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Butter: High-precision genomic alignment of small RNA-seq data
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1016/j.pbi.2014.02.008openalex-snapshot
Seeing the forest for the trees: annotating small RNA producing genes in plants
inferredcites →https://doi.org/10.1016/j.virol.2009.03.024openalex-snapshot
Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: A generic method for diagnosis, discovery and sequencing of viruses
inferredcites →https://doi.org/10.1016/j.ymeth.2013.10.004openalex-snapshot
Identification and annotation of small RNA genes using ShortStack
inferredcites →https://doi.org/10.1038/nature13069openalex-snapshot
miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis
inferredcites →https://doi.org/10.1038/nmeth.1226openalex-snapshot
Mapping and quantifying mammalian transcriptomes by RNA-Seq
inferredcites →https://doi.org/10.1073/pnas.0911353107openalex-snapshot
Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs
inferredcites →https://doi.org/10.1073/pnas.1318131111openalex-snapshot
Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice
inferredcites →https://doi.org/10.1093/bioinformatics/btn223openalex-snapshot
PatMaN: rapid alignment of short sequences to large databases
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btp459openalex-snapshot
RNA-MATE: a recursive mapping strategy for high-throughput RNA-sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/btp692openalex-snapshot
RNA-Seq gene expression estimation with read mapping uncertainty
inferredcites →https://doi.org/10.1093/nar/gkt1181openalex-snapshot
miRBase: annotating high confidence microRNAs using deep sequencing data
inferredcites →https://doi.org/10.1146/annurev-genet-110410-132541openalex-snapshot
Uniting Germline and Stem Cells: The Function of Piwi Proteins and the piRNA Pathway in Diverse Organisms
inferredcites →https://doi.org/10.1186/1471-2105-13-s15-s9openalex-snapshot
A Support Vector Machine based method to distinguish proteobacterial proteins from eukaryotic plant proteins
inferredcites →https://doi.org/10.1186/1471-2105-13-s6-s9openalex-snapshot
A context-based approach to identify the most likely mapping for RNA-seq experiments
inferredcites →https://doi.org/10.1186/gb-2009-10-3-r25openalex-snapshot
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
inferredcites →https://doi.org/10.1261/rna.035279.112openalex-snapshot
ShortStack: Comprehensive annotation and quantification of small RNA genes
inferredcites →https://doi.org/10.1261/rna.1473809openalex-snapshot
Computational and analytical framework for small RNA profiling by high-throughput sequencing
inferredcites →https://doi.org/10.1371/journal.pgen.1004298openalex-snapshot
Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1007/978-1-4939-9818-0_17openalex-snapshot
Isolating Male Meiocytes from Maize and Wheat for “-Omics” Analyses
inferred← citeshttps://doi.org/10.1007/s00705-017-3335-zopenalex-snapshot
Characterization of siRNAs derived from cucumber mosaic virus in infected tobacco plants
inferred← citeshttps://doi.org/10.1016/j.cell.2016.02.057openalex-snapshot
A Tunable Mechanism Determines the Duration of the Transgenerational Small RNA Inheritance in C. elegans
inferred← citeshttps://doi.org/10.1016/j.cell.2019.04.029openalex-snapshot
Neuronal Small RNAs Control Behavior Transgenerationally
inferred← citeshttps://doi.org/10.1016/j.virusres.2015.05.021openalex-snapshot
Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana
inferred← citeshttps://doi.org/10.1016/j.virusres.2015.09.019openalex-snapshot
Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection
inferred← citeshttps://doi.org/10.1016/j.virusres.2018.05.013openalex-snapshot
Profiling of small RNAs derived from cucumber mosaic virus in infected Nicotiana benthamiana plants by deep sequencing
inferred← citeshttps://doi.org/10.1038/srep31857openalex-snapshot
High-fat diet disrupts metabolism in two generations of rats in a parent-of-origin specific manner
inferred← citeshttps://doi.org/10.1098/rstb.2019.0345openalex-snapshot
Mobile genomics: tools and techniques for tackling transposons
inferred← citeshttps://doi.org/10.1101/138800openalex-snapshot
Towards selective-alignment: Bridging the accuracy gap between alignment-based and alignment-free transcript quantification
inferred← citeshttps://doi.org/10.1101/525956openalex-snapshot
Elucidating small RNA pathways in Arabidopsis thaliana egg cells
inferred← citeshttps://doi.org/10.1101/839092openalex-snapshot
The accumulation of chloroplast small RNAs in unicellular alga Chlamydomonas reinhardtii is affected by nitrogen deprivation
inferred← citeshttps://doi.org/10.1111/tpj.12835openalex-snapshot
Highly specific gene silencing in a monocot species by artificial micro RNA s derived from chimeric mi RNA precursors
inferred← citeshttps://doi.org/10.1186/s13059-018-1422-4openalex-snapshot
Investigation into the role of the germline epigenome in the transmission of glucocorticoid-programmed effects across generations
inferred← citeshttps://doi.org/10.1261/rna.055509.115openalex-snapshot
Evaluation of microRNA alignment techniques
inferred← citeshttps://doi.org/10.1261/rna.071324.119openalex-snapshot
Telomeric small RNAs in the genus Caenorhabditis
inferred← citeshttps://doi.org/10.15476/elte.2024.045openalex-snapshot
A növények antivirális RNS csendesítési mechanizmusainak molekuláris vizsgálata
inferred← citeshttps://doi.org/10.3390/biology10090896openalex-snapshot
Bioinformatics and Machine Learning Approaches to Understand the Regulation of Mobile Genetic Elements
inferred← citeshttps://doi.org/10.47749/t/unicamp.2015.947980openalex-snapshot
Estudos genômicos da expressão gênica global do fungo filamentoso Trichoderma reesei crescido em bagaço e colmo de cana-de-açúcar
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