Publications + Datasets

Selected publications

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

Tilgner H*, Jahanbani F*, Gupta I, Collier P, Wei E, Rasmussen M, Snyder M (2017). Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome. Genome Res. 2018 Feb;28(2):231-242. doi: 10.1101/gr.230516.117. Epub 2017 Dec 1.
paper | pubmed

Tilgner H*, Nikolaou C*, Althammer S, Sammeth M, Beato M, Valcárcel J, Guigó R. (2009) Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol. 2009 Sep;16(9):996-­‐1001.
google scholar | pubmed | news&views | cover&paper

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.
google scholar | pubmed | F1000 Recommend | cover&paper

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.
google scholar | pubmed | dataset | F1000 Recommend | cover&paper

Tilgner H*, Grubert F*, Sharon D*, Snyder MP (2014) Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci U S A. 2014 Jul 8;111(27):9869-74.
google scholar | pubmed | dataset | paper

Tilgner H*, Jahanbani F* et al. 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]
google scholar | pubmed | dataset | F1000 Recommend | cover&paper

Tilgner H, Raha D, Habegger L, Mohiuddin M, Gerstein M, Snyder M (2013) Accurate identification and analysis of human mRNA isoforms using deep long read sequencing. G3 (Bethesda). 2013 Mar;3(3):387-97.
google scholar | pubmed | dataset | cover&paper

Pérez-Lluch S*, Blanco E*, Tilgner H*, Curado J*, Ruiz-Romero M, Corominas M, Guigó R. Absence of canonical marks of active chromatin in developmentally regulated genes. Nat Genet. 2015 Oct;47(10):1158-67.
google scholar | pubmed | cover&paper

Curado J*, Iannone C*, Tilgner H*, Valcárcel J, Guigó R. Promoter-like epigenetic signatures in exons displaying cell type-specific splicing. Genome Biol. 2015 Oct 23;16:236.
google scholar | pubmed | paper

Tilgner H, Guigó R (2010). From chromatin to splicing: RNA-processing as a total artwork. Epigenetics. 2010 Apr 1;5(3):180-4.
google scholar | pubmed | paper

Other publications:

Cenik C et al. (including Tilgner H) (2014) Integrative analysis of RNA, translation, and protein levels reveals distinct regulatory variation across humans. Genome Res. 2015 Nov;25(11):1610-21.

Tejedor JR, Tilgner H, Iannone C, Guigó R, Valcárcel J. Role of Six
Single Nucleotide Polymorphisms, Risk Factors in Coronary Disease,
in OLR1 Alternative Splicing. RNA. 2015 Apr 22. [Epub ahead of print]

Derrien T et al. (including Tilgner H) (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression.  Genome Res. 2012 Sep;22(9):1775-89.

Djebali S et al. (including Tilgner H). Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8.

ENCODE Project Consortium (including Tilgner H). An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74.

Maxwell CA et al. (including Tilgner H) (2011) Interplay between BRCA1 and RHAMM regulates epithelial apicobasal polarization and may influence risk of breast cancer. PLoS Biol. 2011 Nov;9(11):e1001199.
ENCODE Project Consortium (including Tilgner H) (2011) A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr;9(4):e1001046.