yusuke1997/dblp-id-title huggingface dataset:
High-throughput feature counting and measurement of roots
FraGAT: a fragment-oriented multi-scale graph attention model for molecular property prediction
Predictive models for population performance on real biological fitness landscapes
Leveraging transcription factor physical proximity for enhancing gene regulation inference
Protein contact prediction by integrating joint evolutionary coupling analysis and supervised learning
Nunchaku: optimally partitioning data into piece-wise contiguous segments
A hypercubic Mk model framework for capturing reversibility in disease, cancer, and evolutionary accumulation modelling
Accurate prediction of protein contact maps by coupling residual two-dimensional bidirectional long short-term memory with convolutional neural networks
A comparative analysis of HGSC and Celera human genome assemblies and gene sets
Structure discovery in PPI networks using pattern-based network decomposition
BioFVM: an efficient, parallelized diffusive transport solver for 3-D biological simulations
Sarment: Python modules for HMM analysis and partitioning of sequences
Dynalogo: an interactive sequence logo with dynamic thresholding of matched quantitative proteomic data
MERIDA: a novel Boolean logic-based integer linear program for personalized cancer therapy
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads
RNAvista: a webserver to assess RNA secondary structures with non-canonical base pairs
VSOT: volume-surface optimization for accurate ultrastructure analysis of dendritic spines
PFRES: protein fold classification by using evolutionary information and predicted secondary structure
A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments
PMUT: a web-based tool for the annotation of pathological mutations on proteins
GRIMM: GRaph IMputation and matching for HLA genotypes
MMFPh: a maximal motif finder for phosphoproteomics datasets
Slider - maximum use of probability information for alignment of short sequence reads and SNP detection
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
Inference of gene regulatory networks and compound mode of action from time course gene expression profiles
SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses
EasyVS: a user-friendly web-based tool for molecule library selection and structure-based virtual screening
A practical false discovery rate approach to identifying patterns of differential expression in microarray data
A model system for studying the integration of molecular biology databases
QOMA: quasi-optimal multiple alignment of protein sequences
Detecting gene clusters under evolutionary constraint in a large number of genomes
The architecture of the gene regulatory networks of different tissues
Differential methylation analysis for BS-seq data under general experimental design
On the analysis of microbiological processes by Monte Carlo simulation techniques
RDP: detection of recombination amongst aligned sequences
SCRIBER: accurate and partner type-specific prediction of protein-binding residues from proteins sequences
Prediction of whole-cell transcriptional response with machine learning
GOHTAM: a website for 'Genomic Origin of Horizontal Transfers, Alignment and Metagenomics'
Prediction of conserved long-range RNA-RNA interactions in full viral genomes
Informed k mer selection for de novo transcriptome assembly
Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins
DeepCEL0 for 2D single-molecule localization in fluorescence microscopy
coMOTIF: a mixture framework for identifying transcription factor and a coregulator motif in ChIP-seq Data
AITL: Adversarial Inductive Transfer Learning with input and output space adaptation for pharmacogenomics
Avoiding cross hybridization by choosing nonredundant targets on cDNA arrays
Realtime analysis and visualization of MinION sequencing data with npReader
Mugsy: fast multiple alignment of closely related whole genomes
Counting pseudoalignments to novel splicing events
STADEERS: a software package for the statistical design of experiments pertaining to the estimation of parameters in rate expressions that describe enzyme-catalyzed processes
MaskerAid : a performance enhancement to RepeatMasker
Automatic assignment of biomedical categories: toward a generic approach
Diametrical clustering for identifying anti-correlated gene clusters
A utility maximizing and privacy preserving approach for protecting kinship in genomic databases
Simulating efficiently the evolution of DNA sequences
Amplicon identification using SparsE representation of multiplex PYROsequencing signal (AdvISER-M-PYRO): application to bacterial resistance genotyping
Identify origin of replication in Saccharomyces cerevisiae using two-step feature selection technique
QDist-quartet distance between evolutionary trees
Software for microbial fingerprinting by means of the infrared spectra
Deep neural networks and distant supervision for geographic location mention extraction
Fast peak error correction algorithms for proteoform identification using top-down tandem mass spectra
Destin: toolkit for single-cell analysis of chromatin accessibility
Varmole: a biologically drop-connect deep neural network model for prioritizing disease risk variants and genes
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
HandAlign: Bayesian multiple sequence alignment, phylogeny and ancestral reconstruction
pyHVis3D: visualising molecular simulation deduced H-bond networks in 3D: application to T-cell receptor interactions
Libaffy: software for processing Affymetrix(R) GeneChip(R) data
Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data
De novo design of peptides and proteins: machine-generated sequences by the PROSA program
Target and biomarker exploration portal for drug discovery
SIAN: software for structural identifiability analysis of ODE models
Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L 2UniFrac
Needle: a fast and space-efficient prefilter for estimating the quantification of very large collections of expression experiments
An effective approach to the identification of subclones of a DNA of known nucleotide sequence
PCAP: probe choice and analysis package - a set of programs to aid in choosing synthetic oligomers for contig mapping
Topology independent structural matching discovers novel templates for protein interfaces
miRCat2: accurate prediction of plant and animal microRNAs from next-generation sequencing datasets
Simultaneous and exact interval estimates for the contrast of two groups based on an extremely high dimensional variable: application to mass spec data
Bioimaging-based detection of mislocalized proteins in human cancers by semi-supervised learning
GCUA: general codon usage analysis
Lipid-Pro: a computational lipid identification solution for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms
Casboundary: automated definition of integral Cas cassettes
ENTRAIN: integrating trajectory inference and gene regulatory networks with spatial data to co-localize the receptor-ligand interactions that specify cell fate
CITEdb: a manually curated database of cell-cell interactions in human
ISCB's initial reaction to New England Journal of Medicine editorial on data sharing
Predicting synergistic effects between compounds through their structural similarity and effects on transcriptomes
GWAF: an R package for genome-wide association analyses with family data
Dug: a semantic search engine leveraging peer-reviewed knowledge to query biomedical data repositories
AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network
Statistical lower bounds on protein copy number from fluorescence expression images
VIRULIGN: fast codon-correct alignment and annotation of viral genomes
Visualization of RNA secondary structures using highly parallel computers
UniSave: the UniProtKB Sequence/Annotation Version database
Automated detection and tracking of many cells by using 4D live-cell imaging data
scanPAV: a pipeline for extracting presence-absence variations in genome pairs
PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance
A comparative genome approach to marker ordering
CMap3D: a 3D visualization tool for comparative genetic maps
Evidence for the regulation of alternative splicing via complementary DNA sequence repeats
Local similarity analysis reveals unique associations among marine bacterioplankton species and environmental factors
JBASE: Joint Bayesian Analysis of Subphenotypes and Epistasis
A semantic web approach applied to integrative bioinformatics experimentation: a biological use case with genomics data
Protein contact map refinement for improving structure prediction using generative adversarial networks
Meta-MEME: motif-based hidden Markov models of protein families
BionoiNet: ligand-binding site classification with off-the-shelf deep neural network
RNAIndel: discovering somatic coding indels from tumor RNA-Seq data
Roundup 2.0: enabling comparative genomics for over 1800 genomes
Realizing privacy preserving genome-wide association studies
FLAS: fast and high-throughput algorithm for PacBio long-read self-correction
BioMake: a GNU make-compatible utility for declarative workflow management
Accelerating reaction-diffusion simulations with general-purpose graphics processing units
Dugong: a Docker image, based on Ubuntu Linux, focused on reproducibility and replicability for bioinformatics analyses
Pepper: cytoscape app for protein complex expansion using protein-protein interaction networks
Sparse Project VCF: efficient encoding of population genotype matrices
Algorithm and computer program Pro_Anal for analysis of relationship between structure and activity in a family of proteins or peptides
A geometric approach to determine association and coherence of the activation times of cell-cycling genes under differing experimental conditions
Model-based analysis of interferon-beta induced signaling pathway
TarHunter, a tool for predicting conserved microRNA targets and target mimics in plants
UNRES-GPU for physics-based coarse-grained simulations of protein systems at biological time- and size-scales
Network predicting drug's anatomical therapeutic chemical code
ReadXplorer - visualization and analysis of mapped sequences
Higher order methylation features for clustering and prediction in epigenomic studies
Prediction of disordered regions in proteins based on the meta approach
Detecting copy number alterations in RNA-Seq using SuperFreq
Dimension reduction methods for microarrays with application to censored survival data
Visual workflows for 13 C-metabolic flux analysis
OntoQuery: easy-to-use web-based OWL querying
pBRIT: gene prioritization by correlating functional and phenotypic annotations through integrative data fusion
RNASeq_similarity_matrix: visually identify sample mix-ups in RNASeq data using a 'genomic' sequence similarity matrix
Protein structural class identification directly from NMR spectra using averaged chemical shifts
HelixGAN a deep-learning methodology for conditional de novo design of α-helix structures
DxFormer: a decoupled automatic diagnostic system based on decoder-encoder transformer with dense symptom representations
Identification of consensus patterns in unaligned DNA sequences known to be functionally related
Identification of differential gene pathways with principal component analysis
rNA: a fast and accurate short reads numerical aligner
Large-scale extraction of brain connectivity from the neuroscientific literature
Accurate and efficient protein sequence design through learning concise local environment of residues
Improved topology prediction using the terminal hydrophobic helices rule
Struct2GO: protein function prediction based on graph pooling algorithm and AlphaFold2 structure information
WGE: a CRISPR database for genome engineering
AFid: a tool for automated identification and exclusion of autofluorescent objects from microscopy images
iCn3D, a web-based 3D viewer for sharing 1D/2D/3D representations of biomolecular structures
HUNER: improving biomedical NER with pretraining
PlasGUN: gene prediction in plasmid metagenomic short reads using deep learning
ProMSED: protein multiple sequence editor for Windows 3.11/95
The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data
ResiCon: a method for the identification of dynamic domains, hinges and interfacial regions in proteins
AlmostSignificant: simplifying quality control of high-throughput sequencing data
Semantic persistence of ambiguous biomedical names in the citation network
GM-DockZn: a geometry matching-based docking algorithm for zinc proteins
indelPost: harmonizing ambiguities in simple and complex indel alignments
Batch equalization with a generative adversarial network
Biologically inspired EM image alignment and neural reconstruction
TADtool: visual parameter identification for TAD-calling algorithms
DeepCOP: deep learning-based approach to predict gene regulating effects of small molecules
DISCOVER: a feature-based discriminative method for motif search in complex genomes
Quantitative densitometry of autoradiograms: digital images representative of optical density
RAD: a web application to identify region associated differentially expressed genes
Sigflow: an automated and comprehensive pipeline for cancer genome mutational signature analysis
Identifying viral integration sites using SeqMap 2.0
Identifiability and experimental design in perturbation studies
Search of periodicities in primary structure of biopolymers: a general Fourier approach
Protein secondary structure prediction by the analysis of variation and conservation in multiple alignments
EMVC-2: an efficient single-nucleotide variant caller based on expectation maximization
A probabilistic model for detecting rigid domains in protein structures
HyperAttentionDTI: improving drug-protein interaction prediction by sequence-based deep learning with attention mechanism
scPreGAN, a deep generative model for predicting the response of single-cell expression to perturbation
genomepy: genes and genomes at your fingertips
PREDAC-H3: a user-friendly platform for antigenic surveillance of human influenza a(H3N2) virus based on hemagglutinin sequences
Deep learning-based classification of breast cancer cells using transmembrane receptor dynamics
Extreme learning machines for reverse engineering of gene regulatory networks from expression time series
DECENT: differential expression with capture efficiency adjustmeNT for single-cell RNA-seq data
Efficient peptide-MHC-I binding prediction for alleles with few known binders
SNPchip : R classes and methods for SNP array data
tigre: Transcription factor inference through gaussian process reconstruction of expression for bioconductor
OWL2Perl: creating Perl modules from OWL class definitions
POPE - a tool to aid high-throughput phylogenetic analysis
Fast overlapping of protein contact maps by alignment of eigenvectors
Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models
specL - an R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics
ProCope - protein complex prediction and evaluation
STARS: statistics on inter-atomic distances and torsion angles in protein secondary structures
MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database
DeepAffinity: interpretable deep learning of compound-protein affinity through unified recurrent and convolutional neural networks
BioMolQuest: integrated database-based retrieval of protein structural and functional information
SEPA: signaling entropy-based algorithm to evaluate personalized pathway activation for survival analysis on pan-cancer data
PEITH(Θ): perfecting experiments with information theory in Python with GPU support
Towards clustering of incomplete microarray data without the use of imputation
Evaluation of haplotype-aware long-read error correction with hifieval
RnaViz 2: an improved representation of RNA secondary structure
JEnsembl: a version-aware Java API to Ensembl data systems
EcoPLOT: dynamic analysis of biogeochemical data
A comparative analysis of relative occurrence of transcription factor binding sites in vertebrate genomes and gene promoter areas
Assessing the application of Ka/Ks ratio test to alternatively spliced exons
Three-dimensional cardiovascular imaging-genetics: a mass univariate framework
ClinVAP: a reporting strategy from variants to therapeutic options
ExpEdit: a webserver to explore human RNA editing in RNA-Seq experiments
massXpert 2 : a cross-platform software environment for polymer chemistry modelling and simulation/analysis of mass spectrometric data
Bayesian modeling of spatial molecular profiling data via Gaussian process
fast_protein_cluster: parallel and optimized clustering of large-scale protein modeling data
Simple, rapid and accurate genotyping-by-sequencing from aligned whole genomes with ArrayMaker
PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance
SelSim: a program to simulate population genetic data with natural selection and recombination
Rseg - an R package to optimize segmentation of SNP array data
MoLPC2: improved prediction of large protein complex structures and stoichiometry using Monte Carlo Tree Search and AlphaFold2
Comparative analyses of population-scale phenomic data in electronic medical records reveal race-specific disease networks
Bacmeta: simulator for genomic evolution in bacterial metapopulations
The Michaelis-Menten equation: computing substrate concentration as a function of time without restrictions on the initial conditions
A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data
CRISPR-RT: a web application for designing CRISPR-C2c2 crRNA with improved target specificity
Fast and accurate inference of local ancestry in Latino populations
Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes
Effects of pooling mRNA in microarray class comparisons
Build a better bootstrap and the RAWR shall beat a random path to your door: phylogenetic support estimation revisited
PyFeat: a Python-based effective feature generation tool for DNA, RNA and protein sequences
TopNEXt: automatic DDA exclusion framework for multi-sample mass spectrometry experiments
TopicNet: a framework for measuring transcriptional regulatory network change
CARE: context-aware sequencing read error correction
An integrated computational approach for metabolic flux analysis coupled with inference of tandem-MS collisional fragments
Time-course network analysis reveals TNF-α can promote G 1 /S transition of cell cycle in vascular endothelial cells
MATE-CLEVER: Mendelian-inheritance-aware discovery and genotyping of midsize and long indels
JEPEGMIX: gene-level joint analysis of functional SNPs in cosmopolitan cohorts
SAMBA: hardware accelerator for biological sequence comparison
BridgeDPI: a novel Graph Neural Network for predicting drug-protein interactions
TROLL-Tandem Repeat Occurrence Locator
SLIMS - a user-friendly sample operations and inventory management system for genotyping labs
THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures
Treephyler: fast taxonomic profiling of metagenomes
Mendel-GPU: haplotyping and genotype imputation on graphics processing units
Deep learning for tumor classification in imaging mass spectrometry
scBatch: batch-effect correction of RNA-seq data through sample distance matrix adjustment
ABCGrid: Application for Bioinformatics Computing Grid
Functional annotation from predicted protein interaction networks
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence
Accelerating screening of 3D protein data with a graph theoretical approach
Protein backbone ensemble generation explores the local structural space of unseen natural homologs
<tt>Oarfish</tt>: enhanced probabilistic modeling leads to improved accuracy in long read transcriptome quantification
GREMA: modelling of emulated gene regulatory networks with confidence levels based on evolutionary intelligence to cope with the underdetermined problem
Unveiling new biological relationships using shared hits of chemical screening assay pairs
Correction to: SVJedi: genotyping structural variations with long reads
CrepHAN: cross-species prediction of enhancers by using hierarchical attention networks
RANKS : a flexible tool for node label ranking and classification in biological networks
Evaluating synteny for improved comparative studies
Complete enumeration of elementary flux modes through scalable demand-based subnetwork definition
icHET: interactive visualization of cytoplasmic heteroplasmy
Profile-based direct kernels for remote homology detection and fold recognition
Comprehensive large-scale assessment of intrinsic protein disorder
Advanced significance analysis of microarray data based on weighted resampling: a comparative study and application to gene deletions in Mycobacterium bovis
Corrigendum to: Probabilistic identification of bacterial essential genes via insertion density using TraDIS data with Tn5 libraries
PGDSpider: an automated data conversion tool for connecting population genetics and genomics programs
TIGA: target illumination GWAS analytics
MiPRIME: an integrated and intelligent platform for mining primer and probe sequences of microbial species
bioWidgets: data interaction components for genomics
parmigene - a parallel R package for mutual information estimation and gene network reconstruction
MetDAT: a modular and workflow-based free online pipeline for mass spectrometry data processing, analysis and interpretation
Estimates of allele-specific expression in Drosophila with a single genome sequence and RNA-seq data
Quality assessment for the putative intrinsic disorder in proteins
Metagene projection characterizes GEN2.2 and CAL-1 as relevant human plasmacytoid dendritic cell models
DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data
Analysis of differential splicing suggests different modes of short-term splicing regulation
Gaussian process regression bootstrapping: exploring the effects of uncertainty in time course data
HALO - a Java framework for precise transcript half-life determination
In silico fine-mapping: narrowing disease-associated loci by intergenomics
Optimal number of features as a function of sample size for various classification rules
End-to-end learning of multiple sequence alignments with differentiable Smith-Waterman
Pareto-optimal phylogenetic tree reconciliation
phRAIDER: Pattern-Hunter based Rapid Ab Initio Detection of Elementary Repeats
KinomeX: a web application for predicting kinome-wide polypharmacology effect of small molecules
CovidGraph: a graph to fight COVID-19
Low-homology protein threading
Reconstructing ribosomal genes from large scale total RNA meta-transcriptomic data
An algorithm for analysing probed partial digestion experiments
DDGemb: predicting protein stability change upon single- and multi-point variations with embeddings and deep learning
The NanoFlow Repository
Tumor heterogeneity assessed by sequencing and fluorescence in situ hybridization (FISH) data
A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
Bioinformatics in structural genomics - Editorial
Supertree algorithms for ancestral divergence dates and nested taxa
PRED-TMBB2: improved topology prediction and detection of beta-barrel outer membrane proteins
Genetdes: automatic design of transcriptional networks
RAINFOREST: a random forest approach to predict treatment benefit in data from (failed) clinical drug trials