Paper Ranking Results

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This issue contains monthly updates to the ranked list of PubMed papers for curation. The full list can be found here. You can view and edit the curated papers file here.

New entries for 2024-07-09 to 2024-08-08:

PubMed ID	Title
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
38979784	DrugDomain: The evolutionary context of drugs and small molecules bound to domains.
39074139	FURNA: A database for functional annotations of RNA structures.
39047988	Knowledge infrastructure for integrated data management and analysis supporting new approach methods in predictive toxicology and risk assessment.
39014503	CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
38991851	PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
39084442	HSADab: A comprehensive database for human serum albumin.
39049520	Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance.
39104826	Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.
38991828	isolateR: an R package for generating microbial libraries from Sanger sequencing data.
39050757	Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily.
39064021	Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review.
39088253	Making Metadata Machine-Readable as the First Step to Providing Findable, Accessible, Interoperable, and Reusable Population Health Data: Framework Development and Implementation Study.
38979651	DIGEP-Pred 2.0: A web application for predicting drug-induced cell signaling and gene expression changes.
39044201	The Digital Atlas of Ancient Rare Diseases (DAARD) and its relevance for current research.
39028894	FragHub: A Mass Spectral Library Data Integration Workflow.
39108676	G-PLIP: Knowledge graph neural network for structure-free protein-ligand bioactivity prediction.
39005357	Alzheimer's Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction.
38984903	Managing macromolecular crystallographic data with a laboratory information management system.

[github-actions[bot]]

New entries for 2024-07-09 to 2024-08-08:

PubMed ID	Title
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
39074139	FURNA: A database for functional annotations of RNA structures.
38979784	DrugDomain: The evolutionary context of drugs and small molecules bound to domains.
39047988	Knowledge infrastructure for integrated data management and analysis supporting new approach methods in predictive toxicology and risk assessment.
39014503	CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.
39084442	HSADab: A comprehensive database for human serum albumin.
38991851	PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
38991828	isolateR: an R package for generating microbial libraries from Sanger sequencing data.
39049520	Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
39104826	Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.
39050757	Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily.
39064021	Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review.
38979651	DIGEP-Pred 2.0: A web application for predicting drug-induced cell signaling and gene expression changes.
39088253	Making Metadata Machine-Readable as the First Step to Providing Findable, Accessible, Interoperable, and Reusable Population Health Data: Framework Development and Implementation Study.
39028894	FragHub: A Mass Spectral Library Data Integration Workflow.
39044201	The Digital Atlas of Ancient Rare Diseases (DAARD) and its relevance for current research.
39005357	Alzheimer's Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction.
39024225	Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.
39010878	MotifbreakR v2: extended capability and database integration.

[github-actions[bot]]

This issue contains monthly updates to the ranked list of PubMed papers for curation. The full list can be found here. You can view and edit the curated papers file here.

New entries for 2024-07-09 to 2024-08-08:

PubMed ID	Title
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
39074139	FURNA: A database for functional annotations of RNA structures.
38979784	DrugDomain: The evolutionary context of drugs and small molecules bound to domains.
39047988	Knowledge infrastructure for integrated data management and analysis supporting new approach methods in predictive toxicology and risk assessment.
39014503	CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.
38991851	PEPhub: a database, web interface, and API for editing, sharing, and validating biological sample metadata.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
39049520	Data set of fraction unbound values in the in vitro incubations for metabolic studies for better prediction of human clearance.
38991828	isolateR: an R package for generating microbial libraries from Sanger sequencing data.
39084442	HSADab: A comprehensive database for human serum albumin.
39050757	Advancing drug discovery through assay development: a survey of tool compounds within the human solute carrier superfamily.
38979651	DIGEP-Pred 2.0: A web application for predicting drug-induced cell signaling and gene expression changes.
39064021	Bioinformatics in Neonatal/Pediatric Medicine-A Literature Review.
39088253	Making Metadata Machine-Readable as the First Step to Providing Findable, Accessible, Interoperable, and Reusable Population Health Data: Framework Development and Implementation Study.
39044201	The Digital Atlas of Ancient Rare Diseases (DAARD) and its relevance for current research.
39005357	Alzheimer's Disease Knowledge Graph Enhances Knowledge Discovery and Disease Prediction.
39028894	FragHub: A Mass Spectral Library Data Integration Workflow.
39044130	Transcription factor binding specificities of the oomycete Phytophthora infestans reflect conserved and divergent evolutionary patterns and predict function.
39113269	Data sharing considerations to maximise use of pathogen biological and genomics resources data for public health.
39024225	Single-fly genome assemblies fill major phylogenomic gaps across the Drosophilidae Tree of Life.

[github-actions[bot]]

This issue contains monthly updates to the ranked list of PubMed papers for curation. The full list can be found here. You can view and edit the curated papers file here.

New entries for 2024-08-02 to 2024-09-01:

PubMed ID	Title
39163546	GMMID: genetically modified mice information database.
39104285	FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants.
39145441	Clustering protein functional families at large scale with hierarchical approaches.
39134728	Glycoscience data content in the NCBI Glycans and PubChem.
39137905	Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.
39174566	An ontology-based knowledge graph for representing interactions involving RNA molecules.
39212696	Toward integration of glycan chemical databases: an algorithm and software tool for extracting sugars from chemical structures.
39126204	The biomedical relationship corpus of the BioRED track at the BioCreative VIII challenge and workshop.
39115390	GENEVIC: GENetic data exploration and visualization via intelli- gent interactive console.
39184336	RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens.
39095357	PatCID: an open-access dataset of chemical structures in patent documents.
39192607	Autoinhibited Protein Database: a curated database of autoinhibitory domains and their autoinhibition mechanisms.
39201310	Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations.
39084442	HSADab: A comprehensive database for human serum albumin.
39104826	Transforming environmental health datasets from the comparative toxicogenomics database into chord diagrams to visualize molecular mechanisms.
39171834	Generation of a high confidence set of domain-domain interface types to guide protein complex structure predictions by AlphaFold.
39143381	Online Mendelian Inheritance in Animals (OMIA): a genetic resource for vertebrate animals.
39176907	Merging Biomedical Ontologies with BioSTransformers.
39184224	What is it that you say you do here? Advocating for the critical role of data scientists in research infrastructure.
39190503	RefXAS: an open access database of X-ray absorption spectra.

[github-actions[bot]]

This issue contains monthly updates to the ranked list of PubMed papers for curation. The full list can be found here. You can view and edit the curated papers file here.

New entries for 2024-09-01 to 2024-10-01:

PubMed ID	Title
39229008	Creating and leveraging bespoke large-scale knowledge graphs for comparative genomics and multi-omics drug discovery with SocialGene.
39294369	Genomics 2 Proteins portal: a resource and discovery tool for linking genetic screening outputs to protein sequences and structures.
39227781	Variant graph craft (VGC): a comprehensive tool for analyzing genetic variation and identifying disease-causing variants.
39230707	GORetriever: reranking protein-description-based GO candidates by literature-driven deep information retrieval for protein function annotation.
39241109	Interactive tools for functional annotation of bacterial genomes.
39237205	CAPRI-Q: The CAPRI resource evaluating the quality of predicted structures of protein complexes.
39339901	Bioinformatics Goes Viral: I. Databases, Phylogenetics and Phylodynamics Tools for Boosting Virus Research.
39345624	Saccharomyces Genome Database: Advances in Genome Annotation, Expanded Biochemical Pathways, and Other Key Enhancements.
39268315	OnetoMap Meta-Data: Healthcare Analytics Through Research.
39228707	Leveraging Generative AI to Accelerate Biocuration of Medical Actions for Rare Disease.
39215721	AnnoDUF: A Web-Based Tool for Annotating Functions of Proteins Having Domains of Unknown Function.
39212696	Toward integration of glycan chemical databases: an algorithm and software tool for extracting sugars from chemical structures.
39235746	A Comprehensive Guide to Quality Assessment and Data Submission for Genomic Surveillance of Enteric Pathogens.
39247978	AARS Online: A collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases.
39279874	BioTextQuest v2.0: An evolved tool for biomedical literature mining and concept discovery.
39304538	The mutant mouse resource and research center (MMRRC) consortium: the US-based public mouse repository system.
39282297	Genome-Wide Mapping of RNA-Protein Associations via Sequencing.
39232149	Deciphering the impact of genomic variation on function.
39345458	The Unified Phenotype Ontology (uPheno): A framework for cross-species integrative phenomics.
39201310	Community Resource: Large-Scale Proteogenomics to Refine Wheat Genome Annotations.

[github-actions[bot]]

This issue contains monthly updates to the ranked list of PubMed papers for curation. The full list can be found here. You can view and edit the curated papers file here.

New entries for 2024-10-02 to 2024-11-01:

PubMed ID	Title
39399372	VCAb: a web-tool for structure-guided exploration of antibodies.
39470706	HSCGD: a comprehensive database of single-cell whole-genome data and metadata.
39401100	IntAct Database for Accessing IMEx's Contextual Metadata of Molecular Interactions.
39436595	Comprehensive Peptide Mapping Is Crucial for Proteogenomics and Proteomics.
39480818	Reference Sequence Browser: An R application with a user-friendly GUI to rapidly query sequence databases.
39464853	Unpacking unstructured data: A pilot study on extracting insights from neuropathological reports of Parkinson's Disease patients using large language models.
39373542	PhageDive: the comprehensive strain database of prokaryotic viral diversity.
39413165	SYNBIP 2.0: epitopes mapping, sequence expansion and scaffolds discovery for synthetic binding protein innovation.
39351883	xQTLatlas: a comprehensive resource for human cellular-resolution multi-omics genetic regulatory landscape.
39441075	20 years of the Bio-Analytic Resource for Plant Biology.
39436034	Dog10K: an integrated Dog10K database summarizing canine multi-omics.
39427279	Perspective: on the importance of extensive, high-quality and reliable deposition of biomolecular NMR data in the age of artificial intelligence.
39436020	DIONYSUS: a database of protein-carbohydrate interfaces.
39436594	Genome Annotation.
39438113	Binding profiles for 961 Drosophila and C. elegans transcription factors reveal tissue-specific regulatory relationships.
39470715	ScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.
39477936	Genome guided, organ-specific transcriptome assembly of the European flounder (P. flesus) from the Baltic Sea.
39389568	The relational modeling of hierarchical data in biodiversity databases.
39431984	DGRPool, a web tool leveraging harmonized Drosophila Genetic Reference Panel phenotyping data for the study of complex traits.
39467848	Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods.