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 41: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 2025. Resolving the three-dimensional interactome of Human Accelerated Regions during human and chimpanzee neurodevelopment. Cell, in press
[ bioRxiv preprint | Press: YaleNews | 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 41: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 ]

(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) ]