Journal Club - Scheduled
JC stands for Journal Club
- JC-Tuesday: theory, AI, etc
- JC-Thursday: bioinformatics, biological models, disease, etc.
BioinfoML stands for the BioinfoML meetings.
- BioinfoML-B bioinformatic session
- BioinfoML-ML Machine Learning Session.
Journal Club - Recorded
2022 11 10th: A time and single-cell resolved model of hematopoiesis
Presenter + Keywords: Ali SC Models. Link to paper.
2022 11 03rd: Cell type-specific inference of differential expression in spatial transcriptomics
Presenter + Keywords: Vincenzo Differential expression Spatial transcriptomics. Link to paper.
2022 10 27th: Pumping the brakes on RNA velocity
Presenter + Keywords: Juan Bernal RNA velocity. Link to paper.
2022 10 20th: Dynamical system theory of cellular reprogramming
Presenter + Keywords: Subash Dynamical systems. Link to paper.
2022 10 13th: Precise Gene Editing Preserves Hematopoietic Stem Cell Function following Transient p53-Mediated DNA Damage Response
Presenter + Keywords: Daniel Gene editing. Link to paper.
2022 09 15th: Systematic functional screening of chromatin factors identifies strong lineage and disease dependencies in normal and malignant haematopoiesis
Presenter + Keywords: Asier, Screening of chromatin. Link to paper.
2022 09 1st: Spatial multi-omic map of human myocardial infarction
Presenter + Keywords: Laura, Spatial multi-omic. Link to paper.
2022 06 30th: NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains
Presenter + Keywords: Aleksandra, Chromatin and transcriptional changes. Link to paper.
2022 06 23rd: Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution
Presenter + Keywords: Sumeer, Integration Spatial and Single Cell. Link to paper.
2022 06 02nd: Data-Driven Patient Clustering and Differential Clinical Outcomes in the Brigham and Women’s Rheumatoid Arthritis Sequential Study Registry
Presenter + Keywords: SaraP, Data-Driven, clinical outcome. Link to paper.
2022 05 21st: Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Presenter + Keywords: Dani, Single-cell, batch identification. Link to paper.
2022 05 5th: A pan-tissue DNA-methylation epigenetic clock based on deep learning
Presenter + Keywords: Estefania, Epiclock, DL, DNA Methylation. Link to paper.
2022 04 7th: Variational Autoencoders Without the Variation
Presenter + Keywords: Sumeer, VAE . Link to paper.
2022 04 21st: Vireo: Bayesian demultiplexing of pooled single-cell RNA-seq data without genotype reference
Presenter + Keywords: Dani, Single-cell, batch identification,. Link to paper.
2022 03 31st: Physics-informed machine learning
Presenter + Keywords: Sandip, Machine Learning and Physical modelling. Link to paper.
2022 03 24th: 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations
Presenter + Keywords: Aleksandra, HiC+CNV . Link to paper.
2022 03 17th: scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies
Presenter + Keywords: Vincenzo, single-cell Power Analysis . Link to paper.
2022 03 10th: Quasi-potential landscape in complex multi-stable systems
Presenter + Keywords: Subash, Complex Systems. Link to paper.
2022 03 3rd: Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation
Presenter + Keywords: Daniel Mouzo, Single-cell. Link to paper.
2022 02 24th: Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.
Presenter + Keywords: Juan Pablo Bernal, RNA Velocity. Link to paper.
2022 02 17th: deepMNN: Deep Learning-Based Single-Cell RNA Sequencing Data Batch Correction Using Mutual Nearest Neighbors
Presenter + Keywords: Xabi + Single-cell DeepLearning. Link to paper.
2022 02 10th: Confronting false discoveries in single-cell differential expression
Presenter + Keywords: Jin + Differential expression Bulk. Link to paper.
2022 02 3rd: Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver
Presenter + Keywords: Laura + Spatial . Link to paper.
2022 01 20th: Benchmarking single-cell RNA-sequencing protocols for cell atlas projects
2021 11 18th: An objective comparison of cell-tracking algorithms
Presenter + Keywords: SaraI + Cell Tracking / Image analysis. Link to paper.
2021 11 11th: STlearn cell-cell interaction
Presenter + Keywords: Laura + Spatial Transcriptomics Analysis link to paper
2021 11 04th: Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench
Presenter + Keywords: Jin + single-cell/Batchcorrection
2021 10 28th: Multiscale and integrative single-cell Hi-C analysis with Higashi
Presenter + Keywords: Aleksandra + HiC/Higashi
2021 10 21st: Mesenchymal stromal cells in the bone marrow niche consist of multi‑populations with distinct transcriptional and epigenetic properties
Presenter + Keywords: Itziar + Single-cell/BMN
2021 10 14th: Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia
Presenter + Keywords: Dani + Single-cell
2021 10 7th: Single-cell metabolic profiling of human cytotoxic T cells
Presenter + Keywords: SaraP + Cytof/Metabolomics
2021 10 5th: High-Resolution Mapping of Chromatin Conformation in Cardiac Myocytes Reveals Structural Remodeling of the Epigenome in Heart Failure
Presenter + Topic: Anqi + HiC
(Old style of enumeration)
Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters
Nuria JC-NB 2021 Sept 30
Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Mapping single-cell data to reference atlases by transfer learning
Sumer JC-KAUST Sep21
Machine Learning to learn models. Review recent ML - Tegmarks work.
The multiple myeloma microenvironment is defined by an inflammatory stromal cell landscapeDynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation
Aleksandra (and introduction by Anqi) JC-NB
Link: Part 1: https://vimeo.com/569813568
Part 2: https://vimeo.com/569813428
Introduction to HiC: https://vimeo.com/569813503
The multiple myeloma microenvironment is defined by an inflammatory stromal cell landscape
Single-Cell Transcriptome Analysis Identifies Ligand-Receptor Pairs Associated With BCP-ALL Prognosis
Intronic variant screening with targeted next-generation sequencing reveals first pseudoexon in LDLR in familial hypercholesterolemia, 10th June 2021
Single-cell atlas of hepatic T cells reveals expansion of liver-resident naive-like CD4+ T cells in primary sclerosing cholangitis, 3rd June 2021
MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks, 3rd June 2021
Sara Palomino JC-NB
Statistical Mechanics meet Single Cell Biology, 27 May 2021
Spatial multi-omic map of human myocardial infarction, 27 May 2021
A single-embryo, single-cell time-resolved model..., 25 May 2021
Technical presentation of BABEL (PNAS 2021) paper, - 22/04/2021
Covid-19 Vaccine Analysis, Matching strategy for cohort analysis, - 08/04/2021
MuTrans-Langevin-Cellular Dynamics - 25/03/2021
Cell2Cell Interaction CellPhoneDB & NATMI - 18/03/2021
ML - generative autoregressive-flow models - 4/03/2021
Xabi and Sumeer
Paper associated: https://arxiv.org/abs/1502.03509
Link to VIMEO: https://vimeo.com/520535100
KNN Single-Cell Plos Comp Bio 2021 paper - 26/02/2021
Link to VIMEO: https://vimeo.com/517808206
Cell2Cell Interaction Introduction - 25/02/2021
EpiMap - 23/02/2021
Atheer Althobaiti, Manjula Thimma, Asima Zia
Link to VIMEO: https://vimeo.com/515813615
ML-RecentDevelopments-Papers-JC - 18/02/2021
Link to VIMEO: https://vimeo.com/517813657
scATAC-seq Review 11/02/2021
From the BioInfo-CompBio-ML journal club. Papers considered:
(i) Bioinfo comparing Methods: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1854-5
(ii) cisTopic methodology: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6517279/
(iii) DL and ATAC: https://www.biorxiv.org/content/10.1101/829481v1.full.pdf
(iv) Multiomics sc: https://pubmed.ncbi.nlm.nih.gov/33098772/
Link to VIMEO: https://vimeo.com/512138351
LIBRA - 2/02/2021
Link to VIMEO: https://vimeo.com/517814735
STREAM - 15/01/2021
Link to VIMEO: https://vimeo.com/512139819
Seurat 4 preprint https://www.biorxiv.org/content/10.1101/2020.10.12.335331v1
Link to VIMEO: https://vimeo.com/514891057
Link to VIMEO: https://vimeo.com/517815478