yusuke1997/dblp-id-title huggingface dataset:
ThreaDNA: predicting DNA mechanics' contribution to sequence selectivity of proteins along whole genomes
MuWU: Mutant-seq library analysis and annotation
A network-based deep learning methodology for stratification of tumor mutations
Reconstructing the temporal progression of HIV-1 immune response pathways
Plasma protein binding prediction focusing on residue-level features and circularity of cyclic peptides by deep learning
Estimation of QTL heritability based on pooled sequencing data
DelPhiForce web server: electrostatic forces and energy calculations and visualization
DEMA: a distance-bounded energy-field minimization algorithm to model and layout biomolecular networks with quantitative features
Quality assessment of protein model-structures using evolutionary conservation
TDFragMapper: a visualization tool for evaluating experimental parameters in top-down proteomics
2SNP: scalable phasing based on 2-SNP haplotypes
OntologyTraverser: an R package for GO analysis
Differential protein expression and peak selection in mass spectrometry data by binary discriminant analysis
A friendly statistics package for microarray analysis
OLOGRAM: determining significance of total overlap length between genomic regions sets
GlobalANCOVA: exploration and assessment of gene group effects
SeqArray - a storage-efficient high-performance data format for WGS variant calls
Causal stability ranking
TEQC: an R package for quality control in target capture experiments
Message from the ISCB: 2016 ISCB Accomplishment by a Senior Scientist Award Given to Søren Brunak
MPSQ: a web tool for protein-state searching
CMAP: Complement Map Database
'Size leap' algorithm: an efficient extraction of the longest common motifs from a molecular sequence set. Application to the DNA sequence reconstruction
Accurate detection of aneuploidies in array CGH and gene expression microarray data
G4HunterApps
Joint estimation of DNA copy number from multiple platforms
FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery
Bayesian inference for dynamic transcriptional regulation; the Hes1 system as a case study
CPSS: a computational platform for the analysis of small RNA deep sequencing data
JXP4BIGI: a generalized, Java XML-based approach for biological information gathering and integration
Icarust, a real-time simulator for Oxford Nanopore adaptive sampling
CentiLib: comprehensive analysis and exploration of network centralities
Multi-class protein fold recognition using support vector machines and neural networks
The JigCell Model Builder and Run Manager
Graph transformation for enzymatic mechanisms
ABEILLE: a novel method for ABerrant Expression Identification empLoying machine LEarning from RNA-sequencing data
HydroPaCe: understanding and predicting cross-inhibition in serine proteases through hydrophobic patch centroids
Predicting physiologically relevant SH3 domain mediated protein-protein interactions in yeast
ACT: aggregation and correlation toolbox for analyses of genome tracks
MiRGOFS: a GO-based functional similarity measurement for miRNAs, with applications to the prediction of miRNA subcellular localization and miRNA-disease association
YY1 is a cis-regulator in the organoid models of high mammographic density
A multi-view graph convolutional network framework based on adaptive adjacency matrix and multi-strategy fusion mechanism for identifying spatial domains
IPEP: an in silico tool to examine proteolytic peptides for mass spectrometry
Automatic rebuilding and optimization of crystallographic structures in the Protein Data Bank
SIMPRO: simple protein homology detection method by using indirect signals
SNP interaction pattern identifier (SIPI): an intensive search for SNP-SNP interaction patterns
WHAP: haplotype-based association analysis
Syllable-PBWT for space-efficient haplotype long-match query
SPAED: harnessing AlphaFold output for accurate segmentation of phage endolysin domains
GeneSpy, a user-friendly and flexible genomic context visualizer
Reducing cost in DNA-based data storage by sequence analysis-aided soft information decoding of variable-length reads
Sc2Mol: a scaffold-based two-step molecule generator with variational autoencoder and transformer
MDSCAN: RMSD-based HDBSCAN clustering of long molecular dynamics
XMSF: Structure-preserving noise reduction and pre-segmentation in microscope tomography
Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors
mb-PHENIX: diffusion and supervised uniform manifold approximation for denoizing microbiota data
Fast probabilistic analysis of sequence function using scoring matrices
Haplotypes histories as pathways of recombinations
Reconstruction of the neuromuscular junction connectome
Coupled Two-way Clustering Server
Multi-profile Bayesian alignment model for LC-MS data analysis with integration of internal standards
IgGeneUsage: differential gene usage in immune repertoires
TE-greedy-nester: structure-based detection of LTR retrotransposons and their nesting
Drug-set enrichment analysis: a novel tool to investigate drug mode of action
Motif-based protein ranking by network propagation
Classical scoring functions for docking are unable to exploit large volumes of structural and interaction data
ICBdocker: a Docker image for proteome annotation and visualization
Is there an acceleration of the CpG transition rate during the mammalian radiation?
Evaluation of linguistic features useful in extraction of interactions from PubMed; Application to annotating known, high-throughput and predicted interactions in I 2 D
AMIN domains have a predicted role in localization of diverse periplasmic protein complexes
A multiobjective method for robust identification of bacterial small non-coding RNAs
Utilizing de Bruijn graph of metagenome assembly for metatranscriptome analysis
A framework and an algorithm to detect low-abundance DNA by a handy sequencer and a palm-sized computer
Identification of a new motif on nucleic acid sequence data using Kohonen's self-organizing map
ValTrendsDB: bringing Protein Data Bank validation information closer to the user
CRDS: Consensus Reverse Docking System for target fishing
PAX2GRAPHML: a python library for large-scale regulation network analysis using BioPAX
GlycoCD: a repository for carbohydrate-related CD antigens
RASP: rapid modeling of protein side chain conformations
Inferring clonal heterogeneity in cancer using SNP arrays and whole genome sequencing
Exome sequencing-based copy-number variation and loss of heterozygosity detection: ExomeCNV
Normalization by distributional resampling of high throughput single-cell RNA-sequencing data
Genetic cooperativity in multi-layer networks implicates cell survival and senescence in the striatum of Huntington's disease mice synchronous to symptoms
KASPspoon: an in vitro and in silico PCR analysis tool for high-throughput SNP genotyping
OLGCG: an OPEN LOOK interface to the GCG sequence analysis package
SLiM on Diet: finding short linear motifs on domain interaction interfaces in Protein Data Bank
Effective dimension reduction methods for tumor classification using gene expression data
Genome-wide analysis of Bkm sequences (GATA repeats): predominant association with sex chromosomes and potential role in higher order chromatin organization and function
RRE: a tool for the extraction of non-coding regions surrounding annotated genes from genomic datasets
MOLGENIS research: advanced bioinformatics data software for non-bioinformaticians
Musket: a multistage k- mer spectrum-based error corrector for Illumina sequence data
Entropy-driven partitioning of the hierarchical protein space
UbiHub: a data hub for the explorers of ubiquitination pathways
A non-stationary model for functional mapping of complex traits
uORF4u: a tool for annotation of conserved upstream open reading frames
DeepGSR: an optimized deep-learning structure for the recognition of genomic signals and regions
A local alignment tool for very long DNA sequences
CCFold: rapid and accurate prediction of coiled-coil structures and application to modelling intermediate filaments
Positive-unlabeled learning for disease gene identification
Incremental window-based protein sequence alignment algorithms
Metabolic pathway analysis web service (Pathway Hunter Tool at CUBIC)
ViroBLAST: a stand-alone BLAST web server for flexible queries of multiple databases and user's datasets
Disulfide connectivity prediction using secondary structure information and diresidue frequencies
Gene-set analysis is severely biased when applied to genome-wide methylation data
Misassembly detection using paired-end sequence reads and optical mapping data
blitzGSEA: efficient computation of gene set enrichment analysis through gamma distribution approximation
Integration of accessibility data from structure probing into RNA-RNA interaction prediction
Calib-RT: an open source python package for peptide retention time calibration in DIA mass spectrometry data
miR-EdiTar: a database of predicted A-to-I edited miRNA target sites
Chainsaw: protein domain segmentation with fully convolutional neural networks
MADGiC: a model-based approach for identifying driver genes in cancer
Stability of gene rankings from RNAi screens
TreeSAPP: the Tree-based Sensitive and Accurate Phylogenetic Profiler
Uncovering the co-evolutionary network among prokaryotic genes
The QDREC web server: determining dose-response characteristics of complex macroparasites in phenotypic drug screens
Synchronous versus asynchronous modeling of gene regulatory networks
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud
Automated protein sequence database classification. I. Integration of compositional similarity search, local similarity search, and multiple sequence alignment
Transposome: a toolkit for annotation of transposable element families from unassembled sequence reads
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology
Single-cell mutation calling and phylogenetic tree reconstruction with loss and recurrence
3Dscript.server: true server-side 3D animation of microscopy images using a natural language-based syntax
Cancer mutational signatures representation by large-scale context embedding
LOCUST: a custom sequence locus typer for classifying microbial isolates
Improved image alignment method in application to X-ray images and biological images
Hybrid huberized support vector machines for microarray classification and gene selection
Finding families for genomic ORFans
Prediction of eukaryotic mRNA translational properties
maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments
Detecting retinal neural and stromal cell classes and ganglion cell subtypes based on transcriptome data with deep transfer learning
OncomiR: an online resource for exploring pan-cancer microRNA dysregulation
Identification of non-Hodgkin's lymphoma prognosis signatures using the CTGDR method
An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types
TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations
Design and implementation of a CORBA-based genome mapping system prototype
Identifying the critical state of complex biological systems by the directed-network rank score method
A protocol for building and evaluating predictors of disease state based on microarray data
Application of compression-based distance measures to protein sequence classification: a methodological study
Partition resampling and extrapolation averaging: approximation methods for quantifying gene expression in large numbers of short oligonucleotide arrays
ayesian automatic relevance determination algorithms for classifying gene expression data
Liftoff: accurate mapping of gene annotations
Post-processing long pairwise alignments
ROBOKOP: an abstraction layer and user interface for knowledge graphs to support question answering
GENIUS: web server to predict local gene networks and key genes for biological functions
TreeAndLeaf: an R/Bioconductor package for graphs and trees with focus on the leaves
ModLoop: automated modeling of loops in protein structures
Prediction of pathogenic single amino acid substitutions using molecular fragment descriptors
Analysis of several key factors influencing deep learning-based inter-residue contact prediction
BlockClust: efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles
Motif independent identification of potential RNA G-quadruplexes by G4RNA screener
Response to comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'
Nezzle: an interactive and programmable visualization of biological networks in Python
An improved algorithm for clustering gene expression data
Graph-based clustering for finding distant relationships in a large set of protein sequences
An approachable, flexible and practical machine learning workshop for biologists
KG4SL: knowledge graph neural network for synthetic lethality prediction in human cancers
Visualization and analysis of protein interactions
RMTL: an R library for multi-task learning
Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation
SemMedDB: a PubMed-scale repository of biomedical semantic predications
Predicting circRNA-disease associations with shared units and multi-channel attention mechanisms
Prediction of novel pre-microRNAs with high accuracy through boosting and SVM
RCSB protein Data Bank: exploring protein 3D similarities via comprehensive structural alignments
A finite-difference computer model of solute diffusion in bacterial films with simultaneous metabolism and chemical reaction
Testing phylogenetic signal with categorical traits and tree uncertainty
Discretized Gaussian mixture for genotyping of microsatellite loci containing homopolymer runs
Compacting de Bruijn graphs from sequencing data quickly and in low memory
DELISHUS: an efficient and exact algorithm for genome-wide detection of deletion polymorphism in autism
Pln24NT: a web resource for plant 24-nt siRNA producing loci
cc SOL omics : a webserver for solubility prediction of endogenous and heterologous expression in Escherichia coli
LOX-DB - a database on lipoxygenases
CalMaTe: a method and software to improve allele-specific copy number of SNP arrays for downstream segmentation
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data
Human-CMouse Gene Searcher: a tool to assist discovery of malformation-associated genes by using phenotype databases
Surfaces: a software to quantify and visualize interactions within and between proteins and ligands
Socrates: identification of genomic rearrangements in tumour genomes by re-aligning soft clipped reads
Pygenprop: a Python library for programmatic exploration and comparison of organism genome properties
SCAN-ATAC-Sim: a scalable and efficient method for simulating single-cell ATAC-seq data from bulk-tissue experiments
DECOD: fast and accurate discriminative DNA motif finding
compendiumdb: an R package for retrieval and storage of functional genomics data
MotifSuite: workflow for probabilistic motif detection and assessment
BasyLiCA: a tool for automatic processing of a Bacterial Live Cell Array
Efficient haplotype matching and storage using the positional Burrows-Wheeler transform (PBWT)
A platform for biological sequence comparison on parallel computers
Semantic Web Service provision: a realistic framework for Bioinformatics programmers
Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P -values
Metaviral SPAdes: assembly of viruses from metagenomic data
Synchronizing a multicellular system by external input: an artificial control strategy
Multiple kernel learning for integrative consensus clustering of omic datasets
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics
RBPPred: predicting RNA-binding proteins from sequence using SVM
Heterogeneous graph inference with matrix completion for computational drug repositioning
LIQUID: an-open source software for identifying lipids in LC-MS/MS-based lipidomics data
Ensemble learning for classifying single-cell data and projection across reference atlases
Significance analysis of functional categories in gene expression studies: a structured permutation approach
BINGO: a blind unmixing algorithm for ultra-multiplexing fluorescence images
ARCS-Motif: discovering correlated motifs from unaligned biological sequences
ParIS Genome Rearrangement server
The Hera database and its use in the characterization of endoplasmic reticulum proteins
ACCUSA - accurate SNP calling on draft genomes
CURVATURE: software for the analysis of curved DNA
Correction to: GTExVisualizer: a web platform for supporting ageing studies
Rediscovering secondary structures as network motifs - an unsupervised learning approach
Compositional symmetries in complete genomes
NCycDB: a curated integrative database for fast and accurate metagenomic profiling of nitrogen cycling genes
Estimating cancer survival and clinical outcome based on genetic tumor progression scores
qgg: an R package for large-scale quantitative genetic analyses
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
Dementia key gene identification with multi-layered SNP-gene-disease network
Shifting and scaling patterns from gene expression data
Identification of metabolites from tandem mass spectra with a machine learning approach utilizing structural features
Augmented Interval List: a novel data structure for efficient genomic interval search
Amplicon: software for designing PCR primers on aligned DNA sequences
Exploring homology detection via k-means clustering of proteins embedded with a large language model
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results
Delineating inter- and intra-antibody repertoire evolution with AntibodyForests
HiRes - a tool for comprehensive assessment and interpretation of metabolomic data
COBREXA.jl: constraint-based reconstruction and exascale analysis
MRHMMs: Multivariate Regression Hidden Markov Models and the variantS
Potent antibiotic design via guided search from antibacterial activity evaluations
Assembly of fingerprint contigs: parallelized FPC
A statistical simulator scDesign for rational scRNA-seq experimental design
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins
Achieving improved accuracy for imputation of ancient DNA
sapFinder: an R/Bioconductor package for detection of variant peptides in shotgun proteomics experiments
Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus
GSMA: software implementation of the genome search meta-analysis method
A collection of well characterised integral membrane proteins
biRte: Bayesian inference of context-specific regulator activities and transcriptional networks
A note on the false discovery rate of novel peptides in proteogenomics
Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone
HCGene: a software tool to support the hierarchical classification of genes
GelMetric: semi-automated electrophoretic mobility analysis
GAPIT: genome association and prediction integrated tool
PRECIS: Protein reports engineered from concise information in SWISS-PROT
DR-SIP: protocols for higher order structure modeling with distance restraints- and cyclic symmetry-imposed packing
Predicting allosteric pockets in protein biological assemblages
FoldNucleus: web server for the prediction of RNA and protein folding nuclei from their 3D structures
Systematic construction of gene coexpression networks with applications to human T helper cell differentiation process
Collecting and managing taxonomic data with NCBI-taxonomist
ImmQuant: a user-friendly tool for inferring immune cell-type composition from gene-expression data
A Tcl-based SRS v.4 interface
CRISPRitz: rapid, high-throughput and variant-aware in silico off-target site identification for CRISPR genome editing
Per-sample standardization and asymmetric winsorization lead to accurate clustering of RNA-seq expression profiles
Integrated databases and computer systems for studying eukaryotic gene expression
Computational approaches to define a human milk metaglycome
TagFinder for the quantitative analysis of gas chromatography - mass spectrometry (GC-MS)-based metabolite profiling experiments
Supervised graph co-contrastive learning for drug-target interaction prediction
Biological network comparison using graphlet degree distribution
FlashPCA2: principal component analysis of Biobank-scale genotype datasets
Global Biobank Engine: enabling genotype-phenotype browsing for biobank summary statistics
optiCall: a robust genotype-calling algorithm for rare, low-frequency and common variants
Continual representation learning for evolving biomedical bipartite networks
A comparison of background correction methods for two-colour microarrays
SEABED: Small molEcule activity scanner weB servicE baseD
Statistical significance of some complex nucleotide combinations: a comparison of DNA models
Machine learning optimization of peptides for presentation by class II MHCs
riboviz 2: a flexible and robust ribosome profiling data analysis and visualization workflow
HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design
Resmap: automated representation of macromolecular interfaces as two-dimensional networks
Sequence search algorithm assessment and testing toolkit (SAT)
BetaAlign: a deep learning approach for multiple sequence alignment
COME: contrastive mapping learning for spatial reconstruction of single-cell RNA sequencing data
nandb - number and brightness in R with a novel automatic detrending algorithm
Context-sensitive network-based disease genetics prediction and its implications in drug discovery
A fast hybrid short read fragment assembly algorithm
Response to comment on 'On the inference of spatial structure from population genetics data'
TIMING 2.0: high-throughput single-cell profiling of dynamic cell-cell interactions by time-lapse imaging microscopy in nanowell grids
GolgiP: prediction of Golgi-resident proteins in plants
Greedy mixture learning for multiple motif discovery in biological sequences
Traitpedia: a collaborative effort to gather species traits
DNA sequence+shape kernel enables alignment-free modeling of transcription factor binding
A comparison of signal sequence prediction methods using a test set of signal peptides
A genetic algorithm for multiple molecular sequence alignment
Displaying the information contents of structural RNA alignments: the structure logos
FunTaxIS-lite: a simple and light solution to investigate protein functions in all living organisms
BamTools: a C++ API and toolkit for analyzing and managing BAM files
StochSens - matlab package for sensitivity analysis of stochastic chemical systems
ExamPle: explainable deep learning framework for the prediction of plant small secreted peptides
Single-cell and spatial multiomic inference of gene regulatory networks using SCRIPro
unifiedWMWqPCR: the unified Wilcoxon-Mann-Whitney test for analyzing RT-qPCR data in R
Protein domain recurrence and order can enhance prediction of protein functions
admixr - R package for reproducible analyses using ADMIXTOOLS
BEST: Bayesian estimation of species trees under the coalescent model
eF-site and PDBjViewer: database and viewer for protein functional sites
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding
proABC-2: PRediction of AntiBody contacts v2 and its application to information-driven docking
chromPlot: visualization of genomic data in chromosomal context
SmartR: an open-source platform for interactive visual analytics for translational research data
ATOM: a powerful gene-based association test by combining optimally weighted markers
Simulation and annotation of global acronyms
PIE the search : searching PubMed literature for protein interaction information