yusuke1997/dblp-id-title huggingface dataset:
Reorganizing heterogeneous information from host-microbe interaction reveals innate associations among samples
Engineering synthetic optogenetic networks for biomedical applications
Population-scale genetic control of alternative polyadenylation and its association with human diseases
Assessing the inhibition efficacy of clinical drugs against the main proteases of SARS-CoV-2 variants and other coronaviruses
The indigenous populations as the model by nature to understand human genomic-phenomics interactions
Tuning hyperparameters of doublet-detection methods for single-cell RNA sequencing data
Imputing not available values in single-cell DNA methylation data using the median is straightforward and effective
ChatGPT opens a new door for bioinformatics
Hierarchical learning of gastric cancer molecular subtypes by integrating multi-modal DNA-level omics data and clinical stratification
Quantifying cell fate change under different stochastic gene activation frameworks
Population dynamics of cancer cells with cell state conversions
Mathematical modeling reveals the mechanisms of feedforward regulation in cell fate decisions in budding yeast
Copy number variation related disease genes
From Phage lambda to human cancer: endogenous molecular-cellular network hypothesis
Molecular docking of cyanine and squarylium dyes with SARS-CoV-2 proteases NSP3, NSP5 and NSP12
Pattern discovery of long non-coding RNAs associated with the herbal treatments in breast and prostate cancers
Perspective on the q-bio Summer School and Conference: 2007-2014 and beyond
Pre-mRNA modifications and their role in nuclear processing
Identification of candidate disease genes in patients with common variable immunodeficiency
Collective motion of bacteria in two dimensions
Lesion region segmentation via weakly supervised learning
Measuring drug similarity using drug-drug interactions
Variation of repetitive cortical spreading depression waves is related with relative refractory period: a computational study
How error correction affects polymerase chain reaction deduplication: A survey based on unique molecular identifier datasets of short reads
Multifaceted roles of complementary sequences on circRNA formation
Quantum conformational transition in biological macromolecule
Transcriptome-wide association studies: a view from Mendelian randomization
Skull ethnic classification by combining skull auxiliary image with deep learning
condLSTM-Q: A novel deep learning model for predicting COVID-19 mortality in fine geographical scale
Comparative analysis of NovaSeq 6000 and MGISEQ 2000 single-cell RNA sequencing data
Stochastic thermodynamics for biological functions
International Workshop on Applications of Probability and Statistics to Biology, July 11-13, 2019
Constructing efficient bacterial cell factories to enable one-carbon utilization based on quantitative biology: A review
Special collection of recent advances in next-generation bioinformatics
Phase separation in synthetic biology
High-throughput quantification of microbial birth and death dynamics using fluorescence microscopy
System identification and parameter estimation in mathematical medicine: examples demonstrated for prostate cancer
Computational methods and applications for quantitative systems pharmacology
Identifying viruses from metagenomic data using deep learning
WIPER: Weighted in-Path Edge Ranking for biomolecular association networks
Modeling the relationship between gene expression and mutational signature
scSCC: A swapped contrastive learning-based clustering method for single-cell gene expression data
DeepDrug: A general graph-based deep learning framework for drug-drug interactions and drug-target interactions prediction
Direct-to-consumer genetic testing in China and its role in GWAS discovery and replication
Transportation, germs, culture: a dynamic graph model of COVID-19 outbreak
Interpretable prediction of drug-cell line response by triple matrix factorization
Network pharmacology research of mechanism of Maxing Shigan Decoction in treating COVID-19
Synthetic gene circuits moving into the clinic
Application of Meta-Mesh on the analysis of microbial communities from human associated-habitats
Chao Tang: a self-motivated scientist pursues interdisciplinary excellence
Integrative modeling of transmitted and de novo variants identifies novel risk genes for congenital heart disease
Characterizing robustness and sensitivity of convolutional neural networks for quantitative analysis of mitochondrial morphology
Prediction and differential analysis of RNA secondary structure
SimHOEPI: A resampling simulator for generating single nucleotide polymorphism data with a high-order epistasis model
Developing bioimaging and quantitative methods to study 3D genome
Light-driven synthetic microbial consortia: playing with an oxygen dilemma
Mathematical modeling of evolution of cell networks in epithelial tissues
A feature extraction framework for discovering pan-cancer driver genes based on multi-omics data
Applications of single-cell technology on bacterial analysis
A comprehensive review of cluster methods for drug-drug interaction network
Deep learning for drug-drug interaction prediction: A comprehensive review
Single-cell analyses reveal impaired type B spermatogonia differentiation and meiotic entry in C-Nap1-null testes
Conductive proteins-based extracellular electron transfer of electroactive microorganisms
Deep learning-based large-scale named entity recognition for anatomical region of mammalian brain
Identifying MiRNA-disease association based on integrating miRNA topological similarity and functional similarity
Single-cell gene regulatory network analysis for mixed cell populations
An effective method for quantification, visualization, and analysis of 3D cell shape during early embryogenesis
Modeling the specificity of protein-DNA interactions
SupraBiology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing
Design of efficient simplified genomic DNA and bisulfite sequencing in large plant populations
MFCN-DDI: Capsule network based on multimodal feature for multitype drug-drug interaction prediction
BMTK: a toolkit for determining modules in biological bipartite networks
Predictive power of cell-to-cell variability
Exploring the interaction patterns among taxa and environments from marine metagenomic data
ASTM: Developing the web service for anthrax related spatiotemporal characteristics and meteorology study
MRHCA: a nonparametric statistics based method for hub and co-expression module identification in large gene co-expression network
Building digital life systems for future biology and medicine
Developing a low-cost milliliter-scale chemostat array for precise control of cellular growth
Physics-informed machine learning for the COVID-19 pandemic: Adherence to social distancing and short-term predictions for eight countries
Differential expression analyses for single-cell RNA-Seq: old questions on new data
Time-scale separation and stochasticity conspire to impact phenotypic dynamics in the canonical and inverted Bacillus subtilis core genetic regulation circuits
Foundation models for bioinformatics
COVIDX: Computer-aided diagnosis of COVID-19 and its severity prediction with raw digital chest X-ray scans
A resistant method for landmark-based analysis of individual asymmetry in two dimensions
Unveiling roles of non-coding RNAs in cancer through advanced technologies
A model of NSCLC microenvironment predicts optimal receptor targets
A digitized catalog of COVID-19 epidemiology data
Advances and challenges towards the study of RNA-RNA interactions in a transcriptome-wide scale
High-throughput metabarcoding of SAR11 assemblages from the southwest Atlantic shelf and arid Patagonia: richness and associated rank abundance distributions
Decoding nervous system by single-cell RNA sequencing
Understanding spatial organizations of chromosomes via statistical analysis of Hi-C data
Commentary to "The human intelligence evolved from proximal cis -regulatory saltations"
Differential methylation analysis for bisulfite sequencing using DSS
HiC-3DViewer: a new tool to visualize Hi-C data in 3D space
Use of artificial neural networks to identify and analyze polymerized actin-based cytoskeletal structures in 3D confocal images
Proteomics techniques in protein biomarker discovery
Identification of genomic regions distorting population structure inference in diverse continental groups
Insights into the antineoplastic mechanism of Chelidonium majus via systems pharmacology approach
Performance-weighted-voting model: an ensemble machine learning method for cancer type classification using whole-exome sequencing mutation
Quantitative functionalization of biosynthetic caged protein materials
The Center for Quantitative Biology at Peking University
Secure and efficient implementation of facial emotion detection for smart patient monitoring system
A comprehensive review of molecular optimization in artificial intelligence-based drug discovery
AMHF-TP: Multifunctional therapeutic peptides prediction based on multi-granularity hierarchical features
Comparison of the experimental methods in haplotype sequencing via next generation sequencing
Exploring the underlying mechanism of action of a traditional Chinese medicine formula, Youdujing ointment, for cervical cancer treatment
Integrating human single-cell data from multiple sources
Delineating the respective impacts of stochastic curl- and grad-forces in a family of idealized core genetic commitment circuits
MTMO: an efficient network-centric algorithm for subtree counting and enumeration
Combination of versatile platforms for the development of synthetic biology
QB: Embracing the future of quantitative understanding and engineering of life
Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas
Functional predictability of universal gene circuits in diverse microbial hosts
Multiple functional linear model for association analysis of RNA-seq with imaging
Mechanistic two-pathway modeling of substrate inhibition in lactic acid bacteria for enhanced fermentation control
Pharmacodynamics simulation of HOEC by a computational model of arachidonic acid metabolic network
Models, methods and tools for ancestry inference and admixture analysis
Regulation by competition: a hidden layer of gene regulatory network
Personal genomes, quantitative dynamic omics and personalized medicine
Identifying early warning signals of cancer formation
CASHeart: A database of single cells chromatin accessibility for the human heart
Forecasting the development of the COVID-19 epidemic by nowcasting: when did things start to get better?
On the possibility of identifying human subjects using behavioural complexity analyses
PMTDS: a computational method based on genetic interaction networks for Precision Medicine Target-Drug Selection in cancer
A clinical trial termination prediction model based on denoising autoencoder and deep survival regression
Current progresses of 3D bioprinting based tissue engineering
Distal nucleotides affect the rate of stop codon read-through
Deterministic modelling of asymptomatic spread and disease stage progression in vaccine preventable infectious diseases
A data-driven sliding-window pairwise comparative approach for the estimation of transmission fitness of SARS-CoV-2 variants and construction of the evolution fitness landscape
EpiFIT: functional interpretation of transcription factors based on combination of sequence and epigenetic information
A penalized integrative deep neural network for variable selection among multiple omics datasets
Current opinions on large cellular models
A survey of web resources and tools for the study of TCM network pharmacology
Special collection of recent advances in next-generation bioinformatics, part II
Cistrome Data Browser and Toolkit: analyzing human and mouse genomic data using compendia of ChIP-seq and chromatin accessibility data
PICB: facing the new challenge and opportunity of big data
Toward an understanding of the relation between gene regulation and 3D genome organization
SynBioEcoli: a comprehensive metabolism network of engineered E. coli in three dimensional visualization
Deciphering the protein-DNA code of bacterial winged helix-turn-helix transcription factors
Target specificity of the CRISPR-Cas9 system
The human intelligence evolved from proximal cis -regulatory saltations
A cell marker-based clustering strategy (cmCluster) for precise cell type identification of scRNA-seq data
A quantitative understanding of microRNA-mediated competing endogenous RNA regulation
Theoretical perspective on synthetic man-made life: Learning from the origin of life
QB: A new inter- and multi-disciplinary forum for modeling, engineering and understanding life
Bistability and oscillations in co-repressive synthetic microbial consortia
Genome-scale metabolic models applied for human health and biopharmaceutical engineering
Plasma proteome profiling reveals biomarkers of chemotherapy resistance in patients with advanced colorectal cancer
Visualization of phage DNA degradation by a type I CRISPR-Cas system at the single-cell level
Modeling information exchange between living and artificial cells
Biclustering by sparse canonical correlation analysis
Synthetic biology: a new approach to study biological pattern formation
Mathematical approaches in studying bicoid gene
Constructing a Boolean implication network to study the interactions between environmental factors and OTUs
A quantitative understanding of lac repressor's binding specificity and flexibility
Special issue on computational biology and bioinformatic applications to the COVID-19 pandemic
Predicting drug-perturbed transcriptional responses using multi-conditional diffusion transformer
Molecular modeling studies of repandusinic acid as potent small molecule for hepatitis B virus through molecular docking and ADME analysis
McSNAC: A software to approximate first-order signaling networks from mass cytometry data
Cellbow: a robust customizable cell segmentation program
How should bioinformatics PIs run wet-labs?
Protocol for simulating the effect of THz electromagnetic field on ion channels
Parameter asymmetry and time-scale separation in core genetic commitment circuits
Loc4Lnc: Accurate prediction of long noncoding RNA subcellular localization via enhanced RNA sequence representation
WaveNano: a signal-level nanopore base-caller via simultaneous prediction of nucleotide labels and move labels through bi-directional WaveNets
OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites
An overview of major metagenomic studies on human microbiomes in health and disease
Cell-based allometry: an approach for evaluation of complexity in morphogenesis
Reflections on the quest to obtain biological information from genomic data
High-throughput quantitative assessment of ABA-responsive elements at single-nucleotide resolution
Rapid identification of multi-strain HBV infection in patient by high-throughput DNA sequencing
On the use of kernel machines for Mendelian randomization
Monitoring and mathematical modeling of mitochondrial ATP in myotubes at single-cell level reveals two distinct population with different kinetics
Mapping and differential expression analysis from short-read RNA-Seq data in model organisms
Quantitative Biology 2019: Dynamic Signaling in Cells and Embryos
Network-based method to infer the contributions of proteins to the etiology of drug side effects
DDI-Transform: A neural network for predicting drug-drug interaction events
Effectiveness of machine learning at modeling the relationship between Hi-C data and copy number variation
The future of genome-scale modeling of yeast through integration of a transcriptional regulatory network
Adaptive total variation constraint hypergraph regularized NMF for single-cell RNA-seq data analysis
Whole-exome sequencing and microRNA profiling reveal PI3K/AKT pathway's involvement in juvenile myelomonocytic leukemia
Polygenic risk scores: effect estimation and model optimization
LIBRA: an adaptative integrative tool for paired single-cell multi-omics data
A study of the COVID-19 epidemic in India using the SEIRD model
Analysis of alternative cleavage and polyadenylation in mature and differentiating neurons using RNA-seq data
IRIS: A method for predicting in vivo RNA secondary structures using PARIS data
DNA methylation meets lineage tracing: History, recent progress, and future directions
A pan-cancer integrative pathway analysis of multi-omics data
RECOGNICER: A coarse-graining approach for identifying broad domains from ChIP-seq data
Analysis of protein features and machine learning algorithms for prediction of druggable proteins
Current challenges and solutions of de novo assembly
Role of ACLY in the development of gastric cancer under hyperglycemic conditions
Biology by the numbers on the Hawaiian Islands
Automated interpretation of metabolic capacity from genome and metagenome sequences
Advanced deep learning methods for molecular property prediction
An introduction to computational tools for differential binding analysis with ChIP-seq data
A systematic analysis of intrinsic regulators for HIV-1 R5 to X4 phenotypic switch
Comprehensive cross cancer analyses reveal mutational signature cancer specificity
Forging the iron-net: Towards a quantitative understanding of microbial communities via siderophore-mediated interactions
Advances and challenges in quantitative delineation of the genetic architecture of complex traits
A survey on biomarker identification based on molecular networks
Revolutionizing multi-omics analysis with artificial intelligence and data processing
Revisiting the false positive rate in detecting recent positive selection
Computational tools for Hi-C data analysis
The methodological challenge in high-throughput profiling and quantifying microRNAs
TACO: Taxonomic prediction of unknown OTUs through OTU co-abundance networks
Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance
A wonderful time - exciting progress made in the past 20 years in genetics powered by the Human Genome Project
Mapping transcriptome-wide protein-RNA interactions to elucidate RNA regulatory programs
Computational study of some potential inhibitors of COVID-19: A DFT analysis
From qualitative to quantitative: the state of the art and challenges for plant synthetic biology
Discrete spread model for COVID-19: the case of Lebanon
Modeling the epidemic dynamics and control of COVID-19 outbreak in China
Special collection of synthetic biology, aiming for quantitative control of cellular systems
A simulated annealing approach for resolution guided homogeneous cryo-electron microscopy image selection
The 7th National Conference on Bioinformatics and Systems Biology of China
Impact of lipid asymmetry on membrane biophysical properties: Insights from molecular dynamics simulations
Control of synthetic gene networks and its applications
Altered cerebral activities and functional connectivity in depression: a systematic review of fMRI studies
Mathematics, genetics and evolution
Meeting report on Synthetic Biology Young Scholar Forum
Imputation of single-cell gene expression with an autoencoder neural network
Fundamental Boolean network modelling for childhood acute lymphoblastic leukaemia pathways
Quantifying E2F1 protein dynamics in single cells
Applications of species accumulation curves in large-scale biological data analysis
A novel method to identify topological domains using Hi-C data
Tracking guided actions recognition for cows
DeepRCI: predicting RNA-chromatin interactions via deep learning with multi-omics data
De novo assembly of transcriptome from next-generation sequencing data
Computational methodology for ChIP-seq analysis
Confidence intervals for Markov chain transition probabilities based on next generation sequencing reads data
Looking back at the first twenty years of genomics
Early bioinformatics research in China
Towards precise reconstruction of gene regulatory networks by data integration
Overlap graphs and de Bruijn graphs: data structures for de novo genome assembly in the big data era
Mathematical modeling and optimal intervention of COVID-19 outbreak
Bridging cross-cultural gaps in scientific exchange through innovative team challenge workshops
Modeling combination chemo-immunotherapy for heterogeneous tumors
SPECIFIC: A systematic framework for engineering cell state-responsive synthetic promoters reveals key regulators of T cell exhaustion
An effective encoding of human medical conditions in disease space provides a versatile framework for deciphering disease associations
Experimental design and model reduction in systems biology
A personal journey on cracking the genomic codes
Transcription regulation by DNA methylation under stressful conditions in human cancer
Selecting near-native protein structures from ab initio models using ensemble clustering
Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions
Metabolic pathway databases and model repositories
Attention emotion recognition via ECG signals
Introduction to bioimaging-based spatial multi-omic novel methods
Action functional as an early warning indicator in the space of probability measures via Schrödinger bridge
Self-organization of active plume lattice in bacterial bioconvection
Functional data analysis: An application to COVID-19 data in the United States in 2020
Physical mechanisms of human brain functions
Modeling stochastic noise in gene regulatory systems
Special issue on RNA processing and regulation
Structural and dynamic properties of the YTH domain in complex with N$lt;sup$gt;6$lt;/sup$gt;-methyladenosine RNA studied by accelerated molecular dynamics simulations
A survey of downstream applications of evolutionary scale modeling protein language models
Power-law multi-wave model for COVID-19 propagation in countries with nonuniform population density
Single molecule fluorescence spectroscopy for quantitative biological applications
Elastic restricted Boltzmann machines for cancer data analysis
ShapeShifter: a novel approach for identifying and quantifying stable lariat intronic species in RNAseq data
CELLO: a longitudinal data analysis toolbox untangling cancer evolution
Imaging genetics - towards discovery neuroscience
Construction of precise support vector machine based models for predicting promoter strength
Predicting enhancer-promoter interaction from genomic sequence with deep neural networks
Multi-chain Fudan-CCDC model for COVID-19 - a revisit to Singapore's case
Recent advances and application in whole-genome multiple displacement amplification
CShaperApp: Segmenting and analyzing cellular morphologies of the developing Caenorhabditis elegans embryo
Transcriptome wide association studies: general framework and methods
Integrated photothermal microcarriers for precise exosome-secreted microRNA profiling in breast cancer diagnosis
Single-cell mitochondrial lineage tracing: Opportunities and challenges
Dynamical network biomarkers for identifying critical transitions and their driving networks of biologic processes
Transcriptome assembly strategies for precision medicine
On why cancer cells require a great amount of glucose
Towards integrated oncogenic marker recognition through mutual information-based statistically significant feature extraction: an association rule mining based study on cancer expression and methylation profiles
Quantitative analysis of gene expression systems
Mapping allosteric pathway in NIa-Pro using computational approach
Germline genomes have a dominant-heritable contribution to cancer immune evasion and immunotherapy response
Computational methods for identifying enhancer-promoter interactions
Variable importance-weighted random forests
Modeling stochastic phenotype switching and bet-hedging in bacteria: stochastic nonlinear dynamics and critical state identification
Toward atomistic models of intact severe acute respiratory syndrome coronavirus 2 via Martini coarse-grained molecular dynamics simulations
A survey of machine learning techniques for detecting and diagnosing COVID-19 from imaging