FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W3037354611> ?p ?o ?g. }

• W3037354611 abstract "Abstract RNA-seq is a modular experimental and computational approach aiming in identifying and quantifying RNA molecules. The modularity of the RNA-seq technology enables adaptation of the protocol to develop new ways to explore RNA biology, but this modularity also brings forth the importance of methodological thoroughness. Liberty of approach comes with the responsibility of choices, and such choices must be informed. Here, we present an approach that identifies gene group-specific quantification biases in current RNA-seq software and references by processing datasets using diverse RNA-seq computational pipelines, and by decomposing these expression datasets with an independent component analysis matrix factorization method. By exploring the RNA-seq pipeline using this systemic approach, we identify genome annotations as a design choice that affects to the same extent quantification results as does the choice of aligners and quantifiers. We also show that the different choices in RNA-seq methodology are not independent, identifying interactions between genome annotations and quantification software. Genes were mainly affected by differences in their sequence, by overlapping genes and genes with similar sequence. Our approach offers an explanation for the observed biases by identifying the common features used differently by the software and references, therefore providing leads for the betterment of RNA-seq methodology." @default.
• W3037354611 created "2020-07-02" @default.
• W3037354611 creator A5041701753 @default.
• W3037354611 creator A5082027663 @default.
• W3037354611 creator A5091333025 @default.
• W3037354611 date "2020-06-01" @default.
• W3037354611 modified "2023-10-16" @default.
• W3037354611 title "Factorial study of the RNA-seq computational workflow identifies biases as technical gene signatures" @default.
• W3037354611 cites W1944771638 @default.
• W3037354611 cites W1981509058 @default.
• W3037354611 cites W1986519709 @default.
• W3037354611 cites W1990293955 @default.
• W3037354611 cites W1997563286 @default.
• W3037354611 cites W1999574084 @default.
• W3037354611 cites W2012034410 @default.
• W3037354611 cites W2022097310 @default.
• W3037354611 cites W2036897871 @default.
• W3037354611 cites W2065128082 @default.
• W3037354611 cites W2065776802 @default.
• W3037354611 cites W2071549023 @default.
• W3037354611 cites W2079517684 @default.
• W3037354611 cites W2087347094 @default.
• W3037354611 cites W2093253451 @default.
• W3037354611 cites W2093575652 @default.
• W3037354611 cites W2096441981 @default.
• W3037354611 cites W2097065948 @default.
• W3037354611 cites W2097860373 @default.
• W3037354611 cites W2097862362 @default.
• W3037354611 cites W2099879295 @default.
• W3037354611 cites W2100305481 @default.
• W3037354611 cites W2100424218 @default.
• W3037354611 cites W2100448568 @default.
• W3037354611 cites W2101735289 @default.
• W3037354611 cites W2102278945 @default.
• W3037354611 cites W2102619694 @default.
• W3037354611 cites W2103441770 @default.
• W3037354611 cites W2104005232 @default.
• W3037354611 cites W2110417468 @default.
• W3037354611 cites W2119204091 @default.
• W3037354611 cites W2123649031 @default.
• W3037354611 cites W2124985265 @default.
• W3037354611 cites W2126144698 @default.
• W3037354611 cites W2131271579 @default.
• W3037354611 cites W2134526812 @default.
• W3037354611 cites W2138207763 @default.
• W3037354611 cites W2140729960 @default.
• W3037354611 cites W2141458291 @default.
• W3037354611 cites W2152239989 @default.
• W3037354611 cites W2154437541 @default.
• W3037354611 cites W2155120241 @default.
• W3037354611 cites W2158717244 @default.
• W3037354611 cites W2169456326 @default.
• W3037354611 cites W2170551349 @default.
• W3037354611 cites W2173732482 @default.
• W3037354611 cites W2179438025 @default.
• W3037354611 cites W2188333210 @default.
• W3037354611 cites W2236822143 @default.
• W3037354611 cites W2272111630 @default.
• W3037354611 cites W2321872593 @default.
• W3037354611 cites W2323326409 @default.
• W3037354611 cites W2399463958 @default.
• W3037354611 cites W2467405197 @default.
• W3037354611 cites W2542446037 @default.
• W3037354611 cites W2571745526 @default.
• W3037354611 cites W2592811885 @default.
• W3037354611 cites W2610975234 @default.
• W3037354611 cites W2731748842 @default.
• W3037354611 cites W2743624002 @default.
• W3037354611 cites W2765745983 @default.
• W3037354611 cites W2767826728 @default.
• W3037354611 cites W2780155440 @default.
• W3037354611 cites W2898598946 @default.
• W3037354611 cites W2901757853 @default.
• W3037354611 cites W2943568104 @default.
• W3037354611 cites W2950254282 @default.
• W3037354611 cites W2950329612 @default.
• W3037354611 cites W2951624434 @default.
• W3037354611 cites W2951781413 @default.
• W3037354611 cites W2964849163 @default.
• W3037354611 cites W2971832717 @default.
• W3037354611 cites W2973374494 @default.
• W3037354611 cites W2996038594 @default.
• W3037354611 cites W4237403594 @default.
• W3037354611 cites W4241874243 @default.
• W3037354611 cites W4247053599 @default.
• W3037354611 doi "https://doi.org/10.1093/nargab/lqaa043" @default.
• W3037354611 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/7671328" @default.
• W3037354611 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/33575596" @default.
• W3037354611 hasPublicationYear "2020" @default.
• W3037354611 type Work @default.
• W3037354611 sameAs 3037354611 @default.
• W3037354611 citedByCount "4" @default.
• W3037354611 countsByYear W30373546112020 @default.
• W3037354611 countsByYear W30373546112021 @default.
• W3037354611 countsByYear W30373546112023 @default.
• W3037354611 crossrefType "journal-article" @default.
• W3037354611 hasAuthorship W3037354611A5041701753 @default.
• W3037354611 hasAuthorship W3037354611A5082027663 @default.
• W3037354611 hasAuthorship W3037354611A5091333025 @default.
• W3037354611 hasBestOaLocation W30373546111 @default.

• next