yusuke1997/dblp-id-title huggingface dataset:
Detecting hidden batch factors through data-adaptive adjustment for biological effects
Metannogen: annotation of biological reaction networks
AQUARIUM: accurate quantification of circular isoforms using model-based strategy
Understanding sequencing data as compositions: an outlook and review
Oligonucleotide properties determination and primer designing: a critical examination of predictions
Piecewise parameter estimation for stochastic models in COPASI
LncRNAnet: long non-coding RNA identification using deep learning
PGAAS: a prokaryotic genome assembly assistant system
An interactive graphic program for calculating the secondary structure content of proteins from circular dichroism spectrum
PAA: an R/bioconductor package for biomarker discovery with protein microarrays
Recognition of characteristic patterns in sets of functionally equivalent DNA sequences
CCmed: cross-condition mediation analysis for identifying replicable trans-associations mediated by cis-gene expression
Kotai Antibody Builder: automated high-resolution structural modeling of antibodies
miRNAkey: a software for microRNA deep sequencing analysis
streammd : fast low-memory duplicate marking using a Bloom filter
Poisson factor models with applications to non-normalized microRNA profiling
Bioinformatics and the Y2K Problem
GRASS: a generic algorithm for scaffolding next-generation sequencing assemblies
Statistical significance of cluster membership for unsupervised evaluation of cell identities
Portable nanopore analytics: are we there yet?
MACiE: a database of enzyme reaction mechanisms
Accurate differential analysis of transcription factor activity from gene expression
µProteInS - a proteogenomics pipeline for finding novel bacterial microproteins encoded by small ORFs
SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces
CentromereArchitect: inference and analysis of the architecture of centromeres
Single feature polymorphism detection using recombinant inbred line microarray expression data
Inference of differential gene regulatory networks based on gene expression and genetic perturbation data
Topological and functional characterization of human translation efficiency covariation network
Literature-based discovery: addressing the issue of the subpar evaluation methodology
NIHBA: a network interdiction approach for metabolic engineering design
Grid computing for improving conformational sampling in NMR structure calculation
EvoLSTM: context-dependent models of sequence evolution using a sequence-to-sequence LSTM
Bioinformatics Education-A UK perspective
DeepCCI: a deep learning framework for identifying cell-cell interactions from single-cell RNA sequencing data
BERTMeSH: deep contextual representation learning for large-scale high-performance MeSH indexing with full text
EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning
A graphical interface for the FoldX forcefield
AGHmatrix: genetic relationship matrices in R
Serpentine: a flexible 2D binning method for differential Hi-C analysis
Improved algorithms for searching restriction maps
GPU-powered model analysis with PySB/cupSODA
genoPlotR: comparative gene and genome visualization in R
Verdant: automated annotation, alignment and phylogenetic analysis of whole chloroplast genomes
Manipulation of FASTQ data with Galaxy
DNAModAnnot: a R toolbox for DNA modification filtering and annotation
Computational design of synthetic gene circuits with composable parts
Assessment of survival prediction models based on microarray data
A computational strategy to adjust for copy number in tumor Hi-C data
MethylMix 2.0: an R package for identifying DNA methylation genes
StrandScript: evaluation of Illumina genotyping array design and strand correction
Fast and accurate gene regulatory network inference by normalized least squares regression
pyGenClean: efficient tool for genetic data clean up before association testing
GERV: a statistical method for generative evaluation of regulatory variants for transcription factor binding
Prediction of ribosome footprint profile shapes from transcript sequences
HYCUD: a computational tool for prediction of effective rotational correlation time in flexible proteins
Differential coexpression analysis using microarray data and its application to human cancer
SNPLINK: multipoint linkage analysis of densely distributed SNP data incorporating automated linkage disequilibrium removal
PROFILER: a tool for automatic searching of internally maintained databases
A hidden Markov support vector machine framework incorporating profile geometry learning for identifying microbial RNA in tiling array data
A graph-theoretic approach to testing associations between disparate sources of functional genomics data
PaReBrick: PArallel REarrangements and BReaks identification toolkit
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data
Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites
High-dimensional bolstered error estimation
Medical concept normalization in clinical trials with drug and disease representation learning
TIPP2: metagenomic taxonomic profiling using phylogenetic markers
Unraveling transcriptional regulatory programs by integrative analysis of microarray and transcription factor binding data
Effusion: prediction of protein function from sequence similarity networks
BRAT-BW: efficient and accurate mapping of bisulfite-treated reads
Conceptual modelling of genomic information
Improved approach for proteochemometrics modeling: application to organic compound - amine G protein-coupled receptor interactions
FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures
An automated tool for obtaining QSAR-ready series of compounds using semantic web technologies
Local multiple alignment by consensus matrix
iEnhancer-XG: interpretable sequence-based enhancers and their strength predictor
Balancing complexity and clarity - towards clinician-ready antibiotic resistance prediction models
BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks
Rule-based modeling with Virtual Cell
ClonoMatch: a tool for identifying homologous immunoglobulin and T-cell receptor sequences in large databases
TADOSS: computational estimation of tandem domain swap stability
An approach to systematic detection of protein structural motifs
SCODE: an efficient regulatory network inference algorithm from single-cell RNA-Seq during differentiation
Improved pathway reconstruction from RNA interference screens by exploiting off-target effects
scHiCNorm: a software package to eliminate systematic biases in single-cell Hi-C data
'Sciencenet' - towards a global search and share engine for all scientific knowledge
SBRML: a markup language for associating systems biology data with models
Analysis of conservation and substitutions of secondary structure elements within protein superfamilies
Changes associated with Ebola virus adaptation to novel species
Sambamba: fast processing of NGS alignment formats
Interactive network visualization in Jupyter notebooks: visJS2jupyter
Decomposition of complex microbial behaviors into resource-based stress responses
Discovering drug-target interaction knowledge from biomedical literature
A unified approach to protein domain parsing with inter-residue distance matrix
GSC: a graphical program for NMR chemical shift comparison
Object-centered representation for species systematics and identification in living systems in nature
Robustness and accuracy of functional modules in integrated network analysis
phyLoSTM: a novel deep learning model on disease prediction from longitudinal microbiome data
P3DOCK: a protein-RNA docking webserver based on template-based and template-free docking
ConSeq: the identification of functionally and structurally important residues in protein sequences
L1EM: a tool for accurate locus specific LINE-1 RNA quantification
meGPS: a multi-omics signature for hepatocellular carcinoma detection integrating methylome and transcriptome data
Extending KNIME for next-generation sequencing data analysis
GIGI-Quick: a fast approach to impute missing genotypes in genome-wide association family data
Fast and SNP-tolerant detection of complex variants and splicing in short reads
MWASTools: an R/bioconductor package for metabolome-wide association studies
Rigid substructure search
Online bias-aware disease module mining with ROBUST-Web
Comments on 'MMFPh: A Maximal Motif Finder for Phosphoproteomics Datasets'
Variant Score Ranker - a web application for intuitive missense variant prioritization
CMap 1.01: a comparative mapping application for the Internet
Processing of big heterogeneous genomic datasets for tertiary analysis of Next Generation Sequencing data
Mass Analysis Peptide Sequence Prediction (MAPSP)
Rgtsp: a generalized top scoring pairs package for class prediction
ADFinder: accurate detection of programmed DNA elimination using NGS high-throughput sequencing data
Regional assignment of genetic markers using a somatic cell hybrid panel: a WWW interactive program available for the pig genome
A universal open-source Electronic Laboratory Notebook
Reference-free prediction of rearrangement breakpoint reads
Rapid motif compliance scoring with match weight sets
OligoArray: genome-scale oligonucleotide design for microarrays
Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP
SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials
read_haps: using read haplotypes to detect same species contamination in DNA sequences
Application of the multiensemble sampling to the equilibrium folding of proteins
Databases, data tombs and dust in the wind
BUILD: a program generator for modelling experimental biological data
Amanida: an R package for meta-analysis of metabolomics non-integral data
Global topological features of cancer proteins in the human interactome
Are graph databases ready for bioinformatics?
Interpretable deep learning architectures for improving drug response prediction performance: myth or reality?
PPUS: a web server to predict PUS-specific pseudouridine sites
Unsupervised classification of noisy chromosomes
All-atom knowledge-based potential for RNA structure prediction and assessment
A multiple alignment program for protein sequences
Btab - a Blast output parser
MCS/SEL/BAS program - an overlapping clustering method with examples from mating type interactions of ciliated protozoa
ArachnoServer 3.0: an online resource for automated discovery, analysis and annotation of spider toxins
Accurate prediction of protein beta-aggregation with generalized statistical potentials
SpaCEM 3 : a software for biological module detection when data is incomplete, high dimensional and dependent
When a single lineage is not enough: Uncertainty-Aware Tracking for spatio-temporal live-cell image analysis
Discovering approximate-associated sequence patterns for protein-DNA interactions
Holistic optimization of an RNA-seq workflow for multi-threaded environments
CrossMap: a versatile tool for coordinate conversion between genome assemblies
projectR: an R/Bioconductor package for transfer learning via PCA, NMF, correlation and clustering
CAR H T A GENE: multipopulation integrated genetic and radiation hybrid mapping
A multi-layer inference approach to reconstruct condition-specific genes and their regulation
FORTE: a profile-profile comparison tool for protein fold recognition
CUT&RUNTools 2.0: a pipeline for single-cell and bulk-level CUT&RUN and CUT&Tag data analysis
NGSphy: phylogenomic simulation of next-generation sequencing data
A phylogenetic C interpreter for TNT
Expertise in expert systems: knowledge acquisition for biological expert systems
AA9int: SNP interaction pattern search using non-hierarchical additive model set
JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data
Linear time-varying models can reveal non-linear interactions of biomolecular regulatory networks using multiple time-series data
RoDiCE: robust differential protein co-expression analysis for cancer complexome
KAPPA, a simple algorithm for discovery and clustering of proteins defined by a key amino acid pattern: a case study of the cysteine-rich proteins
Gimpute: an efficient genetic data imputation pipeline
VARNA: Interactive drawing and editing of the RNA secondary structure
Differential effects of chromatin regulators and transcription factors on gene regulation: a nucleosomal perspective
Comparison of global tests for functional gene sets in two-group designs and selection of potentially effect-causing genes
Density guided importance sampling: application to a reduced model of protein folding
LOCAN: a python library for analyzing single-molecule localization microscopy data
essHi-C: essential component analysis of Hi-C matrices
Identifying molecular markers associated with classification of genotypes by External Logistic Biplots
Improving confidence in lipidomic annotations by incorporating empirical ion mobility regression analysis and chemical class prediction
DIANA - algorithmic improvements for analysis of data-independent acquisition MS data
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods
ClassifyTE: a stacking-based prediction of hierarchical classification of transposable elements
SpatialSort: a Bayesian model for clustering and cell population annotation of spatial proteomics data
BEENE: deep learning-based nonlinear embedding improves batch effect estimation
ProbOnto: ontology and knowledge base of probability distributions
SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip
CellWalker: a user-friendly and modular computational pipeline for morphological analysis of microscopy images
PiDeeL: metabolic pathway-informed deep learning model for survival analysis and pathological classification of gliomas
EDIBLE: experimental design and information calculations in phylogenetics
Comment on: 'Empirical comparison of web-based antimicrobial peptide prediction tools'
Parapred: antibody paratope prediction using convolutional and recurrent neural networks
3DVISION: a program for display of three-dimensional wire models on a PC with VGA display
Estimating gene regulatory networks with pandaR
GSLab: open-source platform for advanced phasor analysis in fluorescence microscopy
PEP_scaffolder: using (homologous) proteins to scaffold genomes
uMELT: prediction of high-resolution melting curves and dynamic melting profiles of PCR products in a rich web application
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants
Efficient inference on known phylogenetic trees using Poisson regression
Shop by image: characterizing visual search in e-commerce
Filtering methods for content-based retrieval on indexed symbolic music databases
Threshold Setting and Performance Optimization in Adaptive Filtering
Related, but not Relevant: Content-Based Collaborative Filtering in TREC-8
Assessing ECG-QRS signal detection algorithm chip and simulation on several FPGAs
Extreme value theory applied to document retrieval from large collections
A secure smart monitoring network for hybrid energy systems using IoT, AI
Snake-shaped robot design and path planning algorithm
Enhanced software change proneness prediction in android applications using balanced data techniques and advanced language models
New unit dot product similarity method and parallelized greedy soup algorithm in the end-to-end automatic speech recognition
Utilizing passage-based language models for ad hoc document retrieval
Simple Bayesian Model for Bitmap Compression
Optimized evaluation of the quality of sensor video internet of things (VIOT) by the integration of big data and artificial intelligence
Boolean semiring key-exchange with BLAKE3 security (BKEX-B3)
Evaluating the effectiveness of relevance feedback based on a user simulation model: effects of a user scenario on cumulated gain value
Complexity Reduction in Lattice-Based Information Retrieval
Ensemble learning with RAG model to reduce redundant question topics in auto-generated exam questions
Applying back-propagation neural network for financial early warning in listed manufacturing companies
Word Spotting in Bitmapped Fax Documents
Information Retrieval Special Issue: Conceptual, Linguistic and Task-Based IR: Research at the University of Tampere
Teaching mathematics for search using a tutorial style of delivery
Deep learning-based occlusion-aware face mask detection for airborne disease control
Scaling Up the TREC Collection
Peak-controlled logits poisoning attack in federated distillation
Optimization of intelligent physical education teaching method based on fuzzy logic and virtual reality
Re-ranking search results using an additional retrieved list
Collaborator recommendation in heterogeneous bibliographic networks using random walks
Optimizing the recency-relevance-diversity trade-offs in non-personalized news recommendations
Introduction to special issue on the second international conference on the theory of information retrieval
A computer-supported learning system to help teachers to teach Fuzzy Information Retrieval Systems
Fewer topics? A million topics? Both?! On topics subsets in test collections
Adaptive invisible steganography for securing medical images leveraging entropy-based image encryption with the mimic octopus adaptive framework (MOAF)
The Probability Ranking Principle Revisited
Cross-lingual training of summarization systems using annotated corpora in a foreign language
Output-sensitive autocompletion search
Word normalization and decompounding in mono- and bilingual IR
Cheating recognition in examination halls based on improved YOLOv8
Design of energy aware crop monitoring clustering mechanism for UAV -based sensor networks by using aperture antenna
A relatedness analysis of government regulations using domain knowledge and structural organization
John Davies, Marko Grobelnik and Dunja Mladenic: Semantic knowledge management - Springer, 2009, 252 pp., Price: $99 (ISBN: 978-3-540-88844-4)
Automatic question answering using the web: Beyond the Factoid
An effective imputation approach for handling missing data using intuitionistic fuzzy clustering algorithms
Identifying top news using crowdsourcing
Keith van Rijsbergen, The Geometry of Information Retrieval
A novel integration of multi-stocked gated variant recurrent units and Kolmogorov-Arnold tuned deep training networks for anchoring the intrusion detection against computer attacks
Enhancing web search in the medical domain via query clarification
Biomedical term extraction: overview and a new methodology
Data-driven prediction of cattle weight gain for evaluating key growth factors with machine learning approaches
Defending recommender systems by influence analysis
Exploring criteria for successful query expansion in the genomic domain
Optimization of frequent item set mining parallelization algorithm based on spark platform
Disinformation detection technology: a survey
Systematic review of recent advances in multimodal sentiment analysis
Session search modeling by partially observable Markov decision process
Clustering small-sized collections of short texts
Leveraging large language model as news sentiment predictor in stock markets: a knowledge-enhanced strategy
Kernelized Type 2 Intuitionistic Fuzzy C Means: a robust approach for brain MRI image segmentation
Measuring Search Engine Quality
The role of cybersecurity as a preventive measure in digital tourism and travel: a systematic literature review
Scale and Translation Invariant Collaborative Filtering Systems
Introduction to the special issue on search intents and diversification
A novel neighborhood based document smoothing model for information retrieval
A spider wasp-based deep neural prediction framework for emotion recognition and sentiment analysis in big data
A Geth-based detection system for ERC20 honeypot contract in Ethereum
Intent-based diversification of web search results: metrics and algorithms
Simple Semantics in Topic Detection and Tracking
Implicit indexing of natural language text by reorganizing bytecodes
Detecting malware evidences through static and dynamic information using extreme machine learning for forensic analysis
Special issue of The Journal of Information Retrieval on web mining for search
IDaTPA: importance degree based thread partitioning approach in thread level speculation
Medicine image classification using deep learning: highlighting the MedNet-MoBiL hybrid model
Search results diversification for effective fair ranking in academic search
Features for image retrieval: an experimental comparison
Design and implementation of a real-time detection system for multi-token sandwich attacks in Ethereum based on Geth client
Dictionary-Based Cross-Language Information Retrieval: Problems, Methods, and Research Findings
Design and evaluation of personalised early childhood mathematics enlightenment games based on deep reinforcement learning
Methods for automatically evaluating answers to complex questions
Retrieving and classifying instances of source code plagiarism
Validating simulated interaction for retrieval evaluation
Using Corpus-Based Approaches in a System for Multilingual Information Retrieval
Understanding the role of AI in Malaysian higher education curricula: an analysis of student perceptions
A model of the relationship between the variations of effectiveness and fairness in information retrieval
Pascal Poncelet, Florent Masseglia, Maguelonne Teisseire: Successes and New Directions in Data Mining
Proposing a framework for blockchain-based implementation in cadastral systems of conflict-impacted communities
A novel cluster of improved frilled lizard optimization and multi-ladder gated networks for the detection of cyber-attacks in computer networks
TIJAH: Embracing IR Methods in XML Databases
A review of text and image retrieval approaches for broadcast news video
A pattern mining approach for information filtering systems
Text Categorization Based on Regularized Linear Classification Methods
Reinforcement online learning to rank with unbiased reward shaping
Automated vehicle fault diagnosis and report generation using hybrid machine learning with multi-step RAG approach
Changes in Search Tactics and Relevance Judgements when Preparing a Research Proposal A Summary of the Findings of a Longitudinal Study
Information retrieval evaluation using test collections
A Hierarchical Document Retrieval Language
A novel HP-Growth model for enhancing community policing in South Africa
Similarity-based ranking of videos from fixed-size one-dimensional video signature
Determining the interests of social media users: two approaches
A deniable and efficient question and answer service over ad hoc social networks
Cross-attention multi branch for Vietnamese sign language recognition: CrossViViT
Secure edge-based smart grid communication using lightweight authentication modeling with autoencoders and real-world data
Effect of OCR error correction on Arabic retrieval
Classifying Amharic webnews
Recommendations for item set completion: on the semantics of item co-occurrence with data sparsity, input size, and input modalities
Blockchain enabled architecture for data privacy preservation in the metaverse environment
Exploiting Manual Indexing to Improve Collection Selection and Retrieval Effectiveness
Interpolation of Erythrocytes and Leukocytes Microscopic image using MsR-CNN with Yolo v9 Model
Exploration of the relationship between SDGs and CSR reports with text mining techniques for stock exchange companies in Taiwan
A supervised learning approach for recommending medical specialists in the healthcare sector for the Afaan Oromo context
William Hersh: Information retrieval: a health and biomedical perspective, 3rd ed - Health and Informatics Series, Springer, 2009, 504 pp, $79.95, ISBN: 978-0-387-78702-2)
Focused retrieval and result aggregation with political data