yusuke1997/dblp-id-title huggingface dataset:
BetaTPred: prediction of beta-TURNS in a protein using statistical algorithms
GraphQA: protein model quality assessment using graph convolutional networks
Definition and identification of homology domains
PreMosa: extracting 2D surfaces from 3D microscopy mosaics
Robust unmixing of tumor states in array comparative genomic hybridization data
Computational analysis of tissue-specific gene networks: application to murine retinal functional studies
MREPATT: detection and analysis of exact consecutive repeats in genomic sequences
BioIE: extracting informative sentences from the biomedical literature
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules
Structural basis of SARS-CoV-2 spike protein induced by ACE2
wgatools : an ultrafast toolkit for manipulating whole-genome alignments
DigiNorthern, digital expression analysis of query genes based on ESTs
Microbench: automated metadata management for systems biology benchmarking and reproducibility in Python
Nonlinear data fusion over Entity-Relation graphs for Drug-Target Interaction prediction
Bringing data from curated pathway resources to Cytoscape with OmniPath
Quality of alignment comparison by COMPASS improves with inclusion of diverse confident homologs
A hybrid approach to protein differential expression in mass spectrometry-based proteomics
2022 ISCB Innovator Award: Núria López-Bigas
Random field modeling of multi-trait multi-locus association for detecting methylation quantitative trait loci
LEVER: software tools for segmentation, tracking and lineaging of proliferating cells
14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides
A dynamic Bayesian Markov model for phasing and characterizing haplotypes in next-generation sequencing
VarChat: the generative AI assistant for the interpretation of human genomic variations
PopFly: the Drosophila population genomics browser
Integrating transformer and imbalanced multi-label learning to identify antimicrobial peptides and their functional activities
GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome
A sequential algorithm to detect diffusion switching along intracellular particle trajectories
Limited conformational space for early-stage protein folding simulation
A deep learning framework for improving long-range residue-residue contact prediction using a hierarchical strategy
Minimal cut sets in biochemical reaction networks
Hamming-Clustering method for signals prediction in 5' and 3' regions of eukaryotic genes
A Poisson model for random multigraphs
MaxSub: an automated measure for the assessment of protein structure prediction quality
TMBleR: a bioinformatic tool to optimize TMB estimation and predictive power
scPretrain: multi-task self-supervised learning for cell-type classification
Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data
Computational identification of natural peptides based on analysis of molecular evolution
Prediction of antimicrobial resistance based on whole-genome sequencing and machine learning
Differentially conserved amino acid positions may reflect differences in SARS-CoV-2 and SARS-CoV behaviour
Modelling-based experiment retrieval: a case study with gene expression clustering
iMetaLab 1.0: a web platform for metaproteomics data analysis
Locuaz: an in silico platform for protein binders optimization
Quantifying heterogeneity of expression data based on principal components
SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy
APSCALE: advanced pipeline for simple yet comprehensive analyses of DNA metabarcoding data
GEInter: an R package for robust gene-environment interaction analysis
Annotating regulatory elements by heterogeneous network embedding
The Transcriptome Analysis and Comparison Explorer - T-ACE: a platform-independent, graphical tool to process large RNAseq datasets of non-model organisms
Discovery and genotyping of novel sequence insertions in many sequenced individuals
Reptile: representative tiling for short read error correction
DEIsoM: a hierarchical Bayesian model for identifying differentially expressed isoforms using biological replicates
StructHDP: automatic inference of number of clusters and population structure from admixed genotype data
Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks
A distributed system for DNA/protein database similarity searches
Drug Targetor: a web interface to investigate the human druggome for over 500 phenotypes
Protein classification using probabilistic chain graphs and the Gene Ontology structure
Combining DNA expression with positional information to detect functional silencing of chromosomal regions
DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning
Detecting and correcting misclassified sequences in the large-scale public databases
BioBayes: A software package for Bayesian inference in systems biology
ABAEnrichment: an R package to test for gene set expression enrichment in the adult and developing human brain
Alternative polyadenylation sites reveal distinct chromatin accessibility and histone modification in human cell lines
Protein secondary structure appears to be robust under in silico evolution while protein disorder appears not to be
Identification of short terminal motifs enriched by antibodies using peptide mass fingerprinting
BISEN: Biochemical Simulation Environment
A flexible two-stage procedure for identifying gene sets that are differentially expressed
An alternative approach to multiple testing for methylation QTL mapping reduces the proportion of falsely identified CpGs
Flashfm-ivis : interactive visualization for fine-mapping of multiple quantitative traits
ipcoal: an interactive Python package for simulating and analyzing genealogies and sequences on a species tree or network
SELAM: simulation of epistasis and local adaptation during admixture with mate choice
PseKNC-General: a cross-platform package for generating various modes of pseudo nucleotide compositions
A divide-and-conquer approach to analyze underdetermined biochemical models
Algorithms for sequence analysis via mutagenesis
WILMA - automated annotation of protein sequences
Integrative transcription start site identification with iTiSS
Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data
Fast and accurate database homology search using upper bounds of local alignment scores
Sequence-specific minimizers via polar sets
Fast spatial ancestry via flexible allele frequency surfaces
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
A tool for gene expression based PubMed search through combining data sources
pong: fast analysis and visualization of latent clusters in population genetic data
SpEED: fast computation of sensitive spaced seeds
Detection and quantification of microorganisms in a heterogeneous foodstuff by image analysis
PyGOLD: a python based API for docking based virtual screening workflow generation
Application of the MAFFT sequence alignment program to large data - reexamination of the usefulness of chained guide trees
Seeing the trees through the forest: sequence-based homo- and heteromeric protein-protein interaction sites prediction using random forest
DeepCRISTL: deep transfer learning to predict CRISPR/Cas9 on-target editing efficiency in specific cellular contexts
Hidden Markov random field models for cell-type assignment of spatially resolved transcriptomics
stVAE deconvolves cell-type composition in large-scale cellular resolution spatial transcriptomics
scMUSCL: multi-source transfer learning for clustering scRNA-seq data
MIMEAnTo: profiling functional RNA in mutational interference mapping experiments
Efficient identification of identical-by-descent status in pedigrees with many untyped individuals
Consensus shapes: an alternative to the Sankoff algorithm for RNA consensus structure prediction
Programs for evaluating and characterising bacterial taxonomic data
Applying family analyses to electronic health records to facilitate genetic research
MethylCoder: software pipeline for bisulfite-treated sequences
A systems-biology model of the tumor necrosis factor (TNF) interactions with TNF receptor 1 and 2
Deep Subspace Mutual Learning for cancer subtypes prediction
AncestralClust: clustering of divergent nucleotide sequences by ancestral sequence reconstruction using phylogenetic trees
MetExploreViz: web component for interactive metabolic network visualization
Deciphering kinase-substrate relationships by analysis of domain-specific phosphorylation network
ABEMUS: platform-specific and data-informed detection of somatic SNVs in cfDNA
A profile-based deterministic sequential Monte Carlo algorithm for motif discovery
Text mining for modeling of protein complexes enhanced by machine learning
An empirical Bayes approach for analysis of diverse periodic trends in time-course gene expression data
Inference of structure in subdivided populations at low levels of genetic differentiation - the correlated allele frequencies model revisited
RSeQC: quality control of RNA-seq experiments
Fast alignment and comparison of RNA structures
ODNA: identification of organellar DNA by machine learning
Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking
Clustering threshold gradient descent regularization: with applications to microarray studies
Airpart: interpretable statistical models for analyzing allelic imbalance in single-cell datasets
MIAmS: microsatellite instability detection on NGS amplicons data
ENACT: End-to-End Analysis of Visium High Definition (HD) Data
SVA: software for annotating and visualizing sequenced human genomes
HAPNEST: efficient, large-scale generation and evaluation of synthetic datasets for genotypes and phenotypes
MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways
ExportAid: database of RNA elements regulating nuclear RNA export in mammals
Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations
Episo: quantitative estimation of RNA 5-methylcytosine at isoform level by high-throughput sequencing of RNA treated with bisulfite
A Hypercard program for the identification of biological specimens [published erratum appears in Comput Appl Biosci 1991 Apr;7(2): 285]
COSSMO: predicting competitive alternative splice site selection using deep learning
Supervised learning on phylogenetically distributed data
Ouroboros: cross-linking protein expression perturbations and cancer histology imaging with generative-predictive modeling
A high-throughput processing service for retention time alignment of complex proteomics and metabolomics LC-MS data
Early bioinformatics: the birth of a discipline - a personal view
Comparing simulation results of SBML capable simulators
A precise and scalable method for querying genes in chromosomal banding regions based on cytogenetic annotations
scTSSR: gene expression recovery for single-cell RNA sequencing using two-side sparse self-representation
Effects of replacing the unreliable cDNA microarray measurements on the disease classification based on gene expression profiles and functional modules
Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays
Computer program designed to predict and plot the secondary structure of proteins
An algorithm for computing the gene tree probability under the multispecies coalescent and its application in the inference of population tree
spiralize: an R package for visualizing data on spirals
MethParquet: an R package for rapid and efficient DNA methylation association analysis adopting Apache Parquet
Differentiating isoform functions with collaborative matrix factorization
PhenoScanner V2: an expanded tool for searching human genotype-phenotype associations
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Rapid genotype refinement for whole-genome sequencing data using multi-variate normal distributions
SharpViSu: integrated analysis and segmentation of super-resolution microscopy data
PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations
FastPval: a fast and memory efficient program to calculate very low P -values from empirical distribution
FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps
Using inferred residue contacts to distinguish between correct and incorrect protein models
Gene Selection and Clustering for Time-course and Dose-response Microarray Experiments Using Order-restricted Inference
SherLoc: high-accuracy prediction of protein subcellular localization by integrating text and protein sequence data
DincRNA: a comprehensive web-based bioinformatics toolkit for exploring disease associations and ncRNA function
FQC Dashboard: integrates FastQC results into a web-based, interactive, and extensible FASTQ quality control tool
ontologyX: a suite of R packages for working with ontological data
PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq)
The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation
BEsTRF: a tool for optimal resolution of terminal-restriction fragment length polymorphism analysis based on user-defined primer-enzyme-sequence databases
A global transcriptomic pipeline decoding core network of genes involved in stages leading to acquisition of drug-resistance to cisplatin in osteosarcoma cells
The CellML Model Repository
Modular decomposition of metabolic reaction networks based on flux analysis and pathway projection
INSECT: IN-silico SEarch for Co-occurring Transcription factors
Modified screening and ranking algorithm for copy number variation detection
A computer algorithm to determine the recognition site of restriction enzymes
Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon
Distance indexing and seed clustering in sequence graphs
De novo identification of highly diverged protein repeats by probabilistic consistency
VAPEX: an interactive web server for the deep exploration of natural virus and phage genomes
Grouper - creation of marker sets for multiplexed genotyping
MetaGeneAlyse: analysis of integrated transcriptional and metabolite data
DMIL-IsoFun: predicting isoform function using deep multi-instance learning
INCLUSive: INtegrated Clustering, Upstream sequence retrieval and motif Sampling
MOCHI: a comprehensive cross-platform tool for amplicon-based microbiota analysis
Top-Down Garbage Collector: a tool for selecting high-quality top-down proteomics mass spectra
NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment
ChromDL: a next-generation regulatory DNA classifier
ctsGE - clustering subgroups of expression data
Sparse non-negative generalized PCA with applications to metabolomics
QuArray: an application for tissue array whole slide image export and signal analysis
Hypothesis testing approaches to the exon prediction problem
Exact coalescent simulation of new haplotype data from existing reference haplotypes
Identification of a small set of plasma signalling proteins using neural network for prediction of Alzheimer's disease
Capturing variation in metagenomic assembly graphs with MetaCortex
NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results
CSBFinder: discovery of colinear syntenic blocks across thousands of prokaryotic genomes
PaGeFinder: quantitative identification of spatiotemporal pattern genes
TFBS: Computational framework for transcription factor binding site analysis
A computational procedure for assessing the significance of RNA secondary structure
Automated detection of apoptotic bodies and cells in label-free time-lapse high-throughput video microscopy using deep convolutional neural networks
Enhanced guide-RNA design and targeting analysis for precise CRISPR genome editing of single and consortia of industrially relevant and non-model organisms
ECCB 2012: The 11 th European Conference on Computational Biology
Informed and automated k -mer size selection for genome assembly
Bipartite tight spectral clustering (BiTSC) algorithm for identifying conserved gene co-clusters in two species
FLINO: a new method for immunofluorescence bioimage normalization
Meta-analysis based on control of false discovery rate: combining yeast ChIP-chip datasets
Automated discovery of 3D motifs for protein function annotation
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
Genome puzzle master (GPM): an integrated pipeline for building and editing pseudomolecules from fragmented sequences
Neural fate decisions mediated by trans -activation and cis -inhibition in Notch signaling
Optimization and profile calculation of ODE models using second order adjoint sensitivity analysis
Few shot domain adaptation for in situ macromolecule structural classification in cryoelectron tomograms
Cysteine separations profiles on protein sequences infer disulfide connectivity
dv-trio: a family-based variant calling pipeline using DeepVariant
An enhanced Java graph applet interface for visualizing interactomes
An ontology for collaborative construction and analysis of cellular pathways
MecCog: a knowledge representation framework for genetic disease mechanism
The Baumgartner-Wei?-Schindler test for the detection of differentially expressed genes in replicated microarray experiments
Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association
Molecular property prediction based on graph structure learning
On the derivation of propensity scales for predicting exposed transmembrane residues of helical membrane proteins
Sequential and parallel algorithms for DNA sequencing
PDEparams: parameter fitting toolbox for partial differential equations in python
The 3DGD: a database of genome 3D structure
GlycoRDF: an ontology to standardize glycomics data in RDF
Structural bioinformatics of DNA: a web-based tool for the analysis of molecular dynamics results and structure prediction
MULTICOMP: a program package for multiple sequence comparison
PrioriTree: a utility for improving phylodynamic analyses in BEAST
Inferring microRNA-mRNA causal regulatory relationships from expression data
PDZBase: a protein?Cprotein interaction database for PDZ-domains
Protease substrate site predictors derived from machine learning on multilevel substrate phage display data
DivPro: diverse protein sequence design with direct structure recovery guidance
Integration of GO annotations in Correspondence Analysis: facilitating the interpretation of microarray data
Differential network analysis for the identification of condition-specific pathway activity and regulation
Challenges in RNA virus bioinformatics
R/qtl: high-throughput multiple QTL mapping
GenoMap, a circular genome data viewer
Rapid multiple protein sequence search by parallel and heterogeneous computation
meRanTK: methylated RNA analysis ToolKit
SENSAAS-Flex: a joint optimization approach for aligning 3D shapes and exploring the molecular conformation space
ChromoViz: multimodal visualization of gene expression data onto chromosomes using scalable vector graphics
Automated assignment grading with large language models: insights from a bioinformatics course
SWAPSC: sliding window analysis procedure to detect selective constraints
PhiHER2: phenotype-informed weakly supervised model for HER2 status prediction from pathological images
RImmPort: an R/Bioconductor package that enables ready-for-analysis immunology research data
Comprehensive study of the exposome and omic data using rexposome Bioconductor Packages
JaDis: computing distances between nucleic acid sequences
OnD-CRF: predicting order and disorder in proteins conditional random fields
Target-align: a tool for plant microRNA target identification
BamView: viewing mapped read alignment data in the context of the reference sequence
On the Importance of Standardisation in Life Sciences
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes
NGL viewer: web-based molecular graphics for large complexes
MetaBMF: a scalable binning algorithm for large-scale reference-free metagenomic studies
Noise-induced cooperative behavior in a multicell system
DeepPASTA: deep neural network based polyadenylation site analysis
Intron-centric estimation of alternative splicing from RNA-seq data
Roundup: a multi-genome repository of orthologs and evolutionary distances
Fluorescent automated DNA sequencers: a file exchange program
PSLpred: prediction of subcellular localization of bacterial proteins
Adjustments and measures of differential expression for microarray data
STELLS2: fast and accurate coalescent-based maximum likelihood inference of species trees from gene tree topologies
Addendum: topology and prediction of RNA pseudoknots
Computational phosphorylation site prediction in plants using random forests and organism-specific instance weights
Structured polychotomous machine diagnosis of multiple cancer types using gene expression
Estimating the power of sequence covariation for detecting conserved RNA structure
TruMatch - a BLAST post-processor that identifies bona fide sequence matches to genome assemblies
Assembly Graph Browser: interactive visualization of assembly graphs
MS 2 PIP: a tool for MS/MS peak intensity prediction
TRAMP: a software package for generating transposon maps
TUGDA: task uncertainty guided domain adaptation for robust generalization of cancer drug response prediction from in vitro to in vivo settings
DeepMeSH: deep semantic representation for improving large-scale MeSH indexing
MS-specific noise model reveals the potential of iTRAQ in quantitative proteomics
A variable selection method for genome-wide association studies
RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification
Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms
TASSEL: software for association mapping of complex traits in diverse samples
GENIE: estimating demographic history from molecular phylogenies
methylR: a graphical interface for comprehensive DNA methylation array data analysis
DrugComboRanker: drug combination discovery based on target network analysis
MultiPaths: a Python framework for analyzing multi-layer biological networks using diffusion algorithms
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects
Genome Detective: an automated system for virus identification from high-throughput sequencing data
MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis
Early immunologic correlates of HIV protection can be identified from computational analysis of complex multivariate T-cell flow cytometry assays
Ragout - a reference-assisted assembly tool for bacterial genomes
Lit-OTAR framework for extracting biological evidences from literature
ProtPOS: a python package for the prediction of protein preferred orientation on a surface
Learning combinatorial transcriptional dynamics from gene expression data
ZIAQ: a quantile regression method for differential expression analysis of single-cell RNA-seq data
PDR: a new genome assembly evaluation metric based on genetics concerns
A sample storage management system for biobanks
A comprehensive evaluation of multicategory classification methods for microarray gene expression cancer diagnosis
Computational antisense oligo prediction with a neural network model