Talk Keyword Index

TALK KEYWORD INDEX

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

Shortcuts: $A B C D E F G H I K L M N O P R S T U V W X

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$\delta$-Hyperbolicity	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
$k$-mer Sets	Fast and Succinct Compression of k-mer Sets with Plain Text Representation of Colored de Bruijn Graphs
A
agent-based model	Simulation of tumor evolution and metastasis at single-cell resolution
Agent-based simulations	Mixed HCV Infection: A novel genetic marker for surveillance of high-risk populations
Alaska	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
alignment-free	DuoHash: fast hashing of spaced seeds with application to spaced k-mers counting
Alpha helix	Improving inter-helical residue contact prediction in α-helical Transmembrane proteins using structural neighborhood crowdedness information
AlphaFold	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
altruism	Antigenic cooperation and cross-immunoreactivity networks
antarctica	Opening an icy black box: diversity and functioning of soil bacteria in Antarctica’s largest ice-free region
Antibiotic Response
antibody design	Improved Graph-Based Antibody-Aware Epitope Prediction with Protein Language Model-Based Embeddings
Arctic	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
ARG	Resistance genes are distinct in protein-protein interaction networks according to drug class and gene mobility
ARIMA	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Association	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Attention Mechanisms	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
B
Backbone Conformation	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
bacteria	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
Bacterial Transcriptomics
batch effect removal	scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Bayesian modeling	Drug-centric prior improves drug response modeling in partially overlapping pharmacogenomic screens
Belarus	Phylodynamics Analysis of HIV Epidemic History in Belarus in 1987-2022
benchmark	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Benchmarking	Benchmarking metagenomic software with the new CAMI web portal
Biobank	Haplotype-based Parallel PBWT for Biobank Scale Data
bioinformatics	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Biomarkers
biosecurity	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
biothreat	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
Breast Cancer Diagnosis	Mammo-Bench: A Large-scale Benchmark Dataset of Mammography Images
bulk RNA Sequencing
C
cancer	Simulation of tumor evolution and metastasis at single-cell resolution The evolution of cancer progression risk: a phylogenetic and machine learning analysis
Cancer evolution	Cancer progression inference from single-cell data with recurrences and mutation losses
Cardiac Arrest Prediction	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
Cardiovascular Simulation	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
CCP	Nearest Neighbor CCP-Based Molecular Sequence Analysis
CD8	HLA class I escape drives the evolution of SARS-CoV-2 in human population
cell fitness	Simulation of tumor evolution and metastasis at single-cell resolution
centralized learning	Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based CT Scan Analysis
Chaos Game Representation	DANCE: Deep Learning-Assisted Analysis of ProteiN Sequences Using Chaos Enhanced Kaleidoscopic Images
Classification	Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
clinical note gen	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
Clique SNV	Applying Genetic Algorithm with Saltations to MAX-3SAT
Clustering	Unsupervised Learning for Tertiary Structure Prediction of Protein Molecules: Systematic Review
ColabFold	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
Colorectal Cancer
Colored Bruijn graphs	Fast and Succinct Compression of k-mer Sets with Plain Text Representation of Colored de Bruijn Graphs
Comorbidity	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Compression	Fast and Succinct Compression of k-mer Sets with Plain Text Representation of Colored de Bruijn Graphs
Computational genomics	DCCNV: Enhanced Copy Number Variation Detection in Single-Cell Sequencing Using Diffusion Processes and Contrastive Learning
Computed Tomography	Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based CT Scan Analysis
Computer-Aided Detection	Mammo-Bench: A Large-scale Benchmark Dataset of Mammography Images
Conditional Mutual Information	Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach
Contact map prediction	Improving inter-helical residue contact prediction in α-helical Transmembrane proteins using structural neighborhood crowdedness information
Contrastive Learning	DCCNV: Enhanced Copy Number Variation Detection in Single-Cell Sequencing Using Diffusion Processes and Contrastive Learning
Copy Number Variations	DCCNV: Enhanced Copy Number Variation Detection in Single-Cell Sequencing Using Diffusion Processes and Contrastive Learning
correlation	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
CoT	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
counting k-mers	DuoHash: fast hashing of spaced seeds with application to spaced k-mers counting
COVID-19	Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences The study of the effects of the full-scale Russian-Ukrainian war on the epidemiological situation and respiratory and intestinal diseases in the Kharkiv region of Ukraine from 2022 to 2024 The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia. Personalized health and genomics libraries for the analysis of long-term effects in COVID-19 patients
COVID-19 data
Cross-Correlation	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
cross-immunoreactivity	Antigenic cooperation and cross-immunoreactivity networks
D
Data Accessibility
Data Augmentation	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
Data Integration	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
Deep Learning	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis DeepGOMeta: Functional Insights into Microbial Communities through Deep Learning From Reads to Enzymes: Exploring Enzymatic Potential in Metagenomes with DNA Language Models Mammo-Bench: A Large-scale Benchmark Dataset of Mammography Images
Degenerate Primers	AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers
Depletion	Assessment of Host and Bacterial Depletion Methods to Enhance RNA Virus Detection by Next-Generation Sequencing
Digital Twin	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based CT Scan Analysis
Dimensionality Reduction	Nearest Neighbor CCP-Based Molecular Sequence Analysis
Disease	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Disease risk prediction	Supervised Poisson Factorization for Uncovering Latent Gene Expression Patterns and Predicting Disease Risk
disentanglement of biological variations	scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Drug response	Drug-centric prior improves drug response modeling in partially overlapping pharmacogenomic screens
Dynamic Gene Regulation
E
earth mover's distance	Earth Mover's Distance to recognize duplicate datasets in an automated molecular epidemiology system
EfficientNet	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
Embedding Analysis	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
Environmental Microbiome	Innovative Tools and Strategies for Outbreak Preparedness: Integrating Environmental Microbiomes and Prospective Pathogen Collections in Hospital Settings
Enzyme function	From Reads to Enzymes: Exploring Enzymatic Potential in Metagenomes with DNA Language Models
Epidemic forecasting
epidemiology	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Epistatic Interactions	Epistatic Density of Viral Variants in Acute and Chronic HCV patients
Epistatic Network	Epistatic Density of Viral Variants in Acute and Chronic HCV patients
epitope prediction	Improved Graph-Based Antibody-Aware Epitope Prediction with Protein Language Model-Based Embeddings
Error correction	HAPLOQ: A simple strategy for correcting sequencing errors on viral amplicons
escape mutations	HLA class I escape drives the evolution of SARS-CoV-2 in human population
evolution	Leveraging Multiple Dimensions of Public Data to Characterize the Evolution of a Staphylococcal Plasmid HLA class I escape drives the evolution of SARS-CoV-2 in human population
Evolutionary jumps	Applying Genetic Algorithm with Saltations to MAX-3SAT
Explainable AI	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
F
FDR Control	AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers
Feature Selection	Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach
Federated Learning	Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based CT Scan Analysis
Federated Transfer Learning	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis Enhancing Privacy Preservation and Reducing Analysis Time with Federated Transfer Learning in Digital Twins-based CT Scan Analysis
Finite State	Cancer progression inference from single-cell data with recurrences and mutation losses
Fitness	Epistatic Density of Viral Variants in Acute and Chronic HCV patients
forecasting	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Foundation model	From Reads to Enzymes: Exploring Enzymatic Potential in Metagenomes with DNA Language Models
Function Prediction	DeepGOMeta: Functional Insights into Microbial Communities through Deep Learning
functional diversity	Opening an icy black box: diversity and functioning of soil bacteria in Antarctica’s largest ice-free region
Fused transformer	A Fused Transformer-based Model for Gene Expression Prediction using Histopathology Images
G
GCN	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Gene expression analysis
Gene expression prediction	A Fused Transformer-based Model for Gene Expression Prediction using Histopathology Images
gene regulation
generative AI	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
Genetic algorithm	Applying Genetic Algorithm with Saltations to MAX-3SAT
Genetic diversity	Evaluation of methods for estimating information entropy from limited sequence data
Genetic Linkage	Hidden Markov Model Analysis of Genetic Linkage
Genetic surveillance	Mixed HCV Infection: A novel genetic marker for surveillance of high-risk populations
Genome-scale Analysis
Genomics	Personalized health and genomics libraries for the analysis of long-term effects in COVID-19 patients
Genotype-phenotype mapping	Evaluation of methods for estimating information entropy from limited sequence data
Geometric Group Theory	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
GHOST	Earth Mover's Distance to recognize duplicate datasets in an automated molecular epidemiology system
Google Trends	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Gradients	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
Granger Test	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
graphs	Improved Graph-Based Antibody-Aware Epitope Prediction with Protein Language Model-Based Embeddings
Group factor analysis	Drug-centric prior improves drug response modeling in partially overlapping pharmacogenomic screens
H
Haplotype Matching	Haplotype-based Parallel PBWT for Biobank Scale Data
Haplotype reconstruction	Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase
hashing	DuoHash: fast hashing of spaced seeds with application to spaced k-mers counting
Health Recommender Systems	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
Hepatitis C virus	Epistatic Density of Viral Variants in Acute and Chronic HCV patients
hepatitis-c	Antigenic cooperation and cross-immunoreactivity networks
Hidden Markov Models	Hidden Markov Model Analysis of Genetic Linkage
Histology images	A Fused Transformer-based Model for Gene Expression Prediction using Histopathology Images
HIV	Phylodynamics Analysis of HIV Epidemic History in Belarus in 1987-2022
hRSV	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
human neural progenitor cells
I
IC	Novel Molecular Markers of the Inferior Colliculus identified via Single Nuclei Transcriptomics
ICD codes	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
In-Silico PCR	AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers
incidence	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Infectious Disease Genomics	Innovative Tools and Strategies for Outbreak Preparedness: Integrating Environmental Microbiomes and Prospective Pathogen Collections in Hospital Settings
Infectious disease models
info retrieval	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
Information Theory	Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach
Integrated	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
Integration
K
k-SAT	Evaluation of methods for estimating information entropy from limited sequence data
Kernel Matrix	Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
Kharkiv	The study of the effects of the full-scale Russian-Ukrainian war on the epidemiological situation and respiratory and intestinal diseases in the Kharkiv region of Ukraine from 2022 to 2024
kraken2	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
L
Language Models
Large Language Model	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
Large language models	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
Large Language Models (LLMs)	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
Learning Framework	A Multi-Model Ensemble Learning Framework with Uncertainty Quantification for Enhanced Poliovirus Surveillance (M-SURE)
Linkage disequilibrium	Hidden Markov Model Analysis of Genetic Linkage
LLMs	Leveraging large language models for predicting viral subtypes from sequence data
local immunodeficiency	Antigenic cooperation and cross-immunoreactivity networks
Long-term effects	Personalized health and genomics libraries for the analysis of long-term effects in COVID-19 patients
M
Machine Learning	The evolution of cancer progression risk: a phylogenetic and machine learning analysis Resistance genes are distinct in protein-protein interaction networks according to drug class and gene mobility
machinelearning	Benchmarking metagenomic software with the new CAMI web portal
Mammogram Dataset	Mammo-Bench: A Large-scale Benchmark Dataset of Mammography Images
Max 3SAT Problem	Applying Genetic Algorithm with Saltations to MAX-3SAT
Medical Imaging	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis Mammo-Bench: A Large-scale Benchmark Dataset of Mammography Images
Melting Temperature	AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers
Metagenome	MetaEdit: Computational Identification of RNA editing in Microbiomes
Metagenome annotation
Metagenomics	DeepGOMeta: Functional Insights into Microbial Communities through Deep Learning Assessing microbial genome representation across various reference databases: a comprehensive evaluation Diversity and Distinctive Characteristics of the Global RNA Virome in Urban Environments From Reads to Enzymes: Exploring Enzymatic Potential in Metagenomes with DNA Language Models Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces Benchmarking metagenomic software with the new CAMI web portal
metastasis	Simulation of tumor evolution and metastasis at single-cell resolution
Metatranscriptome	MetaEdit: Computational Identification of RNA editing in Microbiomes
metatranscriptomics	Diversity and Distinctive Characteristics of the Global RNA Virome in Urban Environments
Methylation
Methylation regulated genes
Metric Space Analysis	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
Microarray Data	Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach
Microbial communities	DeepGOMeta: Functional Insights into Microbial Communities through Deep Learning MetaEdit: Computational Identification of RNA editing in Microbiomes
Microbiome	AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers Model Selection for Sparse Microbial Network Inference using Variational Approximation
midbrain	Novel Molecular Markers of the Inferior Colliculus identified via Single Nuclei Transcriptomics
migration pattern	Simulation of tumor evolution and metastasis at single-cell resolution
Mitogen-activated protein kinase (MAPK) pathway Pharmacogenomics	Drug-centric prior improves drug response modeling in partially overlapping pharmacogenomic screens
mixture models	Model Selection for Sparse Microbial Network Inference using Variational Approximation
Model calibration
Model validation
molecular epidemiology	Phylodynamics Analysis of HIV Epidemic History in Belarus in 1987-2022 Earth Mover's Distance to recognize duplicate datasets in an automated molecular epidemiology system
Molecular Sequence Analysis	DANCE: Deep Learning-Assisted Analysis of ProteiN Sequences Using Chaos Enhanced Kaleidoscopic Images
mortality	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Multiomics	MetaEdit: Computational Identification of RNA editing in Microbiomes
Mutation	Epistatic Density of Viral Variants in Acute and Chronic HCV patients
Mutual Information	Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach
N
nanopore	Nanopore metagenomics as a rapid diagnostic for emerging high-threat bacterial pathogens on environmental interfaces
NCBI SRA	A Multi-Model Ensemble Learning Framework with Uncertainty Quantification for Enhanced Poliovirus Surveillance (M-SURE)
Network	Mixed HCV Infection: A novel genetic marker for surveillance of high-risk populations
networks	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model Antigenic cooperation and cross-immunoreactivity networks
Neural	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Neural Networks Sparsification	Cancer Diseases Classification with Sparse Neural Networks: An Information-Theoretic Approach
neurons	Novel Molecular Markers of the Inferior Colliculus identified via Single Nuclei Transcriptomics
next-generation sequencing	Simulation of tumor evolution and metastasis at single-cell resolution
NGS	Assessment of Host and Bacterial Depletion Methods to Enhance RNA Virus Detection by Next-Generation Sequencing
NLP	Can Language Models Reason about ICD Codes to Guide the Generation of Clinical Notes?
Nuclei isolation protocols
Nucleotides	Nearest Neighbor CCP-Based Molecular Sequence Analysis
O
optimal-leaf-ordering
Ordinary differential equation (ODE) models
orthoflavivirus
Outbreak investigation	Innovative Tools and Strategies for Outbreak Preparedness: Integrating Environmental Microbiomes and Prospective Pathogen Collections in Hospital Settings
P
Parallel Computing	Haplotype-based Parallel PBWT for Biobank Scale Data
pathway
PBWT	Haplotype-based Parallel PBWT for Biobank Scale Data
Personalized Health Recommendations	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
Personalized Healthcare	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
perturbation prediction	scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Phylodynamics	Phylodynamics Analysis of HIV Epidemic History in Belarus in 1987-2022
phylogenetics	The evolution of cancer progression risk: a phylogenetic and machine learning analysis
Phylogeny	Cancer progression inference from single-cell data with recurrences and mutation losses
Plain Text Representation	Fast and Succinct Compression of k-mer Sets with Plain Text Representation of Colored de Bruijn Graphs
Polyploid haplotype assembler	Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase
Population dynamics	Hidden Markov Model Analysis of Genetic Linkage
positive selection	HLA class I escape drives the evolution of SARS-CoV-2 in human population
PPIN	Resistance genes are distinct in protein-protein interaction networks according to drug class and gene mobility
Practical identifiability
Prediction	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Principal Components	A Benchmarking Study of Random Projections and Principal Components for Dimensionality Reduction Strategies in Single Cell Analysis
principle-code
Probabilistic modelling	Supervised Poisson Factorization for Uncovering Latent Gene Expression Patterns and Predicting Disease Risk Probabilistic Assembly and Uncertainty Quantification of Polyploid Haplotype Phase
Profile HMMs	AmpliconHunter: A Scalable Tool for Accurate Amplicon Prediction from Microbiome Samples using Degenerate Primers
progression
Prophet	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Protein Cα Trace	Enhancing Protein Side Chain Packing Using Rotamer Clustering and Machine Learning
Protein Folding	Explaining Protein Folding Networks Using Integrated Gradients and Attention Mechanisms
Protein Function	DeepGOMeta: Functional Insights into Microbial Communities through Deep Learning
Protein Structure	Enhancing Protein Side Chain Packing Using Rotamer Clustering and Machine Learning
Protein structure modeling	Improving inter-helical residue contact prediction in α-helical Transmembrane proteins using structural neighborhood crowdedness information
Protein Tertiary Structure	Unsupervised Learning for Tertiary Structure Prediction of Protein Molecules: Systematic Review
Protein-DNA Binding Prediction	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
Proximity Measure	Unsupervised Learning for Tertiary Structure Prediction of Protein Molecules: Systematic Review
Public Data	Leveraging Multiple Dimensions of Public Data to Characterize the Evolution of a Staphylococcal Plasmid
Punctuated evolution	Applying Genetic Algorithm with Saltations to MAX-3SAT
R
Random Projections	A Benchmarking Study of Random Projections and Principal Components for Dimensionality Reduction Strategies in Single Cell Analysis
Real-time Monitoring	EfficientNet in Digital Twin-based Cardiac Arrest Prediction and Analysis
Reference database	Assessing microbial genome representation across various reference databases: a comprehensive evaluation
Regulatory Genomics
Representation Learning	Evaluating $\delta$-Hyperbolicity of LLM Embeddings for Personalized Health Recommendations
risk modeling	The evolution of cancer progression risk: a phylogenetic and machine learning analysis
RNA editing	MetaEdit: Computational Identification of RNA editing in Microbiomes
RNA LLMs	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
RNA Sequences	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
RNA three-dimensional structure	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
Root Mean Square Deviation	Leveraging RNA LLMs for 3D Structure Prediction via Novel Data Augmentation
rRNA	Assessment of Host and Bacterial Depletion Methods to Enhance RNA Virus Detection by Next-Generation Sequencing
S
Saltations	Applying Genetic Algorithm with Saltations to MAX-3SAT
SARS-CoV-2	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater HLA class I escape drives the evolution of SARS-CoV-2 in human population
scRNA-Seq	A Benchmarking Study of Random Projections and Principal Components for Dimensionality Reduction Strategies in Single Cell Analysis
Sequence Analysis	Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
Sequence Classification	Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences
sequencing	Assessment of Host and Bacterial Depletion Methods to Enhance RNA Virus Detection by Next-Generation Sequencing
sequencing data	Leveraging large language models for predicting viral subtypes from sequence data
seriation
Shannon entropy	Evaluation of methods for estimating information entropy from limited sequence data
Side Chain Packing	Enhancing Protein Side Chain Packing Using Rotamer Clustering and Machine Learning
Side Chain Prediction	Enhancing Protein Side Chain Packing Using Rotamer Clustering and Machine Learning
Side Chain Ro-tamer	Enhancing Protein Side Chain Packing Using Rotamer Clustering and Machine Learning
Simulated annealing	Cancer progression inference from single-cell data with recurrences and mutation losses
simulation	Simulation of tumor evolution and metastasis at single-cell resolution
Single Cell Atlas
Single Cell RNA-Seq
single cell/nuclei	Novel Molecular Markers of the Inferior Colliculus identified via Single Nuclei Transcriptomics
single-cell	Simulation of tumor evolution and metastasis at single-cell resolution
single-cell RNA-sequencing	scDisInFact: disentangled learning for integration and prediction of multi-batch multi-condition single-cell RNA-sequencing data
Single-nucleus RNA sequencing (snRNA-seq)
Sinkhorn Knopp Algorithm	Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm
soil metagenomics	Opening an icy black box: diversity and functioning of soil bacteria in Antarctica’s largest ice-free region
somatic mutation	Simulation of tumor evolution and metastasis at single-cell resolution
spaced seeds	DuoHash: fast hashing of spaced seeds with application to spaced k-mers counting
sparse networks	Model Selection for Sparse Microbial Network Inference using Variational Approximation
Spatial transcriptomics	A Fused Transformer-based Model for Gene Expression Prediction using Histopathology Images
Spike sequence	Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences Nearest Neighbor CCP-Based Molecular Sequence Analysis
Spiking Neural Network	Neuromorphic Spiking Neural Network Based Classification of COVID-19 Spike Sequences
Staphylococcal Plasmid	Leveraging Multiple Dimensions of Public Data to Characterize the Evolution of a Staphylococcal Plasmid
Structural constraints	Phylogenetic inference of migration histories of viral populations under evolutionary and structural constraints
Structural identifiability
Subgraph	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Supervised Analysis	DANCE: Deep Learning-Assisted Analysis of ProteiN Sequences Using Chaos Enhanced Kaleidoscopic Images
Supervised poisson factorization	Supervised Poisson Factorization for Uncovering Latent Gene Expression Patterns and Predicting Disease Risk
Surveillance	A Multi-Model Ensemble Learning Framework with Uncertainty Quantification for Enhanced Poliovirus Surveillance (M-SURE)
Systems Biology
T
Taxonomic discrepancies	Assessing microbial genome representation across various reference databases: a comprehensive evaluation
time series	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.
Time-series Transcriptomics
TM proteins	Improving inter-helical residue contact prediction in α-helical Transmembrane proteins using structural neighborhood crowdedness information
transcription factors
Transcriptional Regulatory Networks
transcriptomics	Novel Molecular Markers of the Inferior Colliculus identified via Single Nuclei Transcriptomics
Transmission tree	Phylogenetic inference of migration histories of viral populations under evolutionary and structural constraints
tumor
tumor evolution	Simulation of tumor evolution and metastasis at single-cell resolution
tumor progression	The evolution of cancer progression risk: a phylogenetic and machine learning analysis
U
Ukraine	The study of the effects of the full-scale Russian-Ukrainian war on the epidemiological situation and respiratory and intestinal diseases in the Kharkiv region of Ukraine from 2022 to 2024
Ultra-deep sequencing	HAPLOQ: A simple strategy for correcting sequencing errors on viral amplicons
Uncertainty propagation
Uncertainty Quantification	A Multi-Model Ensemble Learning Framework with Uncertainty Quantification for Enhanced Poliovirus Surveillance (M-SURE)
Unsupervised learning	Unsupervised Learning for Tertiary Structure Prediction of Protein Molecules: Systematic Review DCCNV: Enhanced Copy Number Variation Detection in Single-Cell Sequencing Using Diffusion Processes and Contrastive Learning
Urban RNA virome	Diversity and Distinctive Characteristics of the Global RNA Virome in Urban Environments
V
variational approximation	Model Selection for Sparse Microbial Network Inference using Variational Approximation
VGAE	Link Prediction in Disease-Disease Interactions Network Using a Hybrid Deep Learning Model
Viral amplicons	HAPLOQ: A simple strategy for correcting sequencing errors on viral amplicons
viral lineage quantification	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Viral population	Phylogenetic inference of migration histories of viral populations under evolutionary and structural constraints
Viral subtyping	Leveraging large language models for predicting viral subtypes from sequence data
virus-host interaction
W
wastewater	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
X
XGBoost	The Use of Google Trends Data to Improve COVID-19 Incidence and Mortality Predictions Over Time in the 50 States of the USA and the District of Columbia.