yusuke1997/dblp-id-title huggingface dataset:
RSCanner: rapid assessment and visualization of RNA structure content
Robust method for detecting differential gene expression in twin studies
QuickTree: building huge Neighbour-Joining trees of protein sequences
A microcomputer program for hydropathic analysis of proteins with I/O through word processing and graphics software
PLiSAGE: enhancing protein-ligand interaction prediction with multimodal surface and geometry encoding
An ensemble approach to microarray data-based gene prioritization after missing value imputation
Identification of coding and non-coding sequences using local Hölder exponent formalism
VisuaLife: library for interactive visualization in rich web applications
Identification of a set of frequent decanucleotides in plants and in animals
UCSC Data Integrator and Variant Annotation Integrator
MASCOT: parameter and state inference under the marginal structured coalescent approximation
BioVLAB-Cancer-Pharmacogenomics: tumor heterogeneity and pharmacogenomics analysis of multi-omics data from tumor on the cloud
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis
Detecting differential binding of transcription factors with ChIP-seq
RNAseqViewer: visualization tool for RNA-Seq data
A global pathway crosstalk network
Mining single-cell time-series datasets with Time Course Inspector
OmicBrowse: a browser of multidimensional omics annotations
vbmp: Variational Bayesian Multinomial Probit Regression for multi-class classification in R
A data-mining approach to spacer oligonucleotide typing of Mycobacterium tuberculosis
Protein backbone angle prediction with machine learning approaches
Use of autocorrelation scanning in DNA copy number analysis
Genome-wide scans for selective sweeps using convolutional neural networks
TimesVector: a vectorized clustering approach to the analysis of time series transcriptome data from multiple phenotypes
Testing the hypothesis of tissue selectivity: the intersection-union test and a Bayesian approach
GIM 3 E: condition-specific models of cellular metabolism developed from metabolomics and expression data
bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby
Estimating transcription factor bindability on DNA
ESA-UbiSite: accurate prediction of human ubiquitination sites by identifying a set of effective negatives
De novo meta-assembly of ultra-deep sequencing data
Locating well-conserved regions within a pairwise alignment
DeNovo: virus-host sequence-based protein-protein interaction prediction
An open-source high-content analysis workflow for CFTR function measurements using the forskolin-induced swelling assay
purgeR: inbreeding and purging in pedigreed populations
RNAscClust: clustering RNA sequences using structure conservation and graph based motifs
A coherent feedforward loop design principle to sustain robustness of biological networks
EnrichNet: network-based gene set enrichment analysis
PASS: a program to align short sequences
Forward-time simulations of non-random mating populations using simuPOP
SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP
Editor's Choice: SNP-SIG 2013: the state of the art of genomic variant interpretation
Fluorescent color factor calculation using dBASE-II
HEMDAG: a family of modular and scalable hierarchical ensemble methods to improve Gene Ontology term prediction
BCdatabaser: on-the-fly reference database creation for (meta-)barcoding
Bastion3: a two-layer ensemble predictor of type III secreted effectors
The Chemical Translation Service - a web-based tool to improve standardization of metabolomic reports
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0
CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences
Identify, quantify and characterize cellular communication from single-cell RNA sequencing data with scSeqComm
IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing
Finding the direct optimal RNA barrier energy and improving pathways with an arbitrary energy model
MIAMI: mutual information-based analysis of multiplex imaging data
DCA: an efficient implementation of the divide-and-conquer approach to simultaneous multiple sequence alignment
Semantic integration of data on transcriptional regulation
ROAST: rotation gene set tests for complex microarray experiments
NRStitcher: non-rigid stitching of terapixel-scale volumetric images
GADGETS: a genetic algorithm for detecting epistasis using nuclear families
Quantitative analysis of one-dimensional gel electrophoresis profiles
H-PoP and H-PoPG: heuristic partitioning algorithms for single individual haplotyping of polyploids
CLAMMS: a scalable algorithm for calling common and rare copy number variants from exome sequencing data
CircSI-SSL: circRNA-binding site identification based on self-supervised learning
Thermodynamically consistent estimation of Gibbs free energy from data: data reconciliation approach
Jutils: a visualization toolkit for differential alternative splicing events
Adaptive one-class Gaussian processes allow accurate prioritization of oncology drug targets
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
Systematic intervention of transcription for identifying network response to disease and cellular phenotypes
Simultaneous alignment and annotation of cis -regulatory regions
Insights from incorporating quantum computing into drug design workflows
EDIR: exome database of interspersed repeats
Detecting and quantifying antibody reactivity in PhIP-Seq data with BEER
The role of CpG island methylator phenotype in the clinical course of hepatocellular carcinoma
In Response to Comment on "Network-constrained regularization and variable selection for analysis of genomic data"
MEME-LaB: motif analysis in clusters
SpliceAid: a database of experimental RNA target motifs bound by splicing proteins in humans
ePCR: an R-package for survival and time-to-event prediction in advanced prostate cancer, applied to real-world patient cohorts
Multifunctional proteins revealed by overlapping clustering in protein interaction network
Bayesian information sharing enhances detection of regulatory associations in rare cell types
dbGSH: a database of S -glutathionylation
A Boolean algebra for genetic variants
Assessing allele-specific expression across multiple tissues from RNA-seq read data
PreTP-2L: identification of therapeutic peptides and their types using two-layer ensemble learning framework
COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data
Inferring population history with DIY ABC : a user-friendly approach to approximate Bayesian computation
AutoBind: automatic extraction of protein-ligand-binding affinity data from biological literature
Quantifying uniformity of mapped reads
PICKLE 3.0: enriching the human meta-database with the mouse protein interactome extended via mouse-human orthology
Computationally feasible estimation of haplotype frequencies from pooled DNA with and without Hardy-Weinberg equilibrium
PAQ: Partition Analysis of Quasispecies
A fast machine learning dataloader for epigenetic tracks from BigWig files
SoDA2: a Hidden Markov Model approach for identification of immunoglobulin rearrangements
Fast and accurate prediction of partial charges using Atom-Path-Descriptor-based machine learning
Prediction of gene expression using histone modification patterns extracted by Particle Swarm Optimization
snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package
AliasServer: a web server to handle multiple aliases used to refer to proteins
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood
CICLOP: a robust and accurate computational framework for protein inner cavity detection
REPETITA: detection and discrimination of the periodicity of protein solenoid repeats by discrete Fourier transform
Evaluation of computational metabolic-pathway predictions for Helicobacter pylori
'Non-destructive' biocomputing security system based on gas-controlled biofuel cell and potentially used for intelligent medical diagnostics
Gene expression trends and protein features effectively complement each other in gene function prediction
Analysis of mass spectral serum profiles for biomarker selection
AGenDA: homology-based gene prediction
multiHiCcompare: joint normalization and comparative analysis of complex Hi-C experiments
STREAM: Static Thermodynamic REgulAtory Model of transcription
Docking cyclic peptides formed by a disulfide bond through a hierarchical strategy
MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes
Ramachandran plot on the web
A multi-objective optimization approach accurately resolves protein domain architectures
Density-based binning of gene clusters to infer function or evolutionary history using GeneGrouper
Joint analysis of expression profiles from multiple cancers improves the identification of microRNA-gene interactions
D3NER: biomedical named entity recognition using CRF-biLSTM improved with fine-tuned embeddings of various linguistic information
MsQuality: an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data
Identifying and removing haplotypic duplication in primary genome assemblies
TSSi - an R package for transcription start site identification from 5′ mRNA tag data
AStream: an R package for annotating LC/MS metabolomic data
An NMR assignment module implemented in the Gifa NMR processing program
PHYLUCE is a software package for the analysis of conserved genomic loci
SNPxGE 2 : a database for human SNP-coexpression associations
EGM: encapsulated gene-by-gene matching to identify gene orthologs and homologous segments in genomes
scHiCDiff: detecting differential chromatin interactions in single-cell Hi-C data
A combined recall and rank framework with online negative sampling for Chinese procedure terminology normalization
Automatic updating of the EMBL database via EMBNet
A noise model for mass spectrometry based proteomics
NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes
DrawTetrado to create layer diagrams of G4 structures
Dizzy-Beats: a Bayesian evidence analysis tool for systems biology
Domain-oriented edge-based alignment of protein interaction networks
AGML Central: web based gel proteomic infrastructure
Representation transfer for differentially private drug sensitivity prediction
Theory and reality for software patents: good in concept, not so good in practice
Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction and a library interface
MILES: a Java tool to extract node-specific enriched subgraphs in biomolecular networks
STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis
Automatic DNA replication tract measurement to assess replication and repair dynamics at the single-molecule level
Fast construction of FM-index for long sequence reads
Iterative Correction of Reference Nucleotides (iCORN) using second generation sequencing technology
COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks
Flexible structural protein alignment by a sequence of local transformations
ESPRESSO: taking into account assessment errors on outcome and exposures in power analysis for association studies
WMDS.net: a network control framework for identifying key players in transcriptome programs
AntigenMap 3D: an online antigenic cartography resource
Machine learning for classifying tuberculosis drug-resistance from DNA sequencing data
Condensing biomedical journal texts through paragraph ranking
Improved genomic island predictions with IslandPath-DIMOB
HYSYS: have you swapped your samples?
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
PPAD: a deep learning architecture to predict progression of Alzheimer's disease
SSpro/ACCpro 6: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, deep learning and structural similarity
Leveraging the structure of the Semantic Web to enhance information retrieval for proteomics
CyDAS: a cytogenetic data analysis system
Predicting promoters in phage genomes using PhagePromoter
simuPOP: a forward-time population genetics simulation environment
Systematic component selection for gene-network refinement
Protein-ligand binding residue prediction enhancement through hybrid deep heterogeneous learning of sequence and structure data
FL-QSAR: a federated learning-based QSAR prototype for collaborative drug discovery
Fast pairwise IBD association testing in genome-wide association studies
Detecting genome-wide epistases based on the clustering of relatively frequent items
PEPerMINT: peptide abundance imputation in mass spectrometry-based proteomics using graph neural networks
Tissue-specific pathway association analysis using genome-wide association study summaries
CRISPI: a CRISPR interactive database
img2net: automated network-based analysis of imaged phenotypes
Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins
ParaMEME: a parallel implementation and a web interface for a DNA and protein motif discovery tool
EthSEQ: ethnicity annotation from whole exome sequencing data
LDA - a java-based linkage disequilibrium analyzer
WebVar: a resource for the rapid estimation of relative site variability from multiple sequence alignments
SpatialDDLS: an R package to deconvolute spatial transcriptomics data using neural networks
DIGREM: an integrated web-based platform for detecting effective multi-drug combinations
Constructing maps between distinct cell fates and parametric conditions by systematic perturbations
RNA secondary structure prediction using highly parallel computers
Human variation database: an open-source database template for genomic discovery
GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression data
CanMethdb: a database for genome-wide DNA methylation annotation in cancers
Using state machines to model the Ion Torrent sequencing process and to improve read error rates
MapView: visualization of short reads alignment on a desktop computer
GeneTree: comparing gene and species phylogenies using reconciled trees
Optimization of co-evolution analysis through phylogenetic profiling reveals pathway-specific signals
Reliability of algorithmic somatic copy number alteration detection from targeted capture data
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide
YETI: Yeast Exploration Tool Integrator
The RNA Newton polytope and learnability of energy parameters
Improving B-cell epitope prediction and its application to global antibody-antigen docking
Rapid motif-based prediction of circular permutations in multi-domain proteins
A calibration method for estimating absolute expression levels from microarray data
Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency
Machine learning accelerates MD-based binding pose prediction between ligands and proteins
Predicting proteolytic sites in extracellular proteins: only halfway there
A cluster validity framework for genome expression data
Two computer programs for rapid entry of DNA sequence data
Haploview: analysis and visualization of LD and haplotype maps
MicroRNA identification based on sequence and structure alignment
The joint distribution of patterns in random sequences with application to the RC-measure for expressivity
BIPSPI: a method for the prediction of partner-specific protein-protein interfaces
Theoretical and practical advances in genome halving
A simple yet accurate correction for winner's curse can predict signals discovered in much larger genome scans
NetExplore: a web server for modeling small network motifs
Identification, semantic annotation and comparison of combinations of functional elements in multiple biological conditions
DDBASE2.0: updated domain database with improved identification of structural domains
Patch-DCA: improved protein interface prediction by utilizing structural information and clustering DCA scores
ComplexViewer: visualization of curated macromolecular complexes
GeneCOST: a novel scoring-based prioritization framework for identifying disease causing genes
GARD: a genetic algorithm for recombination detection
RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree
SEQualyzer: interactive tool for quality control and exploratory analysis of high-throughput RNA structural profiling data
PEAKS: identification of regulatory motifs by their position in DNA sequences
TemStaPro: protein thermostability prediction using sequence representations from protein language models
EDGE: extraction and analysis of differential gene expression
SignalSpider: probabilistic pattern discovery on multiple normalized ChIP-Seq signal profiles
A new method to study the change of miRNA-mRNA interactions due to environmental exposures
SeWeR: a customizable and integrated dynamic HTML interface to bioinformatics services
GPSmatch: an R package for comparing Genomic-binding Profile Similarity among transcriptional regulators using customizable databases
ESPD: a pattern detection model underlying gene expression profiles
Graph-based data integration from bioactive peptide databases of pharmaceutical interest: toward an organized collection enabling visual network analysis
Detecting evolutionary patterns of cancers using consensus trees
A benchmark study of scoring methods for non-coding mutations
CAM3.0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution
DeepLUCIA: predicting tissue-specific chromatin loops using Deep Learning-based Universal Chromatin Interaction Annotator
Classification of protein sequences by their dipeptide composition
DDAP: docking domain affinity and biosynthetic pathway prediction tool for type I polyketide synthases
A causal inference approach for constructing transcriptional regulatory networks
Variant Library Annotation Tool (VaLiAnT): an oligonucleotide library design and annotation tool for saturation genome editing and other deep mutational scanning experiments
Toward heterogeneous information fusion: bipartite graph convolutional networks for in silico drug repurposing
Erratum to: GADGETS: a genetic algorithm for detecting epistasis using nuclear families
RNA-SeQC: RNA-seq metrics for quality control and process optimization
SomaticSiMu: a mutational signature simulator
PStrain: an iterative microbial strains profiling algorithm for shotgun metagenomic sequencing data
TENET: topological feature-based target characterization in signalling networks
ModeRNA server: an online tool for modeling RNA 3D structures
PyCorrFit - generic data evaluation for fluorescence correlation spectroscopy
scSemiGAN: a single-cell semi-supervised annotation and dimensionality reduction framework based on generative adversarial network
RBT - a tool for building refined Buneman trees
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
Ribostral: an RNA 3D alignment analyzer and viewer based on basepair isostericities
A dynamic Bayesian network for identifying protein-binding footprints from single molecule-based sequencing data
rHVDM: an R package to predict the activity and targets of a transcription factor
Optimization method for obtaining nearest-neighbour DNA entropies and enthalpies directly from melting temperatures
MR-Tandem: parallel X!Tandem using Hadoop MapReduce on Amazon Web Services
sc-PDB: a database for identifying variations and multiplicity of 'druggable' binding sites in proteins
Testing clonal relatedness of two tumors from the same patient based on their mutational profiles: update of the Clonality R package
MrBayes 3: Bayesian phylogenetic inference under mixed models
ViQuaS: an improved reconstruction pipeline for viral quasispecies spectra generated by next-generation sequencing
A computational genomics pipeline for prokaryotic sequencing projects
On distance and similarity in fold space
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance
Spectrum: spectral analysis of phylogenetic data
<tt>Crypt4GH-JS</tt>: securely storing sensitive data online with client-side encryption
Predicting runtimes of bioinformatics tools based on historical data: five years of Galaxy usage
SP-DTI: subpocket-informed transformer for drug-target interaction prediction
Mycorrhiza: genotype assignment using phylogenetic networks
Analyzing time series gene expression data
A novel measure of non-coding genome conservation identifies genomic regulatory blocks within primates
Automated generation and refinement of protein signatures: case study with G-protein coupled receptors
ASES: visualizing evolutionary conservation of alternative splicing in proteins
Network-based pathway enrichment analysis with incomplete network information
Kernel approaches for genic interaction extraction
Network neighborhood analysis with the multi-node topological overlap measure
HitWalker: variant prioritization for personalized functional cancer genomics
Cassis: detection of genomic rearrangement breakpoints
Batch mode generation of residue-based diagrams of proteins
SSL-VQ: vector-quantized variational autoencoders for semi-supervised prediction of therapeutic targets across diverse diseases
PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra
The Russian Drug Reaction Corpus and neural models for drug reactions and effectiveness detection in user reviews
The TMCrys server for supporting crystallization of transmembrane proteins
A combinatorial approach for analyzing intra-tumor heterogeneity from high-throughput sequencing data
The Physiome Model Repository 2
SCL: a lattice-based approach to infer 3D chromosome structures from single-cell Hi-C data
A subpopulation model to analyze heterogeneous cell differentiation dynamics
SMGWS 2: improved microcomputer-based three-dimensional stereoscopic macromolecular graphics display
Modular analysis of gene expression data with R
RNA threading with secondary structure and sequence profile
StrainHub: a phylogenetic tool to construct pathogen transmission networks
Audit logs to enforce document integrity in Skyline and Panorama
CoMM: a collaborative mixed model to dissecting genetic contributions to complex traits by leveraging regulatory information
Identification of the idiosyncratic bacterial protein tyrosine kinase (BY-kinase) family signature
Globally Accessible Distributed Data Sharing (GADDS): a decentralized FAIR platform to facilitate data sharing in the life sciences
An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB
Java Treeview - extensible visualization of microarray data
Simulating association studies: a data-based resampling method for candidate regions or whole genome scans
MIB2: metal ion-binding site prediction and modeling server
Protein threading using context-specific alignment potential
Message from the ISCB: ISMB/ECCB Rebooted: 2015 Brings Major Update to the Conference Program
Robust estimation of protein expression ratios with lysate microarray technology
LigDig: a web server for querying ligand-protein interactions
Linguistic approaches to biological sequences
A new criterion to classify globular proteins based on their secondary structure contents
MatrixPlot: visualizing sequence constraints
A grid layout algorithm for automatic drawing of biochemical networks
PERMANOVA-S: association test for microbial community composition that accommodates confounders and multiple distances