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bulkAnalyseR is on biorxiv! | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/news/bulkanalyser-biorxiv23 Feb 2024: Search site. Core Bioinformatics group. bulkAnalyseR is on biorxiv! Submitted by Dr Irina Mohorianu on Fri, 04/02/2022 - 06:20. A new preprint (describing bulkAnalyseR) is on bioarxiv:. “bulkAnalyseR: An accessible, interactive pipeline for -
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 -
imohorianu.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/imohorianujpg23 Feb 2024: Search site. Core Bioinformatics group. imohorianu.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 Cheah -
Group members | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/group-members23 Feb 2024: Research Assistant (2022 - ). MPhil Student in Health Data Science (2022- ); Primary supervisor: Irina Mohorianu. ... Chenge (Joanna) Du (December 2022 - July 2023) Research Assistant, Cambridge Cancer Institute, CRUK. -
Cameron Crawford | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/cameron-crawford23 Feb 2024: Search site. Core Bioinformatics group. Cameron Crawford. I started my Bachelor's degree in Computer Science at the University of Cambridge in 2021 and joined the Core Bioinformatics group as an intern at the end of my first year. Throughout my -
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 -
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 -
dorinmiron.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/dorinmironjpg23 Feb 2024: Search site. Core Bioinformatics group. dorinmiron.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 Cheah -
Data | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/data23 Feb 2024: Search site. Core Bioinformatics group. Data. Core Bioinformatics group. Data. Data acquisition, traceability and curation. We operate a strict policy of experimental record-keeping with traceable identifiers for each experiment that are linked to -
Arash Shahsavari | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/staff/arash-shahsavari23 Feb 2024: Search site. Core Bioinformatics group. Arash Shahsavari. MSc Complex Adaptive Systems (2019). In 2019 I finished my master’s studies at Chalmers University of Technology, in Gothenburg, Sweden, with a thesis on single-cell RNA-seq clustering and -
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 -
KendigSham.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/kendigshamjpg23 Feb 2024: Search site. Core Bioinformatics group. KendigSham.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 Cheah -
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)! -
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. -
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 -
feamiR_ega.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamiregapng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_ega.png. Alt Text:. Summary of features selected by eGA on full H. sapiens positive and negative sets. Title Text:. Summary of features selected by eGA on full H. sapiens positive and negative sets. The -
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. -
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 -
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 -
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:. -
WilliamDunn.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/williamdunnjpg23 Feb 2024: Search site. Core Bioinformatics group. WilliamDunn.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 Cheah -
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 -
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 -
LiviuPirvan.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/liviupirvanpng23 Feb 2024: Search site. Core Bioinformatics group. LiviuPirvan.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 Cheah -
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 -
Clustering evaluation with ClustAssess | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/clustering-evaluation-clustassess23 Feb 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 -
feamiR_ffs.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamirffspng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_ffs.png. Alt Text:. Improvement in performance when adding features, ordered on the x-axis, selected by FFS on a subset of the full H. sapiens dataset. Title Text:. Improvement in performance when -
feamiR - R package for predicting miRNA/mRNA interactions | Core…
https://www.corebioinf.stemcells.cam.ac.uk/news/feamir-r-package-predicting-mirnamrna-interactions23 Feb 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 -
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 -
AndiMunteanu.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/andimunteanupng23 Feb 2024: Search site. Core Bioinformatics group. AndiMunteanu.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 Cheah -
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-december23 Feb 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 -
Single cell RNA-Seq | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/single-cell-rna-seq23 Feb 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. -
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. -
miguel_larraz.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/miguellarrazpng23 Feb 2024: Search site. Core Bioinformatics group. miguel_larraz.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 Cheah -
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 -
Analysis of mRNA-Seq alternative splicing | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/pipelines/analysis-mrna-seq-alternative-splicing23 Feb 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 -
RECOMB_Poster1.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/recombposter1jpg23 Feb 2024: Search site. Core Bioinformatics group. RECOMB_Poster1.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 Cheah -
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-malignancies23 Feb 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. -
RECOMB_Poster2.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/recombposter2jpg23 Feb 2024: Search site. Core Bioinformatics group. RECOMB_Poster2.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 Cheah -
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 -
feamiR is presented at the Heidelberg Non-coding genome symposium by…
https://www.corebioinf.stemcells.cam.ac.uk/news/feamir-presented-heidelberg-non-coding-genome-symposium-eleanor23 Feb 2024: Search site. Core Bioinformatics group. feamiR is presented at the Heidelberg Non-coding genome symposium by Eleanor. Submitted by Dr Irina Mohorianu on Thu, 14/10/2021 - 15:34. The feamiR tool, for predicting microRNA/mRNA interactions is presented -
RECOMB_Scripps.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/recombscrippsjpg23 Feb 2024: Search site. Core Bioinformatics group. RECOMB_Scripps.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 Cheah -
Shiny apps for bulk data with bulkAnalyseR | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/shiny-apps-bulk-data-bulkanalyser23 Feb 2024: Moreover, the app can be easily shared and published, incentivising research reproducibility and allowing others to explore the same processed data. -
rafaelkollyfas.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/rafaelkollyfasjpg23 Feb 2024: Search site. Core Bioinformatics group. rafaelkollyfas.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 Cheah -
Defining the transcriptional signature of esophageal-to-skin lineage…
https://www.corebioinf.stemcells.cam.ac.uk/news/defining-transcriptional-signature-esophageal-skin-lineage-conversion23 Feb 2024: Search site. Core Bioinformatics group. Defining the transcriptional signature of esophageal-to-skin lineage conversion. Submitted by Dr Irina Mohorianu on Sun, 28/03/2021 - 16:18. A new paper in collaboration with Dr Maria Alcolea has been -
miRNA classification with feamiR | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/pipelines-tools/tools/mirna-classification-feamir23 Feb 2024: Search site. Core Bioinformatics group. miRNA classification with feamiR. microRNAs play a key role in RNA interference, the sequence-driven targeting of mRNAs that regulates their translation to proteins, through translation inhibition or the -
AlexCalderwood.jpg | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/alexcalderwoodjpg23 Feb 2024: Search site. Core Bioinformatics group. AlexCalderwood.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 Cheah -
feamiR_rf_gini.png | Core Bioinformatics group
https://www.corebioinf.stemcells.cam.ac.uk/file/feamirrfginipng23 Feb 2024: Search site. Core Bioinformatics group. feamiR_rf_gini.png. Alt Text:. Boxplot showing distribution of mean decrease in Gini index of features across 100 runs on different subsamples of the full H. sapiens dataset. Title Text:. Boxplot showing -
Mapping the biogenesis of forward programmed megakaryocytes from…
https://www.corebioinf.stemcells.cam.ac.uk/news/mapping-biogenesis-forward-programmed-megakaryocytes-induced-pluripotent-stem-cells23 Feb 2024: Search site. Core Bioinformatics group. Mapping the biogenesis of forward programmed megakaryocytes from induced pluripotent stem cells. Submitted by Dr Irina Mohorianu on Mon, 03/05/2021 - 12:02. A new paper in collaboration with Dr Cedric Ghevaert
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