yusuke1997/dblp-id-title huggingface dataset:
Building a high-quality sense inventory for improved abbreviation disambiguation
mdclust-exploratory microarray analysis by multidimensional clustering
A common ancestry for BAP1 and Uch37 regulators
ImgLib2 - generic image processing in Java
CellBRF: a feature selection method for single-cell clustering using cell balance and random forest
A method for visualizing CellML models
Predicting drug-target interactions using restricted Boltzmann machines
SplicingCompass: differential splicing detection using RNA-Seq data
Inferring disease association using clinical factors in a combinatorial manner and their use in drug repositioning
Comparison of single and module-based methods for modeling gene regulatory networks
Simulated single molecule microscopy with SMeagol
FACIL: Fast and Accurate Genetic Code Inference and Logo
Pre-training graph neural networks for link prediction in biomedical networks
Bias in microRNA functional enrichment analysis
Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-Seq significance tool
StatAlign: an extendable software package for joint Bayesian estimation of alignments and evolutionary trees
HyperModules: identifying clinically and phenotypically significant network modules with disease mutations for biomarker discovery
Exploiting the structure of biochemical pathways to investigate dynamical properties with neural networks for graphs
Gene annotation from scientific literature using mappings between keyword systems
TimeXNet Web: identifying cellular response networks from diverse omics time-course data
Improved representation of sequence bloom trees
Edge-based sensitivity analysis of signaling networks by using Boolean dynamics
Mcheza: a workbench to detect selection using dominant markers
miqoGraph: fitting admixture graphs using mixed-integer quadratic optimization
Efficient dynamic variation graphs
RecPhyloXML: a format for reconciled gene trees
Dynamical important residue network (DIRN): network inference via conformational change
STOPGAP: a database for systematic target opportunity assessment by genetic association predictions
adegenet : a R package for the multivariate analysis of genetic markers
Simulation of crosstalk between small GTPase RhoA and EGFR-ERK signaling pathway via MEKK1
Fewer permutations, more accurate P -values
aPEAR : an R package for autonomous visualization of pathway enrichment networks
Somatic mutation effects diffused over microRNA dysregulation
Modeling risk stratification in human cancer
Serial dilution curve: a new method for analysis of reverse phase protein array data
PyPDB: a Python API for the Protein Data Bank
GraphSpace: stimulating interdisciplinary collaborations in network biology
Application of asymmetric statistical potentials to antibody-protein docking
SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction
GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae
SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides
Logomaker: beautiful sequence logos in Python
AntiHunter: searching BLAST output for EST antisense transcripts
Visualizing large hierarchical clusters in hyperbolic space
Phenome-driven disease genetics prediction toward drug discovery
The 2nd international conference on the Bioinformatics of Genome Regulation and Structure (BGRS-2000), Novosibirsk, August 2000
CALLR: a semi-supervised cell-type annotation method for single-cell RNA sequencing data
A global test for groups of genes: testing association with a clinical outcome
Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics
A benchmark for automatic medical consultation system: frameworks, tasks and datasets
INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA
LIBRUS: combined machine learning and homology information for sequence-based ligand-binding residue prediction
APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks
QTL Express: mapping quantitative trait loci in simple and complex pedigrees
Copy number evolution with weighted aberrations in cancer
A Macintosh Hypercard compilation of small subunit ribosomal RNA sequences
Assessing semantic similarity measures for the characterization of human regulatory pathways
PyCoM: a python library for large-scale analysis of residue-residue coevolution data
TDAview: an online visualization tool for topological data analysis
ANTHEPROT: a package for protein sequence analysis using a microcomputer
A fuzzy guided genetic algorithm for operon prediction
Efficient recognition of immunoglobulin domains from amino acid sequences using a neural network
kmacs: the k -mismatch average common substring approach to alignment-free sequence comparison
Deep cross-omics cycle attention model for joint analysis of single-cell multi-omics data
Predicting candidate genes from phenotypes, functions and anatomical site of expression
PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data
No Promoter Left Behind (NPLB): learn de novo promoter architectures from genome-wide transcription start sites
Delta: a new web-based 3D genome visualization and analysis platform
CNAseg - a novel framework for identification of copy number changes in cancer from second-generation sequencing data
Bayesian adaptive sequence alignment algorithms
A RAPID algorithm for sequence database comparisons: application to the identification of vector contamination in the EMBL databases
Symmetry observations in long nucleotide sequences: a commentary on the Discovery Note of Qi and Cuticchia
Systematic inference of highways of horizontal gene transfer in prokaryotes
The binding site distance test score: a robust method for the assessment of predicted protein binding sites
Optimization of drug-target affinity prediction methods through feature processing schemes
Biological sequence modeling with convolutional kernel networks
Whole-proteome interaction mining
PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary
The LabBase system for data management in large scale biology research laboratories
Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using semantic web technologies
Towards Optimal Views of Proteins
PuffAligner: a fast, efficient and accurate aligner based on the Pufferfish index
A3D database: structure-based predictions of protein aggregation for the human proteome
Fast bootstrapping-based estimation of confidence intervals of expression levels and differential expression from RNA-Seq data
Net Nearest Neighbor Analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences
partDSA : deletion/substitution/addition algorithm for partitioning the covariate space in prediction
PharmacoGx: an R package for analysis of large pharmacogenomic datasets
NetLand: quantitative modeling and visualization of Waddington's epigenetic landscape using probabilistic potential
A deductive database system PACADE for analyzing 3-D and secondary structures of protein
Privacy-preserving federated unsupervised domain adaptation with application to age prediction from DNA methylation data
P-cats: prediction of catalytic residues in proteins from their tertiary structures
Capturing biological information with class?Cresponsibility?Ccollaboration cards
tSFM 1.0: tRNA Structure-Function Mapper
Database-driven Multi Locus Sequence Typing (MLST) of bacterial pathogens
Convolutional neural network architectures for predicting DNA-protein binding
mAHTPred: a sequence-based meta-predictor for improving the prediction of anti-hypertensive peptides using effective feature representation
INRICH: interval-based enrichment analysis for genome-wide association studies
Optimal word sizes for dissimilarity measures and estimation of the degree of dissimilarity between DNA sequences
A rate-distortion theory for gene regulatory networks and its application to logic gate consistency
CREMOFAC - a database of chromatin remodeling factors
MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types
PDBpaint, a visualization webservice to tag protein structures with sequence annotations
GeoWaVe: geometric median clustering with weighted voting for ensemble clustering of cytometry data
Estimating the mean in the space of ranked phylogenetic trees
A reformulation of pLSA for uncertainty estimation and hypothesis testing in bio-imaging
Robust linear regression methods in association studies
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
DV-Curve: a novel intuitive tool for visualizing and analyzing DNA sequences
Modeling one thousand intron length distributions with fitild
Identifying functional modules using expression profiles and confidence-scored protein interactions
An ensemble approach to predict binding hotspots in protein-RNA interactions based on SMOTE data balancing and Random Grouping feature selection strategies
Structural RNA alignment by multi-objective optimization
On the viability of unsupervised T-cell receptor sequence clustering for epitope preference
iS-CellR: a user-friendly tool for analyzing and visualizing single-cell RNA sequencing data
Improving peptide identification with single-stage mass spectrum peaks
A random variance model for detection of differential gene expression in small microarray experiments
benchdamic: benchmarking of differential abundance methods for microbiome data
itol.toolkit accelerates working with iTOL (Interactive Tree of Life) by an automated generation of annotation files
An incrementally updatable and scalable system for large-scale sequence search using the Bentley-Saxe transformation
Improving the TFold test for differential shotgun proteomics
FAIRsoft - a practical implementation of FAIR principles for research software
Ontology- and graph-based similarity assessment in biological networks
A finite state machine algorithm for finding restriction sites and other pattern matching applications
phylogeo: an R package for geographic analysis and visualization of microbiome data
Blockwise HMM computation for large-scale population genomic inference
Paircoil2: improved prediction of coiled coils from sequence
Ribopeaks: a web tool for bacterial classification through m/z data from ribosomal proteins
SOLpro: accurate sequence-based prediction of protein solubility
Taxonomy workbench
Analysis assistant for single-molecule force spectroscopy data on membrane proteins - MPTV
GenomeDecoder: inferring segmental duplications in highly repetitive genomic regions
Xlandscape: the graphical display of word frequencies in sequences
ShaKer: RNA SHAPE prediction using graph kernel
Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms
Prediction of viable circular permutants using a graph theoretic approach
FATHMM-XF: accurate prediction of pathogenic point mutations via extended features
Saint: a lightweight integration environment for model annotation
ProVision: a web-based platform for rapid analysis of proteomics data processed by MaxQuant
Codon Optimization OnLine (COOL): a web-based multi-objective optimization platform for synthetic gene design
Selection of oligonucleotides for whole-genome microarrays with semi-automatic update
ELBAMAP: software for management of electrophoresis banding patterns
PROFbval: predict flexible and rigid residues in proteins
Improved pairwise alignments of proteins in the Twilight Zone using local structure predictions
RIsearch: fast RNA-RNA interaction search using a simplified nearest-neighbor energy model
EBImage - an R package for image processing with applications to cellular phenotypes
LPTD: a novel linear programming-based topology determination method for cryo-EM maps
'TransMem': a neural network implemented in Excel spreadsheets for predicting transmembrane domains of proteins
Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths
JCell - a Java-based framework for inferring regulatory networks from time series data
BioTextQuest: a web-based biomedical text mining suite for concept discovery
Fast and accurate short read alignment with Burrows-Wheeler transform
Large-scale structure prediction by improved contact predictions and model quality assessment
Abstracting the dynamics of biological pathways using information theory: a case study of apoptosis pathway
mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data
In vitro versus in vivo compositional landscapes of histone sequence preferences in eucaryotic genomes
Algebraic stability indicators for ranked lists in molecular profiling
Quality estimation of multiple sequence alignments by Bayesian hypothesis testing
The impossible challenge of estimating non-existent moments of the Chemical Master Equation
Lower confidence bounds for prediction accuracy in high dimensions via AROHIL Monte Carlo
Machine learning based prediction for peptide drift times in ion mobility spectrometry
galaxie-CGI scripts for sequence identification through automated phylogenetic analysis
Correction to: Snapper: high-sensitive detection of methylation motifs based on Oxford Nanopore reads
LBIBCell: a cell-based simulation environment for morphogenetic problems
Integrative deep models for alternative splicing
BCE: a tool for software integration
Correcting mistakes in predicting distributions
Phylogenomic branch length estimation using quartets
Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity
PeCoP: automatic determination of persistently conserved positions in protein families
HaploTypo: a variant-calling pipeline for phased genomes
VirPreNet: a weighted ensemble convolutional neural network for the virulence prediction of influenza A virus using all eight segments
Representation and inference of cellular architecture for metabolic reconstruction and modeling
ASAR: visual analysis of metagenomes in R
Simultaneous discovery of cancer subtypes and subtype features by molecular data integration
CistromeMap: a knowledgebase and web server for ChIP-Seq and DNase-Seq studies in mouse and human
Large-scale benchmark of Endeavour using MetaCore maps
MetPA: a web-based metabolomics tool for pathway analysis and visualization
ProtocolNavigator: emulation-based software for the design, documentation and reproduction biological experiments
PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics
HyPhy: hypothesis testing using phylogenies
SPOT-1D-Single: improving the single-sequence-based prediction of protein secondary structure, backbone angles, solvent accessibility and half-sphere exposures using a large training set and ensembled deep learning
Mining frequent stem patterns from unaligned RNA sequences
Is the Bombali virus pathogenic in humans?
FastMix: a versatile data integration pipeline for cell type-specific biomarker inference
BatchI: Batch effect Identification in high-throughput screening data using a dynamic programming algorithm
Flexible algorithm for direct multiple alignment of protein structures and sequences
CellMontage: Similar Expression Profile Search Server
Con-Struct Map: a comparative contact map analysis tool
Embedding-based alignment: combining protein language models with dynamic programming alignment to detect structural similarities in the twilight-zone
Reference panel-guided super-resolution inference of Hi-C data
stringgaussnet: from differentially expressed genes to semantic and Gaussian networks generation
Graspot: a graph attention network for spatial transcriptomics data integration with optimal transport
MIRPIPE: quantification of microRNAs in niche model organisms
DomCut: prediction of inter-domain linker regions in amino acid sequences
NewWave : a scalable R/Bioconductor package for the dimensionality reduction and batch effect removal of single-cell RNA-seq data
MoMA-LoopSampler: a web server to exhaustively sample protein loop conformations
MEDIPIPE: an automated and comprehensive pipeline for cfMeDIP-seq data quality control and analysis
ddPCRclust: an R package and Shiny app for automated analysis of multiplexed ddPCR data
XML, bioinformatics and data integration
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa)
ExaML version 3: a tool for phylogenomic analyses on supercomputers
BalLeRMix +: mixture model approaches for robust joint identification of both positive selection and long-term balancing selection
Knot_pull - python package for biopolymer smoothing and knot detection
Assessing the accuracy of prediction algorithms for classification: an overview
A fast algorithm for evaluating an approximation to the information enclosed within coronas and their sectors in square matrices
PALMA: mRNA to genome alignments using large margin algorithms
Automating candidate gene prioritization with large language models: from naive scoring to literature-grounded validation
Network approach to mutagenesis sheds insight on phage resistance in mycobacteria
Beyond the "best" match: machine learning annotation of protein sequences by integration of different sources of information
Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways
circtools - a one-stop software solution for circular RNA research
PathwAX II: network-based pathway analysis with interactive visualization of network crosstalk
ERGC: an efficient referential genome compression algorithm
PSoL: a positive sample only learning algorithm for finding non-coding RNA genes
DECODE: a computational pipeline to discover T cell receptor binding rules
GraphDTA: predicting drug-target binding affinity with graph neural networks
APL@voro - interactive visualization and analysis of cell membrane simulations
A local multiple alignment method for detection of non-coding RNA sequences
Inter-functional analysis of high-throughput phenotype data by non-parametric clustering and its application to photosynthesis
SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics
Few crucial links assure checkpoint efficiency in the yeast cell-cycle network
Calculating and scoring high quality multiple flexible protein structure alignments
Computational discovery of human coding and non-coding transcripts with conserved splice sites
Tclass: tumor classification system based on gene expression profile
Inferring consensus structure from nucleic acid sequences
COMMO: a web server for the identification and analysis of consensus gene modules across multiple methods
Development of predictive models of laboratory animal growth using artificial neural networks
Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences
LRpath: a logistic regression approach for identifying enriched biological groups in gene expression data
NOrMAL: accurate nucleosome positioning using a modified Gaussian mixture model
Comparisons and validation of statistical clustering techniques for microarray gene expression data
Correction to: Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data
mzRAPP: a tool for reliability assessment of data pre-processing in non-targeted metabolomics
Tasuke: a web-based visualization program for large-scale resequencing data
Comprehensive evaluation of deep learning architectures for prediction of DNA/RNA sequence binding specificities
Noise peak filtering in multi-dimensional NMR spectra using convolutional neural networks
Genomon ITDetector: a tool for somatic internal tandem duplication detection from cancer genome sequencing data
The Bio-Community Perl toolkit for microbial ecology
Comparison of computational methods for the identification of cell cycle-regulated genes
PROMOT: modular modeling for systems biology
Designing hardware for protein sequence analysis
Improved mean estimation and its application to diagonal discriminant analysis
Text similarity: an alternative way to search MEDLINE
Data mining in bioinformatics using Weka
Network analysis of synonymous codon usage
Autoencoder-based phenotyping of ophthalmic images highlights genetic loci influencing retinal morphology and provides informative biomarkers
Accurate haplotype-resolved assembly reveals the origin of structural variants for human trios
Proteomic analysis and prediction of human phosphorylation sites in subcellular level reveal subcellular specificity
A framework for exhaustive modelling of genetic interaction patterns using Petri nets
RPPanalyzer: Analysis of reverse-phase protein array data
An R package to analyse LC/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit)
Erratum to: A data-adaptive Bayesian regression approach for polygenic risk prediction
PatchWorkPlot: simultaneous visualization of local alignments across multiple sequences
kmerPyramid: an interactive visualization tool for nucleobase and k-mer frequencies
ReSimNet: drug response similarity prediction using Siamese neural networks
HIPPIE: a high-throughput identification pipeline for promoter interacting enhancer elements
Disambiguating the species of biomedical named entities using natural language parsers
End-to-end simulation of nanopore sequencing signals with feed-forward transformers
Integrating human and murine anatomical gene expression data for improved comparisons
STAMS: STRING-assisted module search for genome wide association studies and application to autism
2023 Outstanding Contributions to ISCB Award: Shoba Ranganathan
MolPLA: a molecular pretraining framework for learning cores, R-groups and their linker joints
Optimality and identification of dynamic models in systems biology: an inverse optimal control framework
SpaceX: gene co-expression network estimation for spatial transcriptomics
Complete populations of virtual patients for in silico clinical trials
Automatic selection of reference taxa for protein-protein interaction prediction with phylogenetic profiling
EvoAug-TF: extending evolution-inspired data augmentations for genomic deep learning to TensorFlow
The nPYc-Toolbox, a Python module for the pre-processing, quality-control and analysis of metabolic profiling datasets
PQuad - a visual analysis platform for proteomic data exploration of microbial organisms
SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing
Rchange: algorithms for computing energy changes of RNA secondary structures in response to base mutations
KNeMAP: a network mapping approach for knowledge-driven comparison of transcriptomic profiles
Correction to: Joint registration of multiple point clouds for fast particle fusion in localization microscopy
HapMuC: somatic mutation calling using heterozygous germ line variants near candidate mutations
Gene perturbation and intervention in probabilistic Boolean networks
Accurate anchoring alignment of divergent sequences
VIQoR: a web service for visually supervised protein inference and protein quantification
PCN-Miner: an open-source extensible tool for the analysis of Protein Contact Networks
Driver gene detection through Bayesian network integration of mutation and expression profiles
SeqLib: a C ++ API for rapid BAM manipulation, sequence alignment and sequence assembly
Segmentation of long genomic sequences into domains with homogeneous composition with BASIO software
Knowledge representation of signal transduction pathways
Improved model-based, platform-independent feature extraction for mass spectrometry
SpliceMachine: predicting splice sites from high-dimensional local context representations
Enlighten2: molecular dynamics simulations of protein-ligand systems made accessible