the google sheet, those applications will not be considered for interview. Shortlisted candidates will be called for online interview. A web-link with date and time of online interview will be e-mailed to the shortlisted candidates. The candidates must ascertain their eligibility before applying, as ineligible candidates will not be interviewed.

Note

ONLY soft copy of the application in the given format will be accepted. Interview link will only be sent to shortlisted candidates. For any clarification candidates may contact Scientist incharge through e-mail only.

The above positions are completely on a temporary basis and co-terminus with the project. The fellowship/emolument amount for the above positions are as sanctioned in the project and as per DBT/DST norms. The initial appointment will be for one year or till the tenability of the project whichever is earlier and the same can be curtailed/extended on the basis of assessment of the candidate’s performance and discretion of the Competent Authority.

NIPGR reserves the right to select the candidate against the above post depending upon the qualification and experience of the candidate. Reservation of posts shall be as per Govt. of India norms. The appointment may be terminated any time by giving one month notice by either side. The applicants will have no claim implicit or explicit for consideration against any regular position of NIPGR.

Online Form

Download Notification

[cuzunla]

Today I have emailed a prof to be able to attend their workshop on sequencing topics. She said they have reached the maximum amount of people but there will be more of these. They require basic linux and basic knowledge. I do have those but I think I can be ready for the next one. So I want to learn these to attend the workshops:

Basic Linux

https://www.coursera.org/learn/genomic-tools/home/welcome

Bioinformatic Tools

https://www.coursera.org/learn/bioinformatics-methods-1/home/welcome

I want to learn this to be able to deal with my own data for the project:

Data Analysis Python

https://www.freecodecamp.org/learn/data-analysis-with-python/

I want to learn this for my future internship and job. Also for summer opportunities:

Single Cell Gene Expression, RNA-Seq, Differencial Gene Expression

https://www.youtube.com/channel/UCnXs-Nq1dzMZQOKUHKW3rdw/videos

I do want to work hard so lets give one month of deadline and see what happens.

Day 1(23.01.2022)

Learned

-how to download rnaseq data, match it with metadata, arrange the titles, calculate the expression mean and median.

-learned how to bar plot, density plot, scatter plot and heatmap the FPKM values

Couple Days Later(26.01.2022)

Learned

-how to perform basic DESEQ2 analysis and how to plot it

https://lashlock.github.io/compbio/R_presentation.html

-https://genviz.org/module-04-expression/0004/02/01/DifferentialExpression/ (dene)

[cbirt]

Comprehensive data atlases have been made possible by the data-driven nature of biomedical research thanks to large-scale single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST). By facilitating a thorough grasp of biology and pathophysiology, these techniques contribute to the identification of novel targets for therapeutic intervention. However, these technologies’ complexity and sheer amount of data provide analytical difficulties, especially when it comes to reliable cell type, integration, and comprehension of intricate spatial interactions between cells. 

Portrai, Inc. Seoul, researchers created CELLama (Cell Embedding Leverage Language Model Abilities) as a solution to these problems. It is a framework that uses language models to convert cell data into “sentences” that contain gene expressions and metadata, allowing for universal cellular data embedding for a range of analyses.  

The foundation model CELLama overcomes laborious procedures and manual data selection by providing flexible applications for cell typing and spatial context analysis. Its adaptability is demonstrated by the way its potential alters cellular investigation in a variety of scenarios, from identifying cell types to deciphering complex tissue dynamics.

Continue Reading

[evoldir]

Fwd: Course: Online.NGSDataAnalysis.Oct21-25

Begin forwarded message: > From: evoldir@evol.biology.mcmaster.ca > Subject: Course: Online.NGSDataAnalysis.Oct21-25 > Date: 12 September 2024 at 05:56:22 BST > To: rdmpage@gmail.com > > > > Dear all, > > We are excited to announce the Autumn School in Bioinformatics (Online), > taking place from 21-25 October. > > Course website: ( > https://ift.tt/ucf8Q9L ) > > This course focuses on understanding and working with Next Generation > Sequencing (NGS) data, including quality assessment, genome assembly, > RNAseq, differential gene expression, phylogenomics and more. The > course includes hands-on sessions using Illumina, Nanopore, and PacBio > data. Participants will also learn how to make their analysis workflows > fully reproducible using Docker and pipeline workflow managers. > > Only 5 seats available! > > For the full list of our courses and workshops, please visit: ( > https://ift.tt/ucf8Q9L ) > > Best regards, Carlo > > > Carlo Pecoraro, Ph.D > Physalia-courses DIRECTOR > info@physalia-courses.org > mobile: +49 17645230846 > > > "info@physalia-courses.org"