T
Tom Smith
Researcher at University of Cambridge
Publications - 28
Citations - 2024
Tom Smith is an academic researcher from University of Cambridge. The author has contributed to research in topics: RNA & Python (programming language). The author has an hindex of 12, co-authored 27 publications receiving 1241 citations. Previous affiliations of Tom Smith include John Radcliffe Hospital & University of Oxford.
Papers
More filters
Journal ArticleDOI
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
TL;DR: It is shown that errors in the UMI sequence are common and network-based methods to account for these errors when identifying PCR duplicates are introduced, demonstrating the value of properly accounting for errors in UMIs.
Journal ArticleDOI
Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS).
Rayner M. L. Queiroz,Tom Smith,Eneko Villanueva,Maria Marti-Solano,Mie Monti,Mariavittoria Pizzinga,Dan-Mircea Mirea,Manasa Ramakrishna,Robert F. Harvey,Veronica Dezi,Gavin H. Thomas,Anne E. Willis,Kathryn S. Lilley +12 more
TL;DR: Orthogonal organic phase separation (OOPS) is presented, which does not require molecular tagging or capture of polyadenylated RNA, and is applied to recover cross-linked protein–RNA and free protein, or protein-bound RNA and free RNA, in an unbiased way.
Journal ArticleDOI
Alevin efficiently estimates accurate gene abundances from dscRNA-seq data
TL;DR: Alevin’s approach to UMI deduplication considers transcript-level constraints on the molecules from which UMIs may have arisen and accounts for both gene-unique reads and reads that multimap between genes, which addresses the inherent bias in existing tools which discard gene-ambiguous reads.
Journal ArticleDOI
Combining LOPIT with differential ultracentrifugation for high-resolution spatial proteomics
Aikaterini Geladaki,Nina Kočevar Britovšek,Lisa M. Breckels,Tom Smith,Owen L. Vennard,Claire M. Mulvey,Oliver M. Crook,Laurent Gatto,Laurent Gatto,Kathryn S. Lilley +9 more
TL;DR: The authors show that combining the previously developed hyperLOPIT method with differential centrifugation yields protein localisation maps at suborganellar resolution while reducing analysis time and input material.
Journal ArticleDOI
Trans-acting translational regulatory RNA binding proteins.
Robert F. Harvey,Tom Smith,Thomas Mulroney,Rayner M. L. Queiroz,Mariavittoria Pizzinga,Veronica Dezi,Eneko Villenueva,Manasa Ramakrishna,Kathryn S. Lilley,Anne E. Willis +9 more
TL;DR: The protein domains that are responsible for RNA binding as well as the RNA motifs to which they bind, and the role of trans‐acting ribosomal proteins in directing the translation of specific mRNAs are discussed.