yusuke1997/dblp-id-title huggingface dataset:
ChemBioServer 2.0: an advanced web server for filtering, clustering and networking of chemical compounds facilitating both drug discovery and repurposing
ProteinMAE: masked autoencoder for protein surface self-supervised learning
Prediction of transporter targets using efficient RBF networks with PSSM profiles and biochemical properties
Fuzzy C-means Method for Clustering Microarray Data
bpRNA-CosMoS: a robust and efficient RNA structural comparison method using k-mer based cosine similarity
Inferential, robust non-negative matrix factorization analysis of microarray data
Lambda: the local aligner for massive biological data
A multiple-feature framework for modelling and predicting transcription factor binding sites
CROSSalive: a web server for predicting the in vivo structure of RNA molecules
CapiPy: python-based GUI-application to assist in protein immobilization
RxnSim: a tool to compare biochemical reactions
KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours
SVM-dependent pairwise HMM: an application to protein pairwise alignments
Prediction of RNA secondary structure using generalized centroid estimators
ACES: Analysis of Conservation with an Extensive list of Species
Cross-React: a new structural bioinformatics method for predicting allergen cross-reactivity
Inferring protein-protein interactions through high-throughput interaction data from diverse organisms
Cell-connectivity-guided trajectory inference from single-cell data
BioMethyl: an R package for biological interpretation of DNA methylation data
A powerful and flexible approach to the analysis of RNA sequence count data
An expectation-maximization framework for comprehensive prediction of isoform-specific functions
BASIC program for polynomial regression and smoothing
A U-statistics for integrative analysis of multilayer omics data
STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts
annotatr: genomic regions in context
The role of graph topology in the performance of biomedical Knowledge Graph Completion models
Indelign: a probabilistic framework for annotation of insertions and deletions in a multiple alignment
Finding differentially expressed genes for pattern generation
DIGEP-Pred: web service for in silico prediction of drug-induced gene expression profiles based on structural formula
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
TADA: taxonomy-aware dataset aggregator
A modeling framework for embedding-based predictions for compound-viral protein activity
BAUM: improving genome assembly by adaptive unique mapping and local overlap-layout-consensus approach
A mutation profile for top- k patient search exploiting Gene-Ontology and orthogonal non-negative matrix factorization
BCFtools/csq: haplotype-aware variant consequences
PhysioFit: a software to quantify cell growth parameters and extracellular fluxes
PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data
Self-supervised learning of cell type specificity from immunohistochemical images
BiasAway: command-line and web server to generate nucleotide composition-matched DNA background sequences
Evaluating homophily in networks via HONTO (HOmophily Network TOol): a case study of chromosomal interactions in human PPI networks
Characterizing alternative splicing effects on protein interaction networks with LINDA
Exploring high dimensional data with Butterfly: a novel classification algorithm based on discrete dynamical systems
Best practices to evaluate the impact of biomedical research software - metric collection beyond citations
Prediction of transcriptional regulatory sites in the complete genome sequence of Escherichia coli K-12
Cloud bursting galaxy: federated identity and access management
AnnotationSketch : a genome annotation drawing library
Non-transcriptional pathway features reconstructed from secondary effects of RNA interference
localpdb - a Python package to manage protein structures and their annotations
cellCounts: an R function for quantifying 10x Chromium single-cell RNA sequencing data
hybridSPAdes: an algorithm for hybrid assembly of short and long reads
High-throughput modeling and scoring of TCR-pMHC complexes to predict cross-reactive peptides
MultiPLX: automatic grouping and evaluation of PCR primers
Message from the ISCB: 2017 Outstanding Contributions to ISCB Award Given to Fran Lewitter
Two-stage designs for experiments with a large number of hypotheses
WPMIAS: Whole-degradome-based Plant MicroRNA-target Interaction Analysis Server
CORGEN: a FORTRAN-77 generator of standard and non-standard DNA helices from the sequence
Causality modeling for directed disease network
Observing and Interpreting Correlations in Metabolic Networks
Simulation tools for biochemical networks: evaluation of performance and usability
NetControl4BioMed: a web-based platform for controllability analysis of protein-protein interaction networks
WilcoxCV: an R package for fast variable selection in cross-validation
HLA*IMP - an integrated framework for imputing classical HLA alleles from SNP genotypes
Modeling drug combination effects via latent tensor reconstruction
Generalizations of the genomic rank distance to indels
DM-BLD: differential methylation detection using a hierarchical Bayesian model exploiting local dependency
Mining gene expression data based on template theory
Phybase: an R package for species tree analysis
COVoc and COVTriage: novel resources to support literature triage
Large-scale compression of genomic sequence databases with the Burrows-Wheeler transform
Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure
Improved sequence-based prediction of disordered regions with multilayer fusion of multiple information sources
peaks2utr: a robust Python tool for the annotation of 3′ UTRs
Brain annotation toolbox: exploring the functional and genetic associations of neuroimaging results
PeNGaRoo, a combined gradient boosting and ensemble learning framework for predicting non-classical secreted proteins
Where are we at regarding species translation? A review of the sbv IMPROVER challenge
Triplet-based similarity score for fully multilabeled trees with poly-occurring labels
The 2024 ISCB Accomplishments by a Senior Scientist Award - Dr Tandy Warnow
Direct calculation of minimal cut sets involving a specific reaction knock-out
Clustering single-cell multi-omics data with MoClust
A wide repertoire of miRNA binding sites: prediction and functional implications
Fast computation of minimum hybridization networks
A pattern recognition approach to infer time-lagged genetic interactions
MetDisease - connecting metabolites to diseases via literature
13Check_RNA: a tool to evaluate 13C chemical shift assignments of RNA
GAMES identifies and annotates mutations in next-generation sequencing projects
ViCTree: an automated framework for taxonomic classification from protein sequences
An integrated genetic data environment (GDE)-based LINUX interface for analysis of HIV-1 and other microbial sequences
Phandango: an interactive viewer for bacterial population genomics
pFind: a novel database-searching software system for automated peptide and protein identification via tandem mass spectrometry
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
Microcomputer tools for steady-state enzyme kinetics
DRAGON: Database Referencing of Array Genes Online
Adjusting scoring matrices to correct overextended alignments
RAPPPID: towards generalizable protein interaction prediction with AWD-LSTM twin networks
A critical assessment of gene catalogs for metagenomic analysis
SeqDepot: streamlined database of biological sequences and precomputed features
Comparative interactomics analysis of protein family interaction networks using PSIMAP (protein structural interactome map)
A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk
ProBASS - a language model with sequence and structural features for predicting the effect of mutations on binding affinity
Discovering motif pairs at interaction sites from protein sequences on a proteome-wide scale
Pyranose Oxidase Identified as A Member of the GMC Oxidoreductase Family
ogaraK: a population genetics simulator for malaria
DeepPeptide predicts cleaved peptides in proteins using conditional random fields
ESTWeb: bioinformatics services for EST sequencing projects
Automatic display of RNA secondary structures
rBioNet: A COBRA toolbox extension for r econstructing high-quality bio chemical net works
The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation
The size matters? A computational tool to design bivalent ligands
Integrating splice-isoform expression into genome-scale models characterizes breast cancer metabolism
Identification of characteristic oligonucleotides in the bacterial 16S ribosomal RNA sequence dataset
Exon-domain correlation and its corollaries
Motif scraper: a cross-platform, open-source tool for identifying degenerate nucleotide motif matches in FASTA files
Penalized regression with multiple sources of prior effects
A sequential niche multimodal conformational sampling algorithm for protein structure prediction
Classifying next-generation sequencing data using a zero-inflated Poisson model
Multiple-sequence functional annotation and the generalized hidden Markov phylogeny
Specific identification and quantification of circular RNAs from sequencing data
LegumeTFDB: an integrative database of Glycine max , Lotus japonicus and Medicago truncatula transcription factors
Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway
Automatic discovery and classification of bioinformatics Web sources
MITIE: Simultaneous RNA-Seq-based transcript identification and quantification in multiple samples
MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence
Vorescore - fold recognition improved by rescoring of protein structure models
RocaSec: a standalone GUI-based package for robust co-evolutionary analysis of proteins
Corrigendum of 'High throughput analysis of epistasis in genome-wide association studies with BiForce'
Calculation of the photoperiod length
Identifying clusters of functionally related genes in genomes
LINADMIX: evaluating the effect of ancient admixture events on modern populations
Transformation and normalization of oligonucleotide microarray data
Cross-hybridization modeling on Affymetrix exon arrays
Accurate viral population assembly from ultra-deep sequencing data
Greater power and computational efficiency for kernel-based association testing of sets of genetic variants
PINE-SPARKY.2 for automated NMR-based protein structure research
ECOH: An Enzyme Commission number predictor using mutual information and a support vector machine
On the relationship between sequence and structure similarities in proteomics
Cytoscape App Store
A pipeline for RNA-seq data processing and quality assessment
Inferring cancer subnetwork markers using density-constrained biclustering
JMassBalance : mass-balanced randomization and analysis of metabolic networks
RNA movies: visualizing RNA secondary structure spaces
Benchmarking tools for a priori identifiability analysis
Automatic analysis of agarose gel images
A segmental maximum a posteriori approach to genome-wide copy number profiling
ANAIS: Analysis of NimbleGen Arrays Interface
Statistical database analysis of the role of loop dynamics for protein-protein complex formation and allostery
A comprehensive and non-redundant database of protein domain movements
MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory
Genes@Work: an efficient algorithm for pattern discovery and multivariate feature selection in gene expression data
In silico analysis of phytoene synthase and its promoter reveals hints for regulation mechanisms of carotenogenesis in Duanliella bardawil
graphkernels: R and Python packages for graph comparison
A knowledge-based orientation potential for transcription factor-DNA docking
PARA-SITE: a computer algorithm for rapidly analyzing the physical- chemical properties of amino acid sequences at sites of co- and post- translational protein processing
miRBench: novel benchmark datasets for microRNA binding site prediction that mitigate against prevalent microRNA frequency class bias
Classification of small molecules by two- and three-dimensional decomposition kernels
Quintet Rooting: rooting species trees under the multi-species coalescent model
Scrutineer: a computer program that flexibly seeks and describes motifs and profiles in protein sequence databases [published erratum appears in Comput Appl Biosci 1990 Oct;6(4): 431]
The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework
Software for DNA sequencing by hybridization
SPAAN: a software program for prediction of adhesins and adhesin-like proteins using neural networks
The OncoPPi Portal: an integrative resource to explore and prioritize protein-protein interactions for cancer target discovery
PMC text mining subset in BioC: about three million full-text articles and growing
SpectroPipeR - a streamlining post Spectronaut® DIA-MS data analysis R package
DiMoVo: a Voronoi tessellation-based method for discriminating crystallographic and biological protein-protein interactions
Supervised learning of enhancer-promoter specificity based on genome-wide perturbation studies highlights areas for improvement in learning
Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta- algorithm
Improved large-scale prediction of growth inhibition patterns using the NCI60 cancer cell line panel
Unified representation of genetic variants
SSpro/ACCpro 5: almost perfect prediction of protein secondary structure and relative solvent accessibility using profiles, machine learning and structural similarity
GenomeD3Plot: a library for rich, interactive visualizations of genomic data in web applications
PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)
FetalQuant : deducing fractional fetal DNA concentration from massively parallel sequencing of DNA in maternal plasma
DNA sequences and multivariate statistical analysis. Categorical discrimination approach to 5' splice site signals of mRNA precursors in higher eukaryotes' genes
Fur: Find unique genomic regions for diagnostic PCR
ECHO: an application for detection and analysis of oscillators identifies metabolic regulation on genome-wide circadian output
Computing in the biological sciences--a survey
LOTUS, a new domain associated with small RNA pathways in the germline
RVFam: an R package for rare variant association analysis with family data
'Flatten plus': a recent implementation in WSxM for biological research
Computational identification of binding energy hot spots in protein-RNA complexes using an ensemble approach
PlasmoFAB: a benchmark to foster machine learning for Plasmodium falciparum protein antigen candidate prediction
S3V2-IDEAS: a package for normalizing, denoising and integrating epigenomic datasets across different cell types
COPA - cancer outlier profile analysis
The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing
Population-based structural variation discovery with Hydra-Multi
3D graph contrastive learning for molecular property prediction
cgHeliParm: analysis of dsDNA helical parameters for coarse-grained MARTINI molecular dynamics simulations
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP
Exact maximal reduction of stochastic reaction networks by species lumping
Directional allelic imbalance profiling and visualization from multi-sample data with RECUR
CREx: inferring genomic rearrangements based on common intervals
movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples
Quality control and preprocessing of metagenomic datasets
AcImpute: a constraint-enhancing smooth-based approach for imputing single-cell RNA sequencing data
Cellinker: a platform of ligand-receptor interactions for intercellular communication analysis
Mortality Tracker: the COVID-19 case for real time web APIs as epidemiology commons
The mutated subsequence problem and locating conserved genes
Prioritizing predictive biomarkers for gene essentiality in cancer cells with mRNA expression data and DNA copy number profile
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta
PICKY: a novel SVD-based NMR spectra peak picking method
A novel genome-scale repeat finder geared towards transposons
DIMet: an open-source tool for differential analysis of targeted isotope-labeled metabolomics data
Proactive visual and statistical analysis of genomic data in Epiviz
Gene-set association tests for next-generation sequencing data
Computational modelling in health and disease: highlights of the 6th annual SysMod meeting
demuxmix: demultiplexing oligonucleotide-barcoded single-cell RNA sequencing data with regression mixture models
iEnhancer-2L: a two-layer predictor for identifying enhancers and their strength by pseudo k -tuple nucleotide composition
Rapid epistatic mixed-model association studies by controlling multiple polygenic effects
LENS: Landscape of Effective Neoantigens Software
GlyMDB: Glycan Microarray Database and analysis toolset
The effect of genome graph expressiveness on the discrepancy between genome graph distance and string set distance
On genomic repeats and reproducibility
Relational patterns of gene expression via non-metric multidimensional scaling analysis
kc-hits: a tool to aid in the evaluation and classification of chemical carcinogens
caCORE: A common infrastructure for cancer informatics
Unfazed: parent-of-origin detection for large and small de novo variants
MULTICOM: a multi-level combination approach to protein structure prediction and its assessments in CASP8
biospear: an R package for biomarker selection in penalized Cox regression
SEMgraph: an R package for causal network inference of high-throughput data with structural equation models
MEXCOwalk: mutual exclusion and coverage based random walk to identify cancer modules
Artificial neural networks and simulated molecular evolution are potential tools for sequence-oriented protein design
pathClass: an R-package for integration of pathway knowledge into support vector machines for biomarker discovery
Dr.VAE: improving drug response prediction via modeling of drug perturbation effects
SecStAnT: secondary structure analysis tool for data selection, statistics and models building
Compact and evenly distributed k-mer binning for genomic sequences
Automated analysis of protein subcellular location in time series images
GenMiner: mining non-redundant association rules from integrated gene expression data and annotations
SGTK: a toolkit for visualization and assessment of scaffold graphs
Assessing the significance of consistently mis-regulated genes in cancer associated gene expression matrices
ASHLEYS: automated quality control for single-cell Strand-seq data
Bigtools: a high-performance BigWig and BigBed library in Rust
ImSpectR: R package to quantify immune repertoire diversity in spectratype and repertoire sequencing data
STRIKE: evaluation of protein MSAs using a single 3D structure
Relation between sequence and structure in membrane proteins
BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data
GeCo++: a C++ library for genomic features computation and annotation in the presence of variants
The PCR Suite
Lost in translation: an assessment and perspective for computational microRNA target identification
NMRtist: an online platform for automated biomolecular NMR spectra analysis
A knowledge base of the chemical compounds of intermediary metabolism
Novel search method for the discovery of functional relationships
KEGGanim: pathway animations for high-throughput data
Deuteros 2.0: peptide-level significance testing of data from hydrogen deuterium exchange mass spectrometry
Cross-platform comparison of microarray data using order restricted inference
Aether: leveraging linear programming for optimal cloud computing in genomics
LocalAli: an evolutionary-based local alignment approach to identify functionally conserved modules in multiple networks
FaStore: a space-saving solution for raw sequencing data
Transfer learning for drug-target interaction prediction
ScaffoldGraph: an open-source library for the generation and analysis of molecular scaffold networks and scaffold trees
MEME-ChIP: motif analysis of large DNA datasets
missMethyl: an R package for analyzing data from Illumina's HumanMethylation450 platform
Molecular decomposition of complex clinical phenotypes using biologically structured analysis of microarray data
diSTruct v1.0: generating biomolecular structures from distance constraints
Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases
Selection of Oligonucleotide Probes for Protein Coding Sequences
MPEA - metabolite pathway enrichment analysis
In silico sequence evolution with site-specific interactions along phylogenetic trees
A new protein-protein docking scoring function based on interface residue properties
Evolutionary solution for the RNA design problem
LIBRA-WA: a web application for ligand binding site detection and protein function recognition
Computational recognition of potassium channel sequences
WebPHYLIP: a web interface to PHYLIP
DEMETER: efficient simultaneous curation of genome-scale reconstructions guided by experimental data and refined gene annotations
metaGWASmanager: a toolbox for an automated workflow from phenotypes to meta-analysis in GWAS consortia
SST-editing: in silico spatial transcriptomic editing at single-cell resolution
EMDomics: a robust and powerful method for the identification of genes differentially expressed between heterogeneous classes
AlignBucket: a tool to speed up 'all-against-all' protein sequence alignments optimizing length constraints
Validation of double digest selective label database for sequenced prokaryotic genomes
Protein Structures and Information Extraction from Biological Texts: The PASTA System
An unsupervised conditional random fields approach for clustering gene expression time series
A unified ILP framework for core ancestral genome reconstruction problems
Robust biomarker identification for cancer diagnosis with ensemble feature selection methods
Excess positional mutual information predicts both local and allosteric mutations affecting beta lactamase drug resistance
GeneCT: a generalizable cancerous status and tissue origin classifier for pan-cancer biopsies
Möbius: an integrated discrete-event modeling environment
Analyzing marginal cases in differential shotgun proteomics
FSuite: exploiting inbreeding in dense SNP chip and exome data
SubNet: a Java application for subnetwork extraction
mastR: an R package for automated identification of tissue-specific gene signatures in multi-group differential expression analysis
Overlap and diversity in antimicrobial peptide databases: compiling a non-redundant set of sequences
dsRID: in silico identification of dsRNA regions using long-read RNA-seq data
Best-first search guided multistage mass spectrometry-based glycan identification
Proteo-chemometrics interaction fingerprints of protein-ligand complexes predict binding affinity
Robust and efficient identification of biomarkers by classifying features on graphs
CircPro: an integrated tool for the identification of circRNAs with protein-coding potential
Drug repositioning by integrating target information through a heterogeneous network model
Identification of differentially expressed gene sets using the Generalized Berk-Jones statistic
Blood-based multi-tissue gene expression inference with Bayesian ridge regression
Statistical inference of differential RNA-editing sites from RNA-sequencing data by hierarchical modeling