Tag: scATAC-SEQ

Exploring the Latest Advances in Transcriptomics

Since the idea of genetic regulation was first postulated back in the 1950s, our scientific understanding of the transcriptome has deepened greatly.1 Looking into the transcriptome of cells and tissues has helped scientists to understand the biological processes that drive both health and disease; however, the complex and occasionally mysterious…

Continue Reading Exploring the Latest Advances in Transcriptomics

Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

Enhancers control gene expression and play crucial roles in development and homeostasis1–3. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here, we combine deep learning and transfer learning to design tissue-specific enhancers for five tissues in the Drosophila melanogaster embryo – the central nervous…

Continue Reading Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo

Second “Code of Life” Cracked by AI

Understanding how genes are regulated Our DNA code provides the “blueprint” for life, enabling our cellular machinery to produce proteins that carry out essential molecular functions. While each cell possesses the same DNA code, the regulation of specific genes within that cell contribute to its unique function. Genes need to…

Continue Reading Second “Code of Life” Cracked by AI

Study reveals how maternal diabetes affects birth defects at the single-cell level

In a recent study published in Nature Cardiovascular Research, researchers from California used multimodal single-cell analysis in mice to investigate the mechanisms by which maternal diabetes mellitus contributes to congenital abnormalities in the fetus. They found that during embryogenesis, maternal diabetes alters the epigenomic landscape in cardiac and craniofacial progenitors,…

Continue Reading Study reveals how maternal diabetes affects birth defects at the single-cell level

The Biostar Herald for Monday, November 20, 2023

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

Continue Reading The Biostar Herald for Monday, November 20, 2023

MD Anderson Cancer Center hiring Associate Bioinformatics Data Scientist in Houston, TX

SummaryThe University of Texas MD Anderson Cancer Center in Houston is one of the world’s most respected centers focused on cancer patient care, research, education and prevention. It was named the nation’s No. 1 hospital for cancer care in U.S. News & World Report’s 2022-2023 rankings. It is one of…

Continue Reading MD Anderson Cancer Center hiring Associate Bioinformatics Data Scientist in Houston, TX

Error in H5Fopen

Error in H5Fopen 0 Hello– I am trying to run a pipeline against a dataset (ArchR and Arrow Files), however when I use the following: ArrowFiles <- c(“fragments1.arrow”, “fragments2.arrow”, “fragments3.arrow”) proj_CAD1<- ArchRProject( ArrowFiles = ArrowFiles, outputDirectory = “/work/outputDirectory”, copyArrows = TRUE ) I receive the following error: Error in H5Fopen(file,…

Continue Reading Error in H5Fopen

Bioinformatic Scientist | Cleared Careers

Overview Axle is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations nationally and abroad. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

Continue Reading Bioinformatic Scientist | Cleared Careers

J. Craig Venter Institute hiring Bioinformatics Analyst (Zhang Lab) in La Jolla, CA

Position SummaryThe Zhang lab at the JCVI is looking for a highly motivated Bioinformatics Analyst. Projects will focus on integrative computational analysis of single cell multi-omics data, including single cell/nucleus RNA-seq data, using public and in-house experimental data assets. These projects will range across multiple organs and tissues to establish…

Continue Reading J. Craig Venter Institute hiring Bioinformatics Analyst (Zhang Lab) in La Jolla, CA

fragments file generation via Sinto from CellRanger output

fragments file generation via Sinto from CellRanger output 0 Hi, I am following the instructions for the PASTA package (satijalab.org/seurat/articles/pasta_vignette.html). This package uses scRNA-seq data to infer alternative polyadenylation usage from scRNAseq data. It requires among many input files also a fragment file. The authors state the following must be…

Continue Reading fragments file generation via Sinto from CellRanger output

Allen Institute for Immunology hiring Manager, Bioinformatics Operations – Immunology in Seattle, WA

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact…

Continue Reading Allen Institute for Immunology hiring Manager, Bioinformatics Operations – Immunology in Seattle, WA

Compare peaks between clusters in sc-ATAC

Compare peaks between clusters in sc-ATAC 0 Hi So If you have the called peaks per cluster from sc-ATAC and you want to compare between the annotated regions (promoters, enhancers, introns ..etc) between the clusters. Do you use raw peak counts? Do you run differential peak to background? Do you…

Continue Reading Compare peaks between clusters in sc-ATAC

Thymic mimetic cells function beyond self-tolerance

Klein, L., Kyewski, B., Allen, P. M. & Hogquist, K. A. Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see). Nat. Rev. Immunol. 14, 377–391 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  Bornstein, C. et al. Single-cell mapping of the thymic stroma identifies…

Continue Reading Thymic mimetic cells function beyond self-tolerance

Output FindMarkers()

Output FindMarkers() 1 Hi all, Would you please share why I got peaks instead of genes when using this command: compare_0 <- FindMarkers(merged_seurat, ident.1 = ‘WT_0’, ident.2 = ‘MT_0’) head(compare_0) Thank you so much! seurat • 46 views • link updated 9 minutes ago by bk11 &utrif; 670 • written…

Continue Reading Output FindMarkers()

Postdoctoral Associate- Bioinformatics/Cancer Genomics Job in Texas

Summary The Cheng Lab at Baylor College of Medicine is searching for highly motivated and talented postdoctoral candidates to work on Bioinformatics and Computational Biology in Cancer Genomics and Immunology. The position will be involved in the development and/or application of computational approaches to understand the mechanism of cancer…

Continue Reading Postdoctoral Associate- Bioinformatics/Cancer Genomics Job in Texas

Postdoc in Computational Neurogenomics job with Human Technopole

APPLICATION CLOSING DATE: September 1st, 2023. Human Technopole (HT) is a new interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health. HT is composed of five Centers: Computational Biology, Structural Biology, Genomics, Neurogenomics and Health Data Science….

Continue Reading Postdoc in Computational Neurogenomics job with Human Technopole

Bioinformatics Analyst, Sr Analyst or Lead Analyst – Cincinnati

Company Description CincinnatiChildren’sHospitalMedicalCenter is nationally recognized as a leader in pediatric healthcare, with a reputation for excellence in patient care, research and medical education. U.S. News & World Report consistently ranks Cincinnati Children’s as one of the nation’s top three pediatric hospitals in their edition of America’s Best Children’s Hospitals…

Continue Reading Bioinformatics Analyst, Sr Analyst or Lead Analyst – Cincinnati

Bioinformatics Analyst, Sr Analyst or Lead Analyst job with Cincinnati Children’s Hospital

Company Description CincinnatiChildren’sHospitalMedicalCenter is nationally recognized as a leader in pediatric healthcare, with a reputation for excellence in patient care, research and medical education. U.S. News & World Report consistently ranks Cincinnati Children’s as one of the nation’s top three pediatric hospitals in their edition of America’s Best Children’s Hospitals…

Continue Reading Bioinformatics Analyst, Sr Analyst or Lead Analyst job with Cincinnati Children’s Hospital

Junior/ Senior Bioinformatician for computational neurogenomics job with Human Technopole

Job description APPLICATION CLOSING DATE: September 1st, 2023. Human Technopole (HT) is a new interdisciplinary life science research institute, created and supported by the Italian Government, with the aim of developing innovative strategies to improve human health. HT is composed of five Centers: Computational Biology, Structural Biology, Genomics, Neurogenomics and Health…

Continue Reading Junior/ Senior Bioinformatician for computational neurogenomics job with Human Technopole

A universal tool for predicting differentially active features in single-cell and spatial genomics data

singleCellHaystack methodology For a detailed description of the original singleCellHaystack implementation (version 0.3.2) we refer to Vandenbon and Diez19. In brief, singleCellHaystack uses the distribution of cells inside an input space to predict DAFs. First, it infers a reference distribution \(Q\) of all cells in the space by estimating the…

Continue Reading A universal tool for predicting differentially active features in single-cell and spatial genomics data

Bioconductor – ChromSCape

DOI: 10.18129/B9.bioc.ChromSCape     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ChromSCape. Analysis of single-cell epigenomics datasets with a Shiny App Bioconductor version: 3.15 ChromSCape – Chromatin landscape profiling for Single Cells – is a ready-to-launch user-friendly Shiny Application for the analysis…

Continue Reading Bioconductor – ChromSCape

Bioinformatics Scientist job with Active Motif

Position Title: Bioinformatician Scientist Classification: Exempt Reports To: TBD Who is Active Motif? Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. We are committed to providing the highest quality products and superior service & support to serve the life…

Continue Reading Bioinformatics Scientist job with Active Motif

Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis

Tandem duplications and noncoding SNVs at the HCFP1 locus We enrolled families and simplex cases with nonsyndromic congenital facial paresis (CFP, cohort 1 US-based study) and performed genome-wide single-nucleotide polymorphism (SNP) analysis and whole-exome sequencing (WES) in two large dominant pedigrees, family 1 (Fam1) and family 9 (Fam9; Fig. 1a)….

Continue Reading Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis

Bioinformatics Scientist – Active Motif Inc

Position Title: Bioinformatician Scientist Classification: Exempt Reports To: TBD Who is Active Motif? Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. We are committed to providing the highest quality products and superior service & support to serve the life…

Continue Reading Bioinformatics Scientist – Active Motif Inc

Transposons contribute to the acquisition of cell type-specific cis-elements in the brain

De novo motifs with high variability in chromatin accessibility across cells are similar to known binding motifs of neural differentiation-related transcription factors To discover accessible DNA motifs that are important for cell-type specificity in the mouse adult prefrontal cortex (P56), we first investigated whether cell types are characterized by k-mer…

Continue Reading Transposons contribute to the acquisition of cell type-specific cis-elements in the brain

Postdoctoral Associate- Bioinformatics/Cancer Genomics

Summary The Cheng Lab at Baylor College of Medicine is searching for highly motivated and talented post-doc candidates to work on Bioinformatics and Computational Biology in Cancer Genomics and Immunology. The position will be involved in the development and/or application of computational approaches to understand the mechanism of cancer…

Continue Reading Postdoctoral Associate- Bioinformatics/Cancer Genomics

Bioinformatics in Next Generation Sequencing (BiNGS) – Icahn School of Medicine hiring Junior Bioinformatician in New York, New York, United States

Junior Bioinformatician position in BiNGS   We are seeking a junior bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core, to lead transcriptomics and epigenetics data analysis projects related but not limited to cancer biology, skin biology, developmental biology, diabetes, and neuron biology.   The mission…

Continue Reading Bioinformatics in Next Generation Sequencing (BiNGS) – Icahn School of Medicine hiring Junior Bioinformatician in New York, New York, United States

Associate Data Scientist – Genetics (NGS) job with University of Texas MD Anderson Cancer Center

SUMMARY The Genetics Department is a basic science department located in the George and Cynthia Mitchell Basic Sciences Research Building at the world-renowned University of Texas MD Anderson Cancer Center in the heart of the Texas Medical Center. The focus is on advancing knowledge of the molecular genetic mechanisms that…

Continue Reading Associate Data Scientist – Genetics (NGS) job with University of Texas MD Anderson Cancer Center

Bioinformatics Scientist – Carlsbad, CA

Position Title: Bioinformatician Scientist Classification: Exempt Reports To: TBD Who is Active Motif? Active Motif is the industry leader in developing and delivering innovative tools to enable epigenetics and gene regulation research. We are committed to providing the highest quality products and superior service & support to serve the life…

Continue Reading Bioinformatics Scientist – Carlsbad, CA

Analyst/Sr. Analyst, Bioinformatics – Molecular Cardiovascular Biology in Cincinnati, OH for Cincinnati Children’s Hospital Medical Center

Use this area to filter your search results. Each filter option allows for multiple selections. DisciplineAcademic / Research (316)Aerospace Engineering (5)Agricultural Engineering (14)Allied Health (1)Biology (4)Biomedical Engineering (20)Chemical Engineering (4)Civil Engineering (100)Computer Software Engineering (7)Computer and Information Science (17)Conservation Science (2)Construction Trades (1)Electrical Engineering (23)Electronics Engineering (6)Engineering…

Continue Reading Analyst/Sr. Analyst, Bioinformatics – Molecular Cardiovascular Biology in Cincinnati, OH for Cincinnati Children’s Hospital Medical Center

Bioconductor – scMultiome (development version)

DOI: 10.18129/B9.bioc.scMultiome   This is the development version of scMultiome; to use it, please install the devel version of Bioconductor. Collection of Public Single-Cell Multiome (scATAC + scRNAseq) Datasets Bioconductor version: Development (3.17) Single cell multiome data, containing chromatin accessibility (scATAC-seq) and gene expression (scRNA-seq) information analyzed with the ArchR…

Continue Reading Bioconductor – scMultiome (development version)

Too many differential peaks derived from FindMarkers() [Signac]

Too many differential peaks derived from FindMarkers() [Signac] 0 I am currently conducting scATAC-seq downstream analysis and just ran FindMarkers() comparing two biological conditions. In all, the number of diff. peaks turned out as ~5,000 which is rather high (the expected is around 500). How would I go about this?…

Continue Reading Too many differential peaks derived from FindMarkers() [Signac]

Allen Institute Developing Gene Panel Based on Longitudinal scRNA-seq Analytics Platform

NEW YORK – The Allen Institute for Immunology is looking to commercialize a multiomic gene panel to screen for immune disorders based on an internally developed bioinformatics platform for analyzing longitudinal single-cell RNA sequencing data. In doing so, the Seattle-based research institute hopes to make scRNA-seq more accessible as a…

Continue Reading Allen Institute Developing Gene Panel Based on Longitudinal scRNA-seq Analytics Platform

scATAC integration

scATAC integration 0 I am integrating 5 different datasets for a scATAC-seq analysis. I have had the following error persist for weeks; have looked online as well for possible solutions yet nothing has worked. Has anyone run into this issue? The following code is: object.list = list(sample1,sample2, sample3, sample4, sample5)…

Continue Reading scATAC integration

How to aggregate scATAC and multiome scATAC data while preserving the barcodes from the multiome

How to aggregate scATAC and multiome scATAC data while preserving the barcodes from the multiome 0 Hello everyone, I am working on single-cell analysis of my data. From 10X Genomics, I have scATAC-seq data and also multiome (measurements of scRNA + scATAC from the same cell). After using Cell Ranger…

Continue Reading How to aggregate scATAC and multiome scATAC data while preserving the barcodes from the multiome

ATAC Integration Help

ATAC Integration Help 0 Pretty much desperate at this point since I’ve had this error for a week. The output is the following after entering the following command: integration.anchors<- FindIntegrationAnchors( object.list = list(Seurat_1, Seurat_2, Seurat_3), anchor.features = row.names(Seurat_1), assay = c(‘peaks’, ‘peaks’, ‘peaks’), k.filter = NA, reduction = “rlsi”, dims…

Continue Reading ATAC Integration Help

Open PostDoc Position – Innovative Computational Methods for the Joint Analysis of Single-Cell & Spatial Omics Data (m/f/d)

  The Big Data in BioMedicine Group at the Chair of Experimental Bioinformatics (School of Life Sciences, Technical University of Munich (TUM)) invites applications for a postdoctoral position for the development of innovative algorithms for the joint analysis of single-cell & spatial transcriptomic data in the framework of the Novo…

Continue Reading Open PostDoc Position – Innovative Computational Methods for the Joint Analysis of Single-Cell & Spatial Omics Data (m/f/d)

PostDoc Position – Innovative Computational Methods, Germany

PostDoc Position – Innovative Computational Methods: The Big Data in BioMedicine Group at the Chair of Experimental Bioinformatics (School of Life Sciences, Technical University of Munich (TUM)) is seeking a Postdoctoral Researcher to develop innovative algorithms for the joint analysis of single-cell & spatial transcriptomic data in the framework of…

Continue Reading PostDoc Position – Innovative Computational Methods, Germany

MACS to Signac

MACS to Signac 1 Hey guys– Once MACS is completed running, how would I feed the peaks/bed file into Signac for each sample up to merging and finally clustering? I believe the vignette only demonstrates if one were to add *fragment files and I need the peaks file from MACS…

Continue Reading MACS to Signac

MACS Error

MACS Error 1 I’m currently running MACS2 and have the following error: $ macs2 callpeak -f BAMPE -t READS.bed -g hs -n test -B -q 0.01 . . . . **(MACS2/IO/Parser.c:12841)struct.error: unpack requires a string argument of length 4** Any suggestions? I’ve run and re-run this to no avail. scatac-seq…

Continue Reading MACS Error

Dissecting cell identity via network inference and in silico gene perturbation

CellOverview of the Oracle algorithm The CellOracle workflow is made up of several steps. We Tested and implemented CellOracle Python Versions 3.6 and 3.8 were developed and made available for use in the Jupyter Notepad environment CellOracle code can be downloaded open-source on GitHub.github.com/morris-lab/CellOracle), along with detailed descriptions of functions…

Continue Reading Dissecting cell identity via network inference and in silico gene perturbation

Postdoctoral Fellow – Oncology Bioinformatics – Piskol Lab Job Opening in San Pablo, CA at Genentech

The Position The Piskol lab in Genentech’s Research and Early Development organization is looking for an exceptional Postdoctoral Fellow who will pair state-of-the-art single cell assays with computational methods to study the intra-tumoral heterogeneity of metastatic colorectal cancer and the collaborative role of oncogenic signaling pathways in cancer maintenance, progression…

Continue Reading Postdoctoral Fellow – Oncology Bioinformatics – Piskol Lab Job Opening in San Pablo, CA at Genentech

scATAC-seq workflow

scATAC-seq workflow 0 Help. I am still new to the concept of scATAC-seq and was wondering if anyone could provide a straightforward workflow. I am referring to the Signac vignettes but it seems to go back and forth between tutorials. I am starting out with 2 samples– one knockout and…

Continue Reading scATAC-seq workflow

scATAC merging of files

scATAC merging of files 0 Bit of a simple question, however when you are given 2 different treatments of a condition– say Wildtype and the other being a knockout of some sort, would you go through an entire analysis for the wild type and separately another analysis for the knockout;…

Continue Reading scATAC merging of files

CoveragePlot in Signac from MACS2 Object

CoveragePlot in Signac from MACS2 Object 0 I am currently trying to produce a CoveragePlot() to locate a number of transcription factors; however instead of the input being a Chromatin Assay or Seurat Object, I wanted to pass output files passed by MACS2 which was run in the terminal. I…

Continue Reading CoveragePlot in Signac from MACS2 Object

Having a lot of trouble converting Gene Ranges to GeneID.

Having a lot of trouble converting Gene Ranges to GeneID. 0 I’m having trouble converting gene ranges to gene ids for mm10. For example I have a dataframe of “chromosome”, “start”, “end”, and I want the associated “GENE SYMBOL” for each row. I was looking online, which brought me to…

Continue Reading Having a lot of trouble converting Gene Ranges to GeneID.

sr bioinformatics job | United States

linkedin.com Apply on Website The British Dental Journal Bioinformatics Research Scientist to develop and apply innovative analytical approaches to study the mechanisms of normal hematopoiesis and blood diso… Role: Research Scientist, Category: Scientific, Size: 1-10 Sr Bioinformatics Research Scientist: The British Dental Journal Bioinformatics Research Scientist to develop and apply…

Continue Reading sr bioinformatics job | United States

Bioinformatics Analyst I – Job posted on UniversityJobs.com

We are looking for a Bioinformatics Analyst I. The position will involve analysis and visualization of large throughput multi-omics molecular profiles in various human disease models. Data types include single cell transcriptomics, proteomics, metabolomics and epigenomics analysis (MS proteomics and phosphoproteomics, scRNA-Seq, scATAC-Seq, scWGBS-Seq, scCut&Tag), and bulk tissue datasets spanning…

Continue Reading Bioinformatics Analyst I – Job posted on UniversityJobs.com

Senior Scientist Applied Bioinformatics Job In San Francisco, CA 94103| TechCareers

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

Continue Reading Senior Scientist Applied Bioinformatics Job In San Francisco, CA 94103| TechCareers

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…

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

GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq

Hi all, I am new to R and Seurat, and I am following Seurat tutorials to find anchors between RNA-seq and ATAC-seq data according to: Combining the two tutorials is difficult for a cell line data set I am using for SNARE-seq Human here. I managed to run the following…

Continue Reading GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq

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…

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

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…

Continue Reading Research Associate job with KINGS COLLEGE LONDON

HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

Reviewer #1 (Public Review): Droplet-based single-cell method development has stalled in the past years. The field has been overtaken by commercial solutions that optimized performance, but at much higher costs and without any possibility for customization. More recently, combinatorial indexing methods (e.g. SPLIT-seq) have gained popularity, requiring no specialized equipment…

Continue Reading HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics – Karolinska Institute – job portal

Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics Login and apply Do you want to contribute to improving human health? We are looking for an ambitious postdoctoral fellow with solid genome-wide bioinformatics and computational biology skills to join our highly accomplished team. We offer a stimulating environment in…

Continue Reading Postdoctoral position in bioinformatics – focused on single-cell immune transcriptomics – Karolinska Institute – job portal

Decoding gene regulation in the fly brain

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

Continue Reading Decoding gene regulation in the fly brain

Cellular and Molecular Atlas of the Macaque Dorsal Horn

Arokiaraj, Cynthia Mary (2022) Cellular and Molecular Atlas of the Macaque Dorsal Horn. Doctoral Dissertation, University of Pittsburgh. (Unpublished) Abstract The spinal cord dorsal horn occupies a key position in the central nervous system, as it is the first site of integration of somatosensory input from the periphery. Local interneurons…

Continue Reading Cellular and Molecular Atlas of the Macaque Dorsal Horn

tSNE and UMAP of scATAC-seq data looks like spaghetti

tSNE and UMAP of scATAC-seq data looks like spaghetti 0 I would like to use R to generate cluster my 20k cells from a single cell ATAC-seq experiment. I ran PCA then selected the first 50 components, which were put into tSNE’s normalize_input() then Rtsne(). This is the result I…

Continue Reading tSNE and UMAP of scATAC-seq data looks like spaghetti

vanheeringen-lab/seq2science – Giters

Seq2science is the attempt of the van heeringen lab to generate a collection of generic pipelines/workflows which can be used by complete beginners to bioinformatics and experienced bioinformaticians alike. Please take a look at our docs for help with installation, how to run it, and best practices. Our supported workflows:…

Continue Reading vanheeringen-lab/seq2science – Giters

How to interpret Nucleosome banding pattern in scATAC-Seq?

How to interpret Nucleosome banding pattern in scATAC-Seq? 0 Hello, I am following Signac vignette to perform QC on my single cell ATAC-Seq data. As per my understanding the vignette considers all cells with nucleosome signal > 4 to have a high nucleosomal signal strength and nucleosome signal is calculated…

Continue Reading How to interpret Nucleosome banding pattern in scATAC-Seq?

BAMboozle removes genetic variation from human sequence data for open data sharing

Strategy for stripping human sequence data of genetic information To lower the barriers in sharing sequence data, we propose, like others recently17, to remove information on genetic variation that could be used to infer the identity from aligned reads and compromises the privacy of the donor (Fig. 1a). Genetic variation, including…

Continue Reading BAMboozle removes genetic variation from human sequence data for open data sharing

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

Continue Reading Comparative cellular analysis of motor cortex in human, marmoset and mouse

Single cell RNA sequencing (scRNA-seq) in cardiac tissue

Introduction Cardiovascular diseases (CVDs) are the leading cause of death globally, taking an estimated 17.9 million (32.1%) lives in 2015, up from 12.3 million (25.8%) in 1990.1,2 CVDs are highly heterogeneous diseases involving a group of disorders of the heart and blood vessels, which include cardiomyopathy, hypertensive heart disease, heart…

Continue Reading Single cell RNA sequencing (scRNA-seq) in cardiac tissue

Bioinformatics Scientist in Diagenode – GrabJobs

Job Description Diagenode (a Hologic company) is an international biotech company that develops and commercializes innovative instruments and reagents systems for the life science research and molecular diagnostics. Founded in 2003, the Group is headquartered in Liège (Belgium), with subsidiaries in Denville (NJ, USA), in Toyama (Japan) and in Santiago…

Continue Reading Bioinformatics Scientist in Diagenode – GrabJobs

Bioinformatics Research Scientist

Bioinformatics Research Scientist – 93904 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab’s (LBNL, www.lbl.gov/) Joint Genome Institute Division (jgi.doe.gov/) has an opening for a Bioinformatics Research Scientist to join the team. In this exciting role, you will develop new computational methods to investigate gene regulation and regulatory sequence properties…

Continue Reading Bioinformatics Research Scientist

Lab Officer

The Dorrity group at EMBL Heidelberg is seeking a highly motivated computational biologist to act as a Laboratory Officer, helping to set up a new lab that promotes a welcoming and positive atmosphere. Our group uses single-cell genomics as a whole-organism phenotyping tool in zebrafish to (1) understand how different…

Continue Reading Lab Officer

Low mapping rate of 10X scATAC-seq reads

Low mapping rate of 10X scATAC-seq reads 0 Hey Guys, I’m working on a scATAC-seq project using 10X technologies. My samples including several different species. the problem is that for one species (2 sample in total), both of the mapping rate of reads from these 2 samples are very low…

Continue Reading Low mapping rate of 10X scATAC-seq reads

Postdoctoral Position in Immunotherapy, Virology, RNA Biology, Epigenetics, and Drug Design

– Advertisement – Postdoctoral Position in Immunotherapy, Virology, RNA Biology, Epigenetics, and Drug Design is available immediately for highly motivated recent Ph. Ds and/or MDs with strong training in any of the following disciplines: biochemistry, bioinformatics, immunology, molecular and cell biology, virology, medicinal chemistry or chemical biology to participate in the following projects…

Continue Reading Postdoctoral Position in Immunotherapy, Virology, RNA Biology, Epigenetics, and Drug Design

Lab Officer job with EMBL

The Dorrity group at EMBL Heidelberg is seeking a highly motivated computational biologist to act as a Laboratory Officer, helping to set up a new lab that promotes a welcoming and positive atmosphere. Our group uses single-cell genomics as a whole-organism phenotyping tool in zebrafish to (1) understand how different…

Continue Reading Lab Officer job with EMBL

How to merge Bulk ATAC-SEQ with scATAC-SEQ result?

How to merge Bulk ATAC-SEQ with scATAC-SEQ result? 0 Hello, I am using Signac for analyzing scATAC-SEQ for this experiment, we also have some Bulk ATAC-seq data. How can I show the bulk ATAC data as an extra track on Signac browser ? Or Can I merge scATAC-SEQ peak region…

Continue Reading How to merge Bulk ATAC-SEQ with scATAC-SEQ result?

How to generate feature Data(fData)

How to generate feature Data(fData) 0 I’m trying to analyze scATAC-seq data using Cicero, but I lack the metadata for peak(fData). I don’t know how to generate this metadata.Can someone tell me which tool can produce it? Note: This data was not generated using the 10X platform but Fluidigm C1….

Continue Reading How to generate feature Data(fData)

Sequencing file conversion

Sequencing file conversion 0 Hi, friends, I downloaded a set of scATAC-seq BAM files from an article database, and the author said that a BAM file is information about a cell. However, after a few days’ analysis of the script given by the author, I found that a CSV file…

Continue Reading Sequencing file conversion