Publications

Highlighted publications

S Uebbing, AA Kocher, M Baumgartner, Y Ji, S Bai, X Xing, T Nottoli, & JP Noonan (2024). Evolutionary innovations in conserved regulatory elements associate with developmental genes in mammals. Molecular Biology and Evolution, msae199

Here we screened for genetic signatures of evolutionary change in putative enhancer sequences across the mammalian tree-of-life and found that genes involved in gene regulation and development were particularly enriched for evolutionary change.

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

(20) A Pal, MA Noble, M Morales, R Pal, M Baumgartner, JW Yang, KM Yim, S Uebbing, & JP Noonan (2024) Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. bioRxiv 2024.06.25.600691
[ Sequencing data on Gene Expression Omnibus | Code on GitHub part 1 & part 2 and stable versions on Zenodo part 1 & part 2 ]

(19) S Uebbing, AA Kocher, M Baumgartner, Y Ji, S Bai, X Xing, T Nottoli, & JP Noonan (2024). Evolutionary innovations in conserved regulatory elements associate with developmental genes in mammals. Molecular Biology and Evolution, msae199
[ bioRxiv preprint | Code on GitHub | Candidate enhancer dataset on Zenodo ]

(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. Genome Biology 25:156
[ bioRxiv preprint | Code on GitHub and stable version on Zenodo ]

(17) E Geller, MA Noble, M Morales, J Gockley, D Emera, S Uebbing, JL Cotney & JP Noonan (2024). Massively parallel disruption of enhancers active in human neural stem cells Cell Reports 43:113693
[ bioRxiv preprint | Blog post on the Node's December in preprints | Code on GitHub | UCSC Genome Browser Track Hub ]

(16) 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 ]

(15) 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 ]

(14) 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) ]

(13) 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

(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) ]