yusuke1997/dblp-id-title huggingface dataset:
Evaluation of HIV-1 kinetic models using quantitative discrimination analysis
SmashCell: a software framework for the analysis of single-cell amplified genome sequences
Surrogate minimal depth as an importance measure for variables in random forests
HAPRAP: a haplotype-based iterative method for statistical fine mapping using GWAS summary statistics
A software tool for finding locally optimal alignments in protein and nucleic acid sequences
GPCR-GRAPA-LIB-a refined library of hidden Markov Models for annotating GPCRs
MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format
Fast integration of heterogeneous data sources for predicting gene function with limited annotation
Incorporating family disease history and controlling case-control imbalance for population-based genetic association studies
DRIMM-Synteny: decomposing genomes into evolutionary conserved segments
SUBTRACT: a computer program for modeling the process of subtractive hydridization
In silico site of metabolism prediction for human UGT-catalyzed reactions
Enrichment of transcriptional regulatory sites in non-coding genomic region
EBglmnet: a comprehensive R package for sparse generalized linear regression models
POIROT: a powerful test for parent-of-origin effects in unrelated samples leveraging multiple phenotypes
VirBot: an RNA viral contig detector for metagenomic data
T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks
Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients
An empirical comparison of several recent epistatic interaction detection methods
Quartet-based inference is statistically consistent under the unified duplication-loss-coalescence model
InterProSurf: a web server for predicting interacting sites on protein surfaces
Simple stochastic birth andz death models of genome evolution: was there enough time for us to evolve?
JEPEGMIX2: improved gene-level joint analysis of eQTLs in cosmopolitan cohorts
SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data
ORIOGEN: order restricted inference for ordered gene expression data
TreeMap: a structured approach to fine mapping of eQTL variants
Site of metabolism prediction for oxidation reactions mediated by oxidoreductases based on chemical bond
Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data
DiscoverSL: an R package for multi-omic data driven prediction of synthetic lethality in cancers
Estimation of equilibrium constants using automated group contribution methods
GWAlpha: genome-wide estimation of additive effects (alpha) based on trait quantile distribution from pool-sequencing experiments
rScudo: an R package for classification of molecular profiles using rank-based signatures
Riborex: fast and flexible identification of differential translation from Ribo-seq data
A genetic programming-based approach to the classification of multiclass microarray datasets
Importing MAGE-ML format microarray data into BioConductor
Identifying subtle interrelated changes in functional gene categories using continuous measures of gene expression
An in silico genome-wide screen for circadian clock strength in human samples
GPCR-OKB: the G Protein Coupled Receptor Oligomer Knowledge Base
WatFinder : a ProDy tool for protein-water interactions
TreeTime: an extensible C++ software package for Bayesian phylogeny reconstruction with time-calibration
HybridSim-VS: a web server for large-scale ligand-based virtual screening using hybrid similarity recognition techniques
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%
Feature selection for genetic sequence classification
Ribotin: automated assembly and phasing of rDNA morphs
Improving molecular cancer class discovery through sparse non-negative matrix factorization
clustComp, a bioconductor package for the comparison of clustering results
Database of Structural Motifs in Proteins
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
pyPESTO: a modular and scalable tool for parameter estimation for dynamic models
Improving gene recognition accuracy by combining predictions from two gene-finding programs
A varying threshold method for ChIP peak-calling using multiple sources of information
FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution
Haplotype synthesis analysis reveals functional variants underlying known genome-wide associated susceptibility loci
SIMoNe: Statistical Inference for MOdular NEtworks
Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data
Continuous-state HMMs for modeling time-series single-cell RNA-Seq data
A novel approach to local reliability of sequence alignments
MetNetAligner: a web service tool for metabolic network alignments
Insights into structural variations and genome rearrangements in prokaryotic genomes
Inference of Markovian properties of molecular sequences from NGS data and applications to comparative genomics
Transgene-design: a web application for the design of mammalian transgenes
CAMUR: Knowledge extraction from RNA-seq cancer data through equivalent classification rules
SHRiMP2: Sensitive yet Practical Short Read Mapping
GLANET: genomic loci annotation and enrichment tool
TAIJI: approaching experimental replicates-level accuracy for drug synergy prediction
Fast thermodynamically constrained flux variability analysis
Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data
Identification and removal of ribosomal RNA sequences from metatranscriptomes
Model-based clustering of array CGH data
A Julia set model of field-directed morphogenesis: developmental biology and artificial life
SCAssign: a sparky extension for the NMR resonance assignment of aliphatic side-chains of uniformly 13 C, 15 N-labeled large proteins
TLCQA: quantitative study of thin-layer chromatography
iMod: multipurpose normal mode analysis in internal coordinates
Thymine distribution in genes provides novel insight into the functional significance of the proteome of the malaria parasite Plasmodium falciparum 3D7
SoloDel: a probabilistic model for detecting low-frequent somatic deletions from unmatched sequencing data
Frag'r'Us: knowledge-based sampling of protein backbone conformations for de novo structure-based protein design
An annealing mutation operator in the genetic algorithms for RNA folding
Robust biclustering by sparse singular value decomposition incorporating stability selection
Establishing a method of vector contamination identification in database sequences
Genotyping inversions and tandem duplications
smCounter2: an accurate low-frequency variant caller for targeted sequencing data with unique molecular identifiers
GWASinlps: non-local prior based iterative SNP selection tool for genome-wide association studies
Genome-wide association studies pipeline (GWASpi): a desktop application for genome-wide SNP analysis and management
MIX-TPI: a flexible prediction framework for TCR-pMHC interactions based on multimodal representations
genBaRcode: a comprehensive R-package for genetic barcode analysis
RNA 3D structure modeling by fragment assembly with small-angle X-ray scattering restraints
Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic
A novel link prediction algorithm for reconstructing protein-protein interaction networks by topological similarity
Peel learning for pathway-related outcome prediction
BASH: a tool for managing BeadArray spatial artefacts
Privacy-preserving framework for genomic computations via multi-key homomorphic encryption
BioRAT: extracting biological information from full-length papers
Computational methods for the design of effective therapies against drug resistant HIV strains
COMUNET: a tool to explore and visualize intercellular communication
BagBoosting for tumor classification with gene expression data
INFO-RNA - a fast approach to inverse RNA folding
MeConcord: a new metric to quantitatively characterize DNA methylation heterogeneity across reads and CpG sites
RALEE--RNA ALignment Editor in Emacs
opm: an R package for analysing OmniLog ® phenotype microarray data
SVGMap: configurable image browser for experimental data
A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors
High-performance gene name normalization with GENO
An information-based sequence distance and its application to whole mitochondrial genome phylogeny
A Bayesian two-way latent structure model for genomic data integration reveals few pan-genomic cluster subtypes in a breast cancer cohort
Computer programs for exact nonparametric inference
GenBank as a source to monitor and analyze Host-Microbiome data
GOThresher: a program to remove annotation biases from protein function annotation datasets
Chrom-Sig: de-noising 1D genomic profiles by signal processing methods
Memory efficient folding algorithms for circular RNA secondary structures
Small-sample precision of ROC-related estimates
A new approach for displaying identities and differences among aligned amino acid sequences
Improving protein secondary structure prediction using a simple k -mer model
The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
Comments on the analysis of unbalanced microarray data
On the inconsistent treatment of gene-protein-reaction rules in context-specific metabolic models
GenRisk: a tool for comprehensive genetic risk modeling
A personalized microRNA microarray normalization method using a logistic regression model
Genetic network inference as a series of discrimination tasks
kdetrees: non-parametric estimation of phylogenetic tree distributions
LLPSDB v2.0: an updated database of proteins undergoing liquid-liquid phase separation in vitro
Next-generation phenotyping: introducing phecodeX for enhanced discovery research in medical phenomics
An ultra-sensitive T-cell receptor detection method for TCR-Seq and RNA-Seq data
KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor
Tracing the ancestry of operons in bacteria
A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm
ACE: absolute copy number estimation from low-coverage whole-genome sequencing data
mixtureS: a novel tool for bacterial strain genome reconstruction from reads
Erratum to: EpiGraphDB: a database and data mining platform for health data science
Long read alignment based on maximal exact match seeds
Extracting human protein interactions from MEDLINE using a full-sentence parser
Expanded functionality, increased accuracy, and enhanced speed in the de novo genotyping-by-sequencing pipeline GBS-SNP-CROP
FuncFetch: an LLM-assisted workflow enables mining thousands of enzyme-substrate interactions from published manuscripts
Effect of spatial distribution of T-Cells and HIV load on HIV progression
Differential RNA methylation analysis for MeRIP-seq data under general experimental design
Mosaic-PICASSO: accurate crosstalk removal for multiplex fluorescence imaging
Pedstrip: extracting a maximal subset of available, unrelated individuals from a pedigree
pStab: prediction of stable mutants, unfolding curves, stability maps and protein electrostatic frustration
An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry
De novo construction of polyploid linkage maps using discrete graphical models
Chicdiff: a computational pipeline for detecting differential chromosomal interactions in Capture Hi-C data
w4CSeq: software and web application to analyze 4C-seq data
Mathematica packages for simulation of experimental genetics
MESHI: a new library of Java classes for molecular modeling
Combining functional and linkage disequilibrium information in the selection of tag SNPs
NERDD: a web portal providing access to in silico tools for drug discovery
Modeling protein loops with knowledge-based prediction of sequence-structure alignment
Prediction of protein beta-residue contacts by Markov logic networks with grounding-specific weights
Comparative genomics study of inverted repeats in bacteria
dPattern: transcription factor binding site (TFBS) discovery in human genome using a discriminative pattern analysis
Beta-Poisson model for single-cell RNA-seq data analyses
SPSens: a software package for stochastic parameter sensitivity analysis of biochemical reaction networks
CGV: Cancer Genome Viewer, a web service for integrative cancer genome and pharmacogenomic data analysis
OLGA: fast computation of generation probabilities of B- and T-cell receptor amino acid sequences and motifs
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing
A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data
Metatool 5.0: fast and flexible elementary modes analysis
DREIMT: a drug repositioning database and prioritization tool for immunomodulation
Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS
RAG: RNA-As-Graphs database-concepts, analysis, features
lpNet: a linear programming approach to reconstruct signal transduction networks
F-Seq: a feature density estimator for high-throughput sequence tags
HNOXPred: a web tool for the prediction of gas-sensing H-NOX proteins from amino acid sequence
Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways
hotspot: software to support sperm-typing for investigating recombination hotspots
NoRSE: noise reduction and state evaluator for high-frequency single event traces
ProDerAl: reference position dependent alignment
Anonymous nuclear loci in non-model organisms: making the most of high-throughput genome surveys
COVID-2019-associated overexpressed Prevotella proteins mediated host-pathogen interactions and their role in coronavirus outbreak
CPS analysis: self-contained validation of biomedical data clustering
FlowPacker: protein side-chain packing with torsional flow matching
An enhanced loss function simplifies the deep learning model for characterizing the 3D organoid models
RAP: a new computer program for de novo identification of repeated sequences in whole genomes
BFC: correcting Illumina sequencing errors
Design and Assessment of A Fast Algorithm for Identifying Specific Probes for Human and Mouse Genes
Assocplots: a Python package for static and interactive visualization of multiple-group GWAS results
flowCL: ontology-based cell population labelling in flow cytometry
A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human
NoiseMaker: simulated screens for statistical assessment
SECISDesign: a server to design SECIS-elements within the coding sequence
Network-based prediction of metabolic enzymes' subcellular localization
Probabilistic inference of transcription factor concentrations and gene-specific regulatory activities
Statistical analysis of domains in interacting protein pairs
InterProScan 5: genome-scale protein function classification
Erratum. Finding families for genomic ORFans
A tool-kit for cDNA microarray and promoter analysis
Mirage 2.0: fast and memory-efficient reconstruction of gene-content evolution considering heterogeneous evolutionary patterns among gene families
A maximum kernel-based association test to detect the pleiotropic genetic effects on multiple phenotypes
Evaluation of AlphaFold-Multimer prediction on multi-chain protein complexes
Toward better understanding of artifacts in variant calling from high-coverage samples
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
Morbigenous brain region and gene detection with a genetically evolved random neural network cluster approach in late mild cognitive impairment
Metabolite identification and molecular fingerprint prediction through machine learning
Stereo3D: using stereo images to enrich 3D visualization
3DBionotes COVID-19 edition
A cross-species bi-clustering approach to identifying conserved co-regulated genes
A fast coarse filtering method for peptide identification by mass spectrometry
easyFRAP: an interactive, easy-to-use tool for qualitative and quantitative analysis of FRAP data
The UEA sRNA workbench: a suite of tools for analysing and visualizing next generation sequencing microRNA and small RNA datasets
Faucet: streaming de novo assembly graph construction
LEGO-CSM: a tool for functional characterization of proteins
Genome analysis with inter-nucleotide distances
VTUTIN: a full screen gel management editor
Srinivasan (1962-2021) in Bioinformatics and beyond
Deep learning on chaos game representation for proteins
Advancements in computational modelling of biological systems: seventh annual SysMod meeting
Retro: concept-based clustering of biomedical topical sets
Enhanced O-glycosylation site prediction using explainable machine learning technique with spatial local environment
CRNreals: a toolbox for distinguishability and identifiability analysis of biochemical reaction networks
Self-organizing tree growing network for classifying amino acids
BiasViz: visualization of amino acid biased regions in protein alignments
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case
Meta-Storms: efficient search for similar microbial communities based on a novel indexing scheme and similarity score for metagenomic data
Using AnABlast for intergenic sORF prediction in the Caenorhabditis elegans genome
A novel strategy to design highly specific PCR primers based on the stability and uniqueness of 3'-end subsequences
ssSNPer: identifying statistically similar SNPs to aid interpretation of genetic association studies
CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array
CancerSubtypes: an R/Bioconductor package for molecular cancer subtype identification, validation and visualization
Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model
Alignment-free filtering for cfNA fusion fragments
Using biplots to interpret gene expression patterns in plants
WebPARE: web-computing for inferring genetic or transcriptional interactions
FMtree: a fast locating algorithm of FM-indexes for genomic data
Reducing the man-machine barrier: the Sequence Analysis Workbench
iSmaRT: a toolkit for a comprehensive analysis of small RNA-Seq data
SCANMS: adjusting for multiple comparisons in sliding window neutrality tests
Gene set analysis with graph-embedded kernel association test
GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs
Data-driven noise modeling of digital DNA melting analysis enables prediction of sequence discriminating power
A general algorithm to compute multilocus genotype frequencies under various mating systems
Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species
ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles
Software-controlled testing for antidromic activation of single neurones
miRTCat: a comprehensive map of human and mouse microRNA target sites including non-canonical nucleation bulges
PhyloMix: enhancing microbiome-trait association prediction through phylogeny-mixing augmentation
The presence of signal peptide significantly affects transmembrane topology prediction
A parallel and sensitive software tool for methylation analysis on multicore platforms
CellMC - a multiplatform model compiler for the Cell Broadband Engine and x86
GeneLab: Omics database for spaceflight experiments
Three-dimensional reconstruction of helical structures with fast inversion of very large Fourier transforms
RNAG: a new Gibbs sampler for predicting RNA secondary structure for unaligned sequences
Prediction and analysis of nucleotide-binding residues using sequence and sequence-derived structural descriptors
Estimating the Occurrence of False Positives and False Negatives in Microarray Studies by Approximating and Partitioning the Empirical Distribution of P-values
Dynamic modeling of genetic networks using genetic algorithm and S-system
A zero-inflated Poisson model for insertion tolerance analysis of genes based on Tn-seq data
Prediction of protein secondary structure by the hidden Markov model
ASimulatoR: splice-aware RNA-Seq data simulation
Estimation of inbreeding and kinship coefficients via latent identity-by-descent states
Bioinformatics: Biology by other means
A single source k -shortest paths algorithm to infer regulatory pathways in a gene network
Morphologically constrained and data informed cell segmentation of budding yeast
Pasha: a versatile R package for piling chromatin HTS data
PoreLogo: a new tool to analyse, visualize and compare channels in transmembrane proteins
The Cytochrome P450 Engineering Database: a navigation and prediction tool for the cytochrome P450 protein family
TangleSolve: topological analysis of site-specific recombination
SaGePhy: an improved phylogenetic simulation framework for gene and subgene evolution
MSVM-RFE: extensions of SVM-RFE for multiclass gene selection on DNA microarray data
SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data
Microcomputer package for statistical analysis of microbial populations
Moran's I quantifies spatio-temporal pattern formation in neural imaging data
SEMEDA: ontology based semantic integration of biological databases
Biomolecular pleiomorphism probed by spatial interpolation of coarse models
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences
AcrNET: predicting anti-CRISPR with deep learning
GenomeInspector: a new approach to detect correlation patterns of elements on genomic sequences
Repeat-aware evaluation of scaffolding tools
Develop machine learning-based regression predictive models for engineering protein solubility
A two-stage normalization method for partially degraded mRNA microarray data
Completing the E. coli proteome: a database of gene products characterised since the completion of the genome sequence
PredGCN: a Pruning-enabled Gene-Cell Net for automatic cell annotation of single cell transcriptome data
Predicting transcription factor affinities to DNA from a biophysical model
ReMASTER: improved phylodynamic simulation for BEAST 2.7
Inference of missing SNPs and information quantity measurements for haplotype blocks
A novel statistical method for quantitative comparison of multiple ChIP-seq datasets
Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors
PAIPline: pathogen identification in metagenomic and clinical next generation sequencing samples
Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking
Mirroring co-evolving trees in the light of their topologies
GateMeClass: Gate Mining and Classification of cytometry data
RNAloops: a database of RNA multiloops
Graphical model for joint segmentation and tracking of multiple dividing cells
ProFitFun: a protein tertiary structure fitness function for quantifying the accuracies of model structures
Haplotype phasing in single-cell DNA-sequencing data
LINKPHASE3: an improved pedigree-based phasing algorithm robust to genotyping and map errors
Inference of gene networks - application to Bifidobacterium
Parsley: a web app for parsing data from plate readers
Corrigendum to: HALPER facilitates the identification of regulatory element orthologs across species
Integrating patients in time series clinical transcriptomics data
TLM-Tracker: software for cell segmentation, tracking and lineage analysis in time-lapse microscopy movies
A machine learning information retrieval approach to protein fold recognition
Estimating biological elementary flux modes that decompose a flux distribution by the minimal branching property