Categories
Tag: ATAC
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…
Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L
Loss of ASH2L prevents cell proliferation We have studied the molecular and cellular consequences of Ash2l loss in mouse embryo fibroblasts (MEFs) with floxed Ash2l alleles and an inducible Cre-ER recombinase (iMEF-Ash2lfl/fl-Cre-ER). While the knockout of Ash2l was rapid, the downstream effects, including the decrease in promoter-associated H3K4me3, altered gene…
High levels of duplication in ATAC gDNA control?
High levels of duplication in ATAC gDNA control? 0 Hi, I’ve been analysing an ATAC-seq dataset and I’m currently deduplicating the reads (after removing mitochondrial reads). Although I get something on the order of 15% reduction in reads when deduplicating my samples, I’ve gotten about a 90% reduction in reads…
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…
Conserved and divergent gene regulatory programs of the mammalian neocortex
Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…
Single-cell analysis of chromatin accessibility in the adult mouse brain
Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…
Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain
Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…
Topological structures and syntenic conservation in sea anemone genomes
Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article ADS CAS PubMed Google Scholar Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article ADS CAS PubMed PubMed Central Google Scholar Srivastava, M….
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…
Atac-seq shift single-end data
Atac-seq shift single-end data 0 Hi, Atac-seq +4 -5 shift is required when aiming for nucleotide resolution analysis (e.g. TF motif discovery). The available tools (e.g. alignmentSieve from deeptools) look for properly paired reads and perform the shifting. Can this idea anyhow be applied to the single-end data? I know…
Thyroid hormone-regulated chromatin landscape and transcriptional sensitivity of the pituitary gland
Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…
Bioinformatics Software Engineer Consultant Job at ProCogia
ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…
DNA polymerases in precise and predictable CRISPR/Cas9-mediated chromosomal rearrangements | BMC Biology
Cell culture The human endometrial carcinoma HEC-1-B cells were cultured in the modified Eagle’s medium (MEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a 5% (v/v) CO2 incubator. The human embryonic kidney HEK293T cells were cultured in the Dulbecco’s modified Eagle’s medium (DMEM) supplemented…
Senior Bioinformatics Scientist – 127022
UCSD Layoff from Career Appointment: Apply by 12/08/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 12/20/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. This position will work a hybrid schedule which includes a combination…
Downsampling ATAC-seq BAM files
Downsampling ATAC-seq BAM files 0 Hi all, I have two ATAC datasets sequenced on two sequencers with different read depths. I would like to downsample the one with higher read depth to match that of the other dataset as we are observing batch effects following integration. To my understanding, I…
Genetic risk converges on regulatory networks mediating early type 2 diabetes
Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article ADS PubMed Google Scholar Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…
Yes .. BBMap can do that!
NOTE: This collection was originally posted at SeqAnswers.com. Creating a copy here to preserve the information.Part I is available here: Yes .. BBMap can do that! – Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)Part II is available here: Yes .. BBMap can…
Are 10x cellranger-arc ATAC bam files deduplicated?
Are 10x cellranger-arc ATAC bam files deduplicated? 1 I am working with some atac files from cellranger-arc v.2.0. I was wondering whether the atac_possorted_bam.bam produced as the output was deduplicated? I believe the fragment files that are generated detect duplicate reads (as represented by reads with the fifth column >=…
Identification of constrained sequence elements across 239 primate genomes
De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…
Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability
Szekanecz, Z. et al. Autoinflammation and autoimmunity across rheumatic and musculoskeletal diseases. Nat. Rev. Rheumatol. 17, 585–595 (2021). Article CAS PubMed Google Scholar Rosenblum, M. D., Remedios, K. A. & Abbas, A. K. Mechanisms of human autoimmunity. J. Clin. Invest. 125, 2228–2233 (2015). Article PubMed PubMed Central Google Scholar Wang,…
Benchmarking of deep neural networks for predicting personal gene expression from DNA sequence highlights shortcomings
Avsec, Ž. et al. Effective gene expression prediction from sequence by integrating long-range interactions. Nat. Methods 18, 1196–1203 (2021). Article CAS PubMed PubMed Central Google Scholar Avsec, Ž. et al. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nat. Genet. 53, 354–366 (2021). Article CAS PubMed PubMed Central Google…
ProCogia hiring Bioinformatics Software Engineer Consultant in Vancouver, British Columbia, Canada
ProCogia is a data consulting firm headquartered in Vancouver, BC with employees and clients across the United States and Canada. We specialize in Data Operations, Data Engineering, BI & Analytics, Data Science & Bioinformatics across a broad range of industries including Telecom, Pharma, Biotechnology, Retail, Logistics, Technology, Financial Services, Media…
MSL2 ensures biallelic gene expression in mammals
Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…
Epigenetic Changes Dictate Cancer’s Course
Understanding the intricate interplay between genetics and cancer progression has long captivated the scientific community. While genetic mutations have been the main focal point in oncology, recent strides have illuminated the profound influence of epigenetic modifications in the development of cancer. In a recent study published in the journal Nature,…
Reviewing Revvity (NYSE:RVTY) and 10x Genomics (NASDAQ:TXG)
10x Genomics (NASDAQ:TXG – Get Free Report) and Revvity (NYSE:RVTY – Get Free Report) are both medical companies, but which is the better investment? We will contrast the two companies based on the strength of their dividends, risk, analyst recommendations, valuation, institutional ownership, profitability and earnings. Volatility and Risk 10x…
fragments.tsv.gz file in ATAC seq
fragments.tsv.gz file in ATAC seq 0 Hi all, I looked at some tutorials ATAC seq. They use fragments.tsv.gz at the beginning of the analysis. For my ATAC seq data, I have fastq, bam and bw files but not fragment file. So the fragments files will be created from fastq files,…
Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification
Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…
2024 Summer Intern – Oncology Bioinformatics – GRED Job In California – Genentech
The Position 2024 Summer Intern – Oncology Bioinformatics – gRED Oncology Bioinformatics supports and expands oncology research within the larger gRED organization, with our team focusing on cancer immunogenomics and cell therapies. One aspect of these efforts is genomic sequence analysis and optimization, especially in the context of regulatory…
Use of IDR after running MACS3 for ATAC-seq data
Use of IDR after running MACS3 for ATAC-seq data 0 Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice) I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:…
TF Footprinting using HINT ATAC module from RGT
I was successful in running the first three commands of HINT ATAC as shown below following this tutorial github.com/sufyazi/sufyazi.github.io/wiki/TF-Footprinting-Tutorial-using-HINT-ATAC-module-from-RGT-toolbox rgt-hint footprinting –atac-seq –paired-end –organism=mm10 –output-location=/XXX –output-prefix=Afootprints A.mRp.clN.sorted.bam A.mRp.clN_peaks.narrowPeak rgt-hint footprinting –atac-seq –paired-end –organism=mm10 –output-location=/XXX –output-prefix=Afootprints B.mRp.clN.sorted.bam B.mRp.clN_peaks.narrowPeak rgt-motifanalysis matching –organism=mm10 –input-files Afootprints.bed Bfootprints.bed But when I ran the command below…
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…
Diffbind low p-value but high FDR
Diffbind low p-value but high FDR 0 I guess my issue is related to this post support.bioconductor.org/p/85487/#85490. Here is the dba.report(DBA,th=1, bCounts=TRUE) results. One of the peaks clearly shows a significant difference in IGV (And we also expected it to be changed) and has a small p.vaule but the FDR…
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…
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,…
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer
Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…
Predicting cancer subtypes from nucleosome profiling of cell-free DNA
Abstract Modern cancer treatments take advantage of genomic differences between tumors to kill cancer cells using targeted approaches. Typically, this requires a tumor biopsy in order to get tissue for phenotypic and genotypic analysis. However, in late-stage cancer, surgical biopsies of metastases may not be part of the standard of…
University of Alabama at Birmingham hiring BIOINFORMATICIAN I in Birmingham, Alabama, United States
Position Summary: The primary role is to execute a variety of data management and analysis tasks, ensuring the quality, reproducibility, and efficiency of processes related to high-dimensional data. You will collaborate with study investigators and fellow bioinformatics professionals within the department to contribute to high-quality, reproducible research across various scientific…
Transcriptional and epigenetic regulators of human CD8+ T cell function identified through orthogonal CRISPR screens
Developing an epigenetic screening platform in human T cells Staphylococcus aureus Cas9 (SaCas9) has been extensively used for genome editing in vivo as its compact size (3,159 bp) relative to the conventional Streptococcus pyogenes Cas9 (SpCas9) enables packaging into adeno-associated virus26,27,28. However, SaCas9 has not been widely used for targeted gene…
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma
Statistical methods Statistical tests, test statistics and P values are indicated where appropriate in the main text. Categorical associations were established using the chi-squared test of independence if n > 5 for all categories and Fisherʼs exact test otherwise. For both tests, the Python package scipy.stats v1.5.3 implementation was used64. Multiple hypothesis corrections…
argument is of length zero
Hi Diffbind community! I have been encountering some errors creating dba object because the Diffbind package can not load the files. I tried using the aligned bam files after creating sample sheet but have been getting following error: “Error in if ((length(callers) == 1) & (callers[1] == “counts”)) { :…
Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics
Job:Bioinformatics Research Associate in Transcriptomics, Epigenomics and Multi-omics 0 @jp-carter-15371 Last seen 3 hours ago Nashville, TN Creative Data Solutions (Vanderbilt University, Nashville, TN, USA) is seeking a Bioinformatics Research Associate, who will be involved in a variety of life sciences projects and be directly involved in workflows and pipelines…
Insights gained from single-cell analysis of chimeric antigen receptor T-cell immunotherapy in cancer | Military Medical Research
Zhu J, Ke Y, Liu Q, Yang J, Liu F, Xu R, et al. Engineered Lactococcus lactis secreting Flt3L and OX40 ligand for in situ vaccination-based cancer immunotherapy. Nat Commun. 2022;13(1):7466. Article CAS PubMed PubMed Central Google Scholar Evans ER, Bugga P, Asthana V, Drezek R. Metallic nanoparticles for cancer…
The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology job in San Francisco, California at University of California – San Francisco
The Singh Lab – Junior/Assistant/Associate/Full Specialist in Bioinformatics or Computational Biology SCHOOL OF MEDICINE – Department of Anatomy Description The lab of Dr. Param Singh at UCSF (www.singhlabucsf.org) is looking for a Junior/Assistant/Associate/Full Specialist with expertise in bioinformatics or computational biology to join our team and contribute to new and…
DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle
Overview of this study In this study, we measured the DNA methylome from mouse liver and skeletal muscle, integrated the data with the transcriptome and proteome of these mouse tissues22,23, and examined how tissue-dominant protein and gene expression were associated with DNA hypomethylation (Fig. 1). In this study, we measured DNA…
Simplified Single-Cell Isolation
Sponsored content brought to you by Many increasingly used applications, such as cell line engineering and sequencing (including ATAC-seq and RNA-seq) along with single-cell genomics, require single-cell isolation as a starting point. But the cost and complexity of cell sorters have traditionally relegated this technology to larger lab groups or…
CRISPR screening in hematology research: from bulk to single-cell level | Journal of Hematology & Oncology
Transcriptomics CROP-seq [46] Jurkat Poly-A CRISPRko Cas9 119 – 5798 (+ 1320 cells with NT gRNA) Lentiviral DROP-seq RNA Perturb-seq [43, 44] K562 Barcode CRISPRi dCas9-KRAB UPR epistasis screen: 9 triplet combinations UPR Perturb-seq experiment: 91 Up to 3 gRNAs in a single vector UPR epistasis screen: 15006 UPR Perturb-seq experiment:…
Bioinformatics Analyst job with University of Miami
Current Employees: If you are a current Staff, Faculty or Temporary employee at the University of Miami, please click here to log in to Workday to use the internal application process. To learn how to apply for a faculty or staff position using the Career worklet, please review this tip…
Epigenetic regulation during cancer transitions across 11 tumour types
Specimen data All samples for MM, OV, BRCA, PDAC, UCEC, CRC, CESC/AD, SKCM and HNSCC, as well as 2 NATs for GBM and 1 NAT for ccRCC were collected with informed consent in concordance with Institutional Review Board (IRB) approval at the School of Medicine at Washington University in St…
Unable to Generate Motif class for zebrafish scATAC data using Signac package.
Unable to Generate Motif class for zebrafish scATAC data using Signac package. 0 Hi, I am analyzing zebrafish scATAC data using Signac package. The package does not allow me to create motif class. It gives me the following error after running AddMotif function. `ATAC <- AddMotifs( object = ATAC, genome…
Cross validate RNA-seq and ATAC-seq
Cross validate RNA-seq and ATAC-seq 1 Hi, I have RNA-seq and ATAC-seq for the same samples. I wish to cross-validate two datasets. I got DEGs from RNA-seq and DARs from ATAC-seq. I annotated DARs (differentially accessible regions) using Homer, so I got their nearest gene information. Would it be reasonable…
Allen Institute hiring Scientist III – Molecular Biology & Bioinformatics in Seattle, Washington, United States
Scientist III – Molecular Biology & Bioinformatics 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…
Downstream analysis during sc-ATAC seq
Downstream analysis during sc-ATAC seq 0 Hi, I have been analysisg a single-cell ATAC seq data published in a Cell Paper titled “Single-cell analyses reveal key immune cell subsets associated with response to PD-L1 blockade in triple-negative breast cancer” (DOI: 10.1016/j.ccell.2021.09.010), and I have retrieved the ATAC seq data from…
Bioconductor – Bioconductor 3.18 Released
Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…
MICA: a multi-omics method to predict gene regulatory networks in early human embryos
Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…
Mouse mm10 chr4:22,481,383-22,489,763 UCSC Genome Browser v455
Custom Tracks Adiposehidedensesquishpackfull Cerebellumhidedensesquishpackfull Cortexhidedensesquishpackfull Liverhidedensesquishpackfull Lunghidedensesquishpackfull Sintesthidedensesquishpackfull Spleenhidedensesquishpackfull mouse_7_core ATAC Adipose Rep1hidedensefull ATAC Adipose Rep2hidedensefull ATAC Cerebellum Rep1hidedensefull ATAC Cerebellum Rep2hidedensefull ATAC Colon Rep1hidedensefull ATAC Colon Rep2hidedensefull ATAC Cortex Rep1hidedensefull ATAC Cortex Rep2hidedensefull ATAC Heart Rep1hidedensefull ATAC Heart Rep2hidedensefull ATAC Liver Rep1hidedensefull ATAC Liver Rep2hidedensefull ATAC…
How to import filtered_tf_bc_matrix and add it to my anndata object?
Hello, I am analyzing some ATAC samples and I would like to add the motif information to my objects. So far I have imported my fragment files and clustered the cells. I would like to add the filtered_tf_bc_matrix information so I can do differential expression based on the motifs but…
Analytical Scientist in Bioinformatics Software/Pipeline Development at The Institute of Cancer Research
Job Details Under the leadership of Dr Syed Haider, we are seeking to appoint a highly motivated analytical scientist with experience in genomic and transcriptomic data analysis to join our Breast Cancer Research Bioinformatics Group. We employ cutting-edge data-mining techniques in collaboration with experimental investigators to identify new molecular markers of breast…
NGS Training | Top NGS Courses | Online Training | RNASeq | Genome Variant Detection
NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…
Genome-wide epigenetic dynamics during postnatal skeletal muscle growth in Hu sheep
Global changes of the transcriptome during postnatal muscle growth The number of myofibers is thought to remain fixed following birth, muscle fiber hypertrophy growth is the primaryway of muscle growth. The average CSA is generally used to measure the hypertrophy of skeletal muscle fibers. To systematically identify the growth of postnatal…
How to subsample ATAC fragment file?
How to subsample ATAC fragment file? 0 Hello, I have 5 single cell ATAC samples that I have started analyzing with SnapATAC2. My WT samples have about twice the amount of cells as my knock outs and that is why I would like to do the analysis with all the…
What do HAP A1 and HAP A2 mean in plink –freqx output?
What do HAP A1 and HAP A2 mean in plink –freqx output? 0 let’s assume: SNP1 = A/C, SNP2 = T/G, SNP3 = A/G, SNP4 = C/T how do I know what C(HAP A1) C(HAP A2) mean? is HAP A1 = ATAC and HAP A2 = CGGT? This wouldn’t make…
GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership | Genome Biology
Models for single-cell ATAC-seq data In single-cell ATAC-seq data, \(x_{ij}\) is the number of unique reads mapping to peak or region j in cell i. Although \(x_{ij}\) can take non-negative integer values, it is common to “binarize” the accessibility data (e.g., [19, 74, 133,134,135]), meaning that \(x_{ij} = 1\) when…
Chromatin compartmentalization regulates the response to DNA damage
Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…
Bioinformatics Scientist/Analyst/Postdoc – Job posted on PostdocJobs.com
OverviewFounded in 1946, the Oklahoma Medical Research Foundation (OMRF) is among the nation’s oldest, most respected independent, nonprofit biomedical research institutes. OMRF is dedicated to understanding and developing more effective treatments for human diseases, focusing on critical research areas such as Alzheimer’s disease, cancer, lupus, Multiple Sclerosis, and cardiovascular disease….
Research Associate / Postdoc (m/f/x) job with TECHNISCHE UNIVERSITAT DRESDEN (TU DRESDEN)
The Center for Regenerative Therapies Dresden (CRTD), an institute of the Center for Molecular and Cellular Bioengineering (CMCB), is a research center at the TUD Dresden University of Technology with currently over 20 research groups. The research focus of CRTD lies in regeneration and stem cell research from fundamental research…
MUSC College of Health Professions hiring UNIV – Research Specialist III- Bioinformatician – Department of Neuroscience in Charleston, South Carolina, United States
Job Description SummaryThe brand-new MUSC Bioinformatics Core (BioCM) is seeking a superb bioinformatician to develop scientific tools for single cell multiomics and other next-generation sequencing methods. Under the supervision and guidance of BioCM staff and Dr. Stefano Berto, the bioinformatician will contribute to NGS analysis projects, and they will work…
Postdoctoral Fellow – Bioinformatics and Computational Biology – Dr. Maitituoheti Job
Job Description Computational postdoctoral/research associate position is available for a highly motivated candidate with a background in bioinformatics and a passion for exploring the epigenomic alterations in cancer progression and therapy resistance using the single cell and bulk high-throughput ChIP-Sequencing, ATAC-Seq, Hi-ChIP, etc. approaches. Projects will focus on the biology…
Differential gene score in single cell experiment
Hello Biostars’ community, long time not posting here, hope you are all doing well 🙂 I have a single cell multiome (RNA+ATAC in the same nuclei) experiment, made of 20 samples across 4 time points (tpCtrl,tpA,tpB,tpC) of a disease. At a more advanced stage of my analysis, I am not…
Bioinformatics Programmer I – 126046
UCSD Layoff from Career Appointment: Apply by 10/18/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/27/2023. Eligible Special Selection clients should contact their Disability Counselor for assistance. The Moores Cancer Center (MCC) is one of just 54 NCI-designated…
Harvard’s Jason Buenrostro wins MacArthur grant for genetics work
The youngest of this year’s class of MacArthur “genius grant” fellows, 35-year-old Jason Buenrostro was just a graduate student when he pioneered a technique that’s become a mainstay for studying how cells regulate gene expression. While doing his doctoral work at Stanford University, with geneticists William Greenleaf and Howard Chang,…
Senior Bioinformatics Software Engineer, Multi-omic data processing and integration job with Stanford University
Senior Bioinformatics Software Engineer, Multi-omic data processing and integration🔍School of Medicine, Stanford, California, United StatesNew📁Information Technology Services📅4 hours ago Post Date📅101019 Requisition # Stanford University is seeking a Software Developer 1 to join the Kundaje lab in the Department of Genetics to lead and assist with the development of data…
Postdoctoral Associate- Bioinformatics – Job posted on PostdocJobs.com
Postdoctoral Associate- Bioinformatics – Job posted on PostdocJobs.com CONNECT WITH US : Postdoctoral Associate- Bioinformatics Job Number: Date Posted: Oct 12, 2023 Application Deadline: Open Until Filled Baylor College of Medicine Location: Houston, TX Job Number: 7185729 (Ref #: 17415-en_US) Posting Date: Oct 12, 2023 Application Deadline: Open Until Filled…
Postdoctoral Associate- Bioinformatics – Job posted on DiversityWork.com
Job Description Summary We are seeking a highly motivated and skilled Postdoctoral Fellow with a strong background in bioinformatics and a keen interest in single-cell omics. The selected candidate will join a dynamic and interdisciplinary research team dedicated to advancing our understanding of neurological diseases at the single-cell level….
Design model includes sex but only one female
I have a question about how DESeq2 handles design models which include a parameter that only applies to a single sample in the dataset. For context, we are using DESeq2 to capture differential chromatin accessibility due to age differences (adult vs juvenile) using CUT&RUN data from the venom glands of…
Bioinformatics Analyst – NYU Langone Medical Center
NYU Grossman School of Medicine is one of the nation’s top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral part of NYU…
From DNA Damage to Neuron Disruption: MIT’s Comprehensive Alzheimer’s Analysis
MIT scientists conducted an in-depth study on Alzheimer’s, analyzing the genomic, epigenomic, and transcriptomic changes in the disease. Discoveries span from disrupted gene patterns and epigenomic changes to the significance of microglia and DNA damage in neurons. They aim to use AI for drug discovery and have shared their data…
DiffBind dba.count() crash/can’t finish problems
I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet: I run Diffbind with the following codes, but it crashed every time on dba.count . it can finished Computing summits… Recentering peaks… Reads will be counted as Paired-end. But have this…
Senior Bioinformatics Scientist (Hybrid) Job Description
Job Description We are seeking a highly motivated bioinformatics scientist to join our global research team. The scientist will evaluate, develop, and optimize computational methods to analyze next-generation sequencing datasets in support of our drug discovery and development programs, and will produce bioinformatics pipelines that can be operated on high-performance computing…
Post-doctoral Fellow in Chromosome Biology and Epigenetics job with UNIVERSITY OF SOUTHAMPTON
School of Biological Sciences Location: Highfield Campus Salary: £34,980 to £37,099 per annum Full Time Fixed Term for 3 years Closing Date: Thursday 12 October 2023 Interview Date: To be confirmed Reference: 2473223BJ The Yuen lab investigates how chromosomes segregate equally through epigenetic regulation of the centromere. We…
ATAC-Seq and RPKM
ATAC-Seq and RPKM 1 Hi, I want to calculate RPKM of ATAC-Seq data but I do not find any script for that. As I am new to bioinformatics, so would be grateful if somebody guide me. RPKM ATAC-Seq and • 216 views The simplest would be to read the matrix…
SeqMatic Adds Visium Spatial Gene Expression to its 10x Genomics Certified Service Provider Portfolio
Fremont, California – October 2nd, 2023 – SeqMatic, a leading provider of next-generation sequencing (NGS) and omics services, is proud to announce that it has received Visium Spatial Gene Expression and Visium Spatial Gene Expression for FFPE Certifications from 10x Genomics. These certifications further demonstrate SeqMatic’s commitment to delivering efficient…
Microglial states and their impact on Alzheimer’s disease
In a recent study published in Cell, researchers examined 152,459 microglial transcriptomes from 443 individuals, identifying 12 transcriptional states and their relationship to Alzheimer’s disease (AD). Study: Human microglial state dynamics in Alzheimer’s disease progression. Image Credit: Nefedova Tanya/Shutterstock.com Background Microglia play crucial roles in brain cells, changing states to…
Miami University hiring Student Specialist – Bioinformatics in Oxford, Ohio, United States
Job TitleStudent Specialist- BioinformaticsSalary/Grade$12.00 / hrHours Per Week12Duration Of AppointmentAcademic yearJob SummaryBioinformatics analyses of large molecular biology datasets, including, but not limited to RNA-Seq, amplicon (16S, 18S, ITS) metagenomics/microbiome analyses, WES, WGS, ATAC-Seq, and proteomics (MS).Essential DutiesWork independently, good written and oral communication skills, formal report writing, and ability to…
Is APAC Edging Closer to Clinical Application of Single-cell Tech?
Asia Pacific (APAC) is expected to be a major contributor to the growth of single cell technology as the market is driven by factors such as the growing demand for personalised medicine, advancements in sequencing technologies, and the increasing use of single cell analysis in drug discovery. While Japan is…
Do you wonder what 10X data looks like on the newest Illumina sequencer?
in Industry News, Information 18 hours ago 626 Views Single-cell analysis can help tease apart heterogeneity in complex cell populations, distinguishing cell types and revealing dynamic cell states. The 10x Genomics Chromium Single Cell Multiome ATAC + Gene Expression prepares sequencing-ready libraries to simultaneously profile gene expression and chromatin accessibility from the…
Bioinformatics Analyst – St. Jude Children’s Research Hospital
The Laboratory of Dr. Hongbo Chi in the Department of Immunology at St. Jude Children’s Research Hospital is seeking a highly motivated Bioinformatics Analyst to lead the analysis of multi-omics studies in molecular and systems immunology and immuno-oncology. We are particularly interested in understanding the metabolic programs, signaling pathways and…
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively
Why should ATAC-seq mapped reads be shifted +4 and -5 for +strand and -strand, respectively 2 Hello, I have started to analyze ATAC-seq data and I have a quick question about tag-shift process in data processing. In my best knowledge, there is 9-bp duplication created by DNA repair of the…
ATAC-seq +4 -5 shift
ATAC-seq +4 -5 shift 3 Dear all, I saw having the mapped reads have +4 and -5 shift in ATAC-seq is a common practice. Some place says “reads should be shifted + 4 bp and − 5 bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair…
Boston Children’s Hospital hiring Bioinformatics Scientist in Boston, MA
At Boston Children’s Hospital, the quality of our care – and our inclusive hospital working environment – lies in the diversity of our people. With patients from local communities and 160 countries around the world, we’re committed to reflecting the spectrum of their cultures, while opening doors of opportunity for…
The bam file used for DiffBind?
The bam file used for DiffBind? 1 When use DiffBind to compare ATAC-seq data we need bam file for sample sheet. What kind of bam file do we need? Can I use the bam file which already removed duplicates? OR just primary bamfile? DiffBind ATAC-seq • 351 views You should…
Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ?
Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ? 2 Hello everyone, I launched an analysis of some ATACseq data across different conditions. I launch the cf-core ATACseq pipeline v 1.2.1: nf-co.re/atacseq/2.1.2/docs/output In the output I have a PCA generated by…
Methamphetamine-induced region-specific transcriptomic and epigenetic changes in the brain of male rats
Jayanthi, S., McCoy, M. T. & Cadet, J. L. Epigenetic Regulatory Dynamics in Models of Methamphetamine-Use Disorder. Genes 12, 1614 (2021). Article CAS Google Scholar Meredith, C. W., Jaffe, C., Ang-Lee, K. & Saxon, A. J. Implications of chronic methamphetamine use: a literature review. Harv. Rev. Psychiatry 13, 141–154 (2005)….
Single-nucleus transcriptomes reveal spatiotemporal symbiotic perception and early response in Medicago
Nutman, P. S. Centenary lecture. Phil. Trans. R. Soc. B 317, 69–106 (1987). Google Scholar Kelly, S., Radutoiu, S. & Stougaard, J. Legume LysM receptors mediate symbiotic and pathogenic signalling. Curr. Opin. Plant Biol. 39, 152–158 (2017). Article CAS PubMed Google Scholar Roy, S. et al. Celebrating 20 years of…
How-to: Profile the epigenome
The epigenome regulates the expression of genes without altering their underlying DNA sequence. Comprising a dynamic landscape of chemical modifications and structural changes to DNA and its associated histone proteins, the epigenome wields profound influence over cellular identity and function. Epigenetic mechanisms, such as DNA methylation and histone modifications, form…
Acquisition of fluoroquinolone resistance in E. coli
1Division of Clinical Infectious Diseases & Chemotherapy, Tohoku Medical and Pharmaceutical University, Sendai, Japan; 2Department of Pharmacy, Japan Labor Health and Welfare Organization Tohoku Rosai Hospital, Sendai, Japan Correspondence: Takumi Sato, Division of Clinical Infectious Diseases & Chemotherapy, Tohoku Medical and Pharmaceutical University, 4-4-1, Komatsushima, Aoba-ku, Sendai, 981-8558, Japan, Tel…
Spike-in normalization in ATAC-Seq with DiffBind
Spike-in normalization in ATAC-Seq with DiffBind 0 Dear all, we are planning to do an ATAC-Seq experiment in human cell lines and we must correct for batches from different time-points. Therefore, we want to use spike-in normalization as described in the DiffBind vignette. For reasons of practicability, we would prefer…
Silencing Epigenetic Complexes Re-sensitizes Drug-Resistant Cancer Cells
Lung cancers often become resistant to targeted drug therapies. Researchers discovered a way to overcome one type of epigenetic resistance. Targeted anti-cancer therapies dramatically improve patient outcomes in EGFR-mutant lung adenocarcinomas,1 but many tumors acquire resistance to these drugs over time. Because there are numerous ways in which cancers become…
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…
ATAC-seq troubleshoot – Just Noise
ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…
The localization of centromere protein A is conserved among tissues
Earnshaw, W. C. & Migeon, B. R. Three related centromere proteins are absent from the inactive centromere of a stable isodicentric chromosome. Chromosoma 92, 290–296 (1985). Article CAS PubMed Google Scholar Choo, K. H. Centromerization. Trends Cell Biol. 10, 182–188 (2000). Article CAS PubMed Google Scholar Marshall, O. J., Chueh,…