Yifei Huang
Assistant Professor of Biology
Research Summary
Developing novel bioinformatic methods and using them to address fundamental questions in evolutionary genomics and medical genomics.
Huck Graduate Students
Huck Affiliations
Links
Publication Tags
Proteins Genes Conservation Genome Phylogenetics Phylogeny Substitution Reactions Genomics Substitution Protein Model Human Genome Gene Sequence Alignment Rna Sequence Analysis Mutation Linear Models Rate Alleles Scoring Codon Multiple Sequence Alignment Protein Tertiary Structure Gtp Binding Proteins TimeMost Recent Papers
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
Wilfried Guiblet, Michael DeGiorgio, Xiaoheng Cheng, F Chiaromonte, K Eckert, Yi-Fei Huang, K Makova, Genome Research on p. 1136-1149
Dissecting genomic determinants of positive selection with an evolution-guided regression model
Yi-Fei Huang, Molecular Biology and Evolution
Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome
Wilfried M. Guiblet, Michael DeGiorgio, Xiaoheng Cheng, Francesca Chiaromonte, Kristin A. Eckert, Yi Fei Huang, Kateryna D. Makova, 2021, Genome Research on p. 1136-1149
Characterizing RNA stability genome-wide through combined analysis of PRO-seq and RNA-seq data
Amit Blumberg, Yixin Zhao, Yi-Fei Huang, Noah Dukler, Edward Rice, Alexandra Chivu, Katie Krumholz, Charles Danko, Adam Siepel, 2021, BMC Biology on p. 30
Unified inference of missense variant effects and gene constraints in the human genome
Yi Fei Huang, 2020, PLoS Genetics
Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data
Noah Dukler, Yi Fei Huang, Adam Siepel, Sergei Kosakovsky Pond, 2020, Molecular Biology and Evolution on p. 2137-2152
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
Yi Fei Huang, Adam Siepel, 2019, Genome Research on p. 1310-1321
Phastweb
Ritika Ramani, Katie Krumholz, Yi Fei Huang, Adam Siepel, 2019, Bioinformatics on p. 2320-2322
Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution
Han Fang, Yi Fei Huang, Aditya Radhakrishnan, Adam Siepel, Gholson J. Lyon, Michael C. Schatz, 2018, Cell Systems on p. 180-191.e4
Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
Noah Dukler, Gregory T. Booth, Yi Fei Huang, Nathaniel Tippens, Colin T. Waters, Charles G. Danko, John T. Lis, Adam Siepel, 2017, Genome Research on p. 1816-1829
Most-Cited Papers
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
Yi Fei Huang, Brad Gulko, Adam Siepel, 2017, Nature Genetics on p. 618-624
Is a super-enhancer greater than the sum of its parts?
Noah Dukler, Brad Gulko, Yi Fei Huang, Adam Siepel, 2017, Nature Genetics on p. 2-4
Robust high-performance nanoliter-volume single-cell multiple displacement amplification on planar substrates
Kaston Leung, Anders Klaus, Bill K. Lin, Emma Laks, Justina Biele, Daniel Lai, Ali Bashashati, Yi Fei Huang, Radhouane Aniba, Michelle Moksa, Adi Steif, Anne Marie Mes-Masson, Martin Hirst, Sohrab P. Shah, Samuel Aparicio, Carl L. Hansen, 2016, Proceedings of the National Academy of Sciences of the United States of America on p. 8484-8489
Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution
Han Fang, Yi Fei Huang, Aditya Radhakrishnan, Adam Siepel, Gholson J. Lyon, Michael C. Schatz, 2018, Cell Systems on p. 180-191.e4
Phastweb
Ritika Ramani, Katie Krumholz, Yi Fei Huang, Adam Siepel, 2019, Bioinformatics on p. 2320-2322
Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures
Yi Fei Huang, G. Brian Golding, 2014, PLoS Computational Biology on p. e1003429
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
Yi Fei Huang, Adam Siepel, 2019, Genome Research on p. 1310-1321
Func patch: A web server for the fast Bayesian inference of conserved functional patches in protein 3D structures
Yi Fei Huangy, G. Brian Golding, 2015, Bioinformatics on p. 523-531
Nascent RNA sequencing reveals a dynamic global transcriptional response at genes and enhancers to the natural medicinal compound celastrol
Noah Dukler, Gregory T. Booth, Yi Fei Huang, Nathaniel Tippens, Colin T. Waters, Charles G. Danko, John T. Lis, Adam Siepel, 2017, Genome Research on p. 1816-1829
Inferring sequence regions under functional divergence in duplicate genes
Yi Fei Huang, G. Brian Golding, 2012, Bioinformatics on p. 176-183