yusuke1997/dblp-id-title huggingface dataset:
CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs
influx_s: increasing numerical stability and precision for metabolic flux analysis in isotope labelling experiments
Reference descriptions of cellular electrophysiology models
AlertGS: determining alerts for gene sets
Discriminative motif optimization based on perceptron training
Rust-Bio: a fast and safe bioinformatics library
ASPicDB: A database resource for alternative splicing analysis
HD-CNV: hotspot detector for copy number variants
In silico analysis of promoter regions from cold-induced genes in rice ( Oryza sativa L.) and Arabidopsis thaliana reveals the importance of combinatorial control
CRISPR/Cas9 cleavage efficiency regression through boosting algorithms and Markov sequence profiling
Matrix eQTL: ultra fast eQTL analysis via large matrix operations
STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data
An entity tagger for recognizing acquired genomic variations in cancer literature
Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
Probabilistic path ranking based on adjacent pairwise coexpression for metabolic transcripts analysis
IDESS: a toolbox for identification and automated design of stochastic gene circuits
GPViz: dynamic visualization of genomic regions and variants affecting protein domains
NTAP: for NimbleGen tiling array ChIP-chip data analysis
Analysis of E.coli promoter recognition problem in dinucleotide feature space
Benchmarking regulatory network reconstruction with GRENDEL
Using high-throughput multi-omics data to investigate structural balance in elementary gene regulatory network motifs
ProtoCell4P: an explainable prototype-based neural network for patient classification using single-cell RNA-seq
Systematic comparison of ranking aggregation methods for gene lists in experimental results
Robust estimation of the false discovery rate
MareyMap: an R-based tool with graphical interface for estimating recombination rates
Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework
Identifying dispersed epigenomic domains from ChIP-Seq data
Methylation-eQTL analysis in cancer research
SCORE: predicting the core of protein models
InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites
Modular response analysis reformulated as a multilinear regression problem
Algorithm to find gene expression profiles of deregulation and identify families of disease-altered genes
Identify connectome between genotypes and brain network phenotypes via deep self-reconstruction sparse canonical correlation analysis
High resolution scanning of absorbing and fluorescent electrophoresis gels using video image analysis
Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data
BEETL-fastq: a searchable compressed archive for DNA reads
REscan: inferring repeat expansions and structural variation in paired-end short read sequencing data
Metabolite-Investigator: an integrated user-friendly workflow for metabolomics multi-study analysis
DiffChIPL: a differential peak analysis method for high-throughput sequencing data with biological replicates based on limma
msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots
Supervised non-negative matrix factorization methods for MALDI imaging applications
QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks
Evolutionary optimization with data collocation for reverse engineering of biological networks
Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis
PyPCN: protein contact networks in PyMOL
KAnalyze: a fast versatile pipelined K-mer toolkit
A novel algorithm for calling mRNA m 6 A peaks by modeling biological variances in MeRIP-seq data
High-quality sequence clustering guided by network topology and multiple alignment likelihood
BioWAP, mobile Internet service for bioinformatics
Statistical methods for gene set co-expression analysis
GenomeRunner web server: regulatory similarity and differences define the functional impact of SNP sets
Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs
Characterization and improvement of RNA-Seq precision in quantitative transcript expression profiling
GiniQC: a measure for quantifying noise in single-cell Hi-C data
BISANCE: a French service for access to biomolecular sequence databases
Deep convolutional networks for quality assessment of protein folds
Refining Boolean models with the partial most permissive scheme
Response to the letter to the editor: On the feasibility of dynamical analysis of network models of biochemical regulation
A comparison of statistical methods for analysis of high density oligonucleotide array data
ProbeMatchDB-a web database for finding equivalent probes across microarray platforms and species
Measurement error and variant-calling in deep Illumina sequencing of HIV
IgRepertoireConstructor: a novel algorithm for antibody repertoire construction and immunoproteogenomics analysis
The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery
Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach
PSORTb v.2.0: Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis
Designing efficient randstrobes for sequence similarity analyses
A FORTRAN program to simulate the evolution of genetic variability in a small population
A safety framework for flow decomposition problems via integer linear programming
SCALOP: sequence-based antibody canonical loop structure annotation
TandemTools: mapping long reads and assessing/improving assembly quality in extra-long tandem repeats
fastISM: performant in silico saturation mutagenesis for convolutional neural networks
Completing gene trees without species trees in sub-quadratic time
GeneReg: a constraint-based approach for design of feasible metabolic engineering strategies at the gene level
Differential network expression during drug and stress response
Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads
Resolution and reconciliation of non-binary gene trees with transfers, duplications and losses
Data transfer from Beckman LS 5800 liquid scintillation counters to IBM personal computers
ODES: an overlapping dense sub-graph algorithm
A generalized likelihood ratio test to identify differentially expressed genes from microarray data
Thermometer: a webserver to predict protein thermal stability
Anomaly detection in spatial transcriptomics via spatially localized density comparison
PERMORY: an LD-exploiting permutation test algorithm for powerful genome-wide association testing
AIRRSHIP: simulating human B cell receptor repertoire sequences
RabbitKSSD: accelerating genome distance estimation on modern multi-core architectures
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
Predicting and explaining the impact of genetic disruptions and interactions on organismal viability
GeLL: a generalized likelihood library for phylogenetic models
Bacterial Feature Finder (BaFF) - a system for extracting features overrepresented in sets of prokaryotic organisms
Efficient and effective control of confounding in eQTL mapping studies through joint differential expression and Mendelian randomization analyses
Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank
Metagenomic binning with assembly graph embeddings
Learning chromatin states with factorized information criteria
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
DbW: automatic update of a functional family-specific multiple alignment
Double error shrinkage method for identifying protein binding sites observed by tiling arrays with limited replication
Sparse non-negative matrix factorizations via alternating non-negativity-constrained least squares for microarray data analysis
DeepCrystal: a deep learning framework for sequence-based protein crystallization prediction
A network-based drug repurposing method via non-negative matrix factorization
GfaPy: a flexible and extensible software library for handling sequence graphs in Python
Joint amalgamation of most parsimonious reconciled gene trees
XenoSite server: a web-available site of metabolism prediction tool
DD-GUI: a graphical user interface for deep learning-accelerated virtual screening of large chemical libraries (Deep Docking)
Admix-kit: an integrated toolkit and pipeline for genetic analyses of admixed populations
TRStalker: an efficient heuristic for finding fuzzy tandem repeats
REF-LIST: program to list references found in DOS text files of scientific manuscripts
NCMine: Core-peripheral based functional module detection using near-clique mining
Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces
AutoMotif server: prediction of single residue post-translational modifications in proteins
Benchmark of software tools for prokaryotic chromosomal interaction domain identification
Using the structure of genome data in the design of deep neural networks for predicting amyotrophic lateral sclerosis from genotype
SSMAL: similarity searching with alignment graphs
qcCHIP: an R package to identify clonal hematopoiesis variants using cohort-specific data characteristics
ConFunc - functional annotation in the twilight zone
DNAView: a quality assessment tool for the visualization of large sequenced regions
eQTL epistasis: detecting epistatic effects and inferring hierarchical relationships of genes in biological pathways
Edge-group sparse PCA for network-guided high dimensional data analysis
SOSUI: classification and secondary structure prediction system for membrane proteins
A 3D pattern matching algorithm for DNA sequences
Large-scale prokaryotic gene prediction and comparison to genome annotation
MOLECULAR DESIGNER: an interactive program for the display of protein structure on the IBM-PC
Discovery of stable and significant binding motif pairs from PDB complexes and protein interaction datasets
Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability
cl-dash: rapid configuration and deployment of Hadoop clusters for bioinformatics research in the cloud
PRIMe: a method for characterization and evaluation of pleiotropic regions from multiple genome-wide association studies
ScaffoldScaffolder: solving contig orientation via bidirected to directed graph reduction
A powerful approach for association analysis incorporating imprinting effects
A protein secondary structure prediction scheme for the IBM PC and compatibles
Between-group analysis of microarray data
A scalable estimator of SNP heritability for biobank-scale data
Estimating pseudocounts and fold changes for digital expression measurements
Improving the accuracy of transmembrane protein topology prediction using evolutionary information
Obelisc: an identical-by-descent mapping tool based on SNP streak
Visualization of expression clusters using Sammon's non-linear mapping
Seq-SetNet: directly exploiting multiple sequence alignment for protein secondary structure prediction
ScanNeo2: a comprehensive workflow for neoantigen detection and immunogenicity prediction from diverse genomic and transcriptomic alterations
TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures
Identification of bacteriophage genome sequences with representation learning
TAPAS: tools to assist the targeted protein quantification of human alternative splice variants
A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data
Response to Letter to the Editor by Philip Good on To Permute or Not to Permute
Bayesian inference with historical data-based informative priors improves detection of differentially expressed genes
SOMDE: a scalable method for identifying spatially variable genes with self-organizing map
Improved method for predicting ?-turn using support vector machine
GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome
MetalionRNA: computational predictor of metal-binding sites in RNA structures
iCircDA-LTR: identification of circRNA-disease associations based on Learning to Rank
Accounting for ambiguity in ancestral sequence reconstruction
MOUSE (Mitochondrial and Other Useful SEquences) a compilation of population genetic markers
Rapid protein structure classification using one-dimensional structure profiles on the bioSCAN parallel computer
DnaSP, DNA sequence polymorphism: an interactive program for estimating population genetics parameters from DNA sequence data
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology
BALLView: a tool for research and education in molecular modeling
JRmGRN: joint reconstruction of multiple gene regulatory networks with common hub genes using data from multiple tissues or conditions
Side-chain rotamer changes upon ligand binding: common, crucial, correlate with entropy and rearrange hydrogen bonding
MetaQUBIC: a computational pipeline for gene-level functional profiling of metagenome and metatranscriptome
RESQUE: Network reduction using semi-Markov random walk scores for efficient querying of biological networks
Systematic analysis of alternative splicing in time course data using Spycone
Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data
CaSiAn: a Calcium Signaling Analyzer tool
PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations
UniMoG - a unifying framework for genomic distance calculation and sorting based on DCJ
POEAMS: program for outliers elimination in 'anomalous' multidimensional space
OCTID: a one-class learning-based Python package for tumor image detection
Automated protein sequence database classification. II. Delineation Of domain boundaries from sequence similarities
GOR V server for protein secondary structure prediction
Identifying functional miRNA-mRNA regulatory modules with correspondence latent dirichlet allocation
On the organization of bioinformatics core services in biology-based research institutes
PersonaDrive: a method for the identification and prioritization of personalized cancer drivers
An approach to the collection and manipulation of time-based data using the IBM PC and BASICA
Haplotype assembly in polyploid genomes and identical by descent shared tracts
iSFun: an R package for integrative dimension reduction analysis
gsrc: an R package for genome structure rearrangement calling
Match-Box_server: a multiple sequence alignment tool placing emphasis on reliability
Do Current Sequence Analysis Algorithms Disclose Multifunctional (moonlighting) Proteins?
Discovery of candidate KEN-box motifs using Cell Cycle keyword enrichment combined with native disorder prediction and motif conservation
The EMBL sequence version archive
Constructing ontology-driven protein family databases
Modeling interactome: scale-free or geometric?
SpeeDB: fast structural protein searches
Protein function annotation from sequence: prediction of residues interacting with RNA
PREDICT-2ND: a tool for generalized protein local structure prediction
Waggawagga: comparative visualization of coiled-coil predictions and detection of stable single α-helices (SAH domains)
Deep feature extraction of single-cell transcriptomes by generative adversarial network
VarExp: estimating variance explained by genome-wide GxE summary statistics
Automated download and clean-up of family-specific databases for kmer-based virus identification
CymeR: cytometry analysis using KNIME, docker and R
Cyclone: open-source package for simulation and analysis of finite dynamical systems
Phylogenetic double placement of mixed samples
Integration of gene normalization stages and co-reference resolution using a Markov logic network
NVT: a fast and simple tool for the assessment of RNA-seq normalization strategies
Fair molecular feature selection unveils universally tumor lineage-informative methylation sites in colorectal cancer
Meta-analysis for pathway enrichment analysis when combining multiple genomic studies
SneakySnake: a fast and accurate universal genome pre-alignment filter for CPUs, GPUs and FPGAs
Cyto-Sim: a formal language model and stochastic simulator of membrane-enclosed biochemical processes
ADEPTUS: a discovery tool for disease prediction, enrichment and network analysis based on profiles from many diseases
Tablet - next generation sequence assembly visualization
PconsC: combination of direct information methods and alignments improves contact prediction
Graphlet-based edge clustering reveals pathogen-interacting proteins
Inter-species prediction of protein phosphorylation in the sbv IMPROVER species translation challenge
Benchmarking the next generation of homology inference tools
Prediction of metabolic reactions based on atomic and molecular properties of small-molecule compounds
Mapplet: a CORBA-based genome map viewer
A comparison of Radial Basis Function and backpropagation neural networks for identification of marine phytoplankton from multivariate flow cytometry data
Quality of biological images, reconstructed using localization microscopy data
Accurate approximation method for prediction of class I MHC affinities for peptides of length 8, 10 and 11 using prediction tools trained on 9mers
CSB: a Python framework for structural bioinformatics
Specificity and affinity quantification of protein-protein interactions
The development of a high-order Taylor expansion solution to the chemical rate equation for the simulation of complex biochemical systems
G4Hunter web application: a web server for G-quadruplex prediction
Processing and quality control of DNA array hybridization data
On the simultaneous association analysis of large genomic regions: a massive multi-locus association test
Deep structure integrative representation of multi-omics data for cancer subtyping
An R package VIGoR for joint estimation of multiple linear learners with variational Bayesian inference
MolBioLib: a C++11 framework for rapid development and deployment of bioinformatics tasks
Easier threading through web-based comparisons and cross-validations
Inference of protein kinetics by stochastic modeling and simulation of fluorescence recovery after photobleaching experiments
GDPC: connecting researchers with multiple integrated data sources
iCpG-Pos: an accurate computational approach for identification of CpG sites using positional features on single-cell whole genome sequence data
MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline
ProbFold: a probabilistic method for integration of probing data in RNA secondary structure prediction
Gene-Ontology-based clustering of gene expression data
Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer
jMetalCpp: optimizing molecular docking problems with a C++ metaheuristic framework
GateFinder: projection-based gating strategy optimization for flow and mass cytometry
Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules
LPF: a framework for exploring the wing color pattern formation of ladybird beetles in Python
Data mining of effect sizes from PubMed abstracts: a cross-study conceptual replication
Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective
Feature set optimization in biomarker discovery from genome-scale data
SEGID: Identifying Interesting Segments in (Multiple) Sequence Alignments
Predicting miRNA-disease association based on inductive matrix completion
Joint estimation of isoform expression and isoform-specific read distribution using multisample RNA-Seq data
Predicting sub-Golgi localization of type II membrane proteins
ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences
Non-linear classification for on-the-fly fractional mass filtering and targeted precursor fragmentation in mass spectrometry experiments
Open Chrono-Morph Viewer: visualize big bioimage time series containing heterogeneous volumes
CoRegNet: reconstruction and integrated analysis of co-regulatory networks
AC-DIAMOND v1: accelerating large-scale DNA-protein alignment
PinaColada: peptide-inhibitor ant colony ad-hoc design algorithm
TRbase: a database relating tandem repeats to disease genes for the human genome
BleTIES: annotation of natural genome editing in ciliates using long read sequencing
An efficient network querying method based on conditional random fields
On cross-conditional and fluctuation correlations in competitive RNA networks
Curation, integration and visualization of bacterial virulence factors in PATRIC
External control in Markovian genetic regulatory networks: the imperfect information case
A probabilistic framework for aligning paired-end RNA-seq data
ChemDB update - full-text search and virtual chemical space
MSNGO: multi-species protein function annotation based on 3D protein structure and network propagation
AmpUMI: design and analysis of unique molecular identifiers for deep amplicon sequencing
DNASUN: a package of computer programs for the biotechnology laboratory
BnpC: Bayesian non-parametric clustering of single-cell mutation profiles
On the frequency of copy number variants
DIABLO: an integrative approach for identifying key molecular drivers from multi-omics assays
TPES: tumor purity estimation from SNVs
Solving algebraic equations on a microcomputer
GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks
KEPE - a motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors
Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics
POEMS: program for outliers elimination in multidimensional space
Muxstep: an open-source C ++ multiplex HMM library for making inferences on multiple data types
Illoura TM : a software tool for analysis, visualization and semantic querying of cellular and other spatial biological data
Evaluation of drug-human serum albumin binding interactions with support vector machine aided online automated docking
Crowdsourcing for bioinformatics
CytoHiC: a cytoscape plugin for visual comparison of Hi-C networks
SimCT: a generic tool to visualize ontology-based relationships for biological objects
The barcode, UMI, set format and BUStools
Shape component analysis: structure-preserving dimension reduction on biological shape spaces
Accurate estimation of heritability in genome wide studies using random effects models
Finding motifs using DNA images derived from sparse representations
OutSingle: a novel method of detecting and injecting outliers in RNA-Seq count data using the optimal hard threshold for singular values
methyLiftover: cross-platform DNA methylation data integration
Microcomputer BASIC programs for rapid determination of lethal dosages of biocides using logit transformations
Prediction and curation of missing biomedical identifier mappings with Biomappings
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays
Robust clustering of noisy high-dimensional gene expression data for patients subtyping
A set of Alu-free frequent decamers from mammalian genomes enriched in transcription factor signals
Automated construction and analysis of the design space for biochemical systems
Mechanistic insights into mutually exclusive splicing in dynamin 1