Publications

A more comprehensive list of our publications can be found on google scholar.

* denotes equal contributions.

2023
37. Genetics of sexually dimorphic adipose distribution in humans
Hansen GT et al. (2023) Nature Genetics 1-10.

36. Molecular quantitative trait loci
Aguet F, Alasoo K, Li YI,Battle A, Im HK, Montgomery SB, Lappalainen T (2023) Nature Reviews Methods Primers 3 (1), 4.

2022

35. Profiling lariat intermediates reveals genetic determinants of early and late co-transcriptional splicing
Zeng Y, Fair BJ, Zeng H, Krishnamohan A, Hou Y, Hall JM, Ruthenburg AJ, Li YI*, Staley JP* (2022) Molecular Cell 82 (24), 4681-4699

34. RNA editing underlies genetic risk of common inflammatory diseases
Li Q et al. (2022) Nature 608, 569–577.

33. Predicting RNA splicing from DNA sequence using Pangolin.
Zeng T, Li YI (2022) Genome Biology 23 (103) .

2021

32. Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert et al. (2021) Science, 372 (6537).

2020

28. Alternative polyadenylation mediates genetic regulation of gene expression.
Mittleman B, Pott S, Warland S, Zeng T, Mu Z, Kaur M, Gilad Y, Li YI (2020) ELife 9, e57492.

27. LeafCutterMD: an algorithm for outlier splicing detection in rare diseases.
Jenkinson G et al. (2020) Bioinformatics 36, 17.

2019

26. Predicting splicing from primary sequence with deep learning. 
Jaganathan K et al. (2019) Cell 176 (3), 535-548. e24.

25. Characterizing the major structural variant alleles of the human genome. 
Audano PA et al. (2019) Cell 176 (3), 663-675. e19.

24. Trans effects on gene expression can drive omnigenic inheritance. 
Liu X*, Li YI*, Pritchard JK* (2019) Cell 177 (4), 1022-1034. e6.

23. Discovery and characterization of variance QTLs in human induced pluripotent stem cells.
Sarkar AK et al. (2019) PLoS Genetics 15 (4), e1008045.

22. Prioritizing Parkinson’s Disease genes using population-scale transcriptomic data. 
Li YI*, Wong G*, et al. (2019) Nature Communications 10 (1), 994.

21. A Machine-Curated Database of Genome-Wide Association Studies.
Kuleshov V, et al. (2019) Nature Communications 10 (1), 3341.

2018

20. Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility. 
Raj T, Li YI, et al. (2018) Nature Genetics 50 (11), 1584.

19. Impact of regulatory variation across human iPSCs and differentiated cells. 
Banovich NE*, Li YI*, Raj A*, et al. (2018) Genome Research doi: 10.1101/gr.224436.117.

18. Annotation-free quantification of RNA splicing using LeafCutter. 
Li YI*, Knowles DA*, Humphrey J, Barbeira AN, Dickinson SP, Im HK, Pritchard JK. (2018) Nature Genetics doi: 10.1038/s41588-017-0004-9.

2017

17. An expanded view of complex traits: from polygenic to omnigenic. 
Boyle EA*, Li YI*, Pritchard JK*. (2017) Cell 169 June 15, 2017.
[Highlights: The Atlantic, Stanford Med, F1000, Comments & Response]

2016

16. RNA splicing is a primary link between genetic variation and disease. 
Li YI, van de Geijn B, Raj A, Knowles DA, Petti A, Golan D, Gilad Y, Pritchard JK. (2016) Science 352 (6285), 600-604. [Highlights: UChicago Medicine, F1000]

15. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. 
Raj A, Wang S, Shim H, Harpak A, Li YI, Englemann B, Stephens M, Gilad Y, Pritchard JK. (2016) eLife 5, e13328.

14. Structural basis for therapeutic inhibition of complement C5. 
Jore MM, Sheppard D, Barber NM, Johnson S, Li YI, Nunn MA, Elmlund H, Lea SM. (2016)
Nature Structural & Molecular Biology 23(5):378-86.

2015

13. G&T-seq: Separation and parallel sequencing of the genomes and transcriptomes of single cells. 
Macaulay I, Haerty W, Kumar P, Li YI, et al. (2015) Nature methods 12 (6), 519-522. [Highlights: Wikipedia, F1000]

12. Insights into the evolution of longevity from the bowhead whale genome. 
Keane M*, Semeiks J*, Webb AE*, Li YI*, Quesada V* et al. (2015) Cell Reports. 10, 112-122.
[Highlights: NBC News, Science Daily, The Verge]

11. RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts. 
Li YI, Sanchez-Pulido L, Haerty W, Ponting CP. (2015) Genome Research 25 (1), 1-13.
[Highlights: EMBO J]

2014 and older

10. The genomic substrate for adaptive radiation in African cichlid fish. 
Brawand D*, Wagner C*, Li YI*, et al. (2014) Nature 513, 375-381.
[Highlights: Technology.org] 

9. Rapid evolution of beta-keratin genes contribute to phenotypic differences that distinguish turtles and birds from other reptiles. 
Li YI, Kong L, Ponting CP, Haerty W. (2013) Genome biology and evolution 5 (5), 923-933.

8. The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. 
Schaffer HB, et al. (2013) Genome Biology 14 (3), R28.

7. Scaffolding low quality genomes using orthologous protein sequences.
Li YI, Copley RR. (2013) Bioinformatics 29(2):160-5. 

6. Whole transcriptome sequencing of the aging rat brain reveals dynamic RNA changes in the dark matter of the genome.
Wood HS, Craig T, Li Y, Merry B, de Magalhães JP. (2012) Age (Dordr), 1-14.

5. Dissecting the Gene Network of Dietary Restriction to Identify Evolutionary Conserved Pathways and New Functional Genes.
Wuttke D, Connor R, Vora C, Craig T, Li Y, Wood S, Vasieva O, Tang F, de Magalhães JP. (2012) PLoS Genetics 8 (8), e1002834.

4. Accelerated protein evolution analysis reveals genes and pathways associated with the evolution of mammalian longevity.
Li Y, de Magalhães JP. (2011) Age (Dordr), 1-14.

3. RNA Sequencing Reveals Differential Expression of Mitochondrial and Oxidation Reduction Genes in the Long-Lived Naked Mole-Rat When Compared to Mice.
Yu C*, Li Y*, Holmes A, Szafranski K, Faulkes CG, Coen CW, Buffenstein R, Platzer M, de Magalhães JP, Church GM. (2011) PLoS ONE 6(11): e26729.

2. Mitochondrially encoded methionine is inversely related to longevity in mammals.
Aledo JC, Li Y, de Magalhães JP, Ruiz-Camacho M, Perez-Claros JA. (2011) Aging Cell 10:198-207.

1. The Human Ageing Genomic Resources: online databases and tools for biogerontologists.
de Magalhães JP, Budovsky A, Lehmann G, Costa J, Li Y, Fraifeld V, Church GM. (2009) Aging Cell 8(1):65-72.