yusuke1997/dblp-id-title huggingface dataset:
Learning gene regulatory networks using gaussian process emulator and graphical LASSO
Histogram-based Scoring Schemes for Protein Nmr Resonance Assignment
lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics
Fpqrna: Hardware-Accelerated Qrna Package for noncoding RNA Gene Detecting on FPGA
Enhancing Biological Relevance of a Weighted Gene Co-Expression Network for Functional Module Identification
Supersequences of Masks for Oligo-chips
An improved preprocessing algorithm for haplotype inference by pure parsimony
Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery
Better GeneChip microarray Layouts by Combining Probe Placement and Embedding
Cofactor Modification Analysis: a Computational Framework to Identify cofactor specificity Engineering targets for strain Improvement
Many-Atom van der Waals Interactions lead to Direction-Sensitive Interactions of covalent bonds
Incorporating intergenic regions into reversal and transposition distances with indels
Introduction to JBCB Special Issue on BIOINFORMATICS 2019
Discovering Protein-protein Interactions
Deep learning inference of miRNA expression from bulk and single-cell mRNA expression
Parameter estimation analysis of the glioblastoma immune model
Inference of Large-Scale Gene Regulatory Networks Using Regression-Based Network Approach
Constructing a Minimum phylogenetic Network from a Dense triplet Set
Integrating virtual screening and biochemical experimental approach to identify potential anti-cancer agents from drug databank
Protein Subcellular Localization Based on Psi-blast and Machine Learning
A Strategy for Identifying Fluorescence Intensity Profiles of Single Rod-shaped Cells
Refined template selection and combination algorithm significantly improves template-based modeling accuracy
Mathematical Modeling of Auxin Transport in Protoxylem and Protophloem of Arabidopsis thaliana Root tips
Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures
GCMCDTI: Graph convolutional autoencoder framework for predicting drug-target interactions based on matrix completion
Denoising of scanning electron microscope images for biological ultrastructure enhancement
V-ELMpiRNAPred: Identification of human piRNAs by the voting-based extreme learning machine (V-ELM) with a new hybrid feature
Subcellular Localization Charts: a New Visual Methodology for the Semi-Automatic Localization of protein-Related Data Sets
GI-Cluster: Detecting genomic islands via consensus clustering on multiple features
A Fast and Accurate Algorithm for Comparative Analysis of metabolic Pathways
Error Tolerant NMR Backbone Resonance Assignment and Automated Structure Generation
Using binding Profiles to Predict binding sites of Target RNAs
Synthesizing large-scale species trees using the strict consensus approach
Transfer Learning for cytochrome P450 Isozyme Selectivity Prediction
Parallel workflow manager for non-parallel bioinformatic applications to solve large-scale biological problems on a supercomputer
Clustering of Main orthologs for Multiple genomes
Model-Based Clustering with gene Ranking using penalized Mixtures of heavy-tailed Distributions
Genome-Wide Analysis and Modeling of DNA methylation susceptibility in 30 Breast Cancer Cell Lines by using CPG Flanking Sequences
Constrained maximum entropy models to select genotype interactions associated with censored failure times
Prediction model for synergistic anti-tumor multi-compound combinations from traditional Chinese medicine based on extreme gradient boosting, targets and gene expression data
Modeling and Characterization of Multi-charge Mass Spectra for Peptide Sequencing
Exploring the protein Landscape in Ramachandran Space: IT's not Just PSI-phi
Jaguc - a Software package for Environmental Diversity Analyses
Influence of the go-based semantic similarity measures in multi-objective gene clustering algorithm performance
Introduction to the special issue on GIW 2016
Estimation of isoform expression in RNA-seq data using a hierarchical Bayesian model
Use of Gene Networks for Identifying and Validating Drug Targets
Suregene, a Scalable System for Automated Term Disambiguation of Gene and Protein Names
How Multiple Auxin Responsive Elements May Interact in plant promoters: a Reverse Problem solution
Analyzing omics data based on sample network
Influenza A HA's conserved epitopes and broadly neutralizing antibodies: A prediction method
Protein Sub-Cellular Localization Prediction for Special compartments via Optimized Time Series Distances
Recognizing Complex, Asymmetric Functional Sites in Protein Structures Using a Bayesian Scoring Function
EnzDP: Improved enzyme annotation for metabolic network reconstruction based on domain composition profiles
OP-Triplet-ELM: Identification of real and pseudo microRNA precursors using extreme learning machine with optimal features
Patternhunter Ii: Highly Sensitive and Fast Homology Search
Inference of Gene Regulatory Networks Using Boolean-Network Inference Methods
Deppdb - DNA electrostatic Potential Properties Database: electrostatic Properties of genome DNA
Stresses drive a cancer's initiation, progression and metastasis: Critical comments on the book "Cancer Bioinformatics"
Improvement of detection performance of fusion genes from RNA-seq data by clustering short reads
Prediction and validation of avascular tumor growth pattern in different metabolic conditions using in silico and in vitro models
A novel method for predicting DNA N 4 -methylcytosine sites based on deep forest algorithm
Introduction - Some New Results and Tools for Protein Function Prediction, RNA Target Site Prediction, Genotype Calling, Environmental Genomics, and More
The Distribution of Distances between Randomly Constructed genomes: Generating Function, Expectation, Variance and Limits
RiRPSSP: A unified deep learning method for prediction of regular and irregular protein secondary structures
ClEPaps: Fast Pair Alignment of protein Structures Based on conformational Letters
Rnakinetics: a Web Server that Models Secondary Structure Kinetics of an Elongating RNA
Cell cycle period control through modulation of clock inputs
Multiple Rna Structure Alignment
Identifying protein complexes from protein-protein interaction networks based on the gene expression profile and core-attachment approach
On the Computation of Molecular Surface Correlations for protein docking Using Fourier Techniques
Identifying gene-Specific Variations in Biomedical Text
Recognition of Transmembrane Segments in Proteins: Review and Consistency-based Benchmarking of Internet Servers
Comparison of Statistical Significance Criteria
Approximating Metrics with Planar boundary-Labeled Phylogenetic Networks
Development of an Affinity Evaluation and Prediction System by Using the Shape complementarity Characteristic between proteins
Verification of phylogenetic Inference Programs Using Metamorphic Testing
A computational model of the Ca2+ transients and influence of buffering in guinea pig urinary bladder smooth muscle cells
Effective Optimization Algorithms for Fragment-Assembly Based protein Structure Prediction
Stochastic modeling for dynamics of HIV-1 infection using cellular automata: A review
Introduction to Papers Selected from MCCMB'17
A Statistical Framework for Haplotype Block Inference
Integration of autoencoder and graph convolutional network for predicting breast cancer drug response
Comparing the topology of phylogenetic network generators
Hyplosp: a Knowledge-based Approach to Protein Local Structure Prediction
Semiparametric Clustering Method for microarray Data Analysis
Protein fold Classification with Genetic Algorithms and Feature Selection
Systematic investigations of gene effects on both topologies and supports: An Echinococcus illustration
Volcano Plots in Analyzing differential Expressions with mRNA microarrays
Large-Scale metagenomic sequence Clustering on Map-Reduce Clusters
Determining dependency and redundancy for identifying gene-gene interaction associated with complex disease
Global peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using point matching algorithms
Ncrna Consensus Secondary Structure Derivation Using Grammar Strings
Editorial: Guidelines for Credible Machine Learning in Computational Biology
A Different Look at the Quality of Modeled Three-Dimensional protein Structures
A model-based clustering algorithm with covariates adjustment and its application to lung cancer stratification
Conserved water molecules in X-Ray Structures Highlight the Role of water in intramolecular and intermolecular Interactions
Chaos and hyperchaos in simple gene network with negative feedback and time delays
Criteria for an updated Classification of Human transcription factor DNA-binding Domains
Scalable classification of organisms into a taxonomy using hierarchical supervised learners
PAcluster: Clustering polyadenylation site data using canonical correlation analysis
EdClust: A heuristic sequence clustering method with higher sensitivity
Development of software and modification of Q-FISH protocol for estimation of individual telomere length in immunopathology
Family Fingerprints: a Global Approach to Structural Classification
A Heuristic Cluster-Based EM Algorithm for the Planted (L, d) Problem
Protein Complex Prediction Using an Integrative Bioinformatics Approach
An integrated method for identifying essential proteins from multiplex network model of protein-protein interactions
Computational Assignment of Protein Backbone Nmr Peaks Byefficient Bounding and Filtering
Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks
Detecting genetic associations with brain imaging phenotypes in Alzheimer's disease via a novel structured KCCA approach
Symmetric and Asymmetric Multi-modality Biclustering Analysis for Microarray Data Matrix
Duplicated RNA genes in teleost Fish genomes
Ehapp2: Estimate haplotype frequencies from pooled sequencing data with prior database information
Evaluation of Inter-Laboratory and Cross-Platform concordance of DNA microarrays through Discriminating genes and Classifier transferability
Toptmh: Topology Predictor for transmembrane alpha-helices
A Systems Biology Approach for Detecting Toxicity-Related Hotspots inside protein Interaction Networks
Analyzing the performance of short-read classification tools on metagenomic samples toward proper diagnosis of diseases
A Quantum-Inspired Genetic Algorithm Based on Probabilistic Coding for Multiple Sequence Alignment
Mining of structural motifs in proteins using artificial bee colony optimization framework for druggability
Spot Intensity Ratio Statistics in Two-Channel microarray Experiments
Proposing drug fragments for dengue virus NS5 protein
Efficient RNA structure comparison algorithms
Phenosite: a Web Database Integrating the mouse phenotyping Platform and the Experimental Procedures in mice
A Structural Bioinformatics Approach to the Analysis of nonsynonymous Single nucleotide polymorphisms (nsSNPS) and their Relation to Disease
Introduction to Selected Papers from GIW2017
Prokaryote autoimmunity in the context of self-targeting by CRISPR-Cas systems
Chromosome evolution in malaria mosquitoes inferred from physically mapped genome assemblies
The 5th International Conference on Bio-Inspired Models of Network, Information and Computing Systems (Bionetics 2010) Special Track on Bioinformatics
Statistical Comparison of Methods to Estimate the Error Probability in Short-Read Illumina Sequencing
A Unifying Framework for Seed Sensitivity and its Application to Subset Seeds
Gh101 Family of Glycoside hydrolases: subfamily Structure and Evolutionary Connections with Other Families
ADPRtool: A novel predicting model for identification of ASP-ADP-Ribosylation sites of human proteins
Compound property enhancement by virtual compound synthesis
Probe-Level Universal Search (Plus) Algorithm for Gender Differentiation in Affymetrix Datasets
Foreword: Advances in Computational Systems Bioinformatics
NuKit: A deep learning platform for fast nucleus segmentation of histopathological images
Raptor: Optimal Protein Threading by Linear Programming
Some Comments on Instability of False Discovery Rate Estimation
Recurrence Time Statistics: Versatile Tools for Genomic Dna Sequence Analysis
Pops: a Computational Tool for Modeling and Predicting Protease Specificity
Conservation of Amino Acids into Multiple Alignments Involved in Pairwise Interactions in Three-dimensional Protein Structures
Bioie: Retargetable Information Extraction and Ontological Annotation of Biological Interactions from the Literature
Analysis to determine the effect of mutations on binding to small chemical molecules
Symbolic-numeric Estimation of Parameters in Biochemical Models by Quantifier Elimination
KFGRNI: A robust method to inference gene regulatory network from time-course gene data based on ensemble Kalman filter
iCEED: Integrated customized extraction of enzyme data
Robust kernel canonical correlation analysis to detect gene-gene co-associations: A case study in genetics
Practicality and Time Complexity of a Sparsified RNA Folding Algorithm
Tali: Local Alignment of protein Structures Using Backbone Torsion Angles
Polypharmacy side effect prediction based on semi-implicit graph variational auto-encoder
Introduction to the Special Issue on GIW/ABACBS 2019
Feedback-AVPGAN: Feedback-guided generative adversarial network for generating antiviral peptides
Heuristics for the Transposition Distance Problem
Inferring gene regulatory networks using a time-delayed mass action model
Visualization in Simulation Tools: Requirements and a Tool Specification to Support the Teaching of Dynamic Biological Processes
Modeling the impact of point mutations on the stability of proteins
A General Framework for Biclustering Gene Expression Data
Deriving Haplotypes through Recombination and Gene Conversion Pathways
Clinical drug response prediction from preclinical cancer cell lines by logistic matrix factorization approach
Systematic investigation of metabolic reprogramming in different cancers based on tissue-specific metabolic models
A Linear-Time Algorithm for Predicting Functional Annotations from PPI Networks
An Integrative Domain-Based Approach to Predicting protein-protein Interactions
Regularization Strategies for Hyperplane Classifiers: Application to Cancer Classification with gene Expression Data
Prediction of microRNA-binding residues in protein using a Laplacian support vector machine based on sequence information
Interaction of antibodies with Aromatic ligands: the Role of pi-Stacking
Modeling the Optimal Central carbon metabolic pathways under Feedback Inhibition using flux Balance Analysis
From Immunoinformatics to Immunomics
Characterizing the Space of interatomic Distance Distribution Functions Consistent with Solution Scattering Data
A Methodology Based on Molecular Interactions and Pathways to Find Candidate genes Associated to Diseases: its Application to Schizophrenia and Alzheimer's Disease
RPfam: A refiner towards curated-like multiple sequence alignments of the Pfam protein families
Introduction to the CSBio2014 special issue
Flexgrepps - Flexible Greedy peptide Pool Search: Computation of Near-Optimal Sets of degenerate polypeptides for antigenic Screening
Curve-Based Clustering of Time Course Gene Expression Data Using Self-Organizing Maps
Drug synergy model for malignant diseases using deep learning
A machine-learning approach for predicting palmitoylation sites from integrated sequence-based features
Developing Optimal Prediction Models for Cancer Classification Using Gene Expression Data
Dynamic Bayesian Clustering
Computational Construction of Specialized Biological Networks
An Orfome Assembly Approach to Metagenomics Sequences Analysis
The Next Generation of Similarity Measures that Fully Explore the Semantics in Biomedical Ontologies
A new approach to human microRNA target prediction using ensemble pruning and rotation forest
Computing Highly Specific and Noise-tolerant Oligomers Efficiently
Genetack: frameshift Identification in protein-Coding Sequences by the Viterbi Algorithm
A novel method addressing NGS-based mappability bias for sensitive detection of DNA alterations
O-glycosylation site prediction for Homo sapiens by combining properties and sequence features with support vector machine
Using Indirect protein-protein Interactions for protein Complex Prediction
Guest Editor's Introduction: Advanced Techniques for Bioinformatics
Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites
Orthofocus: Program for Identification of orthologs in Multiple genomes in Family-Focused Studies
Drug repurposing and therapeutic anti-microRNA predictions for inhibition of oxidized low-density lipoprotein-induced vascular smooth muscle cell-associated diseases
Multivariate Entropy Distance Method for Prokaryotic Gene Identification
Empirical Potentials for ion Binding in proteins
Dynamic Equilibrium of reconstituting Hematopoietic Stem Cell Populations
Sorting permutations by prefix and suffix rearrangements
Engenius - Environmental genome Informational Utility System
Dynafold: a Dynamic Programming Approach to protein Backbone Structure determination from Minimal Sets of residual Dipolar couplings
Proteomic Biomarker Identification for Diagnosis of Early Relapse in Ovarian Cancer
A novel Arg H52/Tyr H33 conservative motif in antibodies: A correlation between sequence of antibodies and antigen binding
IncMD: Incremental trie-based structural motif discovery algorithm
A Systems Biology Approach to the Study of cisplatin Drug Resistance in Ovarian cancers
Flexible and Robust Networks
PTGAC Model: A machine learning approach for constructing phylogenetic tree to compare protein sequences
Kullback-Leibler Markov Chain Monte Carlo - a New Algorithm for Finite Mixture Analysis and its Application to Gene Expression Data
The potential of family-free rearrangements towards gene orthology inference
Extending hidden Markov models to allow conditioning on previous observations
Searching and Mining Visually Observed Phenotypes of maize Mutants
The method for breast cancer grade prediction and pathway analysis based on improved multiple kernel learning
Systematic analysis and identification of unexpected interactions from the neuroprotein drug interactome in hydrocephalus pharmacological intervention
A Tutorial of Recent Developments in the Seeding of Local Alignment
Impacts of high-quality public data: Special issue on integrating public and in-house biomedical data
EnAMP: A novel deep learning ensemble antibacterial peptide recognition algorithm based on multi-features
Pp i clust: Efficient Clustering of 3D protein-protein Interaction Interfaces
Bioinformatic Analysis of the Neutrality of RNA Secondary Structure Elements across genotypes reveals Evidence for Direct Evolution of Genetic Robustness in HCV
The Incomplete Perfect Phylogeny Haplotype Problem
Probabilistic Ensembles for Improved Inference in protein-Structure Determination
NES-REBS: A novel nuclear export signal prediction method using regular expressions and biochemical properties
From the static interactome to dynamic protein complexes: Three challenges
Bioinformatics research at BGRS\SB-2018
Protein secondary structure prediction improved by recurrent neural networks integrated with two-dimensional convolutional neural networks
Reconstruction of sequence from its circular partial sums for cyclopeptide sequencing problem
Improved Sequence-Based Prediction of Strand residues
Computational analysis and enzyme assay of inhibitor response to disease single nucleotide polymorphisms (SNPs) in lipoprotein lipase
Predicting Antisense Rnas in the Genomes of escherichia Coli and salmonella Typhimurium Using Promoter-search Algorithm Platprom
A Survey of Computational Methods for protein Complex Prediction from protein Interaction Networks
PSOVina: The hybrid particle swarm optimization algorithm for protein-ligand docking
Transformation of FASTA files into feature vectors for unsupervised compression of short reads databases
Research on similarity retrieval method based on mass spectral entropy
Quantitative analysis of the heterogeneous population of endocytic vesicles
Discovery of Functional Genes for Systemic Acquired Resistance in arabidopsis Thaliana through Integrated Data Mining
Characterization of the Existence of Galled-tree Networks
Female reproduction-specific proteins, origins in marine species, and their evolution in the animal kingdom
Human Trash ESTs - Sequences from cDNA Collection that are not Aligned to genome Assembly
Transcriptomic meta-analysis reveals biomarker pairs and key pathways in Tetralogy of Fallot
Search for conserved amino acid residues of the α-crystallin proteins of vertebrates
Multi-omics data analysis reveals the biological implications of alternative splicing events in lung adenocarcinoma
Mining sponge phenomena in RNA expression data
Foundations for Modeling the Dynamics of gene regulatory Networks: a Multilevel-Perspective Review
Whole genome Identity-by-Descent determination
Design and Analysis of Quantitative Differential Proteomics Investigations Using LC-MS Technology
A Hidden Markov Model for Predicting protein Interfaces
Asymptotics of Canonical and Saturated RNA Secondary Structures
Anvaya: a Workflows Environment for Automated genome Analysis
Integrated in silico-in vitro rational design of oncogenic EGFR-derived specific monoclonal antibody-binding peptide mimotopes
Is protein Folding Problem Really a NP-Complete One? First Investigations
MPTM: A tool for mining protein post-translational modifications from literature
Combining Flux and Energy Balance Analysis to Model Large-scale Biochemical Networks
Hidden Markov Models, Grammars, and Biology: a Tutorial
MoRFPred_en: Sequence-based prediction of MoRFs using an ensemble learning strategy
Prediction of adverse drug reactions using drug convolutional neural networks
The impact of simulation time in predicting binding free energies using end-point approaches
Odeion - a Software Module for Structural Identification of Ordinary differential equations
Application of t-SNE to human genetic data
An automated approach to classification of duplex assay for digital droplet PCR
Clustering-Based Approach for Predicting Motif Pairs from protein Interaction Data
Editorial - Data mining in bioinformatics
A symmetry-inclusive algebraic approach to genome rearrangement
PyPredT6: A python-based prediction tool for identification of Type VI effector proteins
An Iterative Algorithm to Quantify Factors Influencing peptide Fragmentation during Tandem Mass Spectrometry
Particle Swarm Optimization Based Approach for Resource Allocation and Scheduling in OFDMA Systems
Parallel Minimax Searching Algorithm for Extremum of Unimodal Unbounded Function
Investigation into the Performance of a MIMO System Equipped with ULA or UCA Antennas: BER, Capacity and Channel Estimation
Two Slot MIMO Configuration for Cooperative Sensor Network
An Energy-Aware Clustering Approach for Wireless Sensor Networks
Beacon-driven Leader Based Protocol over a GE Channel for MAC Layer Multicast Error Control
Ant Colony Optimization Based on Adaptive Volatility Rate of Pheromone Trail
Advances in MIMO Techniques for Mobile Communications - A Survey
Q-Learning-Based Adaptive Waveform Selection in Cognitive Radar
Web Service Generation through Program Slicing
Performance Analysis of Sub-Rating for Handoff Calls in HCN
Performance of Multirate Multicast in Distributed Network
Measurements of Balun and Gap Effects in a Dipole Antenna
Towards High Quality VoIP in 3G Networks An Empirical Approach
Permutation and Complementary Algorithm to Generate Random Sequences for Binary Logic
Average Consensus in Networks of Multi-Agent with Multiple Time-Varying Delays
Analysis of Computer Network Reliability and Criticality: Technique and Features
Protection of Sensitive Messages Based on Quadratic Roots of Gaussians: Groups with Complex Modulus
Block Layering Approach in TAST Codes
An Efficient Routing Tree Algorithm for Combined Uplink and Downlink Subframes on Centralized Scheduling in IEEE 802.16 Based Wireless Mesh Networks
Service Adaptable 3G Turbo Decoder for Indoor/Low Range Outdoor Environment