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 Gene Mutation Sequence Alignment Rna Sequence Analysis Linear Models Tripterine Alleles Scoring Codon Servers Multiple Sequence Alignment Tertiary Protein Structure Time Protein Structure

Most Recent Papers

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, Yifei Huang, Kateryna Dmytrivna Makova, 2021, Genome Research on p. 1136-1149

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

Unified inference of missense variant effects and gene constraints in the human genome

Yi Fei Huang, 2020, PLoS Genetics

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

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

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

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

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

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

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

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

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

Inferring sequence regions under functional divergence in duplicate genes

Yi Fei Huang, G. Brian Golding, 2012, Bioinformatics on p. 176-183

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