Tag: ATAC-SEQ

Bioinformatics Engineer Job Opening in St. Louis, MO at Benson Hill

About Benson HillBenson Hill empowers innovators to develop more healthy, tasty and sustainable food by unlocking the natural genetic diversity of plants. Benson Hill’s CropOS™ platform combines machine learning and big data with advanced breeding techniques and plant biology to drastically accelerate and simplify the product development process. The CropOS…

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Bioconductor – epistack (development version)

DOI: 10.18129/B9.bioc.epistack     This is the development version of epistack; for the stable release version, see epistack. Heatmaps of Stack Profiles from Epigenetic Signals Bioconductor version: Development (3.15) The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq,…

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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:…

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How to define open or close gene in ATAC-seq?

How to define open or close gene in ATAC-seq? 0 May I ask how do you use your ATAC-seq data for post-alignment analysis? Here’s what I’m doing and I have a few problems: For example, there are two groups of samples, WT and KO. In order to define the peak…

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The Biostar Herald for Tuesday, November 23, 2021

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 Mensur Dlakic, Istvan Albert, and was edited…

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QIAGEN hiring Bioinformatics Scientist in United States

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

Retinoic acid affects the transcriptome of zebrafish endodermal cells To identify genes regulated by RA in zebrafish endodermal cells, we used the transgenic Tg(sox17:GFP) line which drives GFP expression in endodermal cells and allows their selection by fluorescence activated cell sorting (FACS). Tg(sox17:GFP) embryos were treated either with RA, BMS493…

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Identification of downstream effectors of retinoic acid specifying the zebrafish pancreas by integrative genomics

Retinoic acid affects the transcriptome of zebrafish endodermal cells To identify genes regulated by RA in zebrafish endodermal cells, we used the transgenic Tg(sox17:GFP) line which drives GFP expression in endodermal cells and allows their selection by fluorescence activated cell sorting (FACS). Tg(sox17:GFP) embryos were treated either with RA, BMS493…

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BIOINFORMATICIAN I PRATT SCHOOL OF ENGINEERING, Duke University Pratt School of Engineering, Durham, North Carolina

Summary We are looking for a talented and motivated individual to work with teams of Researchers and Scientists providing bioinformatics training, consulting, application development and support as part of the Center for Advanced Genomic Technologies (CAGT). Work performed • Contribute to the design, development, implementation, and testing of bioinformatic tools…

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University of Chicago hiring Bioinformatics Specialist in Chicago, Illinois, United States

DepartmentBSD PED – Section Administrator: Hematology, Oncology, and Stem Cell Transplantation About The Department The Section of Pediatric Hematology/Oncology provides care for patients and families with acute and chronic medical conditions, or other hematologic diseases, requiring the specialty knowledge and skills of Hematology, Oncology and Stem Cell Transplantation. Job Summary…

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Zhang Jin’s group reported that rRNA biogenesis regulates the fate transition of mouse ES-2C-like cells

On November 9, 2021, the Stem Cell and Regenerative Medicine Center of the Department of Basic Medicine, Zhejiang University School of Medicine/The First Affiliated Hospital of Zhejiang University School of Medicine/Zhejiang Liangzhu Laboratory Zhang Jin’s research group published a titled ” rRNA Biogenesis ” in Nature Communications . Regulates Mouse…

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CRISPR screens unveil signal hubs for nutrient licensing of T cell immunity

1. Chapman, N. M., Boothby, M. R. & Chi, H. Metabolic coordination of T cell quiescence and activation. Nat. Rev. Immunol. 20, 55–70 (2020). CAS  PubMed  Google Scholar  2. Kim, J. & Guan, K. L. mTOR as a central hub of nutrient signalling and cell growth. Nat. Cell Biol. 21,…

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Can I directly use MACS2 -t -c for ATACseq differential analysis on WT and KO sample?

Can I directly use MACS2 -t -c for ATACseq differential analysis on WT and KO sample? 0 I have ATACseq data from one WT sample and one KO sample, and want to find different peaks between them. Can I just use MACS2 -t -c for this purpose? For example, MACS2…

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ICH GCP – CRA jobs – Senior Scientist Bioinformatics

Parexel International Corporation USA – Any Region – Home Based The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for…

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100% Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks – University of Basel – job portal

100% Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks 2-2.5 year fixed-term contract available immediately or as agreed Understanding how a fertilized egg develops into a complex multicellular organism is one of the most fascinating topics in biology. The current challenge is to understand how genes function as part…

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Senior Scientist Bioinformatics at Parexel

The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for the BGM strategy and interpretation to other SBUs and clients….

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The Shh/Gli3 gene regulatory network precedes the origin of paired fins and reveals the deep homology between distal fins and digits

Significance In this study, we show that the inactivation of the gli3 gene in medaka fish results in the formation of larger dorsal and paired fins. These mutant fins display multiple radial bones and fin rays which resemble polydactyly in Gli3-deficient mice. Our molecular and genetic analyses indicate that the…

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Do you remove blacklisted regions before or after calling peaks?

Do you remove blacklisted regions before or after calling peaks? 0 Hello, I have a question about ATAC-seq processing. I’m working with mouse data where blacklisted regions typically get removed during processing. Some tutorials remove blacklisted regions from the BAM file before calling peaks. Others do this step afterwards on…

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Are scores different between paired and single end ?

TSS enrichement plot : Are scores different between paired and single end ? 0 I’m using this script from ATAqc to compute my TSS enrichment score for ATAC-seq data. But my values are pretty high, around 20+. I was wondering if this script, using the metaseq package was not counting…

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Seqanswers chip-seq

7219 07-11-2021 May 23,  · Although tools like FASTQC presents a graph showing sequence duplication levels understanding and interpreting duplication is complicated for many users by the fact they are working with single-end sequence data, e.g. most RNA-seq or ChIP-seq datasets. In the worst…

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Illumina Sequencing Seminar – NextSeq 2000 Applications for UMN Research

Attend this webinar to learn how to win a NextSeq 2000 P3 200-cycle flow cell for your lab – that’s A BILLION READS of sequencing for FREE. See terms and conditions.  Innovations in next-generation sequencing are helping the UMN genomics community ask – and answer – increasingly complex scientific questions. …

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Advanced Bioinformatics Data Scientist job at BenevolentAI, November 2021

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

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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…

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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…

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Bioconductor – Bioconductor 3.14 Released

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

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Junior Bioinformatician at the Lymphoma Genomic Laboratory

Junior Bioinformatician at the Lymphoma Genomic Laboratory Open position Junior Bioinformatician at the Lymphoma Genomic Laboratory Institute of Oncology Research (IOR) Bellinzona, Switzerland www.ior.usi.ch www.ior.usi.ch The Institute of Oncology Research (IOR) in Bellinzona, Switzerland, is a rapidly evolving,leading center for basic and translational research in oncology in Europe.IOR is affiliated…

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Active Motif hiring Bioinformatics Associate I/II in Carlsbad, California, United States

Position Title Bioinformatics Associate I/II Classification: Exempt Who is Active Motif? Active Motif, Inc. is a privately held global biotechnology company with the vision of bringing the field of epigenetics into personalized and precision medicine. Active Motif’s Bioinformatics group performs specialized transcriptomic- and epigenetics-based analyses for leading academic groups and…

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Measure genome-wide agreement of peaks in

Measure genome-wide agreement of peaks in 0 Is there an approach to measure agreement in epigenomic signals e.g. histone marks (continuous -log10 p-vals after peak calling)? This approach should also work across assays or cell types. For example, how similar is the DNAse-seq signal across Neutrophils, Monocytes and T-cells? Are…

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Scientist II, Cancer Immunologic Data Commons

Scientist II, Cancer Immunologic Data Commons Dana-Farber Cancer Institute Boston, MA Full Time PTL Remote: 2-3 days remote/wk The Department of Data Science seeks a Scientist II to lead the development of the Cancer Immunologic Data Commons at Dana-Farber. The Scientist II will work closely with the laboratories of Drs.Franziska…

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My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening?

My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening? 0 The binding matrix’s peak intervals (all of them) have a width =1 bp. I have set summit=False, summit=0, summit=True. All these parameters return 1 bp width. In fact,…

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Running ATAC-Seq pipeline from ENCODE

Running ATAC-Seq pipeline from ENCODE 1 SLURM is simply a scheduler on HPC systems. You can (probably) just save the script and run it as bash that_script.sh. Alternatively, consider the nf-core ATAC-seq pipeline: nf-co.re/atacseq Login before adding your answer. Traffic: 1212 users visited in the last hour Read more here:…

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why are all DiffBind tutorial’s ATAC-seq peak intervals 400 bp for all intervals?

why are all DiffBind tutorial’s ATAC-seq peak intervals 400 bp for all intervals? 1 I have followed DiffBind tutorial bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf I have found out that the returned count matrix’s peak intervals are always 400bp. Literally, all the peak intervals in the count matrix are 400 bp. I am wondering why…

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Bioinformatics Scientist, Discovery Biology – South San Francisco

Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway.Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from Stanford…

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Staff Bioinformatics Research Engineer and Senior Manager – South San Francisco

As a Staff Bioinformatic Research Engineer and Senior Manager at Freenome, you will lead a team responsible for developing and deploying bioinformatics research on Freenome’s ML research platform. You will lead and manage a team of Research Engineers working large multi-omic datasets, including whole-genome sequencing of cell-free DNA, extracellular small…

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How to import a BED file to ChIPseeker in order to visualize genome coverage plot?

How to import a BED file to ChIPseeker in order to visualize genome coverage plot? 1 Could you please explain how to connect the ATAC-Seq peak results discovered by DiffBind to be imported to ChIPseeker to get CHIP peaks coverage plot? For example, I have the following bed file. chr14…

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BIOINFORMATICS POSTDOC IN EVOLUTIONARY GENOMICS

A postdoctoral position (3 years with possible extensions) is available immediately in the evolutionary genomics group of Henrik Kaessmann. We are seeking highly qualified and enthusiastic applicants with strong skills in computational biology/bioinformatics, ideally also with experience in data mining and comparative or evolutionary genome analyses. We have been interested…

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Confused by MACS2 –scale-to option

Confused by MACS2 –scale-to option 1 Hi all, Quick Q regarding MACS2. The manual states that the –scale-to option serves to “scale the larger sample up to the smaller sample” or vice-versa. What exactly does it mean by this? Is this scaling only applied when multiple samples/reps are given? Or…

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Bioconductor – esATAC

DOI: 10.18129/B9.bioc.esATAC     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…

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BioSpace hiring Bioinformatics Scientist, Discovery Biology in South San Francisco, California, United States

DescriptionSurrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from…

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How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately?

How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately? 0 I am performing some ATAC-seq analysis. I would like to export the output files as a raw abundance profile so that I can analyze them on DESeq2 separately. I am aware that DiffBind contains…

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Our Ability Jobs – HERC: Metro New York & Southern Connecticut Bioinformatics Analyst in Einstein/Resnick

Employer Name: Albert Einstein College of Medicine Specific Responsibilities: Processing and mapping raw NGS RNA-seq, ChIP-seq, ATAC-seq, WGBS and other omics datasets. Analyzing RNA-seq, ChIP-seq, ATAC-seq, WGBS and other omics data sets generated in the lab for investigation of gene and chromatin regulatory networks in stem cells and cancer. Downloading…

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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…

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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

Significance The molecular mechanisms underlying pigmentation patterns in animals is to a large extent an unresolved mystery in biology. For example, compared with mammals, birds show a stunning diversity in pigmentation patterns. This study advances the knowledge concerning the mechanisms creating periodic pigmentation patterns in individual feathers. We show that…

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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…

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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…

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Uni Roles Australia: Grant-Funded Researcher, Bioinformatics

(Level A) $89,610 to $96,007 per annum and (Level B) $100,933 to $119,391 per annum plus an employer contribution of up to 17% superannuation may apply Two fixed-term, full-time positions available for three years Two exciting Bioinformatic opportunities in the newly established Adelaide Centre for Epigenetics (ACE) These two positions…

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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…

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How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect?

How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect? 0 I have processed my ATAC-seq reads and finally obtained MACs2 output bed files. I am at a loss to proceed from here to DESeq2 analysis. I will be thankful to you if could…

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Bioinformatics Scientist – Pittsburgh, PA

Job Description Bioinformatics Scientist Med-Immunology – Pennsylvania-Pittsburgh – (21005833) Computational Immunogenomics Core is seeking a full-time data Bioinformatics Scientist. The candidate will be responsible for developing and deploying analytical workflows for multi-omics data from single-cell and ensemble genomics studies. The candidate will report to the core director and work with…

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Baylor College of Medicine hiring Bioinformatics Analyst I in Houston, Texas, United States

SummaryAn open position for a Bioninformatic Analyst I is available in the Department of Ophthalmology, Baylor College of Medicine, Houston, TX. Will work alongside research scientists and clinicians with diverse backgrounds, including other bioinformaticians and computational biologists, molecular biologists, geneticist and immunologists. The work will focus on harnessing the power…

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NYU Langone Health hiring Bioinformatics Programmer in New York, New York, United States

Job ID: 1080691_RR00048323 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…

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ATAC-seq sample normalization

What you describe seems to be a difference in signal-to-noise ratio which is not uncommon. This is where more elaborate normalization methods such as TMM from edgeR or RLE from DESeq2 come into play. See the following links on why these methods are superior. The videos talk about RNA-seq but…

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Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols

Forum:Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols 2 Published in the RNA Journal in 2020 – this paper argues that if the original RNA amount in the different samples is different, TPM should not be used to find differentially expressed genes. www.ncbi.nlm.nih.gov/pmc/articles/PMC7373998/ Seems like…

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Normalization methods fro ATAC-seq data : bioinformatics

Hi people, Currently, I’m working on analyzing ATACseq data with the following pipeline: fastQC, adapter trimming, etc. BWA mem Remove duplicates, filter MAPQ Call peaks with Genrich for all samples Merge all sample peaks into reference peak set Count Tn5 cut sites with featureCounts At this point I have a…

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AI Rx | Computer Graphics World

Today, we can produce more biomedical data in about three months than we did in the past, with petabytes from just a single hospital. There is a deluge from various sources, such as patients’ medical records, medical instruments, lab work, and more. Likewise, in the research and development space, similar…

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Bioinformaticians (m/f/d) in Bioinformatics Core Unit

We are extending our bioinformatics team and are seeking for two enthusiastic bioinformaticians who would like to build and advance their career in translational cancer genomics and/or spearhead the implementation of next generation sequencing methodologies in routine cancer diagnostics and precision medicine. As a bioinformatician, you will conduct analyses of…

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Is there any software that can use ATAC-seq to identify super enhancer

Is there any software that can use ATAC-seq to identify super enhancer 1 Hello Everyone! Has anyone tried to identify super-enhancers by using ATAC-seq? I am wondering whether some one can recommend some software 🙂 Thanks a lot in advance for your comments and ideas! Best wishes Guandong Shang ATAC-seq…

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Bioinformatics Scientist – verwaltungs-jobs.ch

EPFL, the Swiss Federal Institute of Technology in Lausanne, is one of the most dynamic university campuses in Europe and ranks among the top 20 universities worldwide. The EPFL employs more than 6,000 people supporting the three main missions of the institutions: education, research and innovation. The EPFL campus offers…

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Bioinformatics Training Developer job with The Francis Crick Institute

Bioinformatics and Biostatistics Core Facility   Reports to: Head of Bioinformatics Core Facility   This is a full-time, permanent position on Crick Terms and Conditions of Employment.                                              …

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Bioinformatics Training Developer at The Francis Crick Institute

Short summary The position of Bioinformatics Training Developer will provide support to the bioinformatics training and development needs of research scientists primarily RNA-Seq, ATAC-Seq, ChiP-Seq and single-cell RNA-Seq. There are 2000 research scientists at the Francis Crick Institute. The role-holder will be located within the Bioinformatics and Biostatistics Core in…

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low FRiP(Fraction of Reads in Peaks) score in ATAC-seq

Hi. I’m doing ATAC-seq analysis of colon tissue. I analyzed 1)QC -> 2)Mapping -> 3)Post alignment processing(remove mt reads, duplicated reads, multi-mapped reads) -> 4)Peak calling order. However, as a result of calculating FRiP after peak calling using MACS2, the FRiP score was too low. No major problems were found…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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BIOINFORMATICS SCIENTIST job in in Dubai United Arab Emirates

Description Overview We are looking for a highly motivated and creative bioinformatics research scientist to develop and apply innovative analytical approaches to understand the genetic modifications that drive the development and response to therapy of blood tissues. The scientist will contribute ideas to implement automate and improve existing analysis methods,…

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Calling differential peaks on ATAC-seq data

Calling differential peaks on ATAC-seq data 0 My lab has recently run an ATAC-seq analysis on 3 biological conditions (Day 0, day 1 and day 7) with two replicates assigned to each. Once the data is finally generated, I will need to use some differential peak calling software to identify…

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Manager, Bioinformatics – Brain Science job in Seattle, WA | Allen Institute for Brain Science

Manager, Bioinformatics Brain Science 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…

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Feature selection

Feature selection 0 Hello, I am starting out with bulk ATAC data as bed files that include the read counts. I want to use this data for a package called MOFA, which requires these preprocessing steps: Normalisation: For count-based data such as RNA-seq or ATAC-seq we recommend size factor normalisation…

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edgeR parameters

edgeR parameters 0 I have a doubt regarding filtering results of edgeR I am not getting how to consider whether our genes which we got from edgeR are significant or not.We got 22,000 genes but I need to filter .The parameters set wereMin CPM =1, Log2fc=0,Pvalue adj=0.05. How should I…

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How to get Read Counts from MACS2 output files?

How to get Read Counts from MACS2 output files? 0 Hello, I am working with GEO datasets that supply both bigwig(bw) and bed files for each ATAC sample. I need the read counts/pile up value for downstream analysis, but the 6+4 narrow peak file format from MACS2 does not include…

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Comparative genomics provides insights into the aquatic adaptations of mammals

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (∼375 Mya) or the evolution of arboreal vertebrate species (∼160 Mya). When divergent lineages transition to the…

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Normalization and differential analysis in ATAC-seq data

Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…

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Research reveals a previously unknown role for a key transcription regulator linked to cancer

CTCF is a transcription factor that has been a research target due to its role in regulating a critical oncogene called MYC. Scientists at St. Jude Children’s Research Hospital have found direct evidence that CTCF governs chromatin accessibility, the process of opening tightly spooled DNA so that genes can be…

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Evidence for how a key transcription factor manages access to DNA

Credit: CC0 Public Domain CTCF is a transcription factor that has been a research target due to its role in regulating a critical oncogene called MYC. Scientists at St. Jude Children’s Research Hospital have found direct evidence that CTCF governs chromatin accessibility, the process of opening tightly spooled DNA so…

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Research provides evidence for how a key transcription factor manages access to DNA

Newswise — CTCF is a transcription factor that has been a research target due to its role in regulating a critical oncogene called MYC. Scientists at St. Jude Children’s Research Hospital have found direct evidence that CTCF governs chromatin accessibility, the process of opening tightly spooled DNA so that genes…

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A Closer Look at Type 1 Diabetes Causal Variants

By Allison Proffitt September 7, 2021 | Stephen Rich’s group at the University of Virginia along with John Todd’s team at the University of Oxford, have been tracing the genes responsible for type 1 diabetes for years. In 2009 the team conducted the largest GWAS metanalysis of type 1 diabetes,…

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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…

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Cedars-Sinai hiring Research Bioinformatician II – Knott Lab – Bioinformatics & Functional Genomics in Los Angeles, California, United States

The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II!This position provides excellent opportunities for continued scientific development and contributions at the interface between research and clinical translation in dynamic laboratory environments. At the Knott laboratory,…

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Research Bioinformatician II – Knott Lab

Research Bioinformatician II – Knott Lab – Bioinformatics & Functional Genomics Apply Now Share Requisition # HRC0654414 The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II! This position provides excellent…

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Solvuu hiring Bioinformatics Engineer in United States

Summary At Solvuu, we are building technology to revolutionize bioinformatics and data science. We are seeking an accomplished, self-motivated and ambitious bioinformatics engineer with a strong track record in developing, executing, and maintaining bioinformatics pipelines on AWS for biotech R&D. The successful candidate will have the opportunity to drive and…

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Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS at Agency for Science, Technology and Research Singapore

Job Description Job Responsibilities Familiar with the regulatory requirements specific to the lab. Be highly organized, able to multi-task, and pay close attention to details. Ability to accept direction from reporting officer and work in a collaborative manner to achieve development goals is important. Experience with next generation sequencing techniques…

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Honeycomb Biotechnologies hiring Bioinformatics Scientist, Single-Cell Genomics in Waltham, Massachusetts, United States

Company Description:  Honeycomb Biotechnologies is an early-stage company focused on making scalable solutions for storage and single cell genomic analysis of precious clinical samples. We enable translation of the rich biological information encoded in clinical specimens into high-resolution digital information, which can be queried and analyzed with sequencing. The resulting…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Computational Biologist at Chinook Therapeutics

Apply here Chinook Therapeutics Job Description: Computational Biologist Company: Chinook Therapeutics is a clinical-stage biotechnology company developing precision medicines for patients with kidney diseases. We apply our proprietary research platform to discover and develop therapeutics with novel mechanisms of action against key kidney disease pathways. Our development focus is on…

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Change location of ‘fragments’ in multiome Seurat file

Change location of ‘fragments’ in multiome Seurat file 1 Hello, I have a multiome dataset of RNA +ATAC seq that was given to me as an analysed .RData file by a collaborator. This is already integrated and fully analysed. When I attempt to visualise something in the multiome Seurat object…

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Emory University School of Medicine hiring Bioinformatics Analyst in Atlanta, Georgia, United States

JOB DESCRIPTION: Maintains software, cloud computing, and information networks in a cell and molecular biology laboratory. Applies a range of computational and statistical approaches to analyze complex datasets. Plays a lead role in computational research activities in consultation with Principal Investigator(s) and other lab members.  Establishes and maintains internal databases and…

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Bioinformatics analyst – stem cell biology

The Gracz lab is hiring a bioinformatics analyst to join our group in the Division of Digestive Diseases at Emory University. We are interested in understanding the genetic regulation of stem and progenitor cells in the intestine and liver. Our lab works at the intersection of cell biology and genomics…

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Why are there no peaks for Y chromosome in ATAC-seq?

Why are there no peaks for Y chromosome in ATAC-seq? 0 Hi! This was my first to do the ATAC-seq on a cell culture (which is from a 19-year old male individual). However, after data analysis, there are no peaks for the Y chromosome. Is there any possible explanation for…

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PNAS Papers on Turkish Populations, Pericentromeric Non-Coding RNA, Global Genome Repair

Editor’s Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted this week. An international team tallies genetic variation and population structure in present-day Turkey, using a combination of exome and whole-genome sequencing. Based on exome sequences for…

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Bioconductor – Single.mTEC.Transcriptomes

DOI: 10.18129/B9.bioc.Single.mTEC.Transcriptomes     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Single.mTEC.Transcriptomes. Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Bioconductor version: 3.8 This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data…

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Pericentromeric noncoding RNA changes DNA binding of CTCF and inflammatory gene expression in senescence and cancer

Significance During the aging process, senescent cells secrete inflammatory factors, causing various age-related pathologies. Thus, controlling the senescence-associated secretory phenotype (SASP) can tremendously benefit human health. Although SASP seems to be induced by the alteration of chromosomal organization, its underlying mechanism remains unclear. Here, it has been revealed that noncoding…

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What’s the biology meaning of multi-peak in a region

What’s the biology meaning of multi-peak in a region 0 Hi, everyone Recently, I am anlysising ATAC-seq data. And I find in some region, there will be a phenomenon that mulit peak will link together. While in some region, there may be only one peak. I am very curious what…

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University of Pittsburgh hiring Bioinformatics Scientist in Pittsburgh, Pennsylvania, United States

Computational Immunogenomics Core is seeking a full-time data Bioinformatics Scientist. The candidate will be responsible for developing and deploying analytical workflows for multi-omics data from single-cell and ensemble genomics studies. The candidate will report to the core director and work with interdisciplinary teams to analyze datasets e.g., single-cell and bulk…

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Research Assistant in Bioinformatics and Computational Biology

Job Description Research Assistant in Bioinformatics and Computational Biology 12 month fixed contract, Full time Melbourne, Australia The Peter MacCallum Cancer Centre is Australia’s only public hospital solely dedicated to cancer and one of an elite group of hospitals worldwide to have its own integrated cancer research program and laboratories. …

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Best current tool for deconvolution of bulk sample

Best current tool for deconvolution of bulk sample 0 Just asking around for some general opinions: I will receive bulk RNA-seq and ATAC-seq samples from the spleen (they are all immune cells). To have an idea about the percentages of each individual cell type in the bulk sample, what would…

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