Comparing genomic variant identification protocols for fungi to develop best practices.
Li X, Munoz JF, Gade L, Chow NA, …, Alastruey A, Litvintseva AP , Cuomo CA*.
Microbial Genomics. In preparation
funpipe: a python framework for efficient development of fungal bioinformatic pipelines.
Li X, Munoz J, Cuomo CA*.
Bioinformatics, in preparation.
covsir: an R package for subgenome coverage visualization
Li X, Munoz J, Cuomo CA*.
Bioinformatics, in preparation.
samplyzer: an R package and web application for efficient and interactive quality control of genotype data.
Li X, Segre A, Getz G, Ardlie K*.
Bioinformatics, in preparation.
dispseq: an R package for estimation of expression variation from RNA-seq counts data.
Li X*, Nettleton D*.
Bioinformatics, in prepration.
Tracing the evolutionary history and global expansion of Candida auris using population genomic analyses
Nancy A Chow, José F Muñoz, Lalitha Gade, Elizabeth L Berkow, Xiao Li, Rory M Welsh, Kaitlin Forsberg, Shawn R Lockhart, Rodney Adam, Alexandre Alanio, Ana Alastruey-Izquierdo, Sahar Althawadi, Ana Belén Araúz, Ronen Ben-Ami, Amrita Bharat, Belinda Calvo, Marie Desnos-Ollivier, Patricia Escandón, Dianne Gardam, Revathi Gunturu, Christopher H Heath, Oliver Kurzai, Ronny Martin, Anastasia P Litvintseva, Christina A Cuomo
MBio. (Article, bioRxiv)
The GTEx Consortium atlas of genetic regulatory effects across human tissues
GTEx Consortium
Science (Article)
Cell type–specific genetic regulation of gene expression across human tissues
S Kim-Hellmuth, …, GTEx Consortium, KG Ardlie, T Lappalainen.
Science (Article)
Determinants of telomere length across human tissues
K Demanelis, …, GTEx Consortium, BL Pierce.
Science (Article)
RNA sequence analysis reveals macroscopic somatic clonal expansion across normal tissues
Keren Yizhak, François Aguet, Jaegil Kim, Julian M Hess, Kirsten Kübler, Jonna Grimsby, Ruslana Frazer, Hailei Zhang, Nicholas J Haradhvala, Daniel Rosebrock, Dimitri Livitz, Xiao Li, Eila Arich-Landkof, Noam Shoresh, Chip Stewart, Ayellet V Segrè, Philip A Branton, Paz Polak, Kristin G Ardlie, Gad Getz
Science. (Article)
Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics
Alvaro N. Barbeira, Scott P. Dickinson, Rodrigo Bonazzola, Jiamao Zheng, Heather E. Wheeler, Jason M. Torres, Eric S. Torstenson, Kaanan P. Shah, Tzintzuni Garcia, Todd L. Edwards, Eli A. Stahl, Laura M. Huckins, GTEx Consortium, Dan L. Nicolae, Nancy J. Cox & Hae Kyung Im
Nature Communication.
Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS
Lin H, Liu Q, Li X, Yang J, Liu S, Huang Y, Scanlon MJ, Nettleton D, Schnable PS
Genome Biology (Article)
Genetic effects on gene expression across human tissues.
GTEx Consortium
Nature. (Article)
Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, …, GTEx Consortium, …, MacArthur DG.
Nature. (Article)
Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
Yang F, Wang J, GTEx Consortium, Pierce BL, Chen LS.
Genome Research. (Article)
Colocalization of GWAS and eQTL signals detects target genes
Hormozdiari F, van de Bunt M, Segrè AV, Li X, Joo JWJ, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E.
American Journal of Human Genetics (Article)
ForestPMPlot: a flexible tool for visualizing heterogeneity between studies in meta-analysis
EY Kang, Y Park, X Li, AV Segrè, B Han, E Eskin
G3: Genes, Genomes, Genetics (Article)
Genetic control of morphometric diversity in the maize shoot apical meristem
Leiboff S, Li X, Hu H, Todt N, Yang J, Li X, Yu X, Muehlbauer GJ, Timmermans MCP, Yu J, Schnable PS, Scanlon MJ
Nature Communication. (Article)
A prototypic lysine methyltransferase 4 from archaea with degenerate sequence specificity methylates chromatin proteins Sul7d and Cren7 in different patterns
Y Niu, Y Xia, S Wang, J Li, C Niu, X Li, Y Zhao, H Xiong, Z Li, H Lou, Q Cao.
Journal of Biological Chemistry. (Article)
*: co-first authors or co-corresponding authors. For a full list, click here.