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Floris Johan Maria Roos | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/floris-johan-maria-roos23 Feb 2024: T.M.A.L. Klem and dr. B.P.L. Wijnhoven) and started conducting research into the bile ducts, resulting in his first publication. ... Ludovic Vallier). Currently, he restarted working at the University of Cambridge as a clinical research fellow as well as -
The Split manuscript is presented at UKCBCB, NRP by Eleanor | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/split-manuscript-presented-ukcbcb-nrp-eleanor26 Jul 2024: Institute, Norwich Research Park, UK. -
Bisulfite sequencing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/bisulfite-sequencing26 Jul 2024: Search site. Core Bioinformatics group. Bisulfite sequencing. Bisulfite sequencing (BS) is a technique used to analyse patterns of DNA methylation. As DNA polymerase used in polymerase chain reaction (PCR) during a standard NGS protocol does not -
Image processing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/image-processing23 Feb 2024: Search site. Core Bioinformatics group. Image processing. We are developing an imaging processing pipeline which would help us achieve the 3D localization of the fluorescent molecules analysed with the DHPSF microscope. The video is first stacked -
Bulk mRNA-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/bulk-mrna-seq26 Jul 2024: To increase the visibility of CSCI research in the wider community, we create shiny apps for each bulk mRNA-Seq dataset which can be used to explore data and share more -
Clustering evaluation with ClustAssess | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/clustering-evaluation-clustassess26 Jul 2024: Search site. Core Bioinformatics group. Clustering evaluation with ClustAssess. The transition from bulk to single-cell analyses transformed the computational challenges for high-throughput sequencing data processing. At the core of single-cell -
core-bioinformatics-website-1000.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/core-bioinformatics-website-1000png-223 Feb 2024: Search site. Core Bioinformatics group. core-bioinformatics-website-1000.png. The truth is rarely pure and never simple. Oscar Wilde, The Importance of Being Earnest. core-bioinformatics-website-1000.png. Wellcome - MRC Cambridge Stem Cell -
Cell classification | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/cell-classification23 Feb 2024: Search site. Core Bioinformatics group. Cell classification. The semi-supervised cell classification project is based on a sequencing input. The task is the classification of the cells according to external labels (in this context the labels are -
feamiR - R package for predicting miRNA/mRNA interactions | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/feamir-r-package-predicting-mirnamrna-interactions26 Jul 2024: Search site. Core Bioinformatics group. feamiR - R package for predicting miRNA/mRNA interactions. Submitted by E. Lauzikaite on Tue, 12/01/2021 - 12:28. Our methods paper on feamiR, an R tool for charaterising and predicting miRNA/mRNA interactions -
Excellent end of the year - with two papers accepted in December! |…
https://www.corebioinf.stemcells.cam.ac.uk/news/excellent-end-year-two-papers-accepted-december26 Jul 2024: Search site. Core Bioinformatics group. Excellent end of the year - with two papers accepted in December! Submitted by Dr Irina Mohorianu on Wed, 28/12/2022 - 12:26. Two papers were accepted in December! bulkAnalyseR: An accessible, interactive -
Index sort data | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/index-sort-data23 Feb 2024: Search site. Core Bioinformatics group. Index sort data. For the optimisation of FACS-sorted cell cultures, we have generated a pipeline identifying discriminative genes from index sort data. The pipeline uses the depth distribution of features in -
Single cell RNA-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/single-cell-rna-seq26 Jul 2024: Search site. Core Bioinformatics group. Single cell RNA-Seq. Smart-Seq pipeline. Smart-seq and Smart-Seq2 are popular protocols for single-cell RNA-sequencing. With these protocols, 96-well plates are used with individual cells placed in each well. -
ChIP-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/chip-seq23 Feb 2024: Search site. Core Bioinformatics group. ChIP-Seq. Chromatin immunoprecipitation sequencing (ChIP-Seq) is used to analyse DNA-protein interactions. It infers the positions in a reference genome that are bound by the protein of interest. The list of -
Data denoising with noisyR | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/data-denoising-noisyr23 Feb 2024: Search site. Core Bioinformatics group. Data denoising with noisyR. The NoisyR manuscript was accepted to Nucleic Acids Research (June 2021)! -
The Noise paper is presented at UKCBCB, NRP by Ilias | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/noise-paper-presented-ukcbcb-nrp-ilias23 Feb 2024: Institute, Norwich Research Park, UK. -
Bisulfite sequencing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/bisulfite-sequencing23 Feb 2024: Search site. Core Bioinformatics group. Bisulfite sequencing. Bisulfite sequencing (BS) is a technique used to analyse patterns of DNA methylation. As DNA polymerase used in polymerase chain reaction (PCR) during a standard NGS protocol does not -
The Split manuscript is presented at UKCBCB, NRP by Eleanor | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/split-manuscript-presented-ukcbcb-nrp-eleanor23 Feb 2024: Institute, Norwich Research Park, UK. -
Analysis of mRNA-Seq alternative splicing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/analysis-mrna-seq-alternative-splicing26 Jul 2024: Search site. Core Bioinformatics group. Analysis of mRNA-Seq alternative splicing. Our pipeline uses rMATS to quantify alternative splicing events. rMATS detects five different types of events, as in the figure below. When quantifying events, two -
Bulk mRNA-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/bulk-mrna-seq23 Feb 2024: To increase the visibility of CSCI research in the wider community, we create shiny apps for each bulk mRNA-Seq dataset which can be used to explore data and share more -
NOTCH1 drives immune-escape mechanisms in B cell malignancies | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/notch1-drives-immune-escape-mechanisms-b-cell-malignancies26 Jul 2024: Search site. Core Bioinformatics group. NOTCH1 drives immune-escape mechanisms in B cell malignancies. Submitted by Dr Irina Mohorianu on Mon, 03/05/2021 - 06:28. A new paper in collaboration with Dr Ingo Ringshausen has been submitted to biorXiv.
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