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
2024 03 07th: Time-keeping and decision-making in living cells
Presenter + Keywords: Ali + time keeping. Link to paper.
2024 03 03th: Identifiability Guarantees for Causal Disentanglement from Soft Interventions
Presenter + Keywords: Vincenzo + causal disentaglement. Link to paper.
2024 02 22th: Single-cell multiomics decodes regulatory programs for mouse secondary palate development
Presenter + Keywords: Dani + multiome. Link to paper.
2024 02 08th: Single-cell Mayo Map (scMayoMap): an easy-to-use tool for cell type annotation in single-cell RNA-sequencing data analysis
Presenter + Keywords: Ruben + cell type annotation. Link to paper.
2024 01 31th: DNA synthesis for true random number generation
Presenter + Keywords: Haoling + dna synthesis. Link to paper.
2024 01 18th: Probabilistic embedding, clustering, and alignment for integrating spatial transcriptomics data with PRECAST
Presenter + Keywords: AnaR + probabilistic embedding + spatial. Link to paper.
2024 01 11th: IterPert: Sequential Optimal Experimental Design of Perturbation Screens Guided by Multi-modal Priors
Presenter + Keywords: Reem + perturbation. Link to paper.
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: https://vimeo.com/873610472 (part1) https://vimeo.com/873610589 (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.
Link: https://vimeo.com/770601673
2022 11 03rd: Cell type-specific inference of differential expression in spatial transcriptomics
Presenter + Keywords: Vincenzo Differential expression Spatial transcriptomics. Link to paper.
Link: https://vimeo.com/770601385
2022 10 27th: Pumping the brakes on RNA velocity
Presenter + Keywords: Juan Bernal RNA velocity. Link to paper.
Link: https://vimeo.com/770601196
2022 10 20th: Dynamical system theory of cellular reprogramming
Presenter + Keywords: Subash Dynamical systems. Link to paper.
Link: https://vimeo.com/770601056
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.
Link: https://vimeo.com/770600858
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.
Link: https://vimeo.com/756285925
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
(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
Paper: https://www.sciencedirect.com/science/article/pii/S0092867416313228
Link: https://vimeo.com/621415291
Simultaneous trimodal single-cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq
Miren JC-NB 2021 Sept 23
Paper: https://elifesciences.org/articles/63632
Link: https://vimeo.com/615024971
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
Aleksandra (and introduction by Anqi) JC-NB
Paper: Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation
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
Miren JC-BioinfoML-B
Paper: 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
Paper: MODifieR: an Ensemble R Package for Inference of Disease Modules from Transcriptomics Networks
Statistical Mechanics meet Single Cell Biology, 27 May 2021
Jesper, Statistical mechanics meets single-cell biology
Link to VIMEO: https://vimeo.com/555771991
Spatial multi-omic map of human myocardial infarction, 27 May 2021
Laura
Spatial multi-omic map of human myocardial infarction
Link to VIMEO: https://vimeo.com/555602207
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
Jin Ye
Paper associated CellPhoneDB.
Paper associated NATMI.
Link to VIMEO: https://vimeo.com/525523833
ML - generative autoregressive-flow models - 4/03/2021
Xabi and Sumeer
Paper associated: https://arxiv.org/abs/1502.03509
Paper associated:https://arxiv.org/abs/1606.04934
Paper associated:https://arxiv.org/abs/1705.07057
Paper associated:https://proceedings.neurips.cc/paper/2020/file/9578a63fbe545bd82cc5bbe749636af1-Paper.pdf
Link to VIMEO: https://vimeo.com/520535100
KNN Single-Cell Plos Comp Bio 2021 paper - 26/02/2021
Andreas Tjarnberg
Paper associated: https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008569
Link to VIMEO: https://vimeo.com/517808206
Cell2Cell Interaction Introduction - 25/02/2021
Jin Ye
Paper associated: https://www.nature.com/articles/s41596-020-0292-x
Link to VIMEO: https://vimeo.com/517780650
Laura
Spatial multi-omic map of human myocardial infarction
Link to VIMEO: https://vimeo.com/555602207
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
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
Xabier Martinez-de-Morentin
Paper:https://www.biorxiv.org/content/10.1101/2021.01.27.428400v1.full
Link to VIMEO: https://vimeo.com/517814735
STREAM - 15/01/2021
Marina Ainciburu
Paper: https://www.nature.com/articles/s41467-019-09670-4
Link to VIMEO: https://vimeo.com/512139819
scGSEA Overview - 11th Dec 2020
David Gomez-Cabrero
Link to VIMEO: https://vimeo.com/512139970
CellRank - 22nd Oct 2020
Jesper Tegner
Paper: https://www.biorxiv.org/content/10.1101/2020.10.19.345983v2
Link to VIMEO: https://vimeo.com/512140067
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