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28 matching publication(s)

Publication	Journal	Year	Score	Verdict
TEMP: a computational method for analyzing transposable element polymorphism in populations. PMID 24753423	Nucleic Acids Res	2014	61	L1 61/100
Nucleosome regulatory dynamics in response to TGFβ. PMID 24771338	Nucleic Acids Res	2014	59	L1 59/100
Vespucci: a system for building annotated databases of nascent transcripts. PMID 24304890	Nucleic Acids Res	2013	73	L1 73/100
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program. PMID 22199257	Nucleic Acids Res	2011	86	L1 86/100
Hobbes: optimized gram-based methods for efficient read alignment. PMID 22199254	Nucleic Acids Res	2011	83	L1 83/100
Accurate chromatin marks peak calling with Omnipeak. PMID 41521664	Nucleic Acids Res	2026	77	L1 77/100
A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen. PMID 41505094	Nucleic Acids Res	2026	78	L1 78/100
Rfam 15: RNA families database in 2025. PMID 39526405	Nucleic Acids Res	2025	68	L1 68/100
Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter. PMID 38587191	Nucleic Acids Res	2024	68	L1 68/100
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes. PMID 37602419	Nucleic Acids Res	2023	77	L1 77/100
MirDIP 5.2: tissue context annotation and novel microRNA curation. PMID 36453996	Nucleic Acids Res	2023	89	L1 89/100
COXPRESdb v8: an animal gene coexpression database navigating from a global view to detailed investigations. PMID 36350658	Nucleic Acids Res	2023	84	L1 84/100
Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. PMID 35348734	Nucleic Acids Res	2022	91	L1 91/100
Foster thy young: enhanced prediction of orphan genes in assembled genomes. PMID 34928390	Nucleic Acids Res	2022	84	L1 84/100
An archaeal histone-like protein regulates gene expression in response to salt stress. PMID 34883507	Nucleic Acids Res	2021	94	L1 94/100
Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq. PMID 34875090	Nucleic Acids Res	2022	56	L1 56/100
Frequency and patterns of ribonucleotide incorporation around autonomously replicating sequences in yeast reveal the division of labor of replicative DNA polyme PMID 34551434	Nucleic Acids Res	2021	75	L1 75/100
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. PMID 34019643	Nucleic Acids Res	2021	82	L1 82/100
The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols. PMID 33978761	Nucleic Acids Res	2021	—	L1 No computation
4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans. PMID 33301041	Nucleic Acids Res	2020	78	L1 78/100
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. PMID 32374865	Nucleic Acids Res	2020	61	L1 61/100
Prediction of condition-specific regulatory genes using machine learning. PMID 32329779	Nucleic Acids Res	2020	85	L1 85/100
Octopus-toolkit: a workflow to automate mining of public epigenomic and transcriptomic next-generation sequencing data. PMID 29420797	Nucleic Acids Res	2018	68	L1 68/100
Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. PMID 28398514	Nucleic Acids Res	2017	77	L1 77/100
Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated wit ⚑ PMID 27655631	Nucleic Acids Res	2016	10	L1 10/100 ⚑
Discovery and characterization of Alu repeat sequences via precise local read assembly. PMID 26503250	Nucleic Acids Res	2015	69	L1 69/100
Ribosome A and P sites revealed by length analysis of ribosome profiling data. PMID 25805170	Nucleic Acids Res	2015	81	L1 81/100
Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments. PMID 22064864	Nucleic Acids Res	2011	83	L1 83/100