yusuke1997/dblp-id-title huggingface dataset:
CNGPLD: case-control copy-number analysis using Gaussian process latent difference
ecmtool : fast and memory-efficient enumeration of elementary conversion modes
ADAM: automated data management for research datasets
Testing for presence of known and unknown molecules in imaging mass spectrometry
Accurate flux predictions using tissue-specific gene expression in plant metabolic modeling
Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study
DeMaSk: a deep mutational scanning substitution matrix and its use for variant impact prediction
The Ensembl REST API: Ensembl Data for Any Language
DeepEBV: a deep learning model to predict Epstein-Barr virus (EBV) integration sites
Data pre-processing in liquid chromatography-mass spectrometry-based proteomics
Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming
Image analysis of restriction enzyme fingerprint autoradiograms
EM-stellar: benchmarking deep learning for electron microscopy image segmentation
A method for comparing circular genomes from gene locations: application to mitochondrial genomes
Growing genetic regulatory networks from seed genes
Repitools : an R package for the analysis of enrichment-based epigenomic data
A network-driven approach for genome-wide association mapping
Normalization of metabolomics data with applications to correlation maps
New Leadership for Bioinformatics
A computational search for box C/D snoRNA genes in the Drosophila melanogaster genome
An open letter to the scientific journals
Primerdiffer: a python command-line module for large-scale primer design in haplotype genotyping
Fast alignment of fragmentation trees
LightAssembler: fast and memory-efficient assembly algorithm for high-throughput sequencing reads
MMM: a sequence-to-structure alignment protocol
PCGAN: a generative approach for protein complex identification from protein interaction networks
GTDB-Tk v2: memory friendly classification with the genome taxonomy database
A simple approach for the distribution of computationally intense tasks in an heterogeneous environment: distribution of the MDPP image-processing package
The Fifth Georgia Tech - Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology
ArrayCyGHt: a web application for analysis and visualization of array-CGH data
Model-based design of bistable cell factories for metabolic engineering
A robust AMMI model for the analysis of genotype-by-environment data
SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference
Bioinformatics - Challenges in 2001
High-performance signal peptide prediction based on sequence alignment techniques
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments
A multi-scale convolutional neural network for phenotyping high-content cellular images
An extensive benchmark study on biomedical text generation and mining with ChatGPT
MSIdV: a versatile tool to visualize biological indices from mass spectrometry imaging data
Comment on: 'ERGC: an efficient referential genome compression algorithm'
HAT: haplotype assembly tool using short and error-prone long reads
Flexiplex: a versatile demultiplexer and search tool for omics data
Pairwise RNA secondary structure alignment with conserved stem pattern
SCAMP: a general-purpose simulator and metabolic control analysis program
EBD: an eye biomarker database
Pattern recognition in DNA sequences and its application to consensus foot-printing
Genomic dark matter: the reliability of short read mapping illustrated by the genome mappability score
Context-sensitive data integration and prediction of biological networks
Robust inference of population structure from next-generation sequencing data with systematic differences in sequencing
A neural network method for prediction of ?-turn types in proteins using evolutionary information
Using explainable machine learning to uncover the kinase-substrate interaction landscape
Information theoretic generalized Robinson-Foulds metrics for comparing phylogenetic trees
2022 ISCB Overton Prize: Po-Ru Loh
CMF-Impute: an accurate imputation tool for single cell RNA-seq data
Precision Lasso: accounting for correlations and linear dependencies in high-dimensional genomic data
Model learning to identify systemic regulators of the peripheral circadian clock
3DinSight: an integrated relational database and search tool for the structure, function and properties of biomolecules
Recovering metabolic pathways via optimization
PEGASE: a machine language program for DNA sequence analysis on Apple II microcomputer using a binary coding of nucleotides
PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources
Weakly supervised learning of information structure of scientific abstracts - is it accurate enough to benefit real-world tasks in biomedicine?
Chromaligner: a web server for chromatogram alignment
tttrlib: modular software for integrating fluorescence spectroscopy, imaging, and molecular modeling
NPM: latent batch effects correction of omics data by nearest-pair matching
Mass-spectrometry-based spatial proteomics data analysis using pRoloc and pRolocdata
ProtDec-LTR2.0: an improved method for protein remote homology detection by combining pseudo protein and supervised Learning to Rank
Robust PCA and classification in biosciences
CYSTM, a novel cysteine-rich transmembrane module with a role in stress tolerance across eukaryotes
The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models
ChimeraScan: a tool for identifying chimeric transcription in sequencing data
Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries
FoldUnfold: web server for the prediction of disordered regions in protein chain
Using the plurality of codon positions to identify deleterious variants in human exomes
JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm
MetaABC - an integrated metagenomics platform for data adjustment, binning and clustering
Computational drug repositioning using low-rank matrix approximation and randomized algorithms
Ultranet: efficient solver for the sparse inverse covariance selection problem in gene network modeling
Classifying G-protein coupled receptors with support vector machines
PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and for studying the structure--activity relationships in protein families
A fast and powerful tree-based association test for detecting complex joint effects in case-control studies
ELMER v.2: an R/Bioconductor package to reconstruct gene regulatory networks from DNA methylation and transcriptome profiles
Evolution of amino acid biosynthesis and enzymes with broad substrate specificity
LD Hub: a centralized database and web interface to perform LD score regression that maximizes the potential of summary level GWAS data for SNP heritability and genetic correlation analysis
RNATOPS-W: a web server for RNA structure searches of genomes
A new algorithm for context-based biomedical diagram similarity estimation
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems
Text mining for contexts and relationships in cancer genomics literature
Resolving single-cell heterogeneity from hundreds of thousands of cells through sequential hybrid clustering and NMF
The open targets post-GWAS analysis pipeline
Predicting helix-helix interactions from residue contacts in membrane proteins
Generative probabilistic models for protein-protein interaction networks - the biclique perspective
gene2drug: a computational tool for pathway-based rational drug repositioning
Fast and efficient dynamic nested effects models
matchprobes: a Bioconductor package for the sequence-matching of microarray probe elements
SharePro: an accurate and efficient genetic colocalization method accounting for multiple causal signals
matFR: a MATLAB toolbox for feature ranking
Dynamic applicability domain (dAD): compound-target binding affinity estimates with local conformal prediction
LOCP - locating pilus operons in Gram-positive bacteria
StabilitySort: assessment of protein stability changes on a genome-wide scale to prioritize potentially pathogenic genetic variation
PROSS 2: a new server for the design of stable and highly expressed protein variants
An improved constraint filtering technique for inferring hidden states and parameters of a biological model
Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer
A probabilistic model of nuclear import of proteins
Evaluation of genome-wide association study results through development of ontology fingerprints
Building large updatable colored de Bruijn graphs via merging
ACGT - A Comparative Genomics Tool
Manifold alignment for heterogeneous single-cell multi-omics data integration using Pamona
PIQA: pipeline for Illumina G1 genome analyzer data quality assessment
AncestryView: data-driven visualization of whole-genome local-ancestry
HypercubeME: two hundred million combinatorially complete datasets from a single experiment
Sapling: accelerating suffix array queries with learned data models
Intrinsically disordered C-terminal segments of voltage-activated potassium channels: a possible fishing rod-like mechanism for channel binding to scaffold proteins
Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies
Quaternionic periodicity transform: an algebraic solution to the tandem repeat detection problem
GSA-Lightning: ultra-fast permutation-based gene set analysis
Very low-depth whole-genome sequencing in complex trait association studies
AXE: a program for isolating short segments of long DNA sequences
Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R
A method for de novo nucleic acid diagnostic target discovery
FlaiMapper: computational annotation of small ncRNA-derived fragments using RNA-seq high-throughput data
Large-scale 16S gene assembly using metagenomics shotgun sequences
Domain annotation of trimeric autotransporter adhesins - daTAA
DyNet: visualization and analysis of dynamic molecular interaction networks
BioSilico: an integrated metabolic database system
Optimal seed solver: optimizing seed selection in read mapping
cudaMMC: GPU-enhanced multiscale Monte Carlo chromatin 3D modelling
StochDecomp - Matlab package for noise decomposition in stochastic biochemical systems
Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease
CryptoBench: cryptic protein-ligand binding sites dataset and benchmark
Network-constrained regularization and variable selection for analysis of genomic data
Dotlet: diagonal plots in a Web browser
Positive-unlabeled ensemble learning for kinase substrate prediction from dynamic phosphoproteomics data
Supervised machine learning techniques for the classification of metabolic disorders in newborns
New algorithms for detecting multi-effect and multi-way epistatic interactions
Quantifying the similarity of topological domains across normal and cancer human cell types
Osiris: an integrated promoter database for Oryza sativa L.
RefProtDom: a protein database with improved domain boundaries and homology relationships
SpecieScan: semi-automated taxonomic identification of bone collagen peptides from MALDI-ToF-MS
Prequips - an extensible software platform for integration, visualization and analysis of LC-MS/MS proteomics data
PolarProtPred: predicting apical and basolateral localization of transmembrane proteins using putative short linear motifs and deep learning
Positional sequencing by hybridization
An improved secondary structure computation method and its application to intervening sequence in the human alpha-likeglobin mRNA precursors
ODEN: a program package for molecular evolutionary analysis and database search of DNA and amino acid sequences
Feature-incorporated alignment based ligand-binding residue prediction for carbohydrate-binding modules
Estimating misclassification error with small samples via bootstrap cross-validation
A simulated annealing algorithm for finding consensus sequences
ClusPro: an automated docking and discrimination method for the prediction of protein complexes
Approximate geodesic distances reveal biologically relevant structures in microarray data
LIGAND: chemical database for enzyme reactions
TISIDB: an integrated repository portal for tumor-immune system interactions
ROSO: optimizing oligonucleotide probes for microarrays
Accurate sequence-based prediction of catalytic residues
Response envelope analysis for quantitative evaluation of drug combinations
TRASH: Tandem Repeat Annotation and Structural Hierarchy
Wrangling Galaxy's reference data
CoV-Spectrum: analysis of globally shared SARS-CoV-2 data to identify and characterize new variants
Pathway analysis using random forests with bivariate node-split for survival outcomes
Protein complex prediction based on simultaneous protein interaction network
HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization
Mobyle SNAP Workbench: a web-based analysis portal for population genetics and evolutionary genomics
GenoMetric Query Language: a novel approach to large-scale genomic data management
<tt>tagtango</tt>: an application to compare single-cell annotations
SimMS: a GPU-accelerated cosine similarity implementation for tandem mass spectrometry
Making novel proteins from pseudogenes
Unbiased probabilistic taxonomic classification for DNA barcoding
A stochastic expectation and maximization algorithm for detecting quantitative trait-associated genes
Studying the co-evolution of protein families with the Mirrortree web server
4D nucleome Analysis Toolbox: analysis of Hi-C data with abnormal karyotype and time series capabilities
Visualization and quality assessment of de novo genome assemblies
Tropical principal component analysis on the space of phylogenetic trees
ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
A comparative method for identification of gene structures and alternatively spliced variants
Finding the common structure shared by two homologous RNAs
Mango: a bias-correcting ChIA-PET analysis pipeline
PZLAST: an ultra-fast amino acid sequence similarity search server against public metagenomes
Discovering misannotated lncRNAs using deep learning training dynamics
Joint analysis of multiple phenotypes for extremely unbalanced case-control association studies using multi-layer network
Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets
Genetic Simulation Resources: a website for the registration and discovery of genetic data simulators
The significance of protein sequence similarities
International Society for Computational Biology Honors Goncalo Abecasis with Top Bioinformatics/Computational Biology Award for 2013
Deconvolution of expression for nascent RNA-sequencing data (DENR) highlights pre-RNA isoform diversity in human cells
DeepPurpose: a deep learning library for drug-target interaction prediction
AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions
Assigning spectrum-specific P -values to protein identifications by mass spectrometry
Simulation, power evaluation and sample size recommendation for single-cell RNA-seq
Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks
utr.annotation: a tool for annotating genomic variants that could influence post-transcriptional regulation
PEPSI-Dock: a detailed data-driven protein-protein interaction potential accelerated by polar Fourier correlation
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
CCBuilder: an interactive web-based tool for building, designing and assessing coiled-coil protein assemblies
A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
PanEffect: a pan-genome visualization tool for variant effects in maize
Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions
ModL: exploring and restoring regularity when testing for positive selection
GIMSAN: a Gibbs motif finder with significance analysis
Cell-Dock: high-performance protein-protein docking
Finding steady alignments: similarity and distance
AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs
Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit
BioLingua: a programmable knowledge environment for biologists
OutlierD: an R package for outlier detection using quantile regression on mass spectrometry data
Palantir: a springboard for the analysis of secondary metabolite gene clusters in large-scale genome mining projects
PINdb: a database of nuclear protein complexes from human and yeast
DeepES: deep learning-based enzyme screening to identify orphan enzyme genes
ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization
Genview and Gencode: a pair of programs to test theories of genetic code evolution
Enhanced statistics for local alignment of multiple alignments improves prediction of protein function and structure
nanoTRON: a Picasso module for MLP-based classification of super-resolution data
Phy-Mer: a novel alignment-free and reference-independent mitochondrial haplogroup classifier
A model-based optimization framework for the inference on gene regulatory networks from DNA array data
Compression of genomic sequencing reads via hash-based reordering: algorithm and analysis
An algorithm for modularity analysis of directed and weighted biological networks based on edge-betweenness centrality
OKVAR-Boost: a novel boosting algorithm to infer nonlinear dynamics and interactions in gene regulatory networks
An efficient approach based on multi-sources information to predict circRNA-disease associations using deep convolutional neural network
rtracklayer: an R package for interfacing with genome browsers
The use of gene ontology evidence codes in preventing classifier assessment bias
CAFE 5 models variation in evolutionary rates among gene families
Hexa-Longin domain scaffolds for inter-Rab signalling
An accurate method for identifying recent recombinants from unaligned sequences
Dynamic simulation of protein complex formation on a genomic scale
Multi-indicator comparative evaluation for deep learning-based protein sequence design methods
Improving structure alignment-based prediction of SCOP families using Vorolign Kernels
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
ConsInspector 3.0: new library and enhanced functionality
IPPRED: Server for Proteins Interactions Inference
Predicting citation count of Bioinformatics papers within four years of publication
A secondary and tertiary structure editor for nucleic acids
SARS2020: an integrated platform for identification of novel coronavirus by a consensus sequence-function model
BLSSpeller: exhaustive comparative discovery of conserved cis -regulatory elements
Poorly conserved ORFs in the genome of the archaea Halobacterium sp. NRC-1 correspond to expressed proteins
An active registry for bioinformatics web services
Ontogenomic study of the relationship between number of gene splice variants and GO categorization
ISCB/SPRINGER series in computational biology
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network
ANISE : an application to design mechanobiology simulations of planar epithelia
Vcfexpress: flexible, rapid user-expressions to filter and format VCFs
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields
Identification of transcription factor cooperativity via stochastic system model
MSMAD: a computationally efficient method for the analysis of noisy array CGH data
Rare variant discovery and calling by sequencing pooled samples with overlaps
Evolutionary analysis of enzymes using Chisel
Sputnik: ad hoc distributed computation
rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments
Storing biological sequence databases in relational form
SYNPHONI: scale-free and phylogeny-aware reconstruction of synteny conservation and transformation across animal genomes
Ratio adjustment and calibration scheme for gene-wise normalization to enhance microarray inter-study prediction
Ontology for medicinal materials based on traditional Korean medicine
Multiple alignment of sequences on parallel computers
Curatr: a web application for creating, curating and sharing a mass spectral library
A high-throughput framework to detect synapses in electron microscopy images
An OMICs-based meta-analysis to support infection state stratification
iDBPs: a web server for the identification of DNA binding proteins
The differential activity of biological processes in tissues and cell subsets can illuminate disease-related processes and cell-type identities
A menu-shell for the GCG programs
Markov model recognition and classification of DNA/protein sequences within large text databases
Induction of T-cell memory by a dendritic cell vaccine: a computational model
Extra-binomial variation approach for analysis of pooled DNA sequencing data
pyABC: distributed, likelihood-free inference
An automatic tool to analyze and cluster macromolecular conformations based on self-organizing maps
Mobility-based prediction of hydration structures of protein surfaces
PEAR: a fast and accurate Illumina Paired-End reAd mergeR
Efficient population-scale variant analysis and prioritization with VAPr
GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems
FUN-L: gene prioritization for RNAi screens
A framework for modeling epistatic interaction
SplitMEM: a graphical algorithm for pan-genome analysis with suffix skips
TSpred: a robust prediction framework for TCR-epitope interactions using paired chain TCR sequence data
RNAlign program: alignment of RNA sequences using both primary and secondary structures
Estimating optimal window size for analysis of low-coverage next-generation sequence data
damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets
Structured sparse canonical correlation analysis for brain imaging genetics: an improved GraphNet method
isolateR: an R package for generating microbial libraries from Sanger sequencing data
Charge asymmetry in the proteins of the outer membrane
Cooler: scalable storage for Hi-C data and other genomically labeled arrays
ChAMP: 450k Chip Analysis Methylation Pipeline
NanoStringNorm: an extensible R package for the pre-processing of NanoString mRNA and miRNA data
Defining and predicting structurally conserved regions in protein superfamilies
A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure
rHAT: fast alignment of noisy long reads with regional hashing
Prediction of zinc finger DNA binding protein
Plant 3D (P3D): a plant phenotyping toolkit for 3D point clouds
Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code
Prediction of protein-protein interactions using random decision forest framework
Semi-supervised learning improves gene expression-based prediction of cancer recurrence
NTFD - a stand-alone application for the non-targeted detection of stable isotope-labeled compounds in GC/MS data
glactools: a command-line toolset for the management of genotype likelihoods and allele counts
Quantifying spatial relationships from whole retinal images
QuagmiR: a cloud-based application for isomiR big data analytics
Meisetz and the birth of the KRAB motif
BioSmalltalk: a pure object system and library for bioinformatics