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Rafael Kollyfas | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/rafael-kollyfas23 Feb 2024: My primary research interest lies in the application of machine learning in healthcare, particularly in omics. -
core-bioinformatics-website-1000.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/core-bioinformatics-website-1000png-227 Jul 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 -
feamiR_feature_heatmap.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamirfeatureheatmappng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_feature_heatmap.png. Alt Text:. Heatmap showing the discriminative power of features across the 5 feature-selection methods on the full H. sapiens positive set. Title Text:. Heatmap showing the -
BletchleyFebruary2023_3.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/bletchleyfebruary20233jpg23 Feb 2024: Search site. Core Bioinformatics group. BletchleyFebruary2023_3.jpg. 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 Institute. Jeffrey -
BletchleyFebruary2023_2.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/bletchleyfebruary20232jpg23 Feb 2024: Search site. Core Bioinformatics group. BletchleyFebruary2023_2.jpg. 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 Institute. Jeffrey -
Cell classification | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/cell-classification27 Jul 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 -
cameroncrawford_photo.jpeg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/cameroncrawfordphotojpeg-023 Feb 2024: Search site. Core Bioinformatics group. cameroncrawford_photo.jpeg. 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 Institute. Jeffrey -
Teaching material | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/teaching-material23 Feb 2024: Search site. Core Bioinformatics group. Teaching material. Core Bioinformatics group. Teaching. All teaching materials from the Core Bioinformatics group can be found on our GitHub page. CSCI Teaching. Introduction to RNAseq. This repository -
William (Billy) Dunn | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/william-billy-dunn23 Feb 2024: Search site. Core Bioinformatics group. William (Billy) Dunn. BSc (MedSci) (2013). MBChB (Hons) (2015). MSc Bioinformatics (2017). MRCP (2020). PhD in Stem Cell Biology (2022-present). I completed my intercalated BSc, medical degree and MSc at the -
Kendig (Kenny) Sham | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/kendig-kenny-sham23 Feb 2024: My aim is to expand my Machine Learning skills and apply classic and novel approaches on RNA-seq datasets (at bulk and single-cell level) while working as a Research Assistant -
Ilias Moutsopoulos | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/ilias-moutsopoulos23 Feb 2024: I am currently working with dr. Irina Mohorianu as a research assistant at the Cambridge Stem Cell Institute, developing pipelines for the analysis of diverse types of data. ... Nucleic Acids Research. Contact Details. im383 at cam.ac.uk. Available for -
Toby Milne-Clark | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/toby-milne-clark23 Feb 2024: disciplines. Consequently, I studied for an MSc in Statistics and Data Science with the Université Grenoble Alpes during which I worked in multiple Research Assistant roles for various laboratories at the ... I am keen on applying machine learning -
BletchleyPark_BombeMachine.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/bletchleyparkbombemachinejpg23 Feb 2024: Search site. Core Bioinformatics group. BletchleyPark_BombeMachine.jpg. 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 Institute. -
Index sort data | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/index-sort-data27 Jul 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 -
nclusters-pac-text.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/nclusters-pac-textpng-023 Feb 2024: Search site. Core Bioinformatics group. nclusters-pac-text.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 Institute. Jeffrey -
feamiR_statistical_heatmap.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamirstatisticalheatmappng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_statistical_heatmap.png. Alt Text:. Heatmaps illustrating chi-squared and Fisher exact p-values when assessing differences in positional proportions of single nucleotides (left) and dinucleotides (right) -
bletchleypark_september2023_2.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/bletchleyparkseptember20232jpg23 Feb 2024: Search site. Core Bioinformatics group. bletchleypark_september2023_2.jpg. 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 Institute. -
bletchleypark_september2023_1.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/bletchleyparkseptember20231jpg23 Feb 2024: Search site. Core Bioinformatics group. bletchleypark_september2023_1.jpg. 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 Institute. -
ChIP-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/chip-seq27 Jul 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-noisyr27 Jul 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-ilias27 Jul 2024: Institute, Norwich Research Park, UK. -
Irina Mohorianu | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/irina-mohorianu23 Feb 2024: Nucleic Acids Research. bulkAnalyseR: An accessible, interactive pipeline for analysing and sharing bulk multi-modal sequencing data. -
BletchleyPark_AlanTuringStatue.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/bletchleyparkalanturingstatuejpg23 Feb 2024: Search site. Core Bioinformatics group. BletchleyPark_AlanTuringStatue.jpg. 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 Institute. -
feamiR_kernel_hyperparameter.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamirkernelhyperparameterpng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_kernel_hyperparameter.png. Alt Text:. Performance of SVM model with a variety of kernels on seed features using 10-fold cross-validation on a set of H. sapiens miRNA/mRNA interactions validated by -
noisyR is now published in NAR | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/news/noisyr-now-published-nar23 Feb 2024: Search site. Core Bioinformatics group. noisyR is now published in NAR. Submitted by Dr Irina Mohorianu on Sun, 04/07/2021 - 15:35. Illias' paper was acceped in NAR! Well done, Ilias! noisyR: Enhancing biological signal in sequencing datasets by -
feamiR_numtrees_hyperparameter.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamirnumtreeshyperparameterpng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_numtrees_hyperparameter.png. Alt Text:. Performance of RF model with a range of number of trees, from 1 to 100, using 10-fold cross-validation on a set of H. sapiens miRNA/mRNA interactions validated by -
Publications | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/publications23 Feb 2024: Search site. Core Bioinformatics group. Publications. Core Bioinformatics group. Publications. Methods papers. 2022. ClustAssess: tools for assessing the robustness of single-cell clustering. Arash Shahsavari, Andi Munteanu, Irina Mohorianu. doi:. -
We welcome Alex and Andi! | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/news/we-welcome-alex-and-andi23 Feb 2024: Search site. Core Bioinformatics group. We welcome Alex and Andi! Submitted by Dr Irina Mohorianu on Sun, 04/07/2021 - 15:37. We welcome Alex Calderwood (post-doc) and Andi Munteanu (intern) to the group. We're looking forward to some interesting -
Eleanor Williams | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/eleanor-williams23 Feb 2024: Presented as a poster at RECOMB 2022 (Conference on Research in Computational Molecular Biology) at University of California San Diego, USA. ... Nucleic Acids Research. feamiR: Feature selection based on Genetic Algorithms for predicting miRNA-mRNA -
Nextflow | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/nextflow23 Feb 2024: Search site. Core Bioinformatics group. Nextflow. enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. Nextflow is becoming a powerful -
The Split manuscript is presented at UKCBCB, NRP by Eleanor | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/split-manuscript-presented-ukcbcb-nrp-eleanor27 Jul 2024: Institute, Norwich Research Park, UK. -
Bisulfite sequencing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/bisulfite-sequencing27 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 -
Bulk mRNA-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/bulk-mrna-seq27 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 -
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 -
Clustering evaluation with ClustAssess | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/clustering-evaluation-clustassess27 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 -
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 -
feamiR - R package for predicting miRNA/mRNA interactions | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/feamir-r-package-predicting-mirnamrna-interactions27 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-december27 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 -
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 -
Single cell RNA-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/single-cell-rna-seq27 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. -
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 -
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. -
Analysis of mRNA-Seq alternative splicing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/analysis-mrna-seq-alternative-splicing27 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 -
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-malignancies27 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. -
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. -
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
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