ICCABS 2023: 2023 12TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL ADVANCES IN BIO AND MEDICAL SCIENCES

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

A
abundance estimation	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Adaptive Sampling	Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling
aging brain	Epigenetic regulation of endogenous viral elements in the aging brain
AI	Optimizing Deep Learning for Biomedical Imaging
Alcoholism	Genetic Predisposition to Alcoholism Significantly Alters the Functional Connectivity of the Brain
algorithms	On Multi-Phase Metagenomics Reads Binning Genotyping complex immune loci using integer linear programming
alignment-based HLA typing	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data
alignment-free	On Multi-Phase Metagenomics Reads Binning
Alleles	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data
altruistic virus	Antigenic cooperation and cross-immunoreactivity networks
Alz-heimer’s Disease	AFA: Abstract Functional Analysis Identifies New Microglial Subtypes at Single Cell Level in Alzheimer’s Disease
Alzheimer's Disease	Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective
Amplicon	Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing
Antibiotic resistance	A Hybrid Approach for Antibiotic Resistance Gene Characterization: Leveraging Pre-trained Protein Language Models and Alignment-Based Scoring
Antibiotics	Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies
Assembly	Mitogenome Assembly from Ultraconserved Elements Sequencing Reads
ATAC-seq	Benchmarking computational methods for single-cell chromatin data analysis
Attention Mechanism	Lightweight and Generalizable Model for COVID-19 Detection Using Chest Xray Images
Autoencoder	Decoding Heterogeneity in Quadruple-Negative Breast Cancer: A Data-Driven Clustering Approach A deep neural network to de-noise single-cell RNA sequencing data
B
Balanced background noise	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
Beltrami-Klein model	Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach
benchmark	Benchmarking computational methods for single-cell chromatin data analysis
benchmarking	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Bias in Healthcare	Fast Multi-level Neural Networks to Overcome Bias in Healthcare Applications
biochemical reactions	A Model for Elucidating the Single Molecule Synthesis Process through Temporal Information
Bioinformatics	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data VISTA: An integrated framework for structural variant discovery VISTA: An integrated framework for structural variant discovery
Biological Models	Automated Formalization of Biological Model Properties into Temporal Logics using Large Language Models
Biological Process	AFA: Abstract Functional Analysis Identifies New Microglial Subtypes at Single Cell Level in Alzheimer’s Disease
Biomedical Research	Growing Opportunities for Computational Advancements in Biomedical Research
BioTransformer	Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies
BMPT Prediction Tools	Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies
Brain Connectivity	Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective
Breast Cancer	DNA Methylation Based Subtype Classification of Breast Cancer
Bulk RNA-seq Data Analysis	A Computational Atlas for Transcriptomic Exploration of M. buryatense Using Unsupervised Machine Learning and Interactive Data Visualization
C
Callers	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data
canal segmentation · U-Net deep learning model · explainable artificial	An Explainable Deep Learning Framework for Mandibular Canal Segmentation from Cone Beam Computed Tomography volume
Cancer	A Unified Machine Learning Framework for Multi-subtype Tumour Classification across Diverse Datasets Towards improved reconstruction of single-cell copy number phylogenies
Cancer evolution	Single cell RNA phylogenetics of cancer
Cancer Genome Atlas (TCGA)	Computational and modeling aspects of analyzing high-throughput genomic data
Cancer Research	Enhancing Biomedical Research Using Novel Optical Imaging Technologies and Deep Learning
Cancer Tissue Prediction	Cancer and Tissue Prediction Using Mutational Signatures in Highly Mutated Cancers
Causal inference	Multiomics, Causality, and Longitudinal microbiomics
CD8+ T infiltration	Association of baseline tumor-specific neoantigens and CD8+ T infiltration with immune-related adverse events secondary to immune checkpoint inhibitors
CDR3	Adaptive receptor repertoire profiling methods for RNA sequencing
cell clustering	Single-cell Multiomics Clustering Using Graph Embedded Contrastive Learning
Cell phylogenies	Single cell RNA phylogenetics of cancer
chest CT	Optimizing Deep Learning for Biomedical Imaging
Chest X-Rays	Lightweight and Generalizable Model for COVID-19 Detection Using Chest Xray Images
Chimeric RNA	Identification of Chimeric RNAs: a novel machine learning perspective
Chronic wound	Investigating Microbial Community Functions in Chronic Bacterial Infections
Chronic wounds	Investigating Microbial Community Functions in Chronic Bacterial Infections
classification	A Unified Machine Learning Framework for Multi-subtype Tumour Classification across Diverse Datasets An exact matching method for 16S rRNA taxonomy classification Machine Learning Application for Predicting Smoking Cessation Among US Adults: An Analysis of Waves 1-5 of the PATH Study
Clustering	Clustering-Based Multi-Characteristic Comparative Analysis of COVID-19 Epidemiology in Europe
colon cancer	Computational framework for spatial omics analysis of colon polyp tissue
Comorbidity	Improving Disease Comorbidity Prediction with Biologically Supervised Graph Embedding
Computational Biology	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data VISTA: An integrated framework for structural variant discovery VISTA: An integrated framework for structural variant discovery Genotyping complex immune loci using integer linear programming Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling
Computational Systems Biology	Automated Formalization of Biological Model Properties into Temporal Logics using Large Language Models
Computed Tomography	A 3D Deep Learning Architecture for Denoising Low-Dose CT Scans
Computer-aided Diagnosis	PHViT4Lung: Parallel Hybrid Vision Transformers Augmented by Transfer Learning to Enhance Lung Cancer Diagnosis
contrastive learning	Single-cell Multiomics Clustering Using Graph Embedded Contrastive Learning
Convolution Neural Networks	PHViT4Lung: Parallel Hybrid Vision Transformers Augmented by Transfer Learning to Enhance Lung Cancer Diagnosis
Convolutional Neural Network	Lightweight and Generalizable Model for COVID-19 Detection Using Chest Xray Images
cooperation	Antigenic cooperation and cross-immunoreactivity networks
Copy number variation	Improved inference of single-cell haplotype-aware copy numbers in cancer
COVID-19	Optimizing Deep Learning for Biomedical Imaging Lightweight and Generalizable Model for COVID-19 Detection Using Chest Xray Images Clustering-Based Multi-Characteristic Comparative Analysis of COVID-19 Epidemiology in Europe
Cystic fibrosis	Investigating Microbial Community Functions in Chronic Bacterial Infections Investigating Microbial Community Functions in Chronic Bacterial Infections
D
Data Assimilation	Role of Data Assimilation in Prediction: Potential applications to Biological and Medical Sciences
data augmentation	GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation
data enhancement	SpaNN: a flexible deep neural network framework for predicting the transcript distribution of the spatial transcriptomics
Data Imbalance	FedDP: Secure Federated Learning with Differential Privacy for Disease Prediction
Data Science	Growing Opportunities for Computational Advancements in Biomedical Research
Data Visualization	AFA: Abstract Functional Analysis Identifies New Microglial Subtypes at Single Cell Level in Alzheimer’s Disease
de Bruijn Graphs	On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs
deep learning	A 3D Deep Learning Architecture for Denoising Low-Dose CT Scans Optimizing Deep Learning for Biomedical Imaging GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation Identification of Chimeric RNAs: a novel machine learning perspective mRNA stability prediction A Simple and Interpretable Deep Learning Model for Diagnosing Pneumonia from Chest X-Ray Images Enhancing Biomedical Research Using Novel Optical Imaging Technologies and Deep Learning
deep neural network	SpaNN: a flexible deep neural network framework for predicting the transcript distribution of the spatial transcriptomics
Default Mode Network	Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective
degradation	mRNA stability prediction
Dental Cone Beam Computed Tomography · mandibular	An Explainable Deep Learning Framework for Mandibular Canal Segmentation from Cone Beam Computed Tomography volume
developmental programming	Unraveling the Early-Life Origins of Nonalcoholic Fatty Liver Disease (NAFLD) Using Multi-'Omics Approaches
Differential Privacy	FedDP: Secure Federated Learning with Differential Privacy for Disease Prediction
diffusion models	GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation
Distance computations	A Novel String Map-Based Approach for Distance Calculations with Applications to Faster Record Linkage
Distributed Data Parallel	A 3D Deep Learning Architecture for Denoising Low-Dose CT Scans
DNA Methylation	DNA Methylation Based Subtype Classification of Breast Cancer
drug resistance	PartialFibers: An efficient method for predicting Drug-Drug Interactions
drug-drug combination	PartialFibers: An efficient method for predicting Drug-Drug Interactions
dynamic Bayesian networks	Multiomics, Causality, and Longitudinal microbiomics
E
Early detection	Early detection of emerging viral variants with altered phenotypes using viral epistatic networks
Edit distance	A Novel String Map-Based Approach for Distance Calculations with Applications to Faster Record Linkage
EEG	Multilayer Network Analysis of Brain Signals for Detecting Alzheimer’s Disease Genetic Predisposition to Alcoholism Significantly Alters the Functional Connectivity of the Brain
Electronic health records	A Novel String Map-Based Approach for Distance Calculations with Applications to Faster Record Linkage
electrophysiological testing	How to Record a Phantom Sound - Tinnitus Assessment via Electrophysiology
emerging technologies	Growing Opportunities for Computational Advancements in Biomedical Research
endogenous viral elements	Epigenetic regulation of endogenous viral elements in the aging brain
Epidemiology	Clustering-Based Multi-Characteristic Comparative Analysis of COVID-19 Epidemiology in Europe
Epigenetic regulation	Epigenetic regulation of endogenous viral elements in the aging brain
Epistasis	Early detection of emerging viral variants with altered phenotypes using viral epistatic networks
Epistatic network	Genetic Algorithm with Evolutionary Jumps
Error Correction	ParMEC: A Set of Algorithms for Parallel Metagenomic Error Correction
Evolution	Genetic Algorithm with Evolutionary Jumps Tracking and modeling the dynamics of evolving SARS-CoV-2 Variants
explainable AI	A Simple and Interpretable Deep Learning Model for Diagnosing Pneumonia from Chest X-Ray Images
Extreme value	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
F
Federated Learning	FedDP: Secure Federated Learning with Differential Privacy for Disease Prediction
fiber-based approach	PartialFibers: An efficient method for predicting Drug-Drug Interactions
Formal Models	Automated Formalization of Biological Model Properties into Temporal Logics using Large Language Models
Functional Connectivity	Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective Genetic Predisposition to Alcoholism Significantly Alters the Functional Connectivity of the Brain
G
Gene expression	Single cell RNA phylogenetics of cancer
generative models	GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation
Genetic Algorithm	Genetic Algorithm with Evolutionary Jumps
Genome Graphs	On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs
genomics	GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation Genotyping complex immune loci using integer linear programming
Glycosaminoglycans	Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
GO Analysis	AFA: Abstract Functional Analysis Identifies New Microglial Subtypes at Single Cell Level in Alzheimer’s Disease
Graph Embedding	Improving Disease Comorbidity Prediction with Biologically Supervised Graph Embedding Single-cell Multiomics Clustering Using Graph Embedded Contrastive Learning
graph-based	A computational framework for identifying TCell Receptor specificity in single cell resolution
H
Hamiltonian energy function	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
Haplotype	Improved inference of single-cell haplotype-aware copy numbers in cancer
Hashing	Hashed Embeddings: A Promising Technique for Efficient Protein Sequence Representation
health status	Repeated Measures Latent Dirichlet Allocation for Longitudinal Microbiome Analysis
Healthcare data	Fast Multi-level Neural Networks to Overcome Bias in Healthcare Applications
hepatitis c	Antigenic cooperation and cross-immunoreactivity networks
high-throughput sequencing	Computational and modeling aspects of analyzing high-throughput genomic data
HLA	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
hla-caller	A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
HLA-typing	A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
Human Interactome	Improving Disease Comorbidity Prediction with Biologically Supervised Graph Embedding
Human milk	Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
Human-leukocyte-antigen	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data
Hyaluronan	Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
hyperbolic geometry	Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach
I
Illumina	Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing
image de-noising	Optimizing Deep Learning for Biomedical Imaging
Image Enhancement	A 3D Deep Learning Architecture for Denoising Low-Dose CT Scans
imaging mass spectrometry	Computational framework for spatial omics analysis of colon polyp tissue Role of walnut-derived urolithins in reducing colonic inflammation in a patient cohort elucidated by an integrated omics analysis
immune checkpoint inhibitors	Association of baseline tumor-specific neoantigens and CD8+ T infiltration with immune-related adverse events secondary to immune checkpoint inhibitors
immunogenomics	Genotyping complex immune loci using integer linear programming
immunology	A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
immunoreactivity	Antigenic cooperation and cross-immunoreactivity networks
in silico	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
intelligence · Grad-CAM	An Explainable Deep Learning Framework for Mandibular Canal Segmentation from Cone Beam Computed Tomography volume
Interactive Data Visualization	A Computational Atlas for Transcriptomic Exploration of M. buryatense Using Unsupervised Machine Learning and Interactive Data Visualization
Interspike-interval (ISI) firing rate	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
Isomap	Improving Disease Comorbidity Prediction with Biologically Supervised Graph Embedding
Izhikevich model	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
K
kernel matrix	Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach
Kernel Methods	Preserving Hidden Hierarchical Structures: Poincaré Distance for Enhanced Genomic Sequence Analysis
Knapsack Problem	Genetic Algorithm with Evolutionary Jumps
L
Language model	A Hybrid Approach for Antibiotic Resistance Gene Characterization: Leveraging Pre-trained Protein Language Models and Alignment-Based Scoring
Lasso latent feature model	Computational and modeling aspects of analyzing high-throughput genomic data
latent topic	Repeated Measures Latent Dirichlet Allocation for Longitudinal Microbiome Analysis
lineage inference	Incorporating structural variation into single-cell clonal lineage inference
LLMs	Automated Formalization of Biological Model Properties into Temporal Logics using Large Language Models
localized ablative immunotherapy (LAIT)	Single-cell RNA-sequencing analysis of breast tumor infiltrating lymphocytes treated with localized ablative cancer immunotherapy
long-duration sound (LDS)	How to Record a Phantom Sound - Tinnitus Assessment via Electrophysiology
M
Machine Learning	GenoDiffusion: Conditional Denoising Diffusion Model for Genomic Data Augmentation DNA Methylation Based Subtype Classification of Breast Cancer VISTA: An integrated framework for structural variant discovery VISTA: An integrated framework for structural variant discovery Machine Learning Application for Predicting Smoking Cessation Among US Adults: An Analysis of Waves 1-5 of the PATH Study A Computational Atlas for Transcriptomic Exploration of M. buryatense Using Unsupervised Machine Learning and Interactive Data Visualization
Matching	An exact matching method for 16S rRNA taxonomy classification
Mathematical modeling	Role of Data Assimilation in Prediction: Potential applications to Biological and Medical Sciences
Maximum Flow	Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective
Metabolites	Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies
metabolomics	Role of walnut-derived urolithins in reducing colonic inflammation in a patient cohort elucidated by an integrated omics analysis
Metagenome	ParMEC: A Set of Algorithms for Parallel Metagenomic Error Correction
metagenomics	On Multi-Phase Metagenomics Reads Binning Assessing Microbial Genome Representation Across Various Reference Databases: A Comprehensive Evaluation
Microbial physiology	Investigating Microbial Community Functions in Chronic Bacterial Infections
microbial reference databases	Assessing Microbial Genome Representation Across Various Reference Databases: A Comprehensive Evaluation
microbiome	Unraveling the Early-Life Origins of Nonalcoholic Fatty Liver Disease (NAFLD) Using Multi-'Omics Approaches
microbiome counts	Repeated Measures Latent Dirichlet Allocation for Longitudinal Microbiome Analysis
Microbiomes	Multiomics, Causality, and Longitudinal microbiomics
MiSeq	Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing
Mitochondiral DNA	Mitogenome Assembly from Ultraconserved Elements Sequencing Reads
model	A Unified Machine Learning Framework for Multi-subtype Tumour Classification across Diverse Datasets
mRNA stability	mRNA stability prediction
Multi-level Neural Networks	Fast Multi-level Neural Networks to Overcome Bias in Healthcare Applications
multi-omics	Unraveling the Early-Life Origins of Nonalcoholic Fatty Liver Disease (NAFLD) Using Multi-'Omics Approaches
Multi-Scale Features	Multilayer Network Analysis of Brain Signals for Detecting Alzheimer’s Disease
Multilayer Networks	Multilayer Network Analysis of Brain Signals for Detecting Alzheimer’s Disease
Multiomics	Multiomics, Causality, and Longitudinal microbiomics Single-cell Multiomics Clustering Using Graph Embedded Contrastive Learning
Mutational Signatures	Cancer and Tissue Prediction Using Mutational Signatures in Highly Mutated Cancers
N
Necrotizing enterocolitis	Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
Network	Early detection of emerging viral variants with altered phenotypes using viral epistatic networks
Network analysis	Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
Neural Networks	Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling
Neural-Network	Integrating Neural Networks into DNA Sequence-Based Predictions of RSS Functionality and Activity Level
Neurological Disorder	Functional Connectivity Disruptions in Alzheimer’s Disease: A Maximum Flow Perspective
nonalcoholic fatty liver disease	Unraveling the Early-Life Origins of Nonalcoholic Fatty Liver Disease (NAFLD) Using Multi-'Omics Approaches
Numerical Embedding	Hashed Embeddings: A Promising Technique for Efficient Protein Sequence Representation
O
Optical Imaging	Enhancing Biomedical Research Using Novel Optical Imaging Technologies and Deep Learning
P
Pathogenesis	Investigating Microbial Community Functions in Chronic Bacterial Infections
Pathway	Network-Based Bioinformatics Highlights Broad Importance of Human Milk Hyaluronan
Pattern Matching	On the Hardness of Wildcard Pattern Matching on de Bruijn Graphs
pattern recognition	A Simple and Interpretable Deep Learning Model for Diagnosing Pneumonia from Chest X-Ray Images
persistent virus	Antigenic cooperation and cross-immunoreactivity networks
Phase advance	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
photo-immunotherapy	Single-cell RNA sequencing reveals the atlas of a breast tumor microenvironment and the remodeling by photo-immunotherapy
PHRED	Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing
Pneumonia	A Simple and Interpretable Deep Learning Model for Diagnosing Pneumonia from Chest X-Ray Images
poisson distribution	A deep neural network to de-noise single-cell RNA sequencing data
Polymicrobial infection	Investigating Microbial Community Functions in Chronic Bacterial Infections
Polymicrobial infections	Investigating Microbial Community Functions in Chronic Bacterial Infections
precursor polyps	Computational framework for spatial omics analysis of colon polyp tissue
Prediction	Role of Data Assimilation in Prediction: Potential applications to Biological and Medical Sciences
preprocessing	Benchmarking computational methods for single-cell chromatin data analysis
Primary Metabolism	Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies
Protein	A Hybrid Approach for Antibiotic Resistance Gene Characterization: Leveraging Pre-trained Protein Language Models and Alignment-Based Scoring
Protein Design	Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling
Protein Engineering	Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling
protein sequence classification	Gaussian Beltrami-Klein Model for Protein Sequence Classification: A Hyperbolic Approach
Protein Sequences	Hashed Embeddings: A Promising Technique for Efficient Protein Sequence Representation
proteomics	Role of walnut-derived urolithins in reducing colonic inflammation in a patient cohort elucidated by an integrated omics analysis
pseudotime inference	Computational tumor progression analysis via seriation based trajectory inference
Q
QNBC subtypes	Decoding Heterogeneity in Quadruple-Negative Breast Cancer: A Data-Driven Clustering Approach
Quadruple-Negative Breast Cancer (QNBC)	Decoding Heterogeneity in Quadruple-Negative Breast Cancer: A Data-Driven Clustering Approach
R
Random Forests	Cancer and Tissue Prediction Using Mutational Signatures in Highly Mutated Cancers
read binning	On Multi-Phase Metagenomics Reads Binning
Record linkage (RL)	A Novel String Map-Based Approach for Distance Calculations with Applications to Faster Record Linkage
regularization	A deep neural network to de-noise single-cell RNA sequencing data
relevance aggregation	A Simple and Interpretable Deep Learning Model for Diagnosing Pneumonia from Chest X-Ray Images
repeated measures	Repeated Measures Latent Dirichlet Allocation for Longitudinal Microbiome Analysis
Representation Learning	Preserving Hidden Hierarchical Structures: Poincaré Distance for Enhanced Genomic Sequence Analysis
RNA sequencing	Identification of Chimeric RNAs: a novel machine learning perspective
RNA-Seq	Adaptive receptor repertoire profiling methods for RNA sequencing
RSS-Utilization	Integrating Neural Networks into DNA Sequence-Based Predictions of RSS Functionality and Activity Level
S
SARS-CoV-2	Hashed Embeddings: A Promising Technique for Efficient Protein Sequence Representation Tracking and modeling the dynamics of evolving SARS-CoV-2 Variants A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Scalable Algorithm	ParMEC: A Set of Algorithms for Parallel Metagenomic Error Correction
scRna-seq	A deep neural network to de-noise single-cell RNA sequencing data Computational tumor progression analysis via seriation based trajectory inference
Secondary Metabolism	Predicting Antibiotic Metabolites with One and Two-Steps in Silico Biotransformations to Support Identification of Unknown Chemicals in Exposome and Metabolome Studies
secondary structure	mRNA stability prediction
Semi-Supervised Learning	Exploring Protein Design Landscapes with Semi-Supervised Adaptive Sampling
Sequence Analysis	On Multi-Phase Metagenomics Reads Binning Preserving Hidden Hierarchical Structures: Poincaré Distance for Enhanced Genomic Sequence Analysis
Sequencing	Assessment of PHRED Score Characteristics in Illumina MiSeq Amplicon Sequencing
single cell	A computational framework for identifying TCell Receptor specificity in single cell resolution Benchmarking computational methods for single-cell chromatin data analysis
single cell atlas	Single-cell RNA sequencing reveals the atlas of a breast tumor microenvironment and the remodeling by photo-immunotherapy
Single cell DNA sequencing	Improved inference of single-cell haplotype-aware copy numbers in cancer
Single Cell Gene Expression Data Analysis	AFA: Abstract Functional Analysis Identifies New Microglial Subtypes at Single Cell Level in Alzheimer’s Disease
Single Cell RNA-Seq	Single-cell RNA sequencing reveals the atlas of a breast tumor microenvironment and the remodeling by photo-immunotherapy
single molecule sequencing	A Model for Elucidating the Single Molecule Synthesis Process through Temporal Information
single molecule synthesis	A Model for Elucidating the Single Molecule Synthesis Process through Temporal Information
single-cell	Single-cell Multiomics Clustering Using Graph Embedded Contrastive Learning
single-cell clonal	Incorporating structural variation into single-cell clonal lineage inference
Single-cell phylogeny	Towards improved reconstruction of single-cell copy number phylogenies
Single-cell RNA-sequencing	Single-cell RNA-sequencing analysis of breast tumor infiltrating lymphocytes treated with localized ablative cancer immunotherapy
Single-cell sequencing	Plastic: An easy to use and modular tool for designing tumor phylogeny reconstruction pipelines
Sinusoidal current	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
smoking activity	Machine Learning Application for Predicting Smoking Cessation Among US Adults: An Analysis of Waves 1-5 of the PATH Study
smoking cessation	Machine Learning Application for Predicting Smoking Cessation Among US Adults: An Analysis of Waves 1-5 of the PATH Study
Somatic copy number alterations	Towards improved reconstruction of single-cell copy number phylogenies
spatial transcriptomic sequencing	SpaNN: a flexible deep neural network framework for predicting the transcript distribution of the spatial transcriptomics
spatial transcriptomics	Computational framework for spatial omics analysis of colon polyp tissue Single cell RNA phylogenetics of cancer
Spatiotemporal Patterns	Multilayer Network Analysis of Brain Signals for Detecting Alzheimer’s Disease
statistical model	A Model for Elucidating the Single Molecule Synthesis Process through Temporal Information
structural variation	Incorporating structural variation into single-cell clonal lineage inference
subtype	A Unified Machine Learning Framework for Multi-subtype Tumour Classification across Diverse Datasets
Subtype Classification	DNA Methylation Based Subtype Classification of Breast Cancer
Supervised Embedding	Improving Disease Comorbidity Prediction with Biologically Supervised Graph Embedding
T
T-Cells	A computational framework for identifying TCell Receptor specificity in single cell resolution
taxonomic discrepancies	Assessing Microbial Genome Representation Across Various Reference Databases: A Comprehensive Evaluation
Taxonomy	An exact matching method for 16S rRNA taxonomy classification
TCR	A computational framework for identifying TCell Receptor specificity in single cell resolution
TCR-Seq	Adaptive receptor repertoire profiling methods for RNA sequencing
Temporal Logics	Automated Formalization of Biological Model Properties into Temporal Logics using Large Language Models
tensor completion	PartialFibers: An efficient method for predicting Drug-Drug Interactions
Tinnitus	How to Record a Phantom Sound - Tinnitus Assessment via Electrophysiology
topic models	Repeated Measures Latent Dirichlet Allocation for Longitudinal Microbiome Analysis
Tracking	Tracking and modeling the dynamics of evolving SARS-CoV-2 Variants
trajectory inference	Computational tumor progression analysis via seriation based trajectory inference
Transfer Learning	A 3D Deep Learning Architecture for Denoising Low-Dose CT Scans
transplants	A rigorous benchmarking of alignment-based HLA typing algorithms for RNA-seq data
Tumor evolution	Towards improved reconstruction of single-cell copy number phylogenies
tumor microenvironment	Single-cell RNA sequencing reveals the atlas of a breast tumor microenvironment and the remodeling by photo-immunotherapy
Tumor phylogenetics	Plastic: An easy to use and modular tool for designing tumor phylogeny reconstruction pipelines
tumor-infiltrating T/B cells	Single-cell RNA-sequencing analysis of breast tumor infiltrating lymphocytes treated with localized ablative cancer immunotherapy
tumor-specific neoantigens	Association of baseline tumor-specific neoantigens and CD8+ T infiltration with immune-related adverse events secondary to immune checkpoint inhibitors
Typing	A Rigorous Benchmarking of alignment-based HLA callers for RNA-seq data
U
Ultraconserved Elements	Mitogenome Assembly from Ultraconserved Elements Sequencing Reads
Unsupervised Clustering	Decoding Heterogeneity in Quadruple-Negative Breast Cancer: A Data-Driven Clustering Approach
V
V(D)J-Recombination	Integrating Neural Networks into DNA Sequence-Based Predictions of RSS Functionality and Activity Level
Velocity vector field	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model
Vision Transformers	PHViT4Lung: Parallel Hybrid Vision Transformers Augmented by Transfer Learning to Enhance Lung Cancer Diagnosis
W
wastewater	A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater A rigorous benchmarking of methods for SARS-CoV-2 lineage abundance estimation in wastewater
Workflow design	Plastic: An easy to use and modular tool for designing tumor phylogeny reconstruction pipelines
Z
zero-inflation	A deep neural network to de-noise single-cell RNA sequencing data
ZiPo	A deep neural network to de-noise single-cell RNA sequencing data
γ
γ-γ′ phase plane	Exploring a Solution Curve in the Phase Plane for Extreme Firing Rates in the Izhikevich Model

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