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39 matching publication(s)

Publication	Journal	Year	Score	Verdict
stDyer-image improves clustering analysis of spatially resolved transcriptomics and proteomics with morphological images. PMID 41692960	Bioinformatics	2026	75	L1 75/100
Smart spatial omics (S2-omics) optimizes region of interest selection to capture molecular heterogeneity in diverse tissues. PMID 41298871	Nat Cell Biol	2025	100	L1 100/100
Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material. PMID 41029822	J Transl Med	2025	67	L1 67/100
The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository. PMID 40926267	Genome Biol	2025	99	L1 99/100
Enhanced Generalizability of RNA Secondary Structure Prediction via Convolutional Block Attention Network and Ensemble Learning. PMID 40871599	Molecules	2025	87	L1 87/100
randPedPCA: rapid approximation of principal components from large pedigrees. PMID 40877802	Genet Sel Evol	2025	84	L1 84/100
Chemist: A Domain-Specific Language by Chemists for Chemists. PMID 40815845	J Phys Chem A	2025	89	89/100
Interpretable and integrative analysis of single-cell multiomics with scMKL. PMID 40770488	Commun Biol	2025	65	L1 65/100
Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway. PMID 40699865	Curr Issues Mol Biol	2025	—	L1 No data access
ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae. PMID 40364978	Bio Protoc	2025	100	L1 100/100
Protocol for assessing regulatory elements in murine heart using an AAV9-based massively parallel reporter assay. PMID 40252222	STAR Protoc	2025	93	L1 93/100
GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets. ⚑ PMID 40208796	Gigascience	2025	76	L1 76/100 ⚑
Statistical framework for calling allelic imbalance in high-throughput sequencing data. PMID 39966391	Nat Commun	2025	89	L1 89/100
Single-Cell Hi-C Technologies and Computational Data Analysis. PMID 39887949	Adv Sci (Weinh)	2025	80	L1 80/100
Correcting scale distortion in RNA sequencing data. PMID 39875825	BMC Bioinformatics	2025	76	L1 76/100
RummaGEO: Automatic mining of human and mouse gene sets from GEO. PMID 39569206	Patterns (N Y)	2024	63	L1 63/100
Rfam 15: RNA families database in 2025. PMID 39526405	Nucleic Acids Res	2025	68	L1 68/100
Protocol for the generation of single-nuclei RNA-seq libraries and quantification of heterogeneous cell types activated during social interaction. PMID 39423127	STAR Protoc	2024	78	L1 78/100
Analytical code sharing practices in biomedical research. PMID 38983240	PeerJ Comput Sci	2024	92	L1 92/100
Forseti: a mechanistic and predictive model of the splicing status of scRNA-seq reads. PMID 38940130	Bioinformatics	2024	87	L1 87/100
SGCP: a spectral self-learning method for clustering genes in co-expression networks. ⚑ PMID 38956463	BMC Bioinformatics	2024	51	L1 51/100 ⚑
DeepGSEA: explainable deep gene set enrichment analysis for single-cell transcriptomic data. PMID 38950178	Bioinformatics	2024	40	L1 40/100
PHA4GE quality control contextual data tags: standardized annotations for sharing public health sequence datasets with known quality issues to facilitate testin PMID 38860884	Microb Genom	2024	75	L1 75/100
D2H2: diabetes data and hypothesis hub. PMID 38107655	Bioinform Adv	2023	—	not yet assessed
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. PMID 35193506	BMC Bioinformatics	2022	94	L1 94/100
Preparation of mouse pancreatic tumor for single-cell RNA sequencing and analysis of the data. PMID 34927097	STAR Protoc	2021	50	L1 50/100
TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining. PMID 33705981	Genomics Proteomics Bioinformatics	2021	79	L1 79/100
Integrative network modeling reveals mechanisms underlying T cell exhaustion. PMID 32024856	Sci Rep	2020	59	L1 59/100
RNAmountAlign: Efficient software for local, global, semiglobal pairwise and multiple RNA sequence/structure alignment. PMID 31978147	PLoS One	2020	71	L1 71/100
A Bayesian approach to accurate and robust signature detection on LINCS L1000 data. PMID 32003771	Bioinformatics	2020	37	L1 37/100
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0. PMID 31343654	Invest Ophthalmol Vis Sci	2019	94	L1 94/100
Wx: a neural network-based feature selection algorithm for transcriptomic data. PMID 31324856	Sci Rep	2019	50	L1 50/100
pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. PMID 31114675	F1000Res	2019	90	L1 90/100
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID 31110304	Sci Rep	2019	73	L1 73/100
pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS). PMID 31035919	BMC Bioinformatics	2019	88	L1 88/100
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. PMID 30951143	Database (Oxford)	2019	80	L1 80/100
miRge 2.0 for comprehensive analysis of microRNA sequencing data. PMID 30153801	BMC Bioinformatics	2018	89	L1 89/100
Metavisitor, a Suite of Galaxy Tools for Simple and Rapid Detection and Discovery of Viruses in Deep Sequence Data. PMID 28045932	PLoS One	2017	78	L1 78/100
A robust data scaling algorithm to improve classification accuracies in biomedical data. PMID 27612635	BMC Bioinformatics	2016	87	87/100