JOBIM2025: JOURNéES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHéMATIQUE 2025

This page contains an index consisting of author-provided keywords.

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(meta)genomics	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
3
3’ end	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
3’ RNAseq
4
4C
5
5’ end	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
A
Abundance index	Reindeer2: practical abundance index at scale
active targeting
Acute Myeloid Leukemia
Acute Promyelocytic Leukaemia	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Aedes aegypti
Agent based modelling
Agent-based model
Agent-Based Modelling
Aging
Agroecology
AI
Algorithm
Alpha Diversity	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
Alpha-Satellite DNA	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
alphafold	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction
alternative polyadenylation
amplicon
Amyloids	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
Annotation	GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph
Annotation transfer	GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph
Antibiotic resistance	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Antibody escape	SARS-CoV-2 viral evolution and antibody resilience
Antibody resilience	SARS-CoV-2 viral evolution and antibody resilience
antibody variable regions	AntiBody Sequence Database
Antigen-targeting therapy
Antivirals
Aphid
Applied Mathematics
Arabidopsis thaliana
Arboviruses
archaea
Artificial Intelligence
Ascophyllum nodosum	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Assembly	OReO: Optimizing Read Order for practical compression
Atopic dermatitis
Autoencoder
Autoimmune diseases
Autoimmunity
Automated and scalable pipeline
automatized pipelines
Avian Inlfuenza H7
B
BacDrop
Bacterial pangenome
Bacterial single-cell RNA-seq
bacterial strain dependency	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline
batch effects	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Benchmark	Metatranscriptomic classification in the study of microbial translocation
benchmark comparison	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Benchmarking
binning
bio.tools	Assessing bioinformatics software annotations : bio.tools case-study
bioanalysis
Bioconductor
Biodiversity
Biogeography
Bioinformatics	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
Bioinformatics pipelines
Bioinformatics platform	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Bioinformatics tools
Bioinformatics training	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
Biojava
Biological Resources Centre (BRC)
Biological Systems
biomarkers
Biomass function	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Biomedical knowledge base
Biotherapies
Biotic interactions
Bipolar Disorder	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
boolean network	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic
breast cancer
Breast cancer progression
Bruijn	Selection of test instances for string algorithms
Bulk RNA-seq
C
cancer	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Cancer Cell Signaling
Cancer Genomics
Capacity building	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
Carbon footprint
cell therapy
cell type
Cell type deconvolution
Cell-type deconvolution	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Centenarians
Centromere	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
challenges
chemical communication
Cheminformatics	Open Science Data Processing and Integration Workflows in Metabolomics and Exposomics
Chemosensory receptors
Chimeric Junctions
Chromatin contacts
Chronic Lymphocytic leukemia
Circadian clock
circRNA	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Cis-regulatory elements	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Cistrome
classification
Climate change
clonal evolution
Cloud and containers
Clustering	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
clustering
Coalescent
codon usage
coevolution
Cofactor Segregation	MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
Combinatorial indexing
Community
Community Engagement
comparative genomics	Natural selection acting on gene expression and regulation in mole-rats LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
Comparative transcriptomics	Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Complex ecosystems
compositional data
Compression	OReO: Optimizing Read Order for practical compression
Computational Biology	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Computational modeling
Computing
Condition-specific metabolic reconstruction
confidence intervals
Connectivity score
Consensus sequences reconstruction
conservation
constraint-based metabolic model
constraint-based modeling
constraint-based modelling
Containerization (Docker)
convergent phenotypic evolution	Deciphering the genomic basis of convergent phenotypic evolution
copy number alterations
Copy Number Variation (CNV) Analysis
Core facility	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
core genome	Gratools a tool for easy manipulation of GFA
Core Regulatory Circuits
Cross-sample Contamination	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Culex quinquefasciatus
D
data analysis
Data brokering	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
data integration	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Data Leakage	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
data management
Data submission	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Data Utility
data visualization	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
Data-driven drug discovery
databanks
Database	AntiBody Sequence Database Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
databases	Vizitig: context-rich exploration of sequencing datasets
de Bruijn graph	Vizitig: context-rich exploration of sequencing datasets
De novo assembly
Deep Learning	Models for protein domain embedding Evaluating deep learning models for plant protein function prediction Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction The Pfam protein families database: embracing AI/ML
Deep mutational scanning	SARS-CoV-2 viral evolution and antibody resilience
Defective Viral Genomes detection
Demographic Inference
diagnosis
Diatom
Differential expression signature
differential gene expression	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Differential proportions	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Digital twin
Dinoflagellate
discord
Disease classification	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
Diseases/Phenotypes
Display
diversity statistics
Django
DNA
DNA Damage Response
DNA Double-Strand Breaks
DNA extraction benchmarking
DNA methylation	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder. MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
DNA sequence embedding	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
DNA sequencing benchmarking
DNA-binding
Docker
Dose-Response Assays
Droplet microfluidics
Drug repurposing	Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Drug repurposing
Drug Response Prediction
Drug–target interaction
Duplication
Dynamic programming	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Dynamical systems
E
Early-Onset Alzheimer Disease
Ecological Quality	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
Ecology
EDAM	Assessing bioinformatics software annotations : bio.tools case-study
ELIXIR
Embedding learning	Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering
Endoribonucleolytic cleavage site	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Energy efficiency
enterosignatures
Environmental data
environmental DNA
Epidemiology
Epigenetic Regulation	MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
eukaryote	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
Europe
EuroScienceGateway
evolution	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
evolutionary genomics	Deciphering the genomic basis of convergent phenotypic evolution
Exome sequencing
Exonuclease blockage profiling	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Experience sharing
Exposomics	Open Science Data Processing and Integration Workflows in Metabolomics and Exposomics
Expression regulation
F
FAIR
FAIR bioinformatics software	Assessing bioinformatics software annotations : bio.tools case-study
FAIR data
FAIR data analysis
FAIR database
FAIR Principles
FAIR science
farming practices
Fermentation
Folding potential	Structural Space of Microproteins with Protein Language Models
Food ecosystem
freshwater cyanobacteria	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
FROGS
Functional annotation	LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
G
Galaxy	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Gammaproteobacteria
Gaussian Graphical Models	OneNet—One network to rule them all: Consensus network inference from microbiome data
GBA1 mutation
Gene annotations
Gene conversion
Gene duplication
Gene expression	Natural selection acting on gene expression and regulation in mole-rats
gene expression evolution	Deciphering the genomic basis of convergent phenotypic evolution
Gene family
Gene Ontology	Evaluating deep learning models for plant protein function prediction
Gene Ontology (GO)
Gene Pleiotropy	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
Gene regulation	Natural selection acting on gene expression and regulation in mole-rats
Gene regulatory network	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Gene repertoire
genetic disease
genetic diversity
genetic integrity
genome annotation	Facilitating genome annotation using ANNEXA and long-read RNA sequencing REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
genome assembly
Genome browser
genome portals
Genome Visualization
Genome-scale metabolic models reconstruction	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Genome-wide associations studies	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
Genomic
genomic data
Genomic data visualization
genomic observatories
Genomic Rearrangements
Genomics
Genomics core facility
genotype selection in plants
genotypes	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
Genus Classification
geographic coordinate
geomatics
Glycans
Graph	GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph
graph algorithms	Searching for variable structural motifs in RNA graphs using simple descriptors
Graph Neural Network
Graph Neural Networks
Graph Theory	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Graph-based assembly
Graphical
Growth Forms
growth medium inference
GSM	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline
Guadeloupe
Gut microbiome	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
gut microbiota
GWAS
H
habitat
Haplotyping
HDX-MS
Health
Heterogeneous data
Hi-C
HiFi reads
High pathogenicity
High-performance computing (HPC)
Holobiont	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
Honey bee microbiome
host taxonomy
Hotspots of diversity
Human gut microbiome
I
IDH
Immune cells
Immune response
Immune responses
Immunology
immunotherapy response
in silico pathway screening	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline
Index
Inference
Information System
Information Systems
Information Systems and Data Interoperability
Information Visualization
Infrastructure
Integrase
Interactions
Interactive Data Exploration	SynFlow: a Syri based interactive viewer
Interactome
Intergenic ORFs	Structural Space of Microproteins with Protein Language Models
Interoperability
Interpretability	Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering
Inversions
Inverted repeat	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
IoT LoRaWAN
iPSCs
J
JAK inhibitors
K
K-mer indexing	Reindeer2: practical abundance index at scale
k-mers
keyword1	TBA
keyword2	TBA
keyword3	TBA
Knockoffs	Variable selection in transcriptomics data using knockoffs in a classification framework
knowledge base
Knowledge Graph
Knowledge Graph Embedding	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Knowledge graphs
Krill
L
Lactation biology
lactic acid bacteria	Strain-dependency of metabolic pathways within 1,494 genomes of lactic bacteria evidenced with Prolipipe, an in silico screening pipeline
Large Language Model
Large Language Models
Large-scale Boolean model	Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis
Lasso
Leptin	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
Life Sciences
Ligandability Assessment
linear mixed models
Link Prediction	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Linkage Disequilibrium
linked-reads	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
lncRNAs	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Local Accession Management
Local adaptation
Logical model	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Long-non coding RNA
long-read
long-read nanopore sequencing	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework
Long-read sequencing	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis Facilitating genome annotation using ANNEXA and long-read RNA sequencing
Long-reads
Longevity
M
Machine Learning	jsPCA enables fast, interpretable and parameter-free domain identification in 3D spatial transcriptomics data AntiBody Sequence Database
machine learning
Machine-learning	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
Maize genomic	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Mammalian evolution	Natural selection acting on gene expression and regulation in mole-rats
map viewer
Marine Biodiversity Monitoring	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
marine data
marine organisms
Marine plankton
Markov CLustering	LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
mass spectrometry	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
mast cells
master regulators	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic
Mechanistic Modeling
meningitis
metabarcoding
Metabolic Flux Balance analysis
metabolic fluxes
metabolic modelling	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Metabolic network	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
Metabolic network modelling
metabolic networks
Metabolism	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
Metabolomics	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities Open Science Data Processing and Integration Workflows in Metabolomics and Exposomics
Metadata	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Metagenome assembly
Metagenomic	Metatranscriptomic classification in the study of microbial translocation
metagenomic shotgun
Metagenomics	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Metastases
Metatranscriptomic	Metatranscriptomic classification in the study of microbial translocation
Method database	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
mice
microarray	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
microbial communities
microbial community	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
Microbial ecology	OneNet—One network to rule them all: Consensus network inference from microbiome data
Microbial ecosystems
Microbial guild	OneNet—One network to rule them all: Consensus network inference from microbiome data
microbial guilds
microbial taxonomical annotation comparison
Microbial translocation	Metatranscriptomic classification in the study of microbial translocation
microbiome
microbiome
Microbiota	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
microbiota data	RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
microplastics
Microproteins	Structural Space of Microproteins with Protein Language Models
Misconceptions
MLOps
Model deployment
modeling	HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
Modelling
Molecular clock
MS2 spectra	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
multi-class classification
Multi-genome comparison	SynFlow: a Syri based interactive viewer
Multi-omic data integration
Multi-omics
Multi-omics Integration	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
Multimodal integration
multiomics
multiple myeloma
multiscale modelling
N
Nanopore sequencing
Nematoda
Network dynamics
network expansion
network inference	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic OneNet—One network to rule them all: Consensus network inference from microbiome data
Networking
Neural networks
Neurodegenerative diseases	Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
neuroinflammation
Neurological disease
neuronal differentiation
Neuroscience
Nextflow
NGS data normalization
NIRS
Non-allelic homologous recombination
Non-B DNA
Non-coding variants
Non-model species
Non-target Screening	Open Science Data Processing and Integration Workflows in Metabolomics and Exposomics
normalization
novel CAZymes
O
omics
Omics
Oncology
One Health	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Online tool	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context
Ontologies	Assessing bioinformatics software annotations : bio.tools case-study
Open Education
Open Science	Madbot, a metadata and data brokering online tool to ensure the adoption of standards and FAIR principals in an open science context Open Science Data Processing and Integration Workflows in Metabolomics and Exposomics
open source	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Open-access
Ordering	OReO: Optimizing Read Order for practical compression
Orthology
Oxford Nanopore Technologies
P
PacBio HiFi
Pangenome	Gratools a tool for easy manipulation of GFA GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph Integrating structural variants in genomic studies of rare and complex diseases with long-read sequencing and pangenomes
pangenome graph	Gratools a tool for easy manipulation of GFA GrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph
Pangenome graphs
Pangenome Simulation
pangenomics	Vizitig: context-rich exploration of sequencing datasets
Paraneoplastic Neurological Syndromes
Parkinson disease
pathogenicity
Pathway analysis	Methods for a species-specific genome-scale metabolic modeldesigned for eukaryotes and applied to the Ascophyllum nodosum macroalga
Pathway enrichment	Joint Embedding-Classifier Learning for Interpretable Collaborative Filtering
pattern finding	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
PCHi-C
PDAC
peptide	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction
Peptidomics	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
Personalized medicine (Cancer)
Personalized treatment
Phenology
Phenotype
Phylogenetic evolution
Phylogenetic modelling	Natural selection acting on gene expression and regulation in mole-rats
phylogenetic tree
phylogenetics
Phylogenomics
Phylogeography
PhysiCell
pig
pipeline	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
pitfalls
Plant
Plant Collections and Characterization
Plant Functional Groups
plant-pathogens interaction
Plants
plants domestication
Population Genetics
Post-transcriptional modifications	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
precision medicine
Prediction	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction Developing machine-learning-based amyloidogenicity predictors with Cross-Beta DB
prediction model
prediction of PULs
predomics
Primates	Evolutionary dynamics of centromeric DNA in guenon might end an old anthropocentric dogma
Privacy
Professional Development
prokaryotes	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
Protein annotation	Models for protein domain embedding
Protein domains	Models for protein domain embedding
Protein embedding	Models for protein domain embedding
protein evolution
Protein Families
Protein family	The Pfam protein families database: embracing AI/ML
protein folding
protein function prediction	Evaluating deep learning models for plant protein function prediction
Protein language models	Structural Space of Microproteins with Protein Language Models
protein sequence	AntiBody Sequence Database
protein structures
protein topology
Protein-Protein
Protein-protein interaction modules	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
protein-protein interactions
protein-specific RNA ligands
proteins
Proteomics	SpecPeptidOMS Directly and Rapidly Aligns Mass Spectra on Whole Proteomes and Identifies Peptides That Are Not Necessarily Tryptic: Implications for Peptidomics
provirus
PSSM
Public data	Metatranscriptomic classification in the study of microbial translocation
PWM
python package
Q
quality assessment
Quality control	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
quantitative proteomics
QuantSeq FWD
R
R Markdown notebooks
R packages
R-package	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Random Forests
Rare disease	Integrating structural variants in genomic studies of rare and complex diseases with long-read sequencing and pangenomes
Rare Diseases	Benchmarking Data Leakage on Link Prediction in Biomedical Knowledge Graph Embeddings
Rare variants
Raw milk cheeses
RDF
reads	Selection of test instances for string algorithms
Recombination
recombinations
recursivity
refine
regulatory evolution	Deciphering the genomic basis of convergent phenotypic evolution
Regulatory network	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
remote homologs identification	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
reproducibility	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
reproducibility
reproducible workflows
Research Data Management
Research Support	Ten years of the Pasteur’s Bioinformatics and Biostatistics Hub: achievements and perspectives
Response to water deficit	Regulatory response of maize to water deficit mediated by distal cis-regulatory elements
Restricted Boltzmann Machines	SARS-CoV-2 viral evolution and antibody resilience
reverse ecology
Rheumatoid arthritis	Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis
Rhythmicity
risks analysis
RNA
RNA 3D structure	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
RNA degradation	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
RNA graphs	Searching for variable structural motifs in RNA graphs using simple descriptors
RNA modifications
RNA structural motifs	Searching for variable structural motifs in RNA graphs using simple descriptors
RNA structure
RNA tertiary structure	Searching for variable structural motifs in RNA graphs using simple descriptors
RNA World
RNA-end sequencing	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
RNA-protein interactions
RNA-seq	Bridging the Gap Between R and Python in Bulk Transcriptomic Data Analysis with InMoose
Rshiny	HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures.
S
salmonid species
Sample size	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder.
sample size calculation
SARS-CoV-2	SARS-CoV-2 viral evolution and antibody resilience
Scaffolding
Science Outreach
scRNA-seq
Semantic annotations	Assessing bioinformatics software annotations : bio.tools case-study
Semantic Knowledge Graph	Demonstrating OntoWeaver to Integrate Heterogeneous Information in the OncodashKB Semantic Knowledge Graph for Finding Personalized Actionable Drugs in Ovarian Cancer
Semi-targeted lipidomics
sensory neurons
Sequence alignment	The Pfam protein families database: embracing AI/ML
Sequence motif
Sequence Similarity Network	LAGOON-MCL: A Nextflow pipeline for comprehensive protein sequence annotation and comparison
Sequence size optimization
Sequencing	Integrating structural variants in genomic studies of rare and complex diseases with long-read sequencing and pangenomes
sequencing data analysis	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
SHAP	Explainable AI for Marine Ecological Quality Prediction: Integrating Microbiome Data, Metadata, and Diversity
Shiny application	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data
Short reads
shotgun metagenomics
Similarity
simulation framework	Benchmarking circRNA Detection Tools from Long-Read Sequencing Using Data-Driven and Flexible Simulation Framework RITHMS : An advanced stochastic framework for the simulation of transgenerational hologenomic data
Simulation tool
Single Cell
Single Cell RNA-seq
Single Nucleotide Polymorphism
single-cell
single-cell data science
Single-cell RNA sequencing
SingleCell RNASeq
Small RNA
Snakemake
snoRNA
software	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
SOSA
spatial
spatial
Spatial statistics	jsPCA enables fast, interpretable and parameter-free domain identification in 3D spatial transcriptomics data
Spatial transcriptomics	Interactive toolbox for cell-type deconvolution of spatial transcriptomics data jsPCA enables fast, interpretable and parameter-free domain identification in 3D spatial transcriptomics data
species assignment
spectral preprocessing
Stability selection	OneNet—One network to rule them all: Consensus network inference from microbiome data
standardized	AntiBody Sequence Database
Standardized database
statistical power
statistics
stevioside
structural bioinformatics
structural domains	RNA3DClust: unsupervised segmentation of RNA 3D structures using density-based clustering
Structural properties	Structural Space of Microproteins with Protein Language Models
Structural Variants	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data Integrating structural variants in genomic studies of rare and complex diseases with long-read sequencing and pangenomes
Structural variations	SynFlow: a Syri based interactive viewer
structure analysis
subgraph	Gratools a tool for easy manipulation of GFA
Subtyping
Succinct structures	Reindeer2: practical abundance index at scale
Supervised classification	CroCoDeEL: accurate control-free detection of cross-sample contamination in metagenomics data
Surveillance
Sustainable computing
Sweetpotato virome
Swine Influenza
Symbiosis
Synonymous codon
synteny	SynFlow: a Syri based interactive viewer
Synteny Conservation
Synthetic Data
systematic analysis	A Comprehensive Study of Inverted Repeats in Prokaryotic Genomes: Enrichment, Depletion, and Taxonomic Variations
Systems biology	Metagenome-scale metabolic modelling for the characterization of cross-feeding interactions in freshwater cyanobacteria-associated microbial communities
T
taxonomy
Teaching
Temporal Genomic Data
test instances	Selection of test instances for string algorithms
Tetraploid
Text mining
Therapy resistance	Predictive modelling of Acute Promyelocytic Leukaemia resistance to Retinoic Acid therapy.
Third generation sequencing	OReO: Optimizing Read Order for practical compression
three-dimensional structure	Comparative Analysis of Deep Learning-Based Algorithms for Peptide Structure Prediction
tomato
Toxicogenomic
TP53
Training
Training Environment
trainings
Trans-kingdom
transcription factors	MethMotif 2024 Suite Reveals the Epigenetic Blueprint of Context-Specific Transcription Factor Binding Sites
transcription regulation
Transcription start site	rnaends: an R package targeted to study the exact RNA ends at the nucleotide resolution
Transcriptional Regulatory Networks
Transcriptome
Transcriptomic	Leveraging multi-omics integration to uncover childhood trauma-related mechanisms in bipolar disorder. Variable selection in transcriptomics data using knockoffs in a classification framework
Transcriptomic analysis
transcriptomic data analysis
transcriptomics	Network-centric identification and analysis of a model of post-traumatic stress disorder with NORDic HUMESS: A tool to integrate quantitative transcriptomic and metabolic network modelling to unveil context specific gene signatures. Reindeer2: practical abundance index at scale Vizitig: context-rich exploration of sequencing datasets
Transcriptomics data
Transformer models	MetagenBERT: a Transformer Architecture using Foundational Read Embedding Models to enhance Disease Classification
transformers
transmission
transposable element
transposable elements	REPET v4.0: A Comprehensive Tool for Transposable Element Analysis
treatment resistance
Triticum aestivum
tutorial	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
U
Ultra-conserved element
uncultured bacteria
user ergonomics	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
V
Variable selection	Variable selection in transcriptomics data using knockoffs in a classification framework
Variant Calling
Variant effects	Exhaustive Identification of Pleiotropic Loci for Serum Leptin Levels in the NHGRI-EBI Genome-Wide Association Catalog
variant genotyping	SVJedi-Tag : a novel method for genotyping large inversions with linked-read data
Variants
Variation Graph
Viral adaptation	SARS-CoV-2 viral evolution and antibody resilience
Viral diversity
viral surveillance
Virological surveillance
virtual twin	Building a modular and multi-cellular virtual twin of the synovial joint in Rheumatoid Arthritis
Virus
Virus
visualization	Vizitig: context-rich exploration of sequencing datasets
vizualisation
W
web application	WHOOPER : Web application for Hands-On identification of protein co-Occurrence among Phyla, focused on user ERgonomics.
Web services
Web-service	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
West Africa	A decade of strengthening bioinformatics in West Africa: HPC infrastructure, training, and scientific collaboration
WGS	ABRomics-analysis: a web service for the analysis of Antibiotic Resistance in bacterial genomes
Workflow	Met4J: a library, a toolbox and a workflow suite for graph-based analysis of metabolic networks
workflow
Workflow developments
Workflow Manager
Workflows	Fast answers to simple bioinformatics needs and capacity building in an island context, a focus on microbial omics data analysis
working group
Y
yeast
Z
Zea mays
Zymoseptoria tritici

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