yusuke1997/dblp-id-title huggingface dataset:
Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias
Image library of biological macromolecules
chem16S : community-level chemical metrics for exploring genomic adaptation to environments
SBML and CellML translation in Antimony and JSim
Combinatorial and statistical prediction of gene expression from haplotype sequence
An information theoretic approach for analyzing temporal patterns of gene expression
A Bayesian approach to discriminate between alternative DNA sequence segmentations
Improved enzyme annotation with EC-specific cutoffs using DETECT v2
TCellXTalk facilitates the detection of co-modified peptides for the study of protein post-translational modification cross-talk in T cells
Synggen: fast and data-driven generation of synthetic heterogeneous NGS cancer data
A Comparison of Physical Mapping Algorithms Based on the Maximum Likelihood Model
ScaffMatch: scaffolding algorithm based on maximum weight matching
SANS: high-throughput retrieval of protein sequences allowing 50% mismatches
Correction to: HOMELETTE: a unified interface to homology modelling software
A computer program to calculate and design oligonucleotide primers from amino acid sequences
CDACHIE: chromatin domain annotation by integrating chromatin interaction and epigenomic data with contrastive learning
gargammel: a sequence simulator for ancient DNA
HOPS: high-performance library for (non-)uniform sampling of convex-constrained models
Sparse least trimmed squares regression with compositional covariates for high-dimensional data
GapRepairer: a server to model a structural gap and validate it using topological analysis
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
Dual-dropout graph convolutional network for predicting synthetic lethality in human cancers
Prediction of protein-binding residues: dichotomy of sequence-based methods developed using structured complexes versus disordered proteins
Optimization of minimum set of protein-DNA interactions: a quasi exact solution with minimum over-fitting
PALM: a powerful and adaptive latent model for prioritizing risk variants with functional annotations
CpGFilter: model-based CpG probe filtering with replicates for epigenome-wide association studies
An X windows and UNIX implementation of our sequence analysis package
MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics
Microarray phenotyping in Dictyostelium reveals a regulon of chemotaxis genes
GenCLiP 2.0: a web server for functional clustering of genes and construction of molecular networks based on free terms
HaploGrouper: a generalized approach to haplogroup classification
Markov dynamic models for long-timescale protein motion
Integrate multiple traits to detect novel trait-gene association using GWAS summary data with an adaptive test approach
hiHMM: Bayesian non-parametric joint inference of chromatin state maps
G2S: a web-service for annotating genomic variants on 3D protein structures
HRIBO: high-throughput analysis of bacterial ribosome profiling data
FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps
MONET: a toolbox integrating top-performing methods for network modularization
PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways
Refined algorithm and computer program for calculating all non-negative fluxes admissible in steady states of biochemical reaction systems with or without some flux rates fixed
ARTS: automated randomization of multiple traits for study design
Modeling within-motif dependence for transcription factor binding site predictions
CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences
IntPred: a structure-based predictor of protein-protein interaction sites
Forecasting residue-residue contact prediction accuracy
Evaluation of methods for the prediction of membrane spanning regions
viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
A fast Bayesian change point analysis for the segmentation of microarray data
EPSOL: sequence-based protein solubility prediction using multidimensional embedding
Sparse and skew hashing of K-mers
mimiRNA: a microRNA expression profiler and classification resource designed to identify functional correlations between microRNAs and their targets
Cryo-shift: reducing domain shift in cryo-electron subtomograms with unsupervised domain adaptation and randomization
A fast and memory-efficient implementation of the transfer bootstrap
tmVar 3.0: an improved variant concept recognition and normalization tool
CRANN: detecting adaptive evolution in protein-coding DNA sequences
GraphBin: refined binning of metagenomic contigs using assembly graphs
COBRAC: a fast implementation of convex biclustering with compression
FSSA: a novel method for identifying functional signatures from structural alignments
Organism-specific training improves performance of linear B-cell epitope prediction
simpleaf : a simple, flexible, and scalable framework for single-cell data processing using alevin-fry
FuMa: reporting overlap in RNA-seq detected fusion genes
The Scramble conversion tool
Identifying discriminative classification-based motifs in biological sequences
Network2Canvas: network visualization on a canvas with enrichment analysis
QuickEd: high-performance exact sequence alignment based on bound-and-align
DAPAR & ProStaR: software to perform statistical analyses in quantitative discovery proteomics
A discrete model of bacterial metabolism
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations
SmoothT - a server constructing low-energy pathways from conformational ensembles for interactive visualization and enhanced sampling
Unsupervised topological alignment for single-cell multi-omics integration
Conserved network motifs allow protein-protein interaction prediction
Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data
Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization
Dream: powerful differential expression analysis for repeated measures designs
OBO-Edit - an ontology editor for biologists
A trimming-and-retrieving alignment scheme for reduced representation bisulfite sequencing
muCNV: genotyping structural variants for population-level sequencing
PASPA: a web server for mRNA poly(A) site predictions in plants and algae
sMOL Explorer: an open source, web-enabled database and exploration tool for Small MOLecules datasets
IndeCut evaluates performance of network motif discovery algorithms
ChemDistiller: an engine for metabolite annotation in mass spectrometry
dipwmsearch: a Python package for searching di-PWM motifs
Differential privacy under dependent tuples - the case of genomic privacy
TEAM: efficient two-locus epistasis tests in human genome-wide association study
AnaCoDa: analyzing codon data with Bayesian mixture models
Donuts, scratches and blanks: robust model-based segmentation of microarray images
Privacy preserving protocol for detecting genetic relatives using rare variants
Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks
Automated calibration of consensus weighted distance-based clustering approaches using sharp
Cancer outlier detection based on likelihood ratio test
CANTATA - prediction of missing links in Boolean networks using genetic programming
Unsupervised discovery of phenotype-specific multi-omics networks
j NMFMA: a joint non-negative matrix factorization meta-analysis of transcriptomics data
The automated function prediction SIG looks back at 2013 and prepares for 2014
MTM: a multi-task learning framework to predict individualized tissue gene expression profiles
MetQy - an R package to query metabolic functions of genes and genomes
Detecting critical state before phase transition of complex biological systems by hidden Markov model
How many samples are needed to build a classifier: a general sequential approach
HPOLabeler: improving prediction of human protein-phenotype associations by learning to rank
Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes
VISOR: a versatile haplotype-aware structural variant simulator for short- and long-read sequencing
Beyond accuracy: creating interoperable and scalable text-mining web services
OMSim: a simulator for optical map data
Sfixem - graphical sequence feature display in Java
A unified statistical model to support local sequence order independent similarity searching for ligand-binding sites and its application to genome-based drug discovery
echolocatoR: an automated end-to-end statistical and functional genomic fine-mapping pipeline
IRView: a database and viewer for protein interacting regions
Meltos: multi-sample tumor phylogeny reconstruction for structural variants
Quantifying the biological significance of gene ontology biological processes - implications for the analysis of systems-wide data
ExpTreeDB: Web-based query and visualization of manually annotated gene expression profiling experiments of human and mouse from GEO
onlineFDR: an R package to control the false discovery rate for growing data repositories
atomium - a Python structure parser
Quantifying and correcting slide-to-slide variation in multiplexed immunofluorescence images
LumberJack: a heuristic tool for sequence alignment exploration and phylogenetic inference
LaboImage: a workstation environment for research in image processing and analysis
Signal analysis for genome-wide maps of histone modifications measured by ChIP-seq
A quantitative genotype algorithm reflecting H5N1 Avian influenza niches
Fast integration-based prediction bands for ordinary differential equation models
Discovering molecular functions significantly related to phenotypes by combining gene expression data and biological information
Reproducible and replicable comparisons using SummarizedBenchmark
SigHotSpotter: scRNA-seq-based computational tool to control cell subpopulation phenotypes for cellular rejuvenation strategies
Scalable inference of transcriptional kinetic parameters from MS2 time series data
All-FIT: allele-frequency-based imputation of tumor purity from high-depth sequencing data
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold
SBARS: fast creation of dotplots for DNA sequences on different scales using GA-, GC-content
PhylOligo: a package to identify contaminant or untargeted organism sequences in genome assemblies
gm: a practical tool for automating DNA sequence analysis
REDEMPTION: reduced dimension ensemble modeling and parameter estimation
RNAdraw: an integrated program for RNA secondary structure calculation and analysis under 32-bit Microsoft Windows
Microbiome Modelling Toolbox 2.0: efficient, tractable modelling of microbiome communities
AutoLabDB: a substantial open source database schema to support a high-throughput automated laboratory
MUM&Co: accurate detection of all SV types through whole-genome alignment
EpiSAFARI: sensitive detection of valleys in epigenetic signals for enhancing annotations of functional elements
PanKmer: k -mer-based and reference-free pangenome analysis
Protein-protein interaction site prediction through combining local and global features with deep neural networks
PANTHER-PSEP: predicting disease-causing genetic variants using position-specific evolutionary preservation
Microcomputer simulation of steady-state enzyme kinetics for educational purposes
A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
Prediction error estimation: a comparison of resampling methods
Additional Gene Ontology structure for improved biological reasoning
forqs: forward-in-time simulation of recombination, quantitative traits and selection
pycofitness - Evaluating the fitness landscape of RNA and protein sequences
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data
DOGMA: domain-based transcriptome and proteome quality assessment
GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks
C-It-Loci: a knowledge database for tissue-enriched loci
An Ensemble Spectral Prediction (ESP) model for metabolite annotation
ACE: accurate correction of errors using K -mer tries
Pygenomics: manipulating genomic intervals and data files in Python
A Lasso multi-marker mixed model for association mapping with population structure correction
ALPHA: a toolkit for Automated Local PHylogenomic Analyses
Assembling millions of short DNA sequences using SSAKE
Hierarchical sets: analyzing pangenome structure through scalable set visualizations
hictk: blazing fast toolkit to work with .hic and .cool files
Exploiting transfer learning for the reconstruction of the human gene regulatory network
DeFries-Fulker multiple regression analysis of sibship QTL data: a SAS®macro
Construction of DNA restriction maps based on a simplified experiment
poRe: an R package for the visualization and analysis of nanopore sequencing data
Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry
Access to ground truth at unconstrained size makes simulated data as indispensable as experimental data for bioinformatics methods development and benchmarking
Quantifying cancer progression with conjunctive Bayesian networks
ScribbleDom: using scribble-annotated histology images to identify domains in spatial transcriptomics data
ICMA: an integrated cardiac modeling and analysis platform
Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets
emeraLD: rapid linkage disequilibrium estimation with massive datasets
A comprehensive representation of extensive similarity linkage between large numbers of proteins
Determining parameters for non-linear models of multi-loop free energy change
Revisiting amino acid substitution matrices for identifying distantly related proteins
A system for pattern matching applications on biosequences
NFPws: a web server for delineating broadly neutralizing antibody specificities from serum HIV-1 neutralization data
NAViGaTOR: Network Analysis, Visualization and Graphing Toronto
Combinatorial motif analysis and hypothesis generation on a genomic scale
Squiggle: a user-friendly two-dimensional DNA sequence visualization tool
Protael: protein data visualization library for the web
Custom workflows to improve joint variant calling from multiple related tumour samples: FreeBayesSomatic and Strelka2Pass
Estimation of population genetic parameters using an EM algorithm and sequence data from experimental evolution populations
Estimation of false discovery proportion under general dependence
A MATLAB toolbox for structural kinetic modeling
Protein threading using residue co-variation and deep learning
Graph analysis of fragmented long-read bacterial genome assemblies
Analysis of genomic sequences by Chaos Game Representation
ICBS: a database of interactions between protein chains mediated by ?-sheet formation
FunSiP: a modular and extensible classifier for the prediction of functional sites in DNA
Variable slope normalization of reverse phase protein arrays
GOSSIP: a method for fast and accurate global alignment of protein structures
TOPP - the OpenMS proteomics pipeline
ACME: pan-specific peptide-MHC class I binding prediction through attention-based deep neural networks
Beacon v2 Reference Implementation: a toolkit to enable federated sharing of genomic and phenotypic data
Applying graph theory to protein structures: an Atlas of coiled coils
Genotype calling and mapping of multisite variants using an Atlantic salmon iSelect SNP array
The uniqueome: a mappability resource for short-tag sequencing
AraPath: a knowledgebase for pathway analysis in Arabidopsis
Chromosomal imbalances detected via RNA-sequencing in 28 cancers
NX4: a web-based visualization of large multiple sequence alignments
Dynamic programming algorithms for restriction map comparison
EpiGraphDB: a database and data mining platform for health data science
Simple rules underlying gene expression profiles of more than six subtypes of acute lymphoblastic leukemia (ALL) patients
BAOBAB: a Java editor for large phylogenetic trees
MASH Native: a unified solution for native top-down proteomics data processing
LRCstats, a tool for evaluating long reads correction methods
Simultaneous recognition and segmentation of cells: application in C.elegans
APAlyzer: a bioinformatics package for analysis of alternative polyadenylation isoforms
Phenotypic stability and plasticity in GMP-derived cells as determined by their underlying regulatory network
An RNA Mapping DataBase for curating RNA structure mapping experiments
ISMB-2000: Bioinformatics enters a new millennium
CNV-BAC: Copy number Variation Detection in Bacterial Circular Genome
CLPred: a sequence-based protein crystallization predictor using BLSTM neural network
Automated construction and testing of multi-locus gene-gene associations
On the convergence of a clustering algorithm for protein-coding regions in microbial genomes
ABC-SysBio - approximate Bayesian computation in Python with GPU support
XPRS: a tool for interpretable and explainable polygenic risk score
Message from the ISCB: ISCB Ebola award for important future research on the computational biology of Ebola virus
DOSE: an R/Bioconductor package for disease ontology semantic and enrichment analysis
stringMLST: a fast k-mer based tool for multilocus sequence typing
CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data
DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches
APLOGEN: an object-oriented genetic algorithm performing Monte Carlo optimization
Detection of active transcription factor binding sites with the combination of DNase hypersensitivity and histone modifications
An end-to-end multi-task system of automatic lesion detection and anatomical localization in whole-body bone scintigraphy by deep learning
Pair Matcher (PaM): fast model-based optimization of treatment/case-control matches
HAPLOWSER: a whole-genome haplotype browser for personal genome and metagenome
Construction of simple pathways and simple cycles in ecosystems
FindPath: a Matlab solution for in silico design of synthetic metabolic pathways
ZTR: a new format for DNA sequence trace data
PhenoNet: identification of key networks associated with disease phenotype
Comparative analysis of methods for evaluation of protein models against native structures
MMGraph: a multiple motif predictor based on graph neural network and coexisting probability for ATAC-seq data
Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data
Modeling dependency structures in 450k DNA methylation data
MemLoci: predicting subcellular localization of membrane proteins in eukaryotes
Fast protein structure alignment using Gaussian overlap scoring of backbone peptide fragment similarity
Exploring contingency tables with correspondence analysis
Identification of chromosomal translocation hotspots via scan statistics
UNADON: transformer-based model to predict genome-wide chromosome spatial position
2019 ISCB Innovator Award Recognizes William Stafford Noble
Java bioinformatics analysis web services for multiple sequence alignment - JABAWS: MSA
GEOMETRY: a software package for nucleotide sequence analysis using statistical geometry in sequence space
MotEvo: integrated Bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences
MiCellAnnGELo: annotate microscopy time series of complex cell surfaces with 3D virtual reality
Is cross-validation valid for small-sample microarray classification?
MetaQUAST: evaluation of metagenome assemblies
Robust fingerprinting of genomic databases
Phylesystem: a git-based data store for community-curated phylogenetic estimates
The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
Flux tope analysis: studying the coordination of reaction directions in metabolic networks
SIMCOAL 2.0: a program to simulate genomic diversity over large recombining regions in a subdivided population with a complex history
alona: a web server for single-cell RNA-seq analysis
Correction to: MetaSquare: an integrated metadatabase of 16S rRNA gene amplicon for microbiome taxonomic classification
Differential proteostatic regulation of insoluble and abundant proteins
Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms
Haplotype matching in large cohorts using the Li and Stephens model
MAMOT: hidden Markov modeling tool
Network-based characterization of disease-disease relationships in terms of drugs and therapeutic targets
Segmentation and intensity estimation of microarray images using a gamma-t mixture model
CLIFinder: identification of LINE-1 chimeric transcripts in RNA-seq data
PDB file parser and structure class implemented in Python
Driver network as a biomarker: systematic integration and network modeling of multi-omics data to derive driver signaling pathways for drug combination prediction
Reanalysis of genome sequences of tomato accessions and its wild relatives: development of Tomato Genomic Variation (TGV) database integrating SNPs and INDELs polymorphisms
Micado - a network-oriented database for microbial genomes
Interpretable-ADMET: a web service for ADMET prediction and optimization based on deep neural representation
<tt>k</tt> <tt>mdiff</tt>, large-scale and user-friendly differential k -mer analyses
Condition-specific target prediction from motifs and expression
A supervised approach for identifying discriminating genotype patterns and its application to breast cancer data
Identification of regulatory modules by co-clustering latent variable models: stem cell differentiation
Sequence analysis and membrane partitioning energies of -helical antimicrobial peptides
PCAmatchR: a flexible R package for optimal case-control matching using weighted principal components
A system-level investigation into the cellular toxic response mechanism mediated by AhR signal transduction pathway
Interpretable deep learning in single-cell omics
NExUS: Bayesian simultaneous network estimation across unequal sample sizes
Client-side integration of life science literature resources
Hayai-Annotation Plants: an ultra-fast and comprehensive functional gene annotation system in plants
Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects
TissueViewer: a web-based multiplexed image viewer
Improving phylogenetic analyses by incorporating additional information from genetic sequence databases
GrammR: graphical representation and modeling of count data with application in metagenomics
SmMIP-tools: a computational toolset for processing and analysis of single-molecule molecular inversion probes-derived data
Robust and sparse correlation matrix estimation for the analysis of high-dimensional genomics data
Combining evolutionary information extracted from frequency profiles with sequence-based kernels for protein remote homology detection
Methplotlib: analysis of modified nucleotides from nanopore sequencing
Statistical analysis of a small set of time-ordered gene expression data using linear splines
Prediction of protein group function by iterative classification on functional relevance network
DITOP: drug-induced toxicity related protein database
Improved breast cancer prognosis through the combination of clinical and genetic markers
L 1 regularization facilitates detection of cell type-specific parameters in dynamical systems
CHOISS for selection of single nucleotide polymorphism markers on interval regularity
AptCompare: optimized de novo motif discovery of RNA aptamers via HTS-SELEX