yusuke1997/dblp-id-title huggingface dataset:
MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis
Identifying cancer pathway dysregulations using differential causal effects
SegAnnDB: interactive Web-based genomic segmentation
Evigan: a hidden variable model for integrating gene evidence for eukaryotic gene prediction
Seed: a user-friendly tool for exploring and visualizing microbial community data
MetaFam: a unified classification of protein families. II. Schema and query capabilities
Fast and accurate site frequency spectrum estimation from low coverage sequence data
GenomeWarp: an alignment-based variant coordinate transformation
An efficient graph kernel method for non-coding RNA functional prediction
cnvOffSeq: detecting intergenic copy number variation using off-target exome sequencing data
Differences in gene expression between B-cell chronic lymphocytic leukemia and normal B cells: a meta-analysis of three microarray studies
CODEX: exploration of semantic changes between ontology versions
Using collective expert judgements to evaluate quality measures of mass spectrometry images
Reference-free structural variant detection in microbiomes via long-read co-assembly graphs
Accessible methods for the dynamic time-scale decomposition of biochemical systems
Multi-level mixed effects models for bead arrays
A holistic in silico approach to predict functional sites in protein structures
Improved similarity scores for comparing motifs
Predicting explainable dementia types with LLM-aided feature engineering
Some programs useful for managing data in ecology, taxonomy and zoogeography
A web portal for classification of expression data using maximal margin linear programming
A robust approach to extract biomedical events from literature
Testing significance relative to a fold-change threshold is a TREAT
Improved design and analysis of practical minimizers
Transformation and differential abundance analysis of microbiome data incorporating phylogeny
GLAD: a system for developing and deploying large-scale bioinformatics grid
TALE: Transformer-based protein function Annotation with joint sequence-Label Embedding
CasOT: a genome-wide Cas9/gRNA off-target searching tool
fqtools: an efficient software suite for modern FASTQ file manipulation
Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures
CLARE: Cracking the LAnguage of Regulatory Elements
Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
Protein language models meet reduced amino acid alphabets
CaPSSA: visual evaluation of cancer biomarker genes for patient stratification and survival analysis using mutation and expression data
gCMAP: user-friendly connectivity mapping with R
debCAM: a bioconductor R package for fully unsupervised deconvolution of complex tissues
MomentClosure.jl: automated moment closure approximations in Julia
Pitfalls of machine learning models for protein-protein interaction networks
AEON.py: Python library for attractor analysis in asynchronous Boolean networks
High-dimensional biomarker identification for interpretable disease prediction via machine learning models
Molywood: streamlining the design and rendering of molecular movies
CellBench: R/Bioconductor software for comparing single-cell RNA-seq analysis methods
BeReTa: a systematic method for identifying target transcriptional regulators to enhance microbial production of chemicals
A fast Peptide Match service for UniProt Knowledgebase
BACCardI-a tool for the validation of genomic assemblies, assisting genome finishing and intergenome comparison
HFBSurv: hierarchical multimodal fusion with factorized bilinear models for cancer survival prediction
Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools
Ensemble deep learning of embeddings for clustering multimodal single-cell omics data
Identifying the 3'-terminal exon in human DNA
Improving the accuracy of the structure prediction of the third hypervariable loop of the heavy chains of antibodies
Graph theoretical approach to study eQTL: a case study of Plasmodium falciparum
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts
PConPy - a Python module for generating 2D protein maps
Interaction-site prediction for protein complexes: a critical assessment
A general purpose computer analysis system for chromatographic data
amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool
3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures
Codon Pairs in the Genome of Escherichia Coli
A CitationRank algorithm inheriting Google technology designed to highlight genes responsible for serious adverse drug reaction
MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation
DNAVis: interactive visualization of comparative genome annotations
WeSME: uncovering mutual exclusivity of cancer drivers and beyond
HEALER: homomorphic computation of ExAct Logistic rEgRession for secure rare disease variants analysis in GWAS
Implementation of a practical Markov chain Monte Carlo sampling algorithm in PyBioNetFit
Geometry of gene expression dynamics
Neural network predicts sequence of TP53 gene based on DNA chip
Inferring cellular heterogeneity of associations from single cell genomics
The GenoPred pipeline: a comprehensive and scalable pipeline for polygenic scoring
Computational modeling of immune system of the fish for a more effective vaccination in aquaculture
PepBDB: a comprehensive structural database of biological peptide-protein interactions
Remote homology detection based on oligomer distances
High-throughput and efficient multilocus genome-wide association study on longitudinal outcomes
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Fast tomographic reconstruction on multicore computers
Themisto: a scalable colored k -mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes
LightDock goes information-driven
A spline function approach for detecting differentially expressed genes in microarray data analysis
Transforming a set of biological flat file libraries to a fast access network
CELLBASE: a database management system for the control of cell line storage
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles
DARNED: a DAtabase of RNa EDiting in humans
GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool
Discovering and interpreting transcriptomic drivers of imaging traits using neural networks
Integrating expression data with domain interaction networks
RIP-chip enrichment analysis
iFold: a platform for interactive folding simulations of proteins
BioServices: a common Python package to access biological Web Services programmatically
Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes
Qupe - a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
SKEMPI 2.0: an updated benchmark of changes in protein-protein binding energy, kinetics and thermodynamics upon mutation
PAFway: pairwise associations between functional annotations in biological networks and pathways
CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks
Fast admixture analysis and population tree estimation for SNP and NGS data
An automated model annotation system (AMAS) for SBML models
WhopGenome: high-speed access to whole-genome variation and sequence data in R
Predicting and understanding the stability of G-quadruplexes
Correction to: Optimal adjustment sets for causal query estimation in partially observed biomolecular networks
Wave-spec: a preprocessing package for mass spectrometry data
Observing local and global properties of metabolic pathways: "load points" and "choke points" in the metabolic networks
A nearest neighbor approach for automated transporter prediction and categorization from protein sequences
keras_dna: a wrapper for fast implementation of deep learning models in genomics
ZFIQ: a software package for zebrafish biology
Investigating the human and nonobese diabetic mouse MHC class II immunopeptidome using protein language modeling
MutaProt: a web interface for structural analysis of point mutations
SeedMatchR: identify off-target effects mediated by siRNA seed regions in RNA-seq experiments
Quantification of aneuploidy in targeted sequencing data using ASCETS
SensA: web-based sensitivity analysis of SBML models
Assessing citation integrity in biomedical publications: corpus annotation and NLP models
Explore, edit and leverage genomic annotations using Python GTF toolkit
RERconverge: an R package for associating evolutionary rates with convergent traits
Kinome-wide identification of phosphorylation networks in eukaryotic proteomes
copMEM2: robust and scalable maximum exact match finding
Autoencoder-based drug-target interaction prediction by preserving the consistency of chemical properties and functions of drugs
Rapid simulation and analysis of isotopomer distributions using constraints based on enzyme mechanisms: an example from HT29 cancer cells
GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testing
Ancestral sequence reconstruction: accounting for structural information by averaging over replacement matrices
CircMiner: accurate and rapid detection of circular RNA through splice-aware pseudo-alignment scheme
scNAME: neighborhood contrastive clustering with ancillary mask estimation for scRNA-seq data
flowFit: a Bioconductor package to estimate proliferation in cell-tracking dye studies
ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design
Cleanifier: contamination removal from microbial sequences using spaced seeds of a human pangenome index
BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R
Topological augmentation to infer hidden processes in biological systems
Identification of human-specific transcript variants induced by DNA insertions in the human genome
ADACT: a tool for analysing (dis)similarity among nucleotide and protein sequences using minimal and relative absent words
An experimental evaluation of a loop versus a reference design for two-channel microarrays
The design of Jemboss: a graphical user interface to EMBOSS
A simulation test bed for hypotheses of genome evolution
Gclust: trans -kingdom classification of proteins using automatic individual threshold setting
2023 ISCB innovator award: Dana Pe'er
E-Cell 2: Multi-platform E-Cell simulation system
ProServer: a simple, extensible Perl DAS server
Comment on causality and pathway search in microarray time series experiment
Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0
MACOED: a multi-objective ant colony optimization algorithm for SNP epistasis detection in genome-wide association studies
An optimization model for metabolic pathways
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs
Visualizing information across multidimensional post-genomic structured and textual databases
ProSAT: functional annotation of protein 3D structures
Visualizations for taxonomic and phylogenetic trees
SQUINT: a multiple alignment program and editor
NRGsuite: a PyMOL plugin to perform docking simulations in real time using FlexAID
HykGene: a hybrid approach for selecting marker genes for phenotype classification using microarray gene expression data
Measuring gene functional similarity based on group-wise comparison of GO terms
DiSTect: a Bayesian model for disease-associated gene discovery and prediction in spatial transcriptomics
Position-dependent motif characterization using non-negative matrix factorization
RENANO: a REference-based compressor for NANOpore FASTQ files
IBM microcomputer programs that analyze DNA sequences for tRNA genes
Large-scale analysis of non-synonymous coding region single nucleotide polymorphisms
DOOSS: a tool for visual analysis of data overlaid on secondary structures
Determination of minimum sample size and discriminatory expression patterns in microarray data
Deep learning-based subdivision approach for large scale macromolecules structure recovery from electron cryo tomograms
On the hierarchical classification of G protein-coupled receptors
PhamDB: a web-based application for building Phamerator databases
Minimal cut sets in a metabolic network are elementary modes in a dual network
Discovery of microRNA-mRNA modules via population-based probabilistic learning
ProteomicsBrowser: MS/proteomics data visualization and investigation
MultiP-SChlo: multi-label protein subchloroplast localization prediction with Chou's pseudo amino acid composition and a novel multi-label classifier
Webina: an open-source library and web app that runs AutoDock Vina entirely in the web browser
DIRECTEUR: transcriptome-based prediction of small molecules that replace transcription factors for direct cell conversion
Enrich: software for analysis of protein function by enrichment and depletion of variants
A stochastic model for the evolution of metabolic networks with neighbor dependence
AL2CO: calculation of positional conservation in a protein sequence alignment
Optimal linkage disequilibrium splitting
Characterizing cancer subtypes as attractors of Hopfield networks
An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasis
PopHist: inferring population history from the spectrum of allele frequencies
SEMtree: tree-based structure learning methods with structural equation models
Protein multiple alignments: sequence-based versus structure-based programs
ProtTest: selection of best-fit models of protein evolution
Corrigendum to: HRIBO: high-throughput analysis of bacterial ribosome profiling data
kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome
Multi-modal deep learning improves grain yield prediction in wheat breeding by fusing genomics and phenomics
Robust and accurate estimation of cellular fraction from tissue omics data via ensemble deconvolution
Evaluating reproducibility of differential expression discoveries in microarray studies by considering correlated molecular changes
Biclustering as a method for RNA local multiple sequence alignment
Interactive microbial genome visualization with GView
Symbolic reinterpretation of HLA gene products--impact on interpretation of HLA data at the molecular level
BCov: a method for predicting β-sheet topology using sparse inverse covariance estimation and integer programming
HLA-MA: simple yet powerful matching of samples using HLA typing results
Characterization of the folding degree of proteins
Statistical significance analysis of longitudinal gene expression data
e-Drug3D: 3D structure collections dedicated to drug repurposing and fragment-based drug design
A generalized global alignment algorithm
PiLSL: pairwise interaction learning-based graph neural network for synthetic lethality prediction in human cancers
Predicting the binding preference of transcription factors to individual DNA k -mers
Snowball : strain aware gene assembly of metagenomes
A statistical physics perspective on alignment-independent protein sequence comparison
Reconstructing signaling pathways using regular language constrained paths
Common data model for COVID-19 datasets
CpGtools: a python package for DNA methylation analysis
MatInspector and beyond: promoter analysis based on transcription factor binding sites
SCPC: a method to structurally compare protein complexes
PTL-PRS: an R package for transfer learning of polygenic risk scores with pseudovalidation
A new computational drug repurposing method using established disease-drug pair knowledge
fdrMotif: identifying cis -elements by an EM algorithm coupled with false discovery rate control
PReFerSim: fast simulation of demography and selection under the Poisson Random Field model
miRmine: a database of human miRNA expression profiles
An algorithm for comparing RNA secondary structures and searching for similar substructures
Xolik: finding cross-linked peptides with maximum paired scores in linear time
ASElux: an ultra-fast and accurate allelic reads counter
Rintact: enabling computational analysis of molecular interaction data from the IntAct repository
iPEAP: integrating multiple omics and genetic data for pathway enrichment analysis
Bayesian Inference of Signaling Network Topology in a Cancer Cell Line
A convolutional neural network for common coordinate registration of high-resolution histology images
CAMBIO: software for modelling and simulation of bioprocesses
Associations on the Fly, a new feature aiming to facilitate exploration of the Open Targets Platform evidence
Visual Representation of Database Search Results: The RHIMS Plot
Multidimensional scaling improves distance-based clustering for microbiome data
Fast tumor phylogeny regression via tree-structured dual dynamic programming
Joint estimation of calibration and expression for high-density oligonucleotide arrays
Demixer: a probabilistic generative model to delineate different strains of a microbial species in a mixed infection sample
Expression2Kinases: mRNA profiling linked to multiple upstream regulatory layers
UDSMProt: universal deep sequence models for protein classification
DMEAS: DNA methylation entropy analysis software
HiCForecast: dynamic network optical flow estimation algorithm for spatiotemporal Hi-C data forecasting
iPat: intelligent prediction and association tool for genomic research
TargetMine 2022: a new vision into drug target analysis
VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules
FYPO: the fission yeast phenotype ontology
2DImpute: imputation in single-cell RNA-seq data from correlations in two dimensions
Homology-driven assembly of NOn-redundant protEin sequence sets (NOmESS) for mass spectrometry
Predicting allergenic proteins using wavelet transform
An integrative scoring system for ranking SNPs by their potential deleterious effects
A decoupled, modular and scriptable architecture for tools to curate data platforms
Algorithms for sorting unsigned linear genomes by the DCJ operations
Ceiba : scalable visualization of phylogenies and 2D/3D image collections
MEMO: multi-experiment mixture model analysis of censored data
ShinyGO: a graphical gene-set enrichment tool for animals and plants
A multicellular systems biology model predicts epidermal morphology, kinetics and Ca 2+ flow
APCluster: an R package for affinity propagation clustering
DivBayes and SubT: exploring species diversification using Bayesian statistics
A simple method for predicting the secondary structure of globular proteins: implications and accuracy
Cellenium - a scalable and interactive visual analytics app for exploring multimodal single-cell data
Detecting dispersed duplications in high-throughput sequencing data using a database-free approach
HLA*LA - HLA typing from linearly projected graph alignments
matter: an R package for rapid prototyping with larger-than-memory datasets on disk
Codon optimization: a mathematical programing approach
FOLD: a method to optimize power in meta-analysis of genetic association studies with overlapping subjects
TOXsIgN: a cross-species repository for toxicogenomic signatures
Mollack: a web server for the automated creation of conformational ensembles for intrinsically disordered proteins
Recognition of splice junctions on DNA sequences by BRAIN learning algorithm
Accelerating high-dimensional clustering with lossless data reduction
Cas-analyzer: an online tool for assessing genome editing results using NGS data
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles
MirCure: a tool for quality control, filter and curation of microRNAs of animals and plants
SPECTRE: a suite of phylogenetic tools for reticulate evolution
Study of real-valued distance prediction for protein structure prediction with deep learning
IsoMaTrix: a framework to visualize the isoclines of matrix games and quantify uncertainty in structured populations
Gonomics: uniting high performance and readability for genomics with Go
An optimal peak alignment for comprehensive two-dimensional gas chromatography mass spectrometry using mixture similarity measure
Protlego: a Python package for the analysis and design of chimeric proteins
PseuRECA: genome annotation and gene context analysis for Pseudomonas aeruginosa PAO1
AciDB 1.0: a database of acidophilic organisms, their genomic information and associated metadata
CHROMIXS: automatic and interactive analysis of chromatography-coupled small-angle X-ray scattering data
Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms
An initial strategy for comparing proteins at the domain architecture level
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions
GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text
CONRAD: a method for identification of variable and conserved regions within proteins by scale-space filtering
A pattern-based nearest neighbor search approach for promoter prediction using DNA structural profiles
Using video-oriented instructions to speed up sequence comparison
novoCaller: a Bayesian network approach for de novo variant calling from pedigree and population sequence data
Deep learning of the back-splicing code for circular RNA formation
Analysis of temporal gene expression profiles: clustering by simulated annealing and determining the optimal number of clusters
In response to comment on 'A congruence index for testing topological similarity between trees'
Transcription/replication collisions cause bacterial transcription units to be longer on the leading strand of replication
RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes
flowAI: automatic and interactive anomaly discerning tools for flow cytometry data
h5vc: scalable nucleotide tallies with HDF5
EPGA2: memory-efficient de novo assembler
In silico identification of putative metal binding motifs
An expert system for diagnosis of coronary artery stenosis based on 201Tl scintigrams using the Dempster-Shafer theory of evidence
Growing a classification tree using the apparent misclassification rate
MuGeN: Simultaneous Exploration of Multiple Genomes and Computer Analysis Results
A machine learning-based quantitative model (LogBB_Pred) to predict the blood-brain barrier permeability (logBB value) of drug compounds
The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value
Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides
Whole-genome prokaryotic phylogeny
Unipro UGENE: a unified bioinformatics toolkit
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families
FastPros: screening of reaction knockout strategies for metabolic engineering
Human genomes as email attachments
SCGid: a consensus approach to contig filtering and genome prediction from single-cell sequencing libraries of uncultured eukaryotes
Fast scaffolding with small independent mixed integer programs
AMASS: a database for investigating protein structures
ERNEST: a toolbox for chemical reaction network theory
Recognition of beta-structural motifs using hidden Markov models trained with simulated evolution
Miropeats: graphical DNA sequence comparisons
Reactome enhanced pathway visualization
pyM2aia: Python interface for mass spectrometry imaging with focus on deep learning
Synergy Disequilibrium Plots: graphical visualization of pairwise synergies and redundancies of SNPs with respect to a phenotype
KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping