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:

Journal Club - Recorded

2023 11 23th: Unifying Generative Models with GFlowNets and Beyond

Presenter + Keywords: Vincenzo + Generative Models. Link to paper.


2023 11 16th: Towards Universal cell Embeddings: Integrating Single-cell RNA-seq Datasets across Species with SATURN

Presenter + Keywords: Xabi + SATURN. Link to paper.


2023 11 02nd: A dynamical systems treatment of transcriptomic trajectories in hemotopoiesis

Presenter + Keywords: Ali + transcriptional states. Link to paper.


2023 10 26th: Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq 

Presenter + Keywords: Asier + CaRPool-seq. Link to paper.


2023 10 19th: De novo analysis of bulk RNA-seq data at spatially resolved single-cell resolution

Presenter + Keywords: Aleksandra + Bulk2Space. Link to paper.


2023 10 12th: SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks 

Presenter + Keywords: Mahdi + gene regulatory network. Link to paper.


2023 10 05th: A visual-language foundation model for pathology image analysis using medical Twitter

Presenter + Keywords: Abdelrahman + language image PLIP. Link to paper.


2023 09 28th: Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Presenter + Keywords: JuanB+ veloVI. Link to paper.

Link: (part1) (part2)

2023 09 21st: Biological age is increased by stress and restored upon recovery

Presenter + Keywords: Turki + biological age. Link to paper.


2023 07 27th: Mapping transcriptomic vector fields of single cells

Presenter + Keywords: Ali + JuanB + RNA velocity. Link to paper.


2023 06 15th: scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics

Presenter + Keywords: JuanM + augmentation data. Link to paper.


2023 06 08th: Dissecting cell identity via network inference and in silico gene perturbation

Presenter + Keywords: Asier + cellOracle. Link to paper.


2023 05 25th: Cell-type-specific prediction of 3d chromatin organization enables high-throughput in silico genetic screening

Presenter + Keywords: Aleksandra + cell type prediction. Link to paper.


2023 05 18th: scGPT: Towards Building a Foundation Model for Single-Cell Multi-omics Using Generative AI

Presenter + Keywords: Alberto foundation model. Link to paper.


2023 04 27th: Polygenic risk scores: from research tools to clinical instruments

Presenter + Keywords: Edurne polygenic risk score + imputation. Link to paper.


2023 04 20th: Deep representation learning of electronic health records to unlock patient stratification at scale

Presenter + Keywords: Estefania deep learning stratification. Link to paper.


2023 04 06th: High dimensional co-expression networks enable discovery of transcriptomic drivers in complex biological systems

Presenter + Keywords: Mahdi Networks, biological system. Link to paper.


2023 03 23th: Single-Cell Multimodal Prediction via Transformers

Presenter + Keywords: Sumeer Transformers. Link to paper.


2023 03 16th: GEARS: Predicting transcriptional outcomes of novel multi-gene perturbations

Presenter + Keywords: Reem GEARS, perturbation-data. Link to paper.


2023 03 02nd: DMetaCell: analysis of single-cell RNA-seq data using KNN graph partititons

Presenter + Keywords: Ali MetaCells, SeaCells. Link to paper.


2023 02 16th: Disentanglement via Mechanism Sparsity Regularization: A New Principle for Nonlinear ICA

Presenter + Keywords: Vincenzo causal model. Link to paper.


2023 02 09th: Evaluating single-cell cluster stability using the Jaccard similarity index

Presenter + Keywords: Dani ssclusteval. Link to paper.


2023 02 02th: Distance covariance entropy reveals primed states and bifurcation dynamics in single-cell RNA-Seq data

Presenter + Keywords: Hafeez distance entropy. Link to paper.


2023 01 19th: Learning the dynamics of particle-based systems with Lagrangian Graph Neural Networks

Presenter + Keywords: Sandip graph neural network. Link to paper.


2023 01 12nd: omicsNPC: applying the Non-parametric combination methodology to the integrative analysis of heterogeneous omics data

Presenter + Keywords: Ana omicsNPC. Link to paper.


2022 12 22nd: PerturbNet predicts single-cell responses to unseen chemical and genetic perturbations

Presenter + Keywords: Reem deep generative modeling. Link to paper.


2022 12 1st: A machine learning approach utilizing DNA methylation as an accurate classifier of COVIS-19 disease 

Presenter + Keywords: Mukhtar classifier. Link to paper.


2022 11 17th: MONET: Multi-omic module discovery by omic selection

Presenter + Keywords: Sara P multiomic clustering. Link to paper.



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

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


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

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

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


Babel Paper Babel-PNAS

Link to VIMEO:

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

Sara Palomino

Paper associated Covid-19 Vaccine Analysis

Link to VIMEO:

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

Ali and Jesper

Paper associated MuTrans Preprint.

Link to VIMEO:

Cell2Cell Interaction CellPhoneDB & NATMI - 18/03/2021

Jin Ye

Paper associated CellPhoneDB.

Paper associated NATMI.

Link to VIMEO:

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


Link to VIMEO:


EpiMap - 23/02/2021

Atheer Althobaiti, Manjula Thimma, Asima Zia


Link to VIMEO:

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

Jesper Tegner

Link to VIMEO:


scATAC-seq Review 11/02/2021

From the BioInfo-CompBio-ML journal club. Papers considered:

   (i) Bioinfo comparing  Methods:

   (ii) cisTopic methodology:

   (iii) DL and ATAC:

   (iv) Multiomics sc:

Link to VIMEO:

LIBRA - 2/02/2021

STREAM - 15/01/2021

scGSEA Overview - 11th Dec 2020

David Gomez-Cabrero

Link to VIMEO:

CellRank - 22nd Oct 2020

Seurat4 23/09/2020

Xabier Martinez-de-Morentin

Seurat 4 preprint   

Link to VIMEO:

JC-Paper-Overview 6/09/2020

Jesper Tegner

Link to VIMEO: