Tag: ATAC

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)?

Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me3)? 0 Hi, I have called ChIP-seq broadpeak (H3K9me3, H3K27me3) using SICER2 in mm10. The peak looks good and consistent with the IGV findings. Is there any good tools to annotate these broad peaks to coding genes? I know GREAT(great.stanford.edu/public/html/)…

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Guided exercises to practice ATAC-seq/ChIP-seq analysis?

Guided exercises to practice ATAC-seq/ChIP-seq analysis? 1 Hello everyone! I was wondering if there is any way to practice ATAC-seq/ChIP-seq analysis with guided exercises. Do you know of any resource? RNA-seq would be great too, although I have seen many of them online, if there is any particularly good resource,…

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lazy loading failed, unable to load shared object rtracklayer.so

Hello! I am working on analyzing a dataset I created with the 10x Chromium Single Cell Multiome kit. In order to add gene annotation to the ATAC data, I am trying to install and use the “EnsDb.Mmusculus.v79” and “BSgenome.Mmusculus.UCSC.mm10” packages with bioconductor. The same ERROR has come up repeatedly whenever…

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Scientist, Bioinformatics Job in Carlsbad, CA – Jobot

Scientist, Bioinformatics – ChIP-seq, RNA-seq, Hi-C, ATAC-seq, WGS, Exome-seq This Jobot Job is hosted by: Emmet NittoAre you a fit? Easy Apply now by clicking the “Apply Now” button and sending us your resume.Salary: $90,000 – $115,000 per year A bit about us: Based in Carlsbad, CA, we are a…

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Scientific Manager – Immunology (Nanostring, Exome, RNA, CHIP) job with University of Texas MD Anderson Cancer Center

The Immunology department at MD Anderson Cancer Center seeks to determine the fundamental cellular and molecular mechanisms of a wide range of processes by which the body recognizes and eliminates pathogens and use these findings to unleash the patient’s own immune system against previously treatment-resistant cancers. Treating the immune system…

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Bioinformatics Scientist Job – Karkidi

Experience 2-4 year Salary $170,000-$180,000 Location San Francisco, CA, USA Job Function Bioinformatics Scientist Industry Information Technology Qualification Degree in Computer Science, PhD Degree, Degree in Bioinformatics, Degree in Computational Biology, Degree in Computational Science, Degree in Biomedical Engineering Key Skills Bioconductor, CRISPR technology, Data science techniques, Large data sets,…

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M/F Postdoc In Molecular Biology And Genomics

Description Organisation/Company: CNRS Research Field: Biological sciences › Biological engineering Chemistry › Biochemistry Physics › Biophysics Researcher Profile: First Stage Researcher (R1) Application Deadline: 01/12/2022 23:59 – Europe/Brussels Location: France › MONTPELLIER Type Of Contract: Temporary Job Status: Full-time Hours Per Week: 35 Offer Starting Date: 01/01/2023 – Genomics experiments:…

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Quantifying Peak Height Difference in ATAC-seq

Quantifying Peak Height Difference in ATAC-seq 1 Hi, everyone. How would I go about quantifying the peak height difference of a particular gene between two a wild type and a mutant in ATAC-seq? A colleague mentioned possibly calculating a moving average of read depths for smoothing and then comparing the…

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Bioinformatics Programmer 3 – 119617

UCSD Layoff from Career Appointment: Apply by 10/25/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 11/3/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The Bioinformatics Programmer’s will apply complex bioinformatics concepts to design and…

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Phenotypic plasticity and genetic control in colorectal cancer evolution

Sample preparation and sequencing The method of sample collection and processing is described in a companion article (ref. 23). Sequencing and basic bioinformatic processing of DNA-, RNA- and ATAC-seq data are included there as well. Gene expression normalization and filtering The number of non-ribosomal protein-coding genes on the 23 canonical chromosome pairs…

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Syracuse University Online Employment Site | Post Doc

Job # 076742 Job Title Post Doc – Genomics and Bioinformatics Location Syracuse, NY Pay Range Commensurate with Experience FLSA Status Exempt Hours As determined by PI. Job Type Full-time Rank Post Doc Campus Syracuse, NY Unionized Position Code Not Applicable Job Description The Ahmed-Brimah Lab at Syracuse University invites…

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Butterfly wing pattern ground plan is manipulated by non-coding regulatory DNA, study says

Butterfly wing patterns have a basic plan to them, which is manipulated by non-coding regulatory DNA to create the diversity of wings seen in different species, according to new research. The study, “Deep cis-regulatory homology of the butterfly wing pattern ground plan,” published as the cover story in the Oct….

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Postdoctoral Associate in Plant Genetics, Genomics and Bioinformatics job with University of Florida

Classification Title: Postdoc Aso Job Description: The Institute of Food and Agricultural Sciences is committed to creating an environment of inclusive excellence that affirms diversity across a variety of dimensions, including ability, class, ethnicity/race, gender identity and expression. Inclusive excellence is the active process of including and respecting everyone as…

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Inferring and perturbing cell fate regulomes in human brain organoids

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

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Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements

Baylin, S. B. & Jones, P. A. A decade of exploring the cancer epigenome – biological and translational implications. Nat. Rev. Cancer 11, 726–734 (2011). CAS  PubMed  PubMed Central  Article  Google Scholar  Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease….

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Project Scientist – Knott Lab – Bioinformatics & Functional Genomics

Are you passionate about applying genomics, computer science, and probability theory to study cancer progression? The Knott laboratory at Cedars-Sinai Medical Center is searching for a Project Scientist with a strong background in tumor biology and the immune microenvironment to lead single cell-based omics studies of immunotherapy clinical trials being…

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue.

Abstract Single-nucleus ATAC sequencing (snATAC-seq) employs a hyperactive Tn5 transposase to gain precise information about the cis-regulatory elements in specific cell types. However, the standard protocol of snATAC-seq is not optimized for all tissues, including the brain. Here, we present a modified protocol for single-nuclei isolation from postmortem frozen human…

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Senior/Junior Postdoctoral fellow in Bioinformatics

Highly motivated candidates are invited to apply for a 2-year postdoctoral position (with the possibility of an extension) in the laboratory of Assoc. Professor David Gomez-Cabrero in the Biological and Environmental Sciences and Engineering (BESE) Division at the King Abdullah University of Science and Technology (KAUST) (www.kaust.edu.sa/en/study/faculty/david-gomez-cabrero). The project investigates…

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Broad Institute Study Evaluates Ultima Genomics Sequencer for Single-Cell RNA-Seq

NEW YORK – Results from single-cell RNA sequencing libraries run on the new Ultima Genomics UG100 are “very similar” to those produced on Illumina’s NovaSeq, a new study says. However, the platform shows bias against 3′ gene expression libraries. Led by researchers from the Broad Institute as part of a…

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Differential enrichment of H3K9me3 in intrahepatic cholangiocarcinoma | BMC Medical Genomics

Sia D, Tovar V, Moeini A, Llovet JM. Intrahepatic cholangiocarcinoma: pathogenesis and rationale for molecular therapies. Oncogene. 2013;32(41):4861–70. CAS  Article  Google Scholar  Sungwan P, Lert-Itthiporn W, Silsirivanit A, Klinhom-On N, Okada S, Wongkham S, Seubwai W. Bioinformatics analysis identified CDC20 as a potential drug target for cholangiocarcinoma. PeerJ. 2021;9:e11067. Article …

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Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

lncRNA expression according to breast cancer clinicopathological subtypes To identify lncRNAs expressed by specific breast cancer subtypes or associated with clinicopathological features, we analyzed RNA-sequencing data from two large independent breast cancer cohorts: SCAN-B (n = 3455)17 and TCGA-BRCA (n = 1095). We focused on lncRNAs annotated in the Ensembl18 v93 non-coding reference transcriptome…

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Postdoctoral Research Fellow /Associate – Epigenomics/Bioinformatics in Cincinnati, OH for Cincinnati Children’s Hospital Medical Center

Details Posted: 11-Aug-22 Location: Cincinnati, Ohio Salary: Open Categories: Academic / Research Description Computational postdoctoral positions in bioinformatics and epigenomics (computational/experimental) are available at Dr.Yaping Liu’s lab in the Division of Human Genetics. One of the research directions in Dr. Liu’s group is to study single-cell multi-omics data to understand…

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atac seq – Can I use a tool for highly variable gene selection for selecting highly variable “bins” from an ATACSeq dataset?

I’m working with ATACSeq data from multiple tissue/cell types. The data is binned in 1 megabase bins. I’d like to identify the bins that are “highly variable” across the different tissue types. I can’t seem to find a tool to do this, like there exists for identifying highly variables genes…

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HIC2 controls developmental hemoglobin switching by repressing BCL11A transcription

Orkin, S. H. Globin gene regulation and switching: circa 1990. Cell 63, 665–672 (1990). Sankaran, V. G. & Orkin, S. H. The switch from fetal to adult hemoglobin. Cold Spring Harb. Perspect. Med. 3, a011643 (2013). PubMed  PubMed Central  Article  CAS  Google Scholar  Huang, P. et al. Comparative analysis of…

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Postdoctoral Associate in Bioinformatics, Genomics or AI/Machine Learning

Job Description:    We are seeking a post-doctoral associate in the Intelligent Comparative Oncology Lab directed by Dr. Jon Kim in the College of Veterinary Medicine at the University of Florida (UF). Kim lab focuses on developing novel diagnostic and clinical applications in the field of comparative oncology by utilizing…

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Protocol for single-nucleus ATAC sequencing and bioinformatic analysis in frozen human brain tissue

. 2022 Jun 17;3(3):101491. doi: 10.1016/j.xpro.2022.101491. eCollection 2022 Sep 16. Affiliations Expand Affiliations 1 Department of Neurobiology and Behavior, University of California, Irvine, Irvine, CA, USA. 2 Institute for Memory Impairments and Neurological Disorders (MIND), Irvine, CA, USA. 3 Mathematical, Computational and Systems Biology Program, UC Irvine, Irvine, CA, USA….

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Postdoctoral Associate- Genomics and Bioinformatics job with Baylor College of Medicine

Summary An open position for a Postdoctoral Fellow in human molecular genetics/genomics field is available in the laboratory of Rinki Ratnapriya, Ph.D. at the Department of Ophthalmology, Baylor College of Medicine, Houston, TX. The Ratnapriya lab focuses on harnessing the power of genomic technologies to address translational and clinical bioinformatic…

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Bioinformatics postdoc Position at Harvard Medical School

Our educational programs advance Harvard Medical School’s core mission to alleviate human suffering by nurturing a diverse group of leaders and future leaders in both clinical care and biomedical inquiry. These individuals are on the front lines of medicine and science serving individuals and populations locally, nationally, and globally. Post…

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Postdoctoral Researcher in Computational Biology at Karolinska Institute, Sweden 2022

Postdoctoral Researcher in Computational Biology is available for doctoral degree candidates in Bioinformatics, Computer science, Mathematics, Biostatistics, Neuroscience, or similar field at the Department of Clinical Neuroscience, Karolinska Institute, Sweden 2022 Qualification Details Qualified to be employed as a postdoctor is one who has obtained a doctorate or has equivalent…

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A*STAR RESEARCH ENTITIES hiring #SGUnitedJobs Bioinformatics Specialist, Lab of Cancer Epigenetic Regulation, GIS in Singapore, Singapore

The Laboratory of Cancer Epigenetic Regulation, helmed by GIS Executive Director Patrick Tan, is seeking a Bioinformatician to join a new multi-institutional effort targeting the genetic basis of cancer to create novel therapies and diagnostics. Led by an award-winning thought leader in the field of Asian gastrointestinal cancer research with…

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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…

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Bioinformatics Programmer I – 115257

UCSD Layoff from Career Appointment: Apply by 04/04/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 04/14/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The Department of Medicine (DOM) is the largest department within the…

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SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

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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…

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Bioinformatics Specialist at The University of Chicago in Chicago, IL – 4091

Job Info Department BSD 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…

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Postdoc / Research Scientist in Bioinformatics and Computational Genomics

Job Description Are you a computer geek with a strong interest in genomics? Do you want to use your computational skills to solve human diseases? At the Department of Neurology at Harvard Medical School and Brigham & Women’s Hospital, we have two vacant positions: postdoctoral fellow and research scientist in…

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Nucleic Acids Research Papers on DAVID Update, ChIP-Atlas, RNA Splicing Assay

Researchers at the Frederick National Laboratory for Cancer Research and the National Institutes of Health describe a 2021 update to the bioinformatics tool DAVID, designed for functional annotation and functional gene enrichment analyses. Along with updates to annotation types and other “Knowledgebase” features, the latest version of the DAVID Gene…

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Postdoctoral Scientist – Knott Lab

Details Posted: 09-Apr-22 Location: Los Angeles, California Type: Full-time Salary: Open Categories: Staff/Administrative Internal Number: HRC0544032D Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal…

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Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks

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 of gene regulatory networks (GRNs) that control the proliferation and patterning of progenitor and stem cells during embryonic development….

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Dublin, Ireland | Bioinformatics Research Fellow: Understanding the production of CAR-T cell therapies

Job:Dublin, Ireland | Bioinformatics Research Fellow: Understanding the production of CAR-T cell therapies 0 Cell therapy is the transfer of intact, live cells into a patient to treat or cure a disease. Cell-based immunotherapy and in particular, modified-cell immunotherapy such as CAR-T, has been delivering spectacular results for cancer patients…

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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

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Postdoctoral Fellow – Genomics and Bioinformatics

An open position for a Postdoctoral Fellow in human molecular genetics/genomics field is available in the laboratory of Rinki Ratnapriya, Ph.D. at the Department of Ophthalmology, Baylor College of Medicine, Houston, TX. The successful applicant will work on functional characterization of AMD-GWAS signals to understand the molecular basis of observed…

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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…

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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…

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Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

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Sr. Bioinformatics Scientist-Project Manager – 114267

#114267 Sr. Bioinformatics Scientist-Project Manager Filing Deadline: Mon 2/14/2022 UCSD Layoff from Career Appointment: Apply by 02/02/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 02/14/2022. Eligible Special Selection clients should contact their Disability Counselor for assistance. The UCSD…

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identify and remove adapter sequence

identify and remove adapter sequence 2 Hi all, I am trying to identify the adapter sequences of my ATAC-sequencing data. The way I tried to achieve this was to send the fastq file to FastQC. Hoping the sequence would be picked and showed in the report. In the report, there…

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Droplet Genomics Debuts New Microfluidic Screening Platform, Touting Throughput, Flexibility

NEW YORK – Droplet Genomics, a European technology company headquartered in Vilnius, Lithuania, is rolling out a new droplet microfluidic platform for high-throughput screening for a variety of research applications. CEO Juozas Nainys said the firm delivered the first of the instruments to customers at the end of 2021 after having…

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The Identification of Prognostic and Metastatic Alternative Splicing in Skin Cutaneous Melanoma

Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…

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Postdoctoral Scientist – Knott Lab – Bioinformatics & Functional Genomics

Requisition # HRC0544032C Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient…

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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….

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Bioinformatics Analyst in Evanston, IL for Northwestern University

Details Posted: 23-Dec-21 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Center for Genetic MedSalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to…

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Research Fellow (Computational Biology, Bioinformatics, Machine Learning) at NANYANG TECHNOLOGICAL UNIVERSITY

Job Description A Research Fellow position is available in the Transcription and Chromatin Regulation Laboratory, School of Biological Sciences, Nanyang Technological University, Singapore. We are seeking a talented and motivated Research Fellow in computational biology or data analytics who is interested in developing machine learning approaches to study the changes…

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Arrange the size of subplots in plotHeatmap deeptools figure

Arrange the size of subplots in plotHeatmap deeptools figure 1 Hi all, I am trying to generate a 10×10 (10 bw files + 10 bed files) figure using deeptools but I am having trouble arranging the size of subfigures. I want the subfigures in the same size but if I…

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Research Fellow (Computational Biology, Bioinformatics, Machine Learning)

Research Fellow (Computational Biology, Bioinformatics, Machine Learning) – Career at NTU University in Singapore. Apply for NTU University job and get your career at NTU University! Company: NTU University Job Type: Full Time Work Place: Singapore Salary: SGD 10000 / Month Job Description A Research Fellow position is available in…

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Is there a database of bioinformatics tools & databases?

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

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Diffbind3 dba.plotMA error

Hello, I am analyzing some ATAC-seq from flies using Diffbind3.0.8 and EdgeR. I initially ran dba.analyze() with the default peak size of 401 and was able to graph the results using dba.plotMA and dba.plotVolcano when my contrasts were evaluated using both EdgeR and DESEQ2. After resizing the peaks to 100…

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Bioinformatics Scientist, Discovery Biology job with Surrozen

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…

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Postdoctoral Fellow job with Cleveland Clinic – Genomic Medicine Institute

We are seeking multiple Experimental and Bioinformatics research positions (including Postdoctoral Research Fellows and Research Associate) to join the Alzheimer’s Network Medicine and Artificial Intelligence (AI) research group (www.lerner.ccf.org/gmi/cheng/) led by Dr. Feixiong Cheng at the Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, and Department of Molecular Medicine at…

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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…

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DiffBind in Bioconda

DiffBind in Bioconda 1 @riba-michela-6472 Last seen 7 weeks ago Italy Hi, I was going to check my scripts for differential ATAC-seq Binding Analysis and wanted to install an updated version of “DiffBind” Bioconductor package, in particular version 3.2.6 or 3.2.4 in whcih a specific little bug that was present…

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Lead Bioinformatics Analyst Pharmacogenomics – Great Jobs for Bright People

A Lead Bioinformatics Analyst position is available in the field of pharmacogenomics in the Savic laboratory. The primary research focus of the Savic laboratory involves studying the gene regulatory architecture of pediatric leukemia and genomic responses to antileukemic agents in order to define how the noncoding portion of the human genome impacts…

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Bioinformatics Scientist job with University of Pittsburgh

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 interdisciplinary teams to analyze…

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How to merge samples of the same cell type to do differential peak calling?

How to merge samples of the same cell type to do differential peak calling? 1 Hi! Now I have 6 ATAC-seq samples which have been aligned to hg19 and called peaks by MACS2. 3 of them are from A cells and the other are from B cells. Now I’m going…

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Bioinformatics Postdoctoral Research Associate, Long Lab job with Benaroya Research Institute at Virginia Mason

Benaroya Research Institute at Virginia Mason (BRI) has a bold mission: Predict, prevent, reverse and cure immune system diseases, from autoimmune disease to cancer to COVID-19. We examine the immune system in both health and disease to understand how disorders start and how to rebalance the immune system back to…

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Postdoc (3 years) in Bioinformatics and 3D genome modeling

Position as Postdoctoral Research Fellow available at the Department of Biosciences. The appointment is a fulltime position and is made for a period of three years, and devoted to carrying out a project entitled URGE-3D, funded by the Norwegian Research Council. No one can be appointed for more than one…

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Early Career Scientist – Computational Biology and/or Bioinformatics job with Tsibris Lab, Brigham and Women’s Hospital, Harvard Medical School

We seek an outstanding and highly motivated early-career scientist in the fields of computational biology and/or bioinformatics. The position will involve novel integrated multimodal analyses of single cell datasets in blood immune cells and tissue. Qualified candidates will have an opportunity to design research projects that leverage cutting-edge approaches that…

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Bioinformatics opening at VC-backed Cambridge, USA Bio-IT Startup

The role: As part of the bioinformatics team, you’ll lead the development and prototyping of our flagship bioinformatics workflows (such as: RNAseq (single-cell, bulk, spatial), ChIP-Seq, ATAC-seq (single-cell and bulk), proteomics, etc.). For a given pipeline, you’ll research available analysis methods, compare and contrast existing bioinformatics tooling options, and define…

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Research Fellow in B-cell Epigenomics job with UNIVERSITY OF SOUTHAMPTON

Cancer Sciences Location: Southampton General Hospital Salary: £31,406 Full Time Fixed Term (until 30/09/2022) Closing Date: Monday 06 December 2021 Reference: 1616921CM Applications are invited for a Post-doctoral Research Fellow to join the Cancer Genomics Research Group in the School of Cancer Sciences. This exciting Cancer Research UK-funded post aims…

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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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ecDNA hubs drive cooperative intermolecular oncogene expression

1. Wu, S. et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699–703 (2019). 2. Gorkin, D. U., Leung, D. & Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14, 762–775 (2014). CAS  PubMed  PubMed Central  Google Scholar  3. Zheng, H….

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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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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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