Publications

Highlighted publications

S Uebbing, J Gockley, SK Reilly, AA Kocher, E Geller, N Gandotra, C Scharfe, J Cotney, & JP Noonan (2021). Massively parallel discovery of human-specific substitutions that alter enhancer activity. PNAS, 118:e2007049118

In this paper, we used a massively parallel enhancer assay to interrogate the effects of thousands of human-specific substitutions on the activity of the enhancers in which they reside.

Full publication list

(18) AA Kocher, EV Dutrow, S Uebbing, KM Yim, MF Rosales Larios, M Baumgartner, T Nottoli & JP Noonan (2023). CpG island turnover events predict evolutionary changes in enhancer activity. bioRxiv 2023.05.09.540063

(17) KL Gunawardhana*, L Hong*, T Rugira*, S Uebbing, J Kucharczak, S Mehta, D Karunamuni, B Cabrera-Mendoza, N Gandotra, C Scharfe, R Polimanti, JP Noonan & A Mani (2023). A systems biology approach identifies the role of dysregulated PRDM6 in the development of hypertension. Journal of Clinical Investigations 133:e160036
[ Highlighted in Kidney International | Press: MedicalXpress | Blog post: Tech Explorist ]

(16) EV Dutrow, D Emera, K Yim, S Uebbing, AA Kocher, M Krenzer, T Nottoli, DB Burkhardt, S Krishnaswamy, A Louvi & JP Noonan (2022). Modeling uniquely human gene regulatory function via targeted humanization of the mouse genome. Nature Communications 13:304
[ Highlighted in Nature Communications | bioRxiv preprint | Blog post on the Node's December in preprints | Additional raw data ]

(15) S Uebbing*, J Gockley*, SK Reilly, AA Kocher, E Geller, N Gandotra, C Scharfe, J Cotney & JP Noonan (2021). Massively parallel discovery of human-specific substitutions that alter enhancer activity. PNAS 118:e2007049118
[ Highlighted in This Week in PNAS | bioRxiv preprint | Code on GitHub | UCSC Genome Browser Track Hub | Extended Methods (PDF) ]

(14) J Chen, L Yang, R Zhang, S Uebbing, C Zhang, H Jiang, Y Lei, W Lv, F Tian, K Zhao & S He (2020). Transcriptome-wide patterns of the genetic and expression variation in two sympatric schizothoracine fishes in a Tibetan Plateau glacier lake. Genome Biology and Evolution 12:3725—3737

(13) E Geller, J Gockley, D Emera, S Uebbing, J Cotney & JP Noonan (2019). Massively parallel disruption of enhancers active during human corticogenesis. bioRxiv 852673
[ Blog post on the Node's December in preprints | Code on GitHub | UCSC Genome Browser Track Hub ]

(12) S Uebbing (2019). Stochomys longicaudatus (Rodentia: Muridae). Mammalian Species 51:26—33
[ Used by Wikipedia ]

(11) S Uebbing (2018). Evaluation of RNA-seq normalization methods using challenging datasets. bioRxiv 401679
[ Code on Bitbucket ]

(10) M Wang, S Uebbing, Y Pawitan & DG Scofield (2018). RPASE: Individual-based allele-specific expression detection without prior knowledge of haplotype phase. Molecular Ecology Resources 18:1247—1262
[ Code on GitHub ]

(9) R Sarro, AA Kocher, D Emera, S Uebbing, EV Dutrow, SD Weatherbee, T Nottoli & JP Noonan (2018). Disrupting the three-dimensional regulatory topology of the Pitx1 locus results in overtly normal development. Development 145:dev158550
[ bioRxiv preprint | Blog post on the Node's May in preprints ]

(8) M Wang, S Uebbing & H Ellegren (2017). Bayesian inference of allele-specific gene expression indicates abundant cis-regulatory variation in natural flycatcher populations. Genome Biology and Evolution 9:1266—1279

(7) S Uebbing, A Künstner, H Mäkinen, N Backström, P Bolivar, R Burri, L Dutoit, CF Mugal, A Nater, B Aken, P Flicek, FJ Martin, SMJ Searle & H Ellegren (2016). Divergence in gene expression within and between two closely related flycatcher species. Molecular Ecology 25:2015—2028
[ Code on GitHub ]

(6) S Uebbing*, A Konzer*, L Xu*, N Backström, B Brunström, J Bergquist & H Ellegren (2015). Quantitative mass spectrometry reveals partial translational regulation for dosage compensation in chicken. Molecular Biology and Evolution 32:2716—2725
[ Used by Wikipedia ]

(5) L Smeds, V Warmuth, P Bolivar, S Uebbing, R Burri, A Suh, A Nater, S Bureš, LZ Garamszegi, S Hogner, J Moreno, A Qvarnström, M Ružić, S-A Sæther, G-P Sætre, J Török & H Ellegren (2015). Evolutionary analysis of the female-specific avian W chromosome. Nature Communications 6:7330
[ Press: EurekAlert! and ScienceDaily ]

(4) L Smeds, T Kawakami, R Burri, P Bolivar, A Husby, A Qvarnström, S Uebbing & H Ellegren (2014). Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes. Nature Communications 5:5448
[ Press: Uppsala Nya Tidning (in Swedish) | Selected by Faculty Opinions ]

(3) S Uebbing, A Künstner, H Mäkinen & H Ellegren (2013). Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers. Genome Biology and Evolution 5:1555—1566

(2) J Chen, S Uebbing, N Gyllenstrand, U Lagercrantz, M Lascoux & T Källman (2012). Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms. BMC Genomics 13:589

(1) H Ellegren, L Smeds, R Burri, PI Olason, N Backström, T Kawakami, A Künstner, H Mäkinen, K Nadachowska-Brzyska, A Qvarnström, S Uebbing & JBW Wolf (2012). The genomic landscape of species divergence in Ficedula flycatchers. Nature 491:756—760
[ Highlighted in Current Biology and Heredity | Press: EurekAlert!, ScienceDaily, and Uppsala Nya Tidning (in Swedish) | Recommended twice by Faculty Opinions | Blog post: The Molecular Ecologist | Highly cited paper according to Web of Science | Used by Wikipedia (3x) ]