Selected Publications + Datasets

For a complete list of publications, please see pubmed or google scholar.

3 Papers from before 2016

Tilgner H*, Jahanbani F*, Blauwkamp T, Moshrefi A, Jaeger E, Chen F, Harel I, Bustamante CD, Rasmussen M, Snyder MP. Comprehensive transcriptome analysis using synthetic long read sequencing reveals molecular co-association and conservation of distant splicing events. Nature Biotechnol. 2015 May 18. doi: 10.1038/nbt.3242. [Epub ahead of print]
paper | google scholar | pubmed | F1000 Recommend | cover&paper | covered by genomeweb

Sharon D*, Tilgner H*, Grubert F, Snyder M (2013) A single-molecule long-read survey of the human transcriptome. Nat Biotechnol. 2013 Nov; 31(11):1009-14. doi: 10.1038/nbt.2705. Epub 2013 Oct 13. PMID: 24108091
paper | google scholar | pubmed | F1000 Recommend | cover&paper | covered by genomeweb

Tilgner H, Knowles DG, Johnson R, Davis CA, Chakrabortty S, Djebali S, Curado J, Snyder M, Gingeras TR, Guigó R (2012). Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res. 2012 Sep;22(9):1616-25. doi: 10.1101/gr.134445.111. PMID: 22955974
paper | google scholar | pubmed | F1000 Recommend | cover&paper

3 Papers from 2016-2022

Hardwick SA*, Hu W*, Joglekar A*, Fan L, Collier PG, Foord C, Balacco J, Lanjewar S, Sampson MM, Koopmans F, Prjibelski AD, Mikheenko A, Belchikov N, Jarroux J, Lucas AB, Palkovits M, Luo W, Milner TA, Ndhlovu LC, Smit AB, Trojanowski JQ, Lee VMY, Fedrigo O, Sloan SA, Tombácz D, Ross ME, Jarvis E, Boldogkői Z, Gan L, Tilgner HU. Single-nuclei isoform RNA sequencing unlocks barcoded exon connectivity in frozen brain tissue. Nat Biotechnol. 2022 Jul;40(7):1082-1092. doi: 10.1038/s41587-022-01231-3. Epub 2022 Mar 7. PMID: 35256815.
paper | pubmed | dataset | google scholar | highlighted by Nature Methods

Joglekar A, Prjibelski A, Mahfouz A, Collier P, Lin S, Schlusche AK, Marrocco J, Williams SR, Haase B, Hayes A, Chew JG, Weisenfeld NI, Wong MY, Stein AN, Hardwick SA, Hunt T, Wang Q, Dieterich C, Bent Z, Fedrigo O, Sloan SA, Risso D, Jarvis ED, Flicek P, Luo W, Pitt GS, Frankish A, Smit AB, Ross ME, Tilgner HU (2021). A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain. Nat Commun. 2021 Jan 19;12(1):463. doi: 10.1038/s41467-020-20343-5. PMID: 33469025
paper | pubmed | dataset | google scholar

Gupta I*, Collier PG*, Haase B, Mahfouz A, Joglekar A, Floyd T, Koopmans F, Barres B, Smit AB, Sloan SA, Luo W, Fedrigo O, Ross ME, Tilgner HU (2018). Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells. Nat Biotechnol. 2018 Oct 15. doi: 10.1038/nbt.4259. [Epub ahead of print],
paper | pubmed | dataset | google scholar | covered by genomeweb

3 (almost) Papers 2023-

Prjibelski AD*, Mikheenko A*, Joglekar A, Smetanin A, Jarroux J, Lapidus AL, Tilgner HU. Accurate isoform discovery with IsoQuant using long reads. Nat Biotechnol. 2023 Jan 2. doi: 10.1038/s41587-022-01565-y. Online ahead of print. PMID: 36593406
paper | pubmed | google scholar

Foord C*, Hsu J*, Jarroux J*, Hu W, Belchikov N, Pollard S, He Y, Joglekar A, Tilgner HU. The variables on RNA molecules: concert or cacophony? Answers in long-read sequencing. Nat Methods. 2023 Jan;20(1):20-24. doi: 10.1038/s41592-022-01715-9. PMID: 36635536. This is an outlook on the field in honor of Nature Methods naming long-read sequencing the Method of the Year 2022 - Not original research.
paper | pubmed | google scholar