yusuke1997/dblp-id-title huggingface dataset:
YeATS - a tool suite for analyzing RNA-seq derived transcriptome identifies a highly transcribed putative extensin in heartwood/sapwood transition zone in black walnut
A systematic performance evaluation of clustering methods for single-cell RNA-seq data
The Resource Identification Initiative: A cultural shift in publishing
Data extraction methods for systematic review (semi)automation: A living systematic review
Non-invasive health prediction from visually observable features
Tetranucleotide usage highlights genomic heterogeneity among mycobacteriophages
Constellation Map: Downstream visualization and interpretation of gene set enrichment results
Antecedents of generation Z towards digitalisation. A PLS-SEM analysis
An analysis on the entity annotations in biological corpora
miRcomp-Shiny : Interactive assessment of qPCR-based microRNA quantification and quality control algorithms
IT Service management system for EMBL's European Bioinformatics Institute's IT department
An intelligent decision support system for crop yield prediction using hybrid machine learning algorithms
Enrichment Map - a Cytoscape app to visualize and explore OMICs pathway enrichment results
DRETools: A tool-suite for differential RNA editing detection
iCTNet2: integrating heterogeneous biological interactions to understand complex traits
TicTimer software for measuring tic suppression
Exploring machine learning: A bibliometric general approach using Citespace
Intrinsic negative feedback as a limiting factor for the evolution of higher forms of intelligence
Knowledge management awareness assessment in Nigerian tertiary institutions
2017 Outstanding Contributions to ISCB Award: Fran Lewitter
ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds
HDCytoData: Collection of high-dimensional cytometry benchmark datasets in Bioconductor object formats
Design of chemical space networks incorporating compound distance relationships
Expanding the chemical information science gateway
Feature selection with the R package MXM
A cross-package Bioconductor workflow for analysing methylation array data
An open RNA-Seq data analysis pipeline tutorial with an example of reprocessing data from a recent Zika virus study
An end to end workflow for differential gene expression using Affymetrix microarrays
BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests
Use of routinely collected data in a UK cohort of publicly funded randomised clinical trials
Every scientist is a memory researcher: Suggestions for making research more memorable
Software for web-based tic suppression training
The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research
ROOSTER: An image labeler and classifier through interactive recurrent annotation
archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems
Cyrface : An interface from Cytoscape to R that provides a user interface to R packages
Best practice data life cycle approaches for the life sciences
A new environmental monitoring system for silkworm incubators
META-pipe Authorization service
Evidence of misuse of nonparametric tests in the presence of heteroscedasticity within obesity research
ESforRPD2: Expert System for Rice Plant Disease Diagnosis
Neurosharing: large-scale data sets (spike, LFP) recorded from the hippocampal-entorhinal system in behaving rats
The Neuroimaging Data Model Linear Regression Tool (nidm_linreg): PyNIDM Project
rt-me-fMRI : a task and resting state dataset for real-time, multi-echo fMRI methods development and validation
FALCON: a software package for analysis of nestedness in bipartite networks
Development and interval testing of a naturalistic driving methodology to evaluate driving behavior in clinical research
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
Texture analysis of the developing human brain using customization of a knowledge-based system
TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data
2017 ISCB Innovator Award: Aviv Regev
Design for learning - a case study of blended learning in a science unit
Bringing your tools to CyVerse Discovery Environment using Docker
Community and Code: Nine Lessons from Nine NESCent Hackathons
An R-based reproducible and user-friendly preprocessing pipeline for CyTOF data
Convolutional neural networks for real-time wood plank detection and defect segmentation
Annotation and curation of human genomic variations: an ELIXIR Implementation Study
Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks
Optimised deep neural network model to predict asthma exacerbation based on personalised weather triggers
CELL5M: A geospatial database of agricultural indicators for Africa South of the Sahara
Granite classification using machine learning and edge computing
The protective effectiveness of control interventions for malaria prevention: a systematic review of the literature
PAGAL - Properties and corresponding graphics of alpha helical structures in proteins
Recognizing human activities using light-weight and effective machine learning methodologies
Any neuron can perform linearly non-separable computations
Developing a wintering waterfowl community baseline for environmental monitoring of Narragansett Bay, Rhode Island
Development of a computer-assisted instructional package for life skills to prevent risky sexual behaviors in early adolescents, Bangkok, Thailand
A multi-tool recipe to identify regions of protein-DNA binding and their influence on associated gene expression
Sleep monitoring with the Apple Watch: comparison to a clinically validated actigraph
Open Data and transparency in artificial intelligence and machine learning: A new era of research
Jupyter notebook-based tools for building structured datasets from the Sequence Read Archive
A deep learning segmentation strategy that minimizes the amount of manually annotated images
Who is making clinical trials for treatment or prevention of COVID-19? A review of Clinicaltrials.gov, May 2020
InferCNV, a python web app for copy number inference from discrete gene-level amplification signals noted in clinical tumor profiling reports
Factors that contribute to social media influence within an Internal Medicine Twitter learning community
The ICR142 NGS validation series: a resource for orthogonal assessment of NGS analysis
Collaboration for rare disease drug discovery research
The importance of mentorship and collaboration for scientific capacity-building and capacity-sharing: perspectives of African scientists
Connecting the pieces: Using ORCIDs to improve research impact and repositories
Survey to healthcare professionals on the practicality of AI services for healthcare
CySpanningTree : Minimal Spanning Tree computation in Cytoscape
What is open peer review? A systematic review
Pharmacovigilance in perspective: drug withdrawals, data mining and policy implications
Predicting lithium treatment response in bipolar patients using gender-specific gene expression biomarkers and machine learning
Using different methods to process forced expiratory volume in one second (FEV 1 ) data can impact on the interpretation of FEV 1 as an outcome measure to understand the performance of an adult cystic fibrosis centre: A retrospective chart review
Exploring Vietnamese co-authorship patterns in social sciences with basic network measures of 2008-2017 Scopus data
Make researchers revisit past publications to improve reproducibility
Cross-sectional study of Facebook addiction in a sample of Nepalese population
Investigation of gut microbiome association with inflammatory bowel disease and depression: a machine learning approach
A predictive model of overall survival in patients with metastatic castration-resistant prostate cancer
Recommendations for connecting molecular sequence and biodiversity research infrastructures through ELIXIR
Machine learning algorithms: their applications in plant omics and agronomic traits' improvement
Using citation tracking for systematic literature searching - study protocol for a scoping review of methodological studies and an expert survey
Automated Wormscan
Effective image visualization for publications - a workflow using open access tools and concepts
Improving data transparency in clinical trials using blockchain smart contracts
ImageM: a user-friendly interface for the processing of multi-dimensional images with Matlab
A hybrid recommender system based on data enrichment on the ontology modelling
Conceptual design of smart multi-farm produce dehydrator using a low-cost programmable logic controller and raspberry pi
CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API
BioJS InterMineTable Component : A BioJS component for displaying data from InterMine compatible webservice endpoints
G-Links: a gene-centric link acquisition service
The Mega2R package: R tools for accessing and processing genetic data in common formats
Resource Description Framework reification for trustworthiness in knowledge graphs
BED: a Biological Entity Dictionary based on a graph data model
Bioimage analysis workflows: community resources to navigate through a complex ecosystem
Individual typological differences in a neurally distributed semantic processing system: Revisiting the Science article by Mitchell et al . on computational neurolinguistics
Automating the PathLinker app for Cytoscape
The khmer software package: enabling efficient nucleotide sequence analysis
seqCAT: a Bioconductor R-package for variant analysis of high throughput sequencing data
Badges for sharing data and code at Biostatistics: an observational study
Nonlocal contrast calculated by the second order visual mechanisms and its significance in identifying facial emotions
TCGAbiolinksGUI: A graphical user interface to analyze cancer molecular and clinical data
A biochemical logarithmic sensor with broad dynamic range
Recent advancements in machine vision methods for product code recognition: A systematic review
Working towards a consensus for antibody validation
Tweets from the forest: using Twitter to increase student engagement in an undergraduate field biology course
2019 ISCB Overton Prize: Christophe Dessimoz
A new method for detecting abrupt shifts in time series
Copycat Layout: Network layout alignment via Cytoscape Automation
An analysis of characteristics of post-authorisation studies registered on the ENCePP EU PAS Register
Problematizing Digital Research Evaluation using DOIs in Practice-Based Arts, Humanities and Social Science Research
MinION Analysis and Reference Consortium: Phase 1 data release and analysis
Priority regions for research on dryland cereals and legumes
Porting and using PanGIA for Cytoscape 3: challenges and solutions
Looking into Pandora's Box: The Content of Sci-Hub and its Usage
Procedure and datasets to compute links between genes and phenotypes defined by MeSH keywords
ShinyDiversity - Understanding Alpha and Beta Diversity through Interactive Visualizations
3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0 , an RNA Python library centered on secondary structure elements
Improving agricultural knowledge management: The AgTrials experience
COVID-19 impact: Customised economic stimulus package recommender system using machine learning techniques
Extending TCGA queries to automatically identify analogous genomic data from dbGaP
Performance Analysis of Simulated Annealing and Genetic Algorithm on systems of linear equations
COINSTAC: Decentralizing the future of brain imaging analysis
How 'smart' is smart dentistry?
Advancing the international data science workforce through shared training and education
Machine learning models identify molecules active against the Ebola virus in vitro
Open laboratory notebooks: good for science, good for society, good for scientists
Orchestrating a community-developed computational workshop and accompanying training materials
RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
Data publication consensus and controversies
Biological network analysis with CentiScaPe: centralities and experimental dataset integration
DomainBuilder: the knowledge authoring system for SlideTutor Intelligent Tutoring system
Defeating the 21st century demon "Cybercrime" on corporate bodies in Nigeria: Is security intelligence a weapon? A quantitative study
Smartic: A smart tool for Big Data analytics and IoT
The new alchemy: Online networking, data sharing and research activity distribution tools for scientists
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis
An optimized approach for class imbalance problem in heterogeneous cross project defect prediction
Three general concepts to improve risk prediction: good data, wisdom of the crowd, recalibration
Professional medical writing support and the reporting quality of randomized controlled trial abstracts among high-impact general medical journals
Calcium imaging analysis - how far have we come?
Exploring machine learning: A bibliometric general approach using SciMAT
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
The need for standardisation in life science research - an approach to excellence and trust
Fragger: a protein fragment picker for structural queries
shiny-pred: a server for the prediction of protein disordered regions
Modified recurrent equation-based cubic spline interpolation for missing data recovery in phasor measurement unit (PMU)
SPARClink: an interactive tool to visualize the impact of the SPARC program
In-air Hand Gesture Signature Recognition: An iHGS Database Acquisition Protocol
Exploratory graph analysis of the network data of the Ethereum blockchain
Discovering, Indexing and Interlinking Information Resources
Creating and sharing reproducible research code the workflowr way
epiflows: an R package for risk assessment of travel-related spread of disease
PPI layouts : BioJS components for the display of Protein-Protein Interactions
Developing open-source software for bioimage analysis: opportunities and challenges
FDTool: a Python application to mine for functional dependencies and candidate keys in tabular data
CoNet app: inference of biological association networks using Cytoscape
The 2017 Bioinformatics Open Source Conference (BOSC)
Preprocessed Consortium for Neuropsychiatric Phenomics dataset
RCy3: Network biology using Cytoscape from within R
Repositioning the Chemical Information Science Gateway
Using computation to enhance diagnosis and therapy: a novel mutation operator for real-coded adaptive genetic algorithms
Exploring differential evolution for inverse QSAR analysis
Child psychiatry: A scientometric analysis 1980-2016
Automation of ReactomeFIViz via CyREST API
Ranking the quality of protein structure models using sidechain based network properties
Closing gaps between open software and public data in a hackathon setting: User-centered software prototyping
MSTCN: A multiscale temporal convolutional network for user independent human activity recognition
Does vitamin D deficiency contribute to post-burn bone loss?
Hospital quality monitoring and evaluation system using linked spreadsheets on Microsoft SharePoint
AI in healthcare: A narrative review
Finite-state discrete-time Markov chain models of gene regulatory networks
Upregulation of human β-defensin-3 and cathelicidin LL-37 in Kaposi's sarcoma
Wireless power transfer with transmit diversity
Using agricultural metadata: a novel investigation of trends in sowing date in on-farm research trials using the Online Farm Trials database
Projection layers improve deep learning models of regulatory DNA function
Comment on the "TrialsTracker: Automated ongoing monitoring of failure to share clinical trial results by all major companies and research institutions"
webANIMO: Improving the accessibility of ANIMO
Correlating data from different sensors to increase the positive predictive value of alarms: an empiric assessment
Interactive biomedical segmentation tool powered by deep learning and ImJoy
Progress and challenges for the application of machine learning for neglected tropical diseases
Progress and challenges in the computational prediction of gene function using networks
From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline
Matchmaking in Bioinformatics
Designing and developing an app to perform Hofstee cut-off calculations
An ORCID based synchronization framework for a national CRIS ecosystem
ccbmlib - a Python package for modeling Tanimoto similarity value distributions
An unsupervised disease module identification technique in biological networks using novel quality metric based on connectivity, conductance and modularity
MSL: Facilitating automatic and physical analysis of published scientific literature in PDF format
aMatReader: Importing adjacency matrices via Cytoscape Automation
Umpire 2.0: Simulating realistic, mixed-type, clinical data for machine learning
Possible significance of spatial heterogeneities of local visual features for face perception
FDRestimation: Flexible False Discovery Rate Computation in R
CusVarDB: A tool for building customized sample-specific variant protein database from next-generation sequencing datasets
A curated transcriptome dataset collection to investigate the immunobiology of HIV infection
An interpretable machine learning model of biological age
Algorithm for the anesthetic management of cesarean delivery in patients with unsatisfactory labor epidural analgesia
A novel variable delay Go/No-Go task to study attention, motivation and working memory in the head-fixed rodent
Deep supervised hashing for gait retrieval
Oncoyeasti: a web-based application to translate data obtained from Saccharomyces cerevisiae high-throughput drug screens into cancer therapeutics
2017 ISCB Overton Prize: Christoph Bock
Enterprise resource planning implementation within science and technology park (STP) organisations: an avenue for future research. A systematic review
An ensemble-based Cox proportional hazards regression framework for predicting survival in metastatic castration-resistant prostate cancer (mCRPC) patients
Bibliometrics of the 100 most-cited articles on refugee populations
Comparative evaluation of sensitivity and specificity of immunochromatography kit for the rapid detection of norovirus and rotavirus in Bangladesh
Finding small molecules for the 'next Ebola'
A guide and best practices for R/Bioconductor tool integration in Galaxy
A divide-and-conquer strategy in tumor sampling enhances detection of intratumor heterogeneity in routine pathology: A modeling approach in clear cell renal cell carcinoma
segment_liftover : a Python tool to convert segments between genome assemblies
The impact of the open-access status on journal indices: a review of medical journals
Using Twitter to investigate opinions about multiple sclerosis treatments: a descriptive, exploratory study
Gene Annotation Easy Viewer (GAEV): Integrating KEGG's Gene Function Annotations and Associated Molecular Pathways
Statistical models for the deterioration of kidney function in a primary care population: A retrospective database analysis
Refining the content and design of an alcohol reduction app, Drink Less , to improve its usability and effectiveness: a mixed methods approach
NetMatchStar: an enhanced Cytoscape network querying app
Machine learning methods to predict particulate matter PM 2.5
Online algorithm for assignment of specimens to pooled or individual testing using risk models provides a practical way to increase testing capacity
pyGeno: A Python package for precision medicine and proteogenomics
The Taxonomy of Blockchain-based Technology in the Financial Industry
Journal ratings as predictors of articles quality in Arts, Humanities and Social Sciences: an analysis based on the Italian Research Evaluation Exercise
2019 ISCB Innovator Award recognizes William Stafford Noble
ASaiM-MT: a validated and optimized ASaiM workflow for metatranscriptomics analysis within Galaxy framework
Activity-relevant similarity values for fingerprints and implications for similarity searching
JSim, an open-source modeling system for data analysis
Transcription factor binding site clusters identify target genes with similar tissue-wide expression and buffer against mutations
PressPurt: network sensitivity to press perturbations under interaction uncertainty
AlignmentViewer: Sequence Analysis of Large Protein Families
Robust de novo pathway enrichment with KeyPathwayMiner 5
Machine learning model to predict endophytic colonisation of rice cultivar plant tissues by Beauveria bassiana isolates and their potential as bio-control agents against rice stem borer using existing knowledge
Using complex networks for refining survival prognosis in prostate cancer patient
Centromere detection of human metaphase chromosome images using a candidate based method
Enhancement of digitized X-ray films using Contrast-Limited Adaptive Histogram Equalization (CLAHE)
The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows
Classification of processes involved in sharing individual participant data from clinical trials
scClustViz - Single-cell RNAseq cluster assessment and visualization
Supporting evidence-based analysis for modified risk tobacco products through a toxicology data-sharing infrastructure
bwimage: A package to describe image patterns in natural structures
An a posteriori measure of network modularity
Cytoscape: the network visualization tool for GenomeSpace workflows
Epiviz Web Components: reusable and extensible component library to visualize functional genomic datasets
X-ray versus computerized tomography (CT) images for detection of COVID-19 using deep learning
Long-term preservation of biomedical research data
ranacapa: An R package and Shiny web app to explore environmental DNA data with exploratory statistics and interactive visualizations
rspatialdata: a collection of data sources and tutorials on downloading and visualising spatial data using R
FlyOde - a platform for community curation and interactive visualization of dynamic gene regulatory networks in Drosophila eye development
GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes
Ensemble machine learning modeling for the prediction of artemisinin resistance in malaria
Unbiased K-L estimator for the linear regression model
HeatMapViewer : interactive display of 2D data in biology
BridgeDb app: unifying identifier mapping services for Cytoscape
microbiomeDASim : Simulating longitudinal differential abundance for microbiome data
Alternative miRNAs? Human sequences misidentified as plant miRNAs in plant studies and in human plasma
Nutrition transition in South Asia: the emergence of non-communicable chronic diseases
Cytoscape tools for the web age: D3.js and Cytoscape.js exporters
The InterMine Android app: Cross-organism genomic data in your pocket
Connecting Altmetric: Integrating with Institutional Publications Systems
Nutritional status, survival and mortality in Alzheimer patients - a cross-sectional study
DEVILS: a tool for the visualization of large datasets with a high dynamic range
Semi-automated Modular Program Constructor for physiological modeling: Building cell and organ models
Paging Doctor Google! Heuristics vs. technology
Differential methylation analysis of reduced representation bisulfite sequencing experiments using edgeR
Top 10 metrics for life science software good practices
The F1000Research Antibody Validation Article Collection
(Semi)automated approaches to data extraction for systematic reviews and meta-analyses in social sciences: A living review protocol
flimview : A software framework to handle, visualize and analyze FLIM data
SLiMScape 3.x: a Cytoscape 3 app for discovery of Short Linear Motifs in protein interaction networks