yusuke1997/dblp-id-title huggingface dataset:
Quantitative Early Detection of Diabetic Foot
Structural analysis of PTM hotspots (SAPH-ire): a tool for the prediction of regulatory post-translational modification elements in protein families
ProSol DB: A Protein Solubility Database
Evaluation of different complexity measures for signal detection in genome sequences
Supervised multi-specialist topic model with applications on large-scale electronic health record data
Predicting Breast Cancer Outcome under Different Treatments by Feature Selection Approaches
CNB-MAC'17: The Fourth International Workshop on Computational Network Biology: Modeling, Analysis, and Control
PseudoDomain: identification of processed pseudogenes based on protein domain classification
Towards the Design of Matrix Metalloproteinases (MMP) Antibody Sequences
HarMinMax: Harmonizing Codon Usage to Replicate Local Host Translation
Genomic Sequence Fragment Identification using Quasi-Alignment
Identification of generalizable gene expression biomarkers associated with drug Respose in cell Lines and patients
Prediction of Cell Type Specific Transcription Factor Binding Site Occupancy
Nirvana: Clinical Grade Variant Annotator
Automated Mouse Organ Segmentation: A Deep Learning Based Solution
An integrated optimization framework for inferring two generation kinships and parental genotypes from microsatellite samples
Improved multiple sequence alignments using coupled pattern mining
Performance portability study of epistasis detection using SYCL on NVIDIA GPU
Counting independent motifs in probabilistic networks
A logical exposition of dirac 3-polarizer experiment and its potential impact on computational biology
Inferring ancestry in admixed populations using microarray probe intensities
MinIsoClust: Isoform clustering using minhash and locality sensitive hashing
Integration of Cancer Data through Multiple Mixed Graphical Model
A comprehensive analysis of classification algorithms for cancer prediction from gene expression
Detangling PPI Networks to Uncover Functionally Meaningful Clusters
Pani: a novel algorithm for fast discovery of putative target nodes in signaling networks
Algorithms for optimizing cross-overs in DNA shuffling
Supervised pretraining through contrastive categorical positive samplings to improve COVID-19 mortality prediction
Detecting ECG abnormalities via transductive transfer learning
Development of a generalizable multi-site and multi-modality clinical data cloud infrastructure for pediatric patient care
An Ensemble Machine Learning Approach for Benchmarking and Selection of scRNA-seq Integration Methods
Fast and Highly Scalable Bayesian MDP on a GPU Platform
Influence Function of Multiple Kernel Canonical Analysis to Identify Outliers in Imaging Genetics Data
A Compatibility Approach to Identify Recombination Breakpoints in Bacterial and Viral Genomes
Fleximer: Accurate Quantification of RNA-Seq via Variable-Length k-mers
A computational framework for finding functional modules across multiple biological networks
Biased decoy sampling to aid the selection of near-native protein conformations
High-performance recursive dynamic programming for bioinformatics using MM-like flexible kernels
Evaluating the quality of conformation sampling methods using experimental residual dipolar coupling data
Linearization of Ancestral Genomes with Duplicated Genes
Model-based Transcriptome Engineering
DNA sequence feature selection for intrinsic nucleosome positioning signals using AdaBoost
ParBio'19 - 8th Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine
SNP specific extraction and analysis using shrunken dissimilarity measure
Prediction of candidate genes for neuropsychiatric disorders using feature-based enrichment
ISO: numeric representation of nucleic acid form
A novel network model for molecular prognosis
Automated Breast Cancer Diagnosis Using Deep Learning and Region of Interest Detection (BC-DROID)
Name Similarity for Composite Element Name Matching
Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma
Predicting Breast Cancer Patient Survival Using Machine Learning
Sequence, Structure and Network Methods to Uncover Cancer Genes
Winnow: Interactive Visualization of Temporal Changes in Multidimensional Clinical Data
Pseudotime Based Analysis of Cancer Dynamics
Reconstructing Intra-Tumor Heterogeneity via Convex Optimization and Branch-and-Bound Search
ACM-BCB'18 Tutorial: Making Deep Learning Understandable for Analyzing Sequential Data about Gene Regulation
Unraveling multiple miRNA-mRNA associations through a graph-based approach
Examining effects of variability on systems biology modeling algorithms
The Algorithms of Predicting DNA Binding Site with Combined Feature Encoding and Optimum Decision
SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-Learning
Prefix/Suffix Variation in Retinoic Acid Response Elements
Abstract Mining
An alignment-free approach to cluster proteins using frequency of conserved k-mers
NcRNA homology search using Hamming distance seeds
Generation of novel Chagas vaccines: evolving studies/work in progress
Evaluating theoretical models of protein interaction network evolution without seed graphs
Random forest-based prediction of protein sumoylation sites from sequence features
Topological analysis of structural roles of proteins in interactome networks
A collective ranking method for genome-wide association studies
RImmPort: enabling ready-for-analysis immunology research data
Surveillance of COVID-19 pandemic using social media: a reddit study in North Carolina
Pairwise structure alignment specifically tuned for surface pockets and interaction interfaces
Towards Independent Particle Reconstruction from Cryogenic Transmission Electron Microscopy
Using Similarity Metrics on Real World Data to Recommend the Next Treatment
Identifying gene functions using functional expression profiles obtained by voxelation
Parallel stochastic simulations of budding yeast cell cycle: load balancing strategies and theoretical analysis
A deep framework for bacterial image segmentation and classification
DynMap: mapping short reads to multiple related genomes
A comparative study of codon adaptation in ssDNA and dsDNA phages
Optimal protospacer sequences recommended by ensemble deep learning for high-efficiency base editing
Are Profile Hidden Markov Models Identifiable?
A multi-resolution graph convolution network for contiguous epitope prediction
Real-Time Monitoring of Health Security Attacks with R-based Data Visualization Dashboard
Pulmonary artery smooth muscle responses to KCl under normoxic and hypoxic conditions studied by means of a spatial network model
Ring optimization of edit metric codes in DNA
LSHvec: a vector representation of DNA sequences using locality sensitive hashing and FastText word embeddings
Target Gene Prediction of Transcription Factor Using a New Neighborhood-regularized Tri-factorization One-class Collaborative Filtering Algorithm
Challenges in adapting text mining for full text articles to assist pathway curation
glu-RNA: aliGn highLy strUctured ncRNAs using only sequence similarity
Mechanistic model demonstrates importance of autocrine IL-8 secretion by neutrophils
Incremental network querying in biological networks
Immunoinformatic analysis of Chinese hamster ovary (CHO) protein contaminants in therapeutic protein formulations
Highlights Talks at ACM BCB 2017
Semi-automated Constraint-based Metabolic Model Generation
Identification of protein coding regions in RNA transcripts
Amb-EM: a SNP-based prediction of HLA alleles using ambiguous HLA data
Improving identification of key players in aging via network de-noising
Simulating Uncertainty of Early Warning Scores in Sepsis Detection
Gene set analysis using principal components
Personalized medicine - challenges and opportunities for informatics research
PseudoLasso: leveraging read alignment in homologous regions to correct pseudogene expression estimates via RNASeq
MULTICOM: a large-scale conformation sampling and evaluation server for protein tertiary structure prediction
Co-MEAL: Cost-Optimal Multi-Expert Active Learning Architecture for Mobile Health Monitoring
fMRI image registration with AFNI's 3dQwarp
An improved algorithm for the sorting by reversals and transpositions problem
Towards biophysical validation of constraint modeling for rigidity analysis of proteins
SVMPT: A Hybrid Approach to Sparse and Irregular Clinical Data Learning with Selective Variable-wise Message Passing and Transformer
Identification of therapeutic targets for muscle atrophy via analyzing transcriptomic profiles with systems biology approaches
An integrative framework for structure-based prediction of biological effects mediated by antipeptide antibodies
Meta-analysis of Genomic and Proteomic Features to Predict Synthetic Lethality of Yeast and Human Cancer
Biological network clustering by robust NMF
Cost-Sensitive Deep Active Learning for Epileptic Seizure Detection
AT[N]-net: multimodal spatiotemporal network for subtype identification in Alzheimer's disease
Revealing Multi-biological Subtypes of Schizophrenia through a Data-Driven Clustering
Stochastic Modeling and Simulation of Reaction-Diffusion System with Hill Function Dynamics
CytoSet: predicting clinical outcomes via set-modeling of cytometry data
Investigating statistical analysis for network motifs
gLIMS: Google cloud-based laboratory information management system for NMR metabolomics
Towards dynamic simulation of a whole cell model
Emulation of biological networks in reconfigurable hardware
SeqAnt: Cloud-Based Whole-Genome Annotation and Search
Numerically stable algorithm for Inverse Kinematics of 6R problem and its applications to macrocycles
GANDALF: A Prototype of a GAN-based Peptide Design Method
A parameter estimation approach for non-linear systems biology models using spline approximation
Algorithms for pseudoknot classification
A Text-Mining System for Concept Annotation in Biomedical Full Text Articles
A collaborative filtering approach to assess individual condition risk based on patients' social network data
Multi-target protein-chemical interaction prediction using task-regularized and boosted multi-task learning
Identifying protein complexes in AP-MS data with negative evidence via soft Markov clustering
MultiRBP: multi-task neural network for protein-RNA binding prediction
Computing interaction probabilities in signaling networks
Biomarker Discovery via Optimal Bayesian Feature Filtering for Structured Multiclass Data
MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads
DDI2PPI: an integrated web server for protein-protein interaction and residue contact matrix predictions
Ranking docked models of protein-protein complexes using predicted partner-specific protein-protein interfaces: a preliminary study
Developing a modified version of generative adversarial network to predict the potential anti-viral drug of COVID-19
A continuum hard-sphere model of protein adsorption
Clinical knowledgebase to interprete genomic variations from targeted exome sequencing of patient tumor samples
PepGPL: A Multi-Task Framework for Identifying Peptide-Protein Interactions and Corresponding Binding Residues
Using motion planning to rank ligand binding affinity
An integrative analysis of ATAC-seq and RNA-seq data in activated, CD4+CD45RO+CD196+ human T cells treated with IL-1B and IL-23 with or without PGE2
MVAR: a mouse variation registry
Statistical Analysis of Computed Energy Landscapes to Understand Dysfunction in Pathogenic Protein Variants
Remote homology detection on alpha-structural proteins using simulated evolution
Detecting Chromosomal Inversions from Dense SNPs by Combining PCA and Association Tests
Deep Learning for High-Order Drug-Drug Interaction Prediction
miHA-match: computational detection of tissue-specific minor histocompatibility antigens
Phylogenetic and functional divergence analysis of vertebrate IRAK family members
Scalable non-invasive pediatric cerebral visual impairment screening with the higher visual function question inventory (HVFQI)
Predicting prognostic markers for glioma using gene co-expression network analysis
Explaining large-for-gestational-age births: a random forest classifier with a novel local interpretation method
A Visual Analytics Framework for Analysis of Patient Trajectories
Identifying causal variants at loci with multiple signals of association
Dynamic Phylogenetic Inference for Sequence-based Typing Data
A computational metabolic model of the NG108-15 cell for high content drug screening with electrophysiological readout
PINet: Privileged Information Improve the Interpretablity and generalization of structural MRI in Alzheimer's Disease
Correlation Imputation in Single cell RNA-seq using Auxiliary Information and Ensemble Learning
How TV advertising and social network help tobacco control campaigns influence more
BCB '20: 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Virtual Event, USA, September 21-24, 2020
The Atomizer: Extracting Implicit Molecular Structure from Reaction Network Models
An Algorithm for Constructing Hypothetical Evolutionary Trees Using Common Mutation Similarity Matrices
Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignments
Leveraging hierarchy in medical codes for predictive modeling
Beta-Binomial Modeling of CRISPR Pooled Screen Data Identifies Target Genes with Greater Sensitivity and fewer False Negatives
Protein subcellular localization prediction with associative classification and multi-class SVM
Efficient data reduction for large-scale genetic mapping
Poster abstract: RNA thermodynamic conformational entropy
Transparent single-cell set classification with kernel mean embeddings
Human immunodeficiency virus (HIV) proteomics resource at BioAfrica
Computational identification of functional network modules associated with the pathogenicity of Fusarium verticillioides
A Sparse Latent Regression Approach for Integrative Analysis of Glycomic and Glycotranscriptomic Data
GPU-Optimized Hybrid Neighbor/Cell List Algorithm for Coarse-Grained MD Simulations of Protein and RNA Folding and Assembly
Study of Antidepressant Molecular Structure Leading to Safer Dosing
Initial Results In Using de Novo Motif Inference to Detect Cis-Regulatory Modules
Protein blocks versus hydrogen bonds based alphabets for protein structure classification
The impact of sample size and tissue type on the reproducibility of gene co-expression networks
Tensor-Factorization-Based Phenotyping using Group Information: Case Study on the Efficacy of Statins
Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2016, Seattle, WA, USA, October 2-5, 2016
Predicting possible directed-graph patterns of gene expressions in studies involving multiple treatments
Disease named entity recognition and normalization with DNorm
Exploring Frequented Regions in Pan-Genomic Graphs
Novel Generated Peptides for COVID-19 Targets
Network-Based Modeling of Sepsis: Quantification and Evaluation of Simultaneity of Organ Dysfunctions
Scalable Optimal Bayesian Classification of Single-Cell Trajectories under Regulatory Model Uncertainty
Computational Modeling of pH-dependent gp120-CD4 Interactions in Founder and Chronic HIV Strains
Fusion Lasso and Its Applications to Cancer Subtype and Stage Prediction
A fast computation of pairwise sequence alignment scores between a protein and a set of single-locus variants of another protein
TCGA Lung Cancer Analysis Pipeline
CellCom: A web server for prediction, visualization, and evaluation of cell-cell communication mediated by ligand-receptor pairs
A Qualitative Evaluation of Language Models on Automatic Question-Answering for COVID-19
Geometric Sampling Framework for Exploring Molecular Walker Energetics and Dynamics
mHMM (multivariate hidden Markov model) application in studying BRD4 and JMJD6 function cooperatively on promoter-proximal polymerase-II (Pol II) pausing release
Classification of Helpful Comments on Online Suicide Watch Forums
ClinicalAgent: Clinical Trial Multi-Agent System with Large Language Model-based Reasoning
Combining spectral clustering and large cut algorithms to find compensatory functional modules from yeast physical and genetic interaction data with GLASS
PRASE: PageRank-based Active Subnetwork Extraction
Towards Instructing Disease-Drug Link Prediction with Social Determinants of Health
Rethinking Radiology Report Generation via Causal Inspired Counterfactual Augmentation
Ranking differential genes in co-expression networks
Unsupervised manifold alignment for single-cell multi-omics data
SimConcept: a hybrid approach for simplifying composite named entities in biomedicine
Towards Smartphone-Based Monitoring of Micronutrient Status
Com-DNB: A novel method for identifying critical states of complex biological processes and its parallelization
Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, BCB 2018, Washington, DC, USA, August 29 - September 01, 2018
Bayesian Hyperparameter Optimization for Machine Learning Based eQTL Analysis
Graphery: a Biological Network Algorithm Tutorial Webservice
Analysis of Molecular Structure Data]{Systematic Study of Different Design Decisions in Markov Model-based Analysis of Molecular Structure Data: Extended Abstract
A graph model and an exact algorithm for finding transcription factor modules
Improving decoy databases for protein folding algorithms
Domain specific information retrieval and text mining in medical document
A graph and hierarchical clustering based approach for population structure inference
Serum antibody repertoire profiling using virtual antigen screen
A generalized lattice model for clustering metagenomic sequences
The TREC Medical Records Track
PCMA: A New Mediation Analysis Method Effectively Identifies Relevant Pathways Connecting Microbiota and Diseases
Co-occurrence Clusters of Aligned Pattern Clusters
Copy number variation estimation from multiple next-generation sequencing samples
Multi-core dynamic parallelism for multiple sequence alignment and counting metrics
454 and SOLiD™ complementary used to filter and build the draft genome of highly abundant cyanobacteria in biological desert crust
PopCover: a method for selecting of peptides with optimal population and pathogen coverage
Time to Reactivation of Latent Tuberculosis Infection Varies by Lineage
Multi-modal Predictive Models of Diabetes Progression
Exact Algorithms for Duplication-Transfer-Loss Reconciliation with Non-Binary Gene Trees
Tutorial: Rapidly Identifying Disease-associated Rare Variants using Annotation and Machine Learning at Whole-genome Scale Online
A whole genome simulator of prokaryote genome evolution
Automatic detection of vaccine adverse reactions by incorporating historical medical conditions
EvoVGM: a deep variational generative model for evolutionary parameter estimation
Towards a natural walking monitor for pulmonary patients using simple smart phones
Ir-Man: An Information Retrieval Framework for Marine Animal Necropsy Analysis
CAPTURE: A Clustered Adaptive Patchwork Technique for Unified Registration Enhancement in Biological Imaging
A Bayesian decision fusion approach for microRNA target prediction
Comparing and optimizing transcriptome assembly pipeline for diploid wheat
An experimental design to reduce dynamics uncertainty in genomic networks
Antidote application: an educational system for treatment of common toxin overdose
Leveraging Treatment Patterns to Predict Survival of Patients with Advanced Non-Small-Cell Lung Cancer
Pre-Phaser: Precise Cell-Cycle Phase Detector for scRNA-seq
Three Co-expression Pattern Types across Microbial Transcriptional Networks of Plankton in Two Oceanic Waters
A mobile sensor system for gait analysis supporting the assessment of rehabilitation measures
Structural representations of DNA regulatory substrates can enhance sequence-based algorithms by associating functional sequence variants
A Cross-Platform System Architecture for Form Design and Data Analytics for Public Health
Classification of Alzheimer Diagnosis from ADNI Plasma Biomarker Data
Towards an extensible ontology for streaming sensor data for clinical trials
PathoEye: a novel deep learning framework for histopathological image analysis of skin tissue
MixEHR-Nest: Identifying Subphenotypes within Electronic Health Records through Hierarchical Guided-Topic Modeling
Identifying Experimental Evidence in Biomedical Abstracts Relevant to Drug-Drug Interactions
Microbial source tracking by molecular fingerprinting
Automated peak alignment for nucleic acid capillary electrophoresis data by dynamic programming
Uncovering Key Features of Individuals Who Benefit from Polygenic Risk Scores in Prostate Cancer Prediction
Strand : fast sequence comparison using mapreduce and locality sensitive hashing
How to build regulatory networks from single-cell gene expression data
Discovering Inconsistencies in PubMed Abstracts through Ontology-Based Information Extraction
CCR5/CXCR4 discriminating sites in the HIV-1 gp120 core
Alzheimer's disease target selection: a data integration approach
Concurrent imputation and prediction on EHR data using bi-directional GANs: Bi-GANs for EHR imputation and prediction
Generation of synthetic data in evaluating interactions for association studies
A Constrained K-shortest Path Algorithm to Rank the Topologies of the Protein Secondary Structure Elements Detected in CryoEM Volume Maps
Retrieval-Augmented Large Language Models for Adolescent Idiopathic Scoliosis Patients in Shared Decision-Making
A Multi-Objective Flow Cytometry Profiling for B-Cell Lymphoma Diagnosis
Pheno2GRN: a workflow for phenotype to gene network study and reverse engineering comparison
Integrative Deep Learning for PanCancer Molecular Subtype Classification Using Histopathological Images and RNAseq Data
Inferring species trees from gene duplication episodes
Interpreting Negative Data on Antipeptide Paratope Binding to Support Development of B-Cell Epitope Prediction for Vaccine Design and Other Translational Applications
Association between response to brief trastuzumab exposure in cell lines and early stage HER2+ breast tumors
An Integrated Approach for Efficient Multi-Omics Joint Analysis
Smartphone-based Pupillometry for Diagnosis of Ischemic and Hemorrhagic Stroke
An exploratory graph query interface for biomedical data
Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence Data
Workshop on Microbiomics, Metagenomics, and Metabolomics
Relapsing-remitting multiple scleroris and the role of vitamin D: an agent based model
ACM International Conference on Bioinformatics, Computational Biology and Biomedicine, BCB' 11, Chicago, IL, USA - July 31 - August 03, 2011
Genomics information retrieval using a Bayesian model for learning and re-ranking
Data mining for electroencephalogram signal processing and analysis
Sub-Class Differences of PH-Dependent HIV GP120-CD4 Interactions
ShareTrace: an iterative message passing algorithm for efficient and effective disease risk assessment on an interaction graph
Semi-supervised sequence classification using abstraction augmented Markov models
Statistical Methods for Ambiguous Sequence Mappings
Using ontologies for supporting genomic sequence annotation projects
Assigning ICD-O-3 codes to pathology reports using neural multi-task training with hierarchical regularization
Predicting drug resistance in M. tuberculosis using a long-term recurrent convolutional network
Parallelization of the spectral deconvolution stage of the proteomic discovery process
Variational Autoencoders for Protein Structure Prediction
An integrative approach to infer regulation programs in a transcription regulatory module network
TAPESTRY: Network-centric Target Prioritization in Disease-related Signaling Networks
The MEGADOCK project: Ultra-high-speed protein-protein interaction prediction tools on supercomputing environments
Challenges and Opportunities of Amazon Serverless Lambda Services in Bioinformatics
Classification and feature selection for craniosynostosis