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.
Link to all JCs are here: vimeo.com/user/133636169/folder/3668602
 

Journal Club - Recorded

 

2022 09 1st: Spatial multi-omic map of human myocardial infarction

Presenter + Keywords: Laura, Spatial multi-omic. Link to paper.

Link: https://vimeo.com/748477792

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.

Link: https://vimeo.com/733884010

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.

Link: https://vimeo.com/725582852

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.

Link: https://vimeo.com/718677698

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.

Link: https://vimeo.com/712543229

2022 05 5th: A pan-tissue DNA-methylation epigenetic clock based on deep learning

Presenter + Keywords: Estefania, Epiclock, DL, DNA Methylation. Link to paper.

Link: https://vimeo.com/712542876

 

2022 04 7th: Variational Autoencoders Without the Variation

Presenter + Keywords: Sumeer, VAE . Link to paper.

Link: 

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.

Link: https://vimeo.com/712543229

2022 03 31st: Physics-informed machine learning

Presenter + Keywords: Sandip, Machine Learning and Physical modelling. Link to paper.

Link: https://vimeo.com/697701720

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.

Link: https://vimeo.com/697700527

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.

Link: https://vimeo.com/697700016

2022 03 10th: Quasi-potential landscape in complex multi-stable systems

Presenter + Keywords: Subash, Complex Systems. Link to paper.

Link: https://vimeo.com/697699464

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.

Link: https://vimeo.com/697699152

2022 02 24th: Preprocessing choices affect RNA velocity results for droplet scRNA-seq data.

Presenter + Keywords: Juan Pablo Bernal, RNA Velocity. Link to paper.

Link: https://vimeo.com/697698697

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.

Link: https://vimeo.com/679675735

2022 02 10th: Confronting false discoveries in single-cell differential expression

Presenter + Keywords: Jin + Differential expression Bulk. Link to paper.

Link: https://vimeo.com/679675568

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.

Link: https://vimeo.com/679675520

2022 01 20th: Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

Presenter + Keywords: Miren + Multiomics. Link to paper. And link.

Link: https://vimeo.com/672351770

2021 11 18th: An objective comparison of cell-tracking algorithms

Presenter + Keywords: SaraI + Cell Tracking / Image analysis. Link to paper.

Link: https://vimeo.com/648285029

2021 11 11th: STlearn cell-cell interaction

Presenter + Keywords: Laura + Spatial Transcriptomics Analysis link to paper

Link: https://vimeo.com/648284934

2021 11 04th: Flexible comparison of batch correction methods for single-cell RNA-seq using BatchBench

Presenter + Keywords: Jin + single-cell/Batchcorrection

Link: https://vimeo.com/644658086

2021 10 28th: Multiscale and integrative single-cell Hi-C analysis with Higashi

Presenter + Keywords: Aleksandra + HiC/Higashi

Link: https://vimeo.com/644658042

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

Link: https://vimeo.com/644657385

2021 10 14th: Extensive Remodeling of the Immune Microenvironment in B Cell Acute Lymphoblastic Leukemia

Presenter + Keywords: Dani + Single-cell

Link: https://vimeo.com/634264766

2021 10 7th: Single-cell metabolic profiling of human cytotoxic T cells

Presenter + Keywords: SaraP + Cytof/Metabolomics

Link: https://vimeo.com/630095808

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

Link: https://vimeo.com/630095672

(Old style of enumeration)

Lineage-Specific Genome Architecture Links Enhancers and Non-coding Disease Variants to Target Gene Promoters

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

Paper:

    https://www.nature.com/articles/s41587-021-01001-7

    Link: https://vimeo.com/615874097

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

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

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

Sally

Babel Paper Babel-PNAS

Link to VIMEO: https://vimeo.com/544913466

Covid-19 Vaccine Analysis, Matching strategy for cohort analysis, - 08/04/2021

Sara Palomino

Paper associated Covid-19 Vaccine Analysis

Link to VIMEO: https://vimeo.com/535444091

MuTrans-Langevin-Cellular Dynamics - 25/03/2021

Ali and Jesper

Paper associated MuTrans Preprint.

Link to VIMEO: https://vimeo.com/530255170

Cell2Cell Interaction CellPhoneDB & NATMI - 18/03/2021

Jin Ye

Paper associated CellPhoneDB.

Paper associated NATMI.

Link to VIMEO: https://vimeo.com/525523833

ML - generative autoregressive-flow models - 4/03/2021

KNN Single-Cell Plos Comp Bio 2021 paper - 26/02/2021

Cell2Cell Interaction Introduction - 25/02/2021

TotalVI - 25/02/2021

Xabier Martiner-de-Morentin

Paper: https://www.nature.com/articles/s41592-020-01050-x

Link to VIMEO: https://vimeo.com/517775729

 

EpiMap - 23/02/2021

Atheer Althobaiti, Manjula Thimma, Asima Zia

Paper: https://www.nature.com/articles/s41586-020-03145-z

Link to VIMEO: https://vimeo.com/515813615

ML-RecentDevelopments-Papers-JC - 18/02/2021

Jesper Tegner

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

STREAM - 15/01/2021

scGSEA Overview - 11th Dec 2020

David Gomez-Cabrero

Link to VIMEO: https://vimeo.com/512139970

CellRank - 22nd Oct 2020

Seurat4 23/09/2020

Xabier Martinez-de-Morentin

Seurat 4 preprint  https://www.biorxiv.org/content/10.1101/2020.10.12.335331v1   

Link to VIMEO: https://vimeo.com/514891057

JC-Paper-Overview 6/09/2020

Jesper Tegner

Link to VIMEO: https://vimeo.com/517815478