yusuke1997/dblp-id-title huggingface dataset:
YADA: a tool for taking the most out of high-resolution spectra
Pythoscape: a framework for generation of large protein similarity networks
Cancer classification of single-cell gene expression data by neural network
Mechanisms to protect the privacy of families when using the transmission disequilibrium test in genome-wide association studies
Snowball: resampling combined with distance-based regression to discover transcriptional consequences of a driver mutation
Combining multiple positive training sets to generate confidence scores for protein-protein interactions
Prediction of histone post-translational modifications using deep learning
SScore : an R package for detecting differential gene expression without gene expression summaries
JBrowseR: an R interface to the JBrowse 2 genome browser
KABOOM! A new suffix array based algorithm for clustering expression data
Mutual learning for joint disease detection and severity prediction reveals multimodal pathogenesis for neurodegenerative disorders
Method for identifying transcription factor binding sites in yeast
Large scale genotype-phenotype correlation analysis based on phylogenetic trees
Preserving full spectrum information in imaging mass spectrometry data reduction
BEST: Binding-site Estimation Suite of Tools
TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types
GBPARSE: a parser for the GenBank flat-file format with the new feature table format
KG-Hub - building and exchanging biological knowledge graphs
Simultaneous modeling of pharmacokinetics and pharmacodynamics: an improved algorithm
MEDELLER: homology-based coordinate generation for membrane proteins
Multiple Alignment of protein structures and sequences for VMD
PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures
CoRC: the COPASI R Connector
SMI-BLAST: a novel supervised search framework based on PSI-BLAST for protein remote homology detection
Mclip: motif detection based on cliques of gapped local profile-to-profile alignments
An assessment of the uses of homologous interactions
ACPred-FL: a sequence-based predictor using effective feature representation to improve the prediction of anti-cancer peptides
Multiple sequence alignment with user-defined constraints at GOBICS
Modeling clinical and molecular covariates of mutational process activity in cancer
R PheWAS: data analysis and plotting tools for phenome-wide association studies in the R environment
APTANI: a computational tool to select aptamers through sequence-structure motif analysis of HT-SELEX data
Use of within-array replicate spots for assessing differential expression in microarray experiments
Automated tracking and analysis of centrosomes in early Caenorhabditis elegans embryos
Classifying short gene expression time-courses with Bayesian estimation of piecewise constant functions
A robust model for read count data in exome sequencing experiments and implications for copy number variant calling
A framework for analytical characterization of monoclonal antibodies based on reactivity profiles in different tissues
Corrigendum to: ASpli: Integrative analysis of splicing landscapes through RNA-Seq assays
Accurate peptide fragmentation predictions allow data driven approaches to replace and improve upon proteomics search engine scoring functions
PAMOGK: a pathway graph kernel-based multiomics approach for patient clustering
Gaussian interaction profile kernels for predicting drug-target interaction
Omics community detection using multi-resolution clustering
Modeling and predicting transcriptional units of <$O_SSF>Escherichia coli<$C_SSF>genes using hidden Markov models
GBOOST: a GPU-based tool for detecting gene-gene interactions in genome-wide case control studies
flowLearn: fast and precise identification and quality checking of cell populations in flow cytometry
scTIM: seeking cell-type-indicative marker from single cell RNA-seq data by consensus optimization
PRALINE TM : a strategy for improved multiple alignment of transmembrane proteins
LDassoc: an online tool for interactively exploring genome-wide association study results and prioritizing variants for functional investigation
FAVA: high-quality functional association networks inferred from scRNA-seq and proteomics data
Classification of protein quaternary structure with support vector machine
Meshable : searching PubMed abstracts by utilizing MeSH and MeSH-derived topical terms
SimSCSnTree: a simulator of single-cell DNA sequencing data
Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information
Integrative Metabolic-Flux Platform for Analysis, Contextualization, and Targeting (IMPACT): bridging untargeted and targeted flux analysis
Simulation-assisted machine learning
Molecular signatures-based prediction of enzyme promiscuity
Cellsnp-lite: an efficient tool for genotyping single cells
Deep mining heterogeneous networks of biomedical linked data to predict novel drug-target associations
Utility library for structural bioinformatics
Vaeda computationally annotates doublets in single-cell RNA sequencing data
Multi-locus match probability in a finite population: a fundamental difference between the Moran and Wright-Fisher models
A web application for the unspecific detection of differentially expressed DNA regions in strand-specific expression data
Joint learning dimension reduction and clustering of single-cell RNA-sequencing data
Breakpoint identification and smoothing of array comparative genomic hybridization data
OligoFaktory: a visual tool for interactive oligonucleotide design
Population-scale detection of non-reference sequence variants using colored de Bruijn graphs
BioQuery: An Object Framework for Building Queries to Biomedical Databases
Scaling read aligners to hundreds of threads on general-purpose processors
NGSView: an extensible open source editor for next-generation sequencing data
Regression analysis for comparing protein samples with 16 O/ 18 O stable-isotope labeled mass spectrometry
ASICS: an R package for a whole analysis workflow of 1D 1H NMR spectra
The caBIG® Life Science Business Architecture Model
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data
ITM Probe: analyzing information flow in protein networks
Genome Visualization Made Fast and Simple
Badger - an accessible genome exploration environment
Clustering of change patterns using Fourier coefficients
A novel method for automatic functional annotation of proteins
FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking
VANO: a volume-object image annotation system
Network-based integration of multi-omics data for prioritizing cancer genes
TFBScluster: a resource for the characterization of transcriptional regulatory networks
DeepMHCII: a novel binding core-aware deep interaction model for accurate MHC-II peptide binding affinity prediction
HierCC: a multi-level clustering scheme for population assignments based on core genome MLST
IsoResolve: predicting splice isoform functions by integrating gene and isoform-level features with domain adaptation
Discovery of multi-operon colinear syntenic blocks in microbial genomes
TASIC: determining branching models from time series single cell data
Querying multiple sets of P-values through composed hypothesis testing
NeuroPID: a predictor for identifying neuropeptide precursors from metazoan proteomes
StrBioLib: a Java library for development of custom computational structural biology applications
An effective statistical evaluation of ChIPseq dataset similarity
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis
AttOmics: attention-based architecture for diagnosis and prognosis from omics data
Evaluation of the gene-specific dye bias in cDNA microarray experiments
CSO validator: improving manual curation workflow for biological pathways
bwtool: a tool for bigWig files
EuGene: maximizing synthetic gene design for heterologous expression
Unsupervised technique for robust target separation and analysis of DNA microarray spots through adaptive pixel clustering
Annotation of tandem mass spectrometry data using stochastic neural networks in shotgun proteomics
Finite mixtures of matrix variate Poisson-log normal distributions for three-way count data
Fast gap-affine pairwise alignment using the wavefront algorithm
Greedy method for inferring tandem duplication history
STRING: finding tandem repeats in DNA sequences
mzML2ISA & nmrML2ISA: generating enriched ISA-Tab metadata files from metabolomics XML data
LogoJS: a Javascript package for creating sequence logos and embedding them in web applications
LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor
MGEScan: a Galaxy-based system for identifying retrotransposons in genomes
Comparing co-evolution methods and their application to template-free protein structure prediction
A correction for estimating error when using the Local Pooled Error Statistical Test
InterPro-an integrated documentation resource for protein families, domains and functional sites
Sensitivity, principal component and flux analysis applied to signal transduction: the case of epidermal growth factor mediated signaling
APART: Automated Preprocessing for NMR Assignments with Reduced Tedium
Subnetwork hierarchies of biochemical pathways
A novel structural position-specific scoring matrix for the prediction of protein secondary structures
An efficient algorithm for the extraction of HGVS variant descriptions from sequences
Lean and deep models for more accurate filtering of SNP and INDEL variant calls
PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
Fitting a geometric graph to a protein-protein interaction network
Correction to: KR4SL: knowledge graph reasoning for explainable prediction of synthetic lethality
In search of the small ones: improved prediction of short exons in vertebrates, plants, fungi and protists
Methods for evaluating exon-protein correspondences
A new way to protect privacy in large-scale genome-wide association studies
Quantifying reproducibility for differential proteomics: noise analysis for protein liquid chromatography-mass spectrometry of human serum
Phitest for analyzing the homogeneity of single-cell populations
TiQuant: software for tissue analysis, quantification and surface reconstruction
RNF: a general framework to evaluate NGS read mappers
Coupled Two-way Clustering Analysis of Breast Cancer and Colon Cancer Gene Expression Data
A scalable method for parameter identification in kinetic models of metabolism using steady-state data
ImagePy: an open-source, Python-based and platform-independent software package for bioimage analysis
shinyCircos: an R/Shiny application for interactive creation of Circos plot
Representing mutations for predicting cancer drug response
Iterative feature representations improve N4-methylcytosine site prediction
Improving the performance and interpretability on medical datasets using graphical ensemble feature selection
PolishEM: image enhancement in FIB-SEM
GR-Align: fast and flexible alignment of protein 3D structures using graphlet degree similarity
Efficient similarity search in protein structure databases by k-clique hashing
Analysis of CFSE time-series data using division-, age- and label-structured population models
MorphOT: transport-based interpolation between EM maps with UCSF ChimeraX
Accurate deep learning off-target prediction with novel sgRNA-DNA sequence encoding in CRISPR-Cas9 gene editing
Predicting post-translational lysine acetylation using support vector machines
Compressed indexing and local alignment of DNA
Supervised learning is an accurate method for network-based gene classification
Trowel: a fast and accurate error correction module for Illumina sequencing reads
The necessity of adjusting tests of protein category enrichment in discovery proteomics
On the biases in predictions of protein stability changes upon variations: the INPS test case
spatialTIME and iTIME: R package and Shiny application for visualization and analysis of immunofluorescence data
DL4papers: a deep learning approach for the automatic interpretation of scientific articles
Effects of spaced k-mers on alignment-free genotyping
Optimal algorithms for haplotype assembly from whole-genome sequence data
SplAdder : identification, quantification and testing of alternative splicing events from RNA-Seq data
MolDy: molecular dynamics simulation made easy
Gaining confidence in biological interpretation of the microarray data: the functional consistence of the significant GO categories
Haloferax volcanii PitA: an example of functional interaction between the Pfam chlorite dismutase and antibiotic biosynthesis monooxygenase families?
AFRESh: an adaptive framework for compression of reads and assembled sequences with random access functionality
ExScript: An 'EX'-Centric Approach to the Description of Transcript Diversity
Privacy-preserving and robust watermarking on sequential genome data using belief propagation and local differential privacy
CTX-BLAST: context sensitive version of protein BLAST
Supervised identification of allergen-representative peptides for in silico detection of potentially allergenic proteins
M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci
Cas-Database: web-based genome-wide guide RNA library design for gene knockout screens using CRISPR-Cas9
Flavitrack: an annotated database of flavivirus sequences
TargetFinder: a software for antisense oligonucleotide target site selection based on MAST and secondary structures of target mRNA
Combining evidence using p-values: application to sequence homology searches
BEM: Mining Coregulation Patterns in Transcriptomics via Boolean Matrix Factorization
Cardinality optimization in constraint-based modelling: application to human metabolism
NdPASA: a pairwise sequence alignment server for distantly related proteins
Accurate spliced alignment of long RNA sequencing reads
DeepSF: deep convolutional neural network for mapping protein sequences to folds
ALIGNSEC: viewing protein secondary structure predictions within large multiple sequence alignments
Deep-learning method for data association in particle tracking
Cellular phenotype database: a repository for systems microscopy data
Prediction of protein secondary structure using the 3D-1D compatibility algorithm
MetaCoMET: a web platform for discovery and visualization of the core microbiome
Computation of recurrent minimal genomic alterations from array-CGH data
Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures
Chimera: a Bioconductor package for secondary analysis of fusion products
Predicting homologous signaling pathways using machine learning
pyRMSD: a Python package for efficient pairwise RMSD matrix calculation and handling
A Pascal microcomputer program for prediction of protein secondary structure and hydropathic segments
A genetic algorithm for designing gene family-specific oligonucleotide sets used for hybridization: the G protein-coupled receptor protein superfamily
A new statistic for identifying batch effects in high-throughput genomic data that uses guided principal component analysis
Automated classification of alternative splicing and transcriptional initiation and construction of visual database of classified patterns
Identifying associations between amino acid changes and meta information in alignments
Z extensions to the RHMAPPER package
Interactive and fuzzy search: a dynamic way to explore MEDLINE
Gencrypt: one-way cryptographic hashes to detect overlapping individuals across samples
libSBOLj3: a graph-based library for design and data exchange in synthetic biology
A geometric approach for classification and comparison of structural variants
Guide tree optimization with genetic algorithm to improve multiple protein 3D-structure alignment
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions
High-performance hardware implementation of a parallel database search engine for real-time peptide mass fingerprinting
Structural genomics meets computational biology
SJARACNe: a scalable software tool for gene network reverse engineering from big data
MPRAscore: robust and non-parametric analysis of massively parallel reporter assays
A new representation of protein structure: vector diagram
PipeVal: light-weight extensible tool for file validation
COMPASS : a program for generating serial samples under an infinite sites model
Using 2 k + 2 bubble searches to find single nucleotide polymorphisms in k -mer graphs
HiSpOD: probe design for functional DNA microarrays
Q-Gene: Processing Quantitative Real-time RT-PCR Data
PdbAlign, PdbDist and DistAlign: tools to aid in relating sequence variability to structure
Response to comment on 'Can sugars be produced from fatty acids? A test case for pathway analysis tools'
DeepSymmetry: using 3D convolutional networks for identification of tandem repeats and internal symmetries in protein structures
DOCKGROUND protein-protein docking decoy set
DendroPy: a Python library for phylogenetic computing
cMap: the comparative genetic map viewer
Molecular causes of transcriptional response: a Bayesian prior knowledge approach
SQC: secure quality control for meta-analysis of genome-wide association studies
Pybedtools: a flexible Python library for manipulating genomic datasets and annotations
Doing sequence analysis with your printer
Deconvolution of multiple infections in Plasmodium falciparum from high throughput sequencing data
Robust Cluster Analysis of Microarray Gene Expression Data with the Number of Clusters Determined Biologically
Predicting phenotypes from microarrays using amplified, initially marginal, eigenvector regression
HAMdetector: a Bayesian regression model that integrates information to detect HLA-associated mutations
Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR
Embed-Search-Align: DNA sequence alignment using Transformer models
MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments
Annotation-Modules: a tool for finding significant combinations of multisource annotations for gene lists
Quantitative trait association study for mean telomere length in the South Asian genomes
Infernal 1.1: 100-fold faster RNA homology searches
pathSCOUTTM: exploration and analysis of biochemical pathways
Improving protein function prediction using protein sequence and GO-term similarities
HHfrag: HMM-based fragment detection using HHpred
PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools
SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction
Novel algorithms for efficient subsequence searching and mapping in nanopore raw signals towards targeted sequencing
fmcsR: mismatch tolerant maximum common substructure searching in R
ENViz: a Cytoscape App for integrated statistical analysis and visualization of sample-matched data with multiple data types
Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins
Modeling the interplay of single-stranded binding proteins and nucleic acid secondary structure
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
Integrating genome assemblies with MAIA
Varanto: variant enrichment analysis and annotation
Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment
Corpus domain effects on distributional semantic modeling of medical terms
Robust smooth segmentation approach for array CGH data analysis
LipiDisease: associate lipids to diseases using literature mining
Constraining volume by matching the moments of a distance distribution
Bio3d: an R package for the comparative analysis of protein structures
MUGAN: multi-GPU accelerated AmpliconNoise server for rapid microbial diversity assessment
Large-scale automated identification of mouse brain cells in confocal light sheet microscopy images
QuasiSeq: profiling viral quasispecies via self-tuning spectral clustering with PacBio long sequencing reads
Graphical interface to the genetic network database GeNet
rnaCrosslinkOO: an object-oriented R package for the analysis of RNA structural data generated by RNA crosslinking experiments
RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling
Comment on 'Bayesian parentage analysis with systematic accountability of genotyping error, missing data and false matching'
Identification of drug-target interaction from interactome network with 'guilt-by-association' principle and topology features
Detection of cis -element clusters in higher eukaryotic DNA
EcoTransLearn: an R-package to easily use transfer learning for ecological studies - a plankton case study
Computational identification of MoRFs in protein sequences
Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation
Analyzing genome coverage profiles with applications to quality control in metagenomics
Phage display can select over-hydrophobic sequences that may impair prediction of natural domain-peptide interactions
CoCoNet: an efficient deep learning tool for viral metagenome binning
Statistical test of structured continuous trees based on discordance matrix
HybridNET: a tool for constructing hybridization networks
CoNtRol: an open source framework for the analysis of chemical reaction networks
Origins of introns based on the definition of exon modules and their conserved interfaces
Clustering-based model of cysteine co-evolution improves disulfide bond connectivity prediction and reduces homologous sequence requirements
Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus
Scoring-and-unfolding trimmed tree assembler: concepts, constructs and comparisons
MetalPredator: a web server to predict iron-sulfur cluster binding proteomes
Machaon CVE: cluster validation for gene expression data
An efficient framework to identify key miRNA-mRNA regulatory modules in cancer
Thermodynamic database for protein-nucleic acid interactions (ProNIT)
The art of pedigree drawing: algorithmic aspects
EasyModel: user-friendly tool for building and analysis of simple mathematical models in systems biology
GAVISUNK: genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
A bacterial identification teaching exercise revisited
Scope+: an open source generalizable architecture for single-cell RNA-seq atlases at sample and cell levels
UEP: an open-source and fast classifier for predicting the impact of mutations in protein-protein complexes
MetaBridge: enabling network-based integrative analysis via direct protein interactors of metabolites
Automatic extension of Gene Ontology with flexible identification of candidate terms
LocTree2 predicts localization for all domains of life
Looking at the BiG picture: incorporating bipartite graphs in drug response prediction
Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy
Dhaka: variational autoencoder for unmasking tumor heterogeneity from single cell genomic data
The adapted Activity-By-Contact model for enhancer-gene assignment and its application to single-cell data
SYNBADm: a tool for optimization-based automated design of synthetic gene circuits
HiLive: real-time mapping of illumina reads while sequencing
DeepGenGrep: a general deep learning-based predictor for multiple genomic signals and regions
DnaSP, DNA polymorphism analyses by the coalescent and other methods
An extended IUPAC nomenclature code for polymorphic nucleic acids
PHAT: a transmembrane-specific substitution matrix
U-PASS: unified power analysis and forensics for qualitative traits in genetic association studies