yusuke1997/dblp-id-title huggingface dataset:
Cancer diagnosis marker extraction for soft tissue sarcomas based on gene expression profiling data by using projective adaptive resonance theory (PART) filtering method
Magic-BLAST, an accurate RNA-seq aligner for long and short reads
Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection
ASPIC: a novel method to predict the exon-intron structure of a gene that is optimally compatible to a set of transcript sequences
Semi-supervised prediction of protein subcellular localization using abstraction augmented Markov models
GeFaST: An improved method for OTU assignment by generalising Swarm's fastidious clustering approach
fcScan: a versatile tool to cluster combinations of sites using genomic coordinates
Mayday - integrative analytics for expression data
CNN-based ranking for biomedical entity normalization
multiDE: a dimension reduced model based statistical method for differential expression analysis using RNA-sequencing data with multiple treatment conditions
DNAfusion: an R/Bioconductor package for increased sensitivity of detecting gene fusions in liquid biopsies
Support Vector Machines for predicting protein structural class
EnCOUNTer: a parsing tool to uncover the mature N-terminus of organelle-targeted proteins in complex samples
Building Markov state models with solvent dynamics
MATria: a unified centrality algorithm
Modeling of 2D diffusion processes based on microscopy data: parameter estimation and practical identifiability analysis
Assessment of composite motif discovery methods
Control of false discoveries in grouped hypothesis testing for eQTL data
Pydna: a simulation and documentation tool for DNA assembly strategies using python
mAPKL: R/ Bioconductor package for detecting gene exemplars and revealing their characteristics
Taxon ordering in phylogenetic trees: a workbench test
Outcome prediction based on microarray analysis: a critical perspective on methods
Optimization and expansion of non-negative matrix factorization
Integrating multiple molecular sources into a clinical risk prediction signature by extracting complementary information
Peak shape clustering reveals biological insights
Bottom-up GGM algorithm for constructing multilayered hierarchical gene regulatory networks that govern biological pathways or processes
Machine learning-based prediction of survival prognosis in cervical cancer
Assessing transcriptomic heterogeneity of single-cell RNASeq data by bulk-level gene expression data
Exploratory analysis of protein translation regulatory networks using hierarchical random graphs
Review of the selected proceedings of the Fifth International Workshop on Data Integration in the Life Sciences 2008
Virtual Screening of potential drug-like inhibitors against Lysine/DAP pathway of Mycobacterium tuberculosis
Examining the significance of fingerprint-based classifiers
Prediction of regulatory elements in mammalian genomes using chromatin signatures
Learning misclassification costs for imbalanced classification on gene expression data
Ancestry inference using reference labeled clusters of haplotypes
Highlights from the 6th International Society for Computational Biology Student Council Symposium at the 18th Annual International Conference on Intelligent Systems for Molecular Biology
Protected Research Information Management Environment (PRIME) provides a secure open source data management option for clinical and scientific research
Incorporating biological information in sparse principal component analysis with application to genomic data
getphylo: rapid and automatic generation of multi-locus phylogenetic trees
Detecting microRNA activity from gene expression data
Parallel multiplicity and error discovery rate (EDR) in microarray experiments
Efficient haplotype block recognition of very long and dense genetic sequences
Assessment of k -mer spectrum applicability for metagenomic dissimilarity analysis
ParallABEL: an R library for generalized parallelization of genome-wide association studies
Automatic plankton image classification combining multiple view features via multiple kernel learning
New resampling method for evaluating stability of clusters
IonCRAM: a reference-based compression tool for ion torrent sequence files
Probabilistic Principal Component Analysis for Metabolomic Data
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives
Cluster oligonucleotide signatures for rapid identification by sequencing
APTE: identification of indirect read-out A-DNA promoter elements in genomes
SWS: accessing SRS sites contents through Web Services
Amino acid "little Big Bang": Representing amino acid substitution matrices as dot products of Euclidian vectors
Identifying collateral and synthetic lethal vulnerabilities within the DNA-damage response
Inference of Chromosome-Specific Copy Numbers Using Population Haplotypes
A new strategy for better genome assembly from very short reads
ANCAC: amino acid, nucleotide, and codon analysis of COGs - a tool for sequence bias analysis in microbial orthologs
Towards mainstreaming of biodiversity data publishing: recommendations of the GBIF Data Publishing Framework Task Group
SplicerAV: a tool for mining microarray expression data for changes in RNA processing
Reduction strategies for hierarchical multi-label classification in protein function prediction
HebbPlot: an intelligent tool for learning and visualizing chromatin mark signatures
Fuzzy support vector machine: an efficient rule-based classification technique for microarrays
MS4 - Multi-Scale Selector of Sequence Signatures: An alignment-free method for classification of biological sequences
Evaluation of vicinity-based hidden Markov models for genotype imputation
Improvement of variables interpretability in kernel PCA
Gene finding in the chicken genome
Machine learning-based donor permission extraction from informed consent documents
TRIg: a robust alignment pipeline for non-regular T-cell receptor and immunoglobulin sequences
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data
A signal processing approach for enriched region detection in RNA polymerase II ChIP-seq data
Evolutionary distance estimation and fidelity of pair wise sequence alignment
GenMasterTable: a user-friendly desktop application for filtering, summarising, and visualising large-scale annotated genetic variants
IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico
H 3 NGST: a fully automated, web-based platform for end-to-end ChIP-seq analysis
UbiProt: a database of ubiquitylated proteins
Integrating multiple immunogenetic data sources for feature extraction and mining somatic hypermutation patterns: the case of "towards analysis" in chronic lymphocytic leukaemia
Highlights from the Student Council Symposium 2011 at the International Conference on Intelligent Systems for Molecular Biology and European Conference on Computational Biology
Use of DNA melting simulation software for in silico diagnostic assay design: targeting regions with complex melting curves and confirmation by real-time PCR using intercalating dyes
An Eigenvalue test for spatial principal component analysis
Integrated olfactory receptor and microarray gene expression databases
Biclustering fMRI time series: a comparative study
A fast algorithm for the multiple genome rearrangement problem with weighted reversals and transpositions
MassComp, a lossless compressor for mass spectrometry data
Meta-analytic approach to the accurate prediction of secreted virulence effectors in Gram-negative bacteria
Integrating alternative splicing detection into gene prediction
Efficient Sequential and Parallel Algorithms for Planted Motif Search
Correction to: Combining heterogeneous subgroups with graph-structured variable selection priors for Cox regression
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations
Most of the tight positional conservation of transcription factor binding sites near the transcription start site reflects their co-localization within regulatory modules
CryGetter: a tool to automate retrieval and analysis of Cry protein data
DNAscan: personal computer compatible NGS analysis, annotation and visualisation
Approximate Bayesian computation schemes for parameter inference of discrete stochastic models using simulated likelihood density
An attention-based effective neural model for drug-drug interactions extraction
coda4microbiome: compositional data analysis for microbiome cross-sectional and longitudinal studies
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data
Evolutionary programming as a platform for in silico metabolic engineering
Analytical results on the Beauchemin model of lymphocyte migration
RAFTS3G: an efficient and versatile clustering software to analyses in large protein datasets
PAPAyA: a platform for breast cancer biomarker signature discovery, evaluation and assessment
Association of genomewide newborn DNA methylation patterns with maternal and newborn characteristics
Gene prioritization and clustering by multi-view text mining
Versatile and declarative dynamic programming using pair algebras
Filtering de novo indels in parent-offspring trios
VarRanker: rapid prioritization of sequence variations associated with human disease
Random forests for the analysis of matched case-control studies
Computing and visually analyzing mutual information in molecular co-evolution
Normal modes analysis and surface electrostatics of haemagglutinin proteins as fingerprints for high pathogenic type A influenza viruses
Analytics and visualization tools to characterize single-cell stochasticity using bacterial single-cell movie cytometry data
A risk factor attention-based model for cardiovascular disease prediction
PrimedSherlock: a tool for rapid design of highly specific CRISPR-Cas12 crRNAs
Agile methods in biomedical software development: a multi-site experience report
AllesTM: predicting multiple structural features of transmembrane proteins
iLAP: a workflow-driven software for experimental protocol development, data acquisition and analysis
A metadata-aware application for remote scoring and exchange of tissue microarray images
Identification of new members of hydrophobin family using primary structure analysis
CpGcluster : a distance-based algorithm for CpG-island detection
DNAVaxDB: the first web-based DNA vaccine database and its data analysis
Identifying cancer mutation targets across thousands of samples: MuteProc, a high throughput mutation analysis pipeline
Mammalian piRNA target prediction using a hierarchical attention model
A computational approach for identifying pathogenicity islands in prokaryotic genomes
BIOZON: a system for unification, management and analysis of heterogeneous biological data
Optimal dimensionality selection for independent component analysis of transcriptomic data
Characterization and identification of ubiquitin conjugation sites with E3 ligase recognition specificities
Primary orthologs from local sequence context
SOAPTyping: an open-source and cross-platform tool for sequence-based typing for HLA class I and II alleles
Bayesian detection of periodic mRNA time profiles without use of training examples
Visual Gene Developer: a fully programmable bioinformatics software for synthetic gene optimization
HMMF: a hybrid multi-modal fusion framework for predicting drug side effect frequencies
Non-nucleosidic inhibition of Herpes simplex virus DNA polymerase: mechanistic insights into the anti-herpetic mode of action of herbal drug withaferin A
Unsupervised reduction of random noise in complex data by a row-specific, sorted principal component-guided method
DisBind: A database of classified functional binding sites in disordered and structured regions of intrinsically disordered proteins
Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility
Self-analysis of repeat proteins reveals evolutionarily conserved patterns
Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation
MPrime: efficient large scale multiple primer and oligonucleotide design for customized gene microarrays
Local alignment of two-base encoded DNA sequence
A novel radiomics based on multi-parametric magnetic resonance imaging for predicting Ki-67 expression in rectal cancer: a multicenter study
Survival prediction from clinico-genomic models - a comparative study
Identification of the cuproptosis-related molecular subtypes and an immunotherapy prognostic model in hepatocellular carcinoma
rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics
antaRNA - Multi-objective inverse folding of pseudoknot RNA using ant-colony optimization
Towards the prediction of essential genes by integration of network topology, cellular localization and biological process information
OSCI: standardized stem cell ontology representation and use cases for stem cell investigation
Improved algorithms for approximate string matching (extended abstract)
CoPub Mapper: mining MEDLINE based on search term co-publication
Subject level clustering using a negative binomial model for small transcriptomic studies
Statistical Methods for Analyzing Immunosignatures
Boosting K-nearest neighbor regression performance for longitudinal data through a novel learning approach
Decoy selection for protein structure prediction via extreme gradient boosting and ranking
Prior knowledge driven Granger causality analysis on gene regulatory network discovery
Permutation test for periodicity in short time series data
A manually curated database of tetrapod mitochondrially encoded tRNA sequences and secondary structures
A statistical approach to detection of copy number variations in PCR-enriched targeted sequencing data
Detecting disease associated modules and prioritizing active genes based on high throughput data
Semantic Inference using Chemogenomics Data for Drug Discovery
Deterministic Effects Propagation Networks for reconstructing protein signaling networks from multiple interventions
Research on RNA secondary structure predicting via bidirectional recurrent neural network
Trustworthiness and metrics in visualizing similarity of gene expression
Genes2FANs: connecting genes through functional association networks
A deep learning method for counting white blood cells in bone marrow images
TSEBRA: transcript selector for BRAKER
Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics
Semantic annotation of consumer health questions
Reflections on a journey: a retrospective of the ISCB Student Council symposium series
Optimal cDNA microarray design using expressed sequence tags for organisms with limited genomic information
DeepPVP: phenotype-based prioritization of causative variants using deep learning
Profile-based short linear protein motif discovery
Randomization techniques for assessing the significance of gene periodicity results
Differential expression of microRNAs as predictors of glioblastoma phenotypes
DiffLogo: a comparative visualization of sequence motifs
In silico design of MHC class I high binding affinity peptides through motifs activation map
Grace-AKO: a novel and stable knockoff filter for variable selection incorporating gene network structures
Correction to: CDSnake: Snakemake pipeline for retrieval of annotated OTUs from paired-end reads using CD-HIT utilities
Thresher: determining the number of clusters while removing outliers
Grid-based prediction of torsion angle probabilities of protein backbone and its application to discrimination of protein intrinsic disorder regions and selection of model structures
py_ped_sim: a flexible forward pedigree and genetic simulator for complex family pedigree analysis
PyEvolve: a toolkit for statistical modelling of molecular evolution
ProCKSI: a decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information
Correction: NanoBERTa-ASP: predicting nanobody paratope based on a pretrained RoBERTa model
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model
Consistency of metagenomic assignment programs in simulated and real data
Development and production of an oligonucleotide MuscleChip: use for validation of ambiguous ESTs
Efficient discovery of abundant post-translational modifications and spectral pairs using peptide mass and retention time differences
Information management for high content live cell imaging
Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data
SVM-RFE: selection and visualization of the most relevant features through non-linear kernels
InTAD: chromosome conformation guided analysis of enhancer target genes
The 'un-shrunk' partial correlation in Gaussian graphical models
Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays
Prediction of RNA secondary structure with pseudoknots using integer programming
Var2GO: a web-based tool for gene variants selection
End-to-end protein-ligand complex structure generation with diffusion-based generative models
Reconstituting protein interaction networks using parameter-dependent domain-domain interactions
CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis
Linear-time computation of minimal absent words using suffix array
Confident difference criterion: a new Bayesian differentially expressed gene selection algorithm with applications
PASS2: an automated database of protein alignments organised as structural superfamilies
SAG-QC: quality control of single amplified genome information by subtracting non-target sequences based on sequence compositions
Current trend and development in bioinformatics research
BLASTGrabber: a bioinformatic tool for visualization, analysis and sequence selection of massive BLAST data
Bi-objective integer programming for RNA secondary structure prediction with pseudoknots
A heuristic model for computational prediction of human branch point sequence
cuRnet: an R package for graph traversing on GPU
PHDcleav: a SVM based method for predicting human Dicer cleavage sites using sequence and secondary structure of miRNA precursors
Filling gaps of genome scaffolds via probabilistic searching optical maps against assembly graph
3D: diversity, dynamics, differential testing - a proposed pipeline for analysis of next-generation sequencing T cell repertoire data
Using contextual and lexical features to restructure and validate the classification of biomedical concepts
Integrating protein structures and precomputed genealogies in the Magnum database: Examples with cellular retinoid binding proteins
SMILE: systems metabolomics using interpretable learning and evolution
Vertical Decomposition with Genetic Algorithm for Multiple Sequence Alignment
INSnet: a method for detecting insertions based on deep learning network
Maximum parsimony reconciliation in the DTLOR model
Meta-analysis of variables affecting mouse protection efficacy of whole organism Brucella vaccines and vaccine candidates
Selective Phenotyping, Entropy Reduction and the Mastermind Game
GRIBCG: a software for selection of sgRNAs in the design of balancer chromosomes
Robust classification using average correlations as features (ACF)
Quadratic variance models for adaptively preprocessing SELDI-TOF mass spectrometry data
iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
Ab initio identification of putative human transcription factor binding sites by comparative genomics
EMDL_m6Am: identifying N6,2′-O-dimethyladenosine sites based on stacking ensemble deep learning
A distance-field based automatic neuron tracing method
Down-weighting overlapping genes improves gene set analysis
Quality evaluation of extracted ion chromatograms and chromatographic peaks in liquid chromatography/mass spectrometry-based metabolomics data
Modelling the effect of subcellular mutations on the migration of cells in the colorectal crypt
An evaluation methodology for machine learning-based tandem mass spectra similarity prediction
Topology-aware illumination design for volume rendering
Drug repositioning for enzyme modulator based on human metabolite-likeness
Identifying transcription factor and microRNA mediated synergetic regulatory networks in lung cancer
Finding reproducible cluster partitions for the k-means algorithm
Automated prediction of HIV drug resistance from genotype data
Prioritization of cancer driver gene with prize-collecting steiner tree by introducing an edge weighted strategy in the personalized gene interaction network
Identifying Cancer genes by combining two-rounds RWR based on multiple biological data
FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform
WebNetCoffee: a web-based application to identify functionally conserved proteins from Multiple PPI networks
Computational purification of tumor gene expression data
Bios2mds: an R package for comparing orthologous protein families by metric multidimensional scaling
Fast and accurate genome-wide predictions and structural modeling of protein-protein interactions using Galaxy
mySyntenyPortal: an application package to construct websites for synteny block analysis
KRLMM: an adaptive genotype calling method for common and low frequency variants
Directed acyclic graph kernels for structural RNA analysis
Disease Pathway Cut for Multi-Target drugs
An improved sequence based prediction protocol for DNA-binding proteins using SVM and comprehensive feature analysis
Fast and exact quantification of motif occurrences in biological sequences
Clustering gene expression data with a penalized graph-based metric
ANGSD: Analysis of Next Generation Sequencing Data
A Formal Concept Analysis Approach to Consensus Clustering of Multi-Experiment Expression Data
MRI-based brain tumor segmentation using FPGA-accelerated neural network
A direct comparison of protein interaction confidence assignment schemes
SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas
EMD: an ensemble algorithm for discovering regulatory motifs in DNA sequences
An open-source representation for 2-DE-centric proteomics and support infrastructure for data storage and analysis
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis
Automatic generation of 3D motifs for classification of protein binding sites
Hotspot Hunter: a computational system for large-scale screening and selection of candidate immunological hotspots in pathogen proteomes
Determining gene response patterns of time series gene expression data using R
NightShift: NMR Shift Inference by General Hybrid Model Training - a Framework for NMR Chemical Shift Prediction
4Pipe4 - A 454 data analysis pipeline for SNP detection in datasets with no reference sequence or strain information
PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants
Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain
ProMiner: rule-based protein and gene entity recognition
Predicting drug side-effect profiles: a chemical fragment-based approach
MOIRAI: A Compact Workflow System for CAGE Analysis
MIGREW: database on molecular identification of genes for resistance in wheat
MultiToxPred 1.0: a novel comprehensive tool for predicting 27 classes of protein toxins using an ensemble machine learning approach
Biclustering of gene expression data using reactive greedy randomized adaptive search procedure
Modeling Escherichia coli signal peptidase complex with bound substrate: determinants in the mature peptide influencing signal peptide cleavage
Assessment of genome annotation using gene function similarity within the gene neighborhood