A deep learning framework for predicting human essential genes from population and functional genomic data
Troy M LaPolice, Yi-Fei Huang✉
bioRxiv (2021)
Mixture Density Regression reveals frequent recent adaptation in the human genome
Diego F Salazar-Tortosa, Yi-Fei Huang✉, David Enard✉
bioRxiv (2021)
Transcription factor binding sites are frequently under accelerated evolution in primates
Xinru Zhang✉, Bohao Fang, Yi-Fei Huang✉
Nature Communications 14:783 (2023)
Extreme purifying selection against point mutations in the human genome
Noah Dukler*, Mehreen R Mughal*, Ritika Ramani, Yi-Fei Huang, Adam Siepel✉
Nature Communications 13:4312 (2022)
Dissecting genomic determinants of positive selection with an evolution-guided regression model
Yi-Fei Huang✉
Molecular Biology and Evolution 39:msab291 (2022)
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✉
Genome Research 31:1136-1149 (2021)
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, Katie Krumholz, Charles G. Danko and Adam Siepel✉
BMC biology 19:1-17 (2021)
Non-B DNA: a major contributor to small-and large-scale variation in nucleotide substitution frequencies across the genome
Wilfried M Guiblet*, Marzia A Cremona*, Robert S Harris, Di Chen, Kristin A Eckert, Francesca Chiaromonte✉, Yi-Fei Huang✉, Kateryna D Makova✉
Nucleic Acids Research 49:1497-1516 (2021)
Unified inference of missense variant effects and gene constraints in the human genome
Yi-Fei Huang✉
PLoS Genetics 16:e1008922 (2020)
Phylogenetic modeling of regulatory element turnover based on epigenomic data
Noah Dukler, Yi-Fei Huang and Adam Siepel✉
Molecular Biology and Evolution 37:2137-2152 (2020)
Estimation of allele-specific fitness effects across human protein-coding sequences and implications for disease
Yi-Fei Huang and Adam Siepel✉
Genome Research 29:1310-1321 (2019)
PhastWeb: a web interface for evolutionary conservation scoring of multiple sequence alignments using phastCons and phyloP
Ritika Ramani, Katie Krumholz, Yi-Fei Huang, and Adam Siepel✉
Bioinformatics 35:2320-2322 (2019)
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, and Michael C Schatz✉
Cell systems 6:180-191 (2018)
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data
Yi-Fei Huang, Brad Gulko, and Adam Siepel✉
Nature Genetics 49:618-624 (2017)
Is a super-enhancer greater than the sum of its parts?
Noah Dukler*, Brad Gulko*, Yi-Fei Huang*, and Adam Siepel✉
Nature Genetics 49:2-3 (2017)
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✉, and Adam Siepel✉
Genome Research 27:1816-1829 (2017)
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, and Carl L Hansen✉
Proceedings of the National Academy of Sciences 113:8484-8489 (2016)
FuncPatch: a web server for the fast Bayesian inference of conserved functional patches in protein 3D structures
Yi-Fei Huang and G. Brian Golding✉
Bioinformatics 31:523-531 (2015)
Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures
Yi-Fei Huang and G. Brian Golding✉
PLoS Computational Biology 10:e1003429 (2014)
Inferring sequence regions under functional divergence in duplicate genes
Yi-Fei Huang and G. Brian Golding✉
Bioinformatics 28:176-183 (2012)
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
Yi-Fei Huang and Deng-Ke Niu✉
BMC Evolutionary Biology 8:154 (2008)
*: co-first author
✉: corresponding author
Underscore: lab member/alumnus