Yifei Huang

Assistant Professor of Biology

yuh371@psu.edu

Research Summary

Developing novel bioinformatic methods and using them to address fundamental questions in evolutionary genomics and medical genomics.

Huck Graduate Students

Huck Affiliations

Molecular, Cellular, and Integrative Biosciences

Bioinformatics and Genomics

Publication Tags

Genome Proteins Genes Conservation Genomics Human Genome Nucleotides Mutation Phylogeny Phylogenetics Rna Dna Rate Model Protein Substitution Sequence Alignment Rna Sequence Analysis Linear Models Servers Time Tertiary Protein Structure Efficiency Alleles Protein Structure

Most Recent Publications

Extreme purifying selection against point mutations in the human genome

Noah Dukler, Mehreen R. Mughal, Ritika Ramani, Yi Fei Huang, Adam Siepel, 2022, Nature Communications

Dissecting Genomic Determinants of Positive Selection with an Evolution-Guided Regression Model

Yi Fei Huang, 2022, Molecular Biology and Evolution

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 J. Rice, Alexandra G. Chivu, Katie Krumholz, Charles G. Danko, Adam Siepel, 2021, BMC Biology

Non-B DNA: A major contributor to small-and large-scale variation in nucleotide substitution frequencies across the genome

Wilfried Guiblet, Marzia Cremona, Robert Harris, Di Chen, Kristin A. Eckert, Francesca Chiaromonte, Yi Fei Huang, Kateryna D. Makova, 2021, Nucleic Acids Research on p. 1497--1516

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

Wilfried M. Guiblet, Michael DeGiorgio, Michael , Xiaoheng Cheng, Francesca Chiaromonte, Kristin A. Eckert, Yi Fei Huang, Kateryna D. 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: A web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

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

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

Non-B DNA: A major contributor to small-and large-scale variation in nucleotide substitution frequencies across the genome

Wilfried Guiblet, Marzia Cremona, Robert Harris, Di Chen, Kristin A. Eckert, Francesca Chiaromonte, Yi Fei Huang, Kateryna D. Makova, 2021, Nucleic Acids Research on p. 1497--1516

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: A web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP

Ritika Ramani, Katie Krumholz, Yi Fei Huang, Adam Siepel, 2019, Bioinformatics on p. 2320-2322

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

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

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

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

News Articles Featuring Yifei Huang

Feb 04, 2021

Unusual DNA folding increases the rates of mutations

DNA sequences that can fold into shapes other than the classic double helix tend to have higher mutation rates than other regions in the human genome. New research by a team of Penn State scientists shows that the elevated mutation rate in these sequences plays a major role in determining regional variation in mutation rates across the genome.

Full Article