Template-based prediction of protein structure with deep learning

by Haicang Zhang, Yufeng Shen
Published 2020-12-01

Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing.

by Yufeng Shen, Sumeet Sarin, Ye Liu, Oliver Hobert, Itsik Pe'er
Published 2008-01-01

Rare variant phasing and haplotypic expression from RNA sequencing with phASER

by Stephane E. Castel, Pejman Mohammadi, Wendy K. Chung, Yufeng Shen, Tuuli Lappalainen
Published 2016-09-01

Distinct epigenomic patterns are associated with haploinsufficiency and predict risk genes of developmental disorders

by Xinwei Han, Siying Chen, Elise Flynn, Shuang Wu, Dana Wintner, Yufeng Shen
Published 2018-05-01

A pan-cancer analysis of driver gene mutations, DNA methylation and gene expressions reveals that chromatin remodeling is a major mechanism inducing global changes in cancer epigen...

by Ahrim Youn, Kyung In Kim, Raul Rabadan, Benjamin Tycko, Yufeng Shen, Shuang Wang
Published 2018-11-01

Characterizing immunoglobulin repertoire from whole blood by a personal genome sequencer.

by Fan Gao, Edwin Lin, Yaping Feng, William J Mack, Yufeng Shen, Kai Wang
Published 2013-01-01

Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose

by Wenji Ma, Jaeyop Lee, Daniel Backenroth, Yu Jerry Zhou, Erin Bush, Peter Sims, Kang Liu, Yufeng Shen
Published 2019-06-01

ABC transporters and the proteasome complex are implicated in susceptibility to Stevens-Johnson syndrome and toxic epidermal necrolysis across multiple drugs.

by Paola Nicoletti, Mukesh Bansal, Celine Lefebvre, Paolo Guarnieri, Yufeng Shen, Itsik Pe'er, Andrea Califano, Aris Floratos
Published 2015-01-01

MVP predicts the pathogenicity of missense variants by deep learning

by Hongjian Qi, Haicang Zhang, Yige Zhao, Chen Chen, John J. Long, Wendy K. Chung, Yongtao Guan, Yufeng Shen
Published 2021-01-01

Congenital diaphragmatic hernias: from genes to mechanisms to therapies

by Gabrielle Kardon, Kate G. Ackerman, David J. McCulley, Yufeng Shen, Julia Wynn, Linshan Shang, Eric Bogenschutz, Xin Sun, Wendy K. Chung
Published 2017-08-01

Non-cancer-related pathogenic germline variants and expression consequences in ten-thousand cancer genomes

by Zishan Wang, Xiao Fan, Yufeng Shen, Meghana S Pagadala, Rebecca Signer, Kamil J. Cygan, William G. Fairbrother, Hannah Carter, Wendy K. Chung, Kuan-lin Huang
Published 2021-09-01

Deep whole-genome sequencing of multiple proband tissues and parental blood reveals the complex genetic etiology of congenital diaphragmatic hernias

by Eric L. Bogenschutz, Zac D. Fox, Andrew Farrell, Julia Wynn, Barry Moore, Lan Yu, Gudrun Aspelund, Gabor Marth, Mark Yandell, Yufeng Shen, Wendy K. Chung, Gabrielle Kardon
Published 2020-10-01

Genotype and defects in microtubule-based motility correlate with clinical severity in KIF1A-associated neurological disorder

by Lia Boyle, Lu Rao, Simranpreet Kaur, Xiao Fan, Caroline Mebane, Laura Hamm, Andrew Thornton, Jared T. Ahrendsen, Matthew P. Anderson, John Christodoulou, Arne Gennerich, Yufeng Shen, Wendy K. Chung
Published 2021-04-01

Blood peptidome-degradome profile of breast cancer.

by Yufeng Shen, Nikola Tolić, Tao Liu, Rui Zhao, Brianne O Petritis, Marina A Gritsenko, David G Camp, Ronald J Moore, Samuel O Purvine, Francisco J Esteva, Richard D Smith
Published 2010-10-01

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

by Brahma V. Kumar, Wenji Ma, Michelle Miron, Tomer Granot, Rebecca S. Guyer, Dustin J. Carpenter, Takashi Senda, Xiaoyun Sun, Siu-Hong Ho, Harvey Lerner, Amy L. Friedman, Yufeng Shen, Donna L. Farber
Published 2017-09-01

Nanodroplet processing platform for deep and quantitative proteome profiling of 10–100 mammalian cells

by Ying Zhu, Paul D. Piehowski, Rui Zhao, Jing Chen, Yufeng Shen, Ronald J. Moore, Anil K. Shukla, Vladislav A. Petyuk, Martha Campbell-Thompson, Clayton E. Mathews, Richard D. Smith, Wei-Jun Qian, Ryan T. Kelly
Published 2018-02-01

Novel risk genes and mechanisms implicated by exome sequencing of 2572 individuals with pulmonary arterial hypertension

by Na Zhu, Michael W. Pauciulo, Carrie L. Welch, Katie A. Lutz, Anna W. Coleman, Claudia Gonzaga-Jauregui, Jiayao Wang, Joseph M. Grimes, Lisa J. Martin, Hua He, PAH Biobank Enrolling Centers’ Investigators, Yufeng Shen, Wendy K. Chung, William C. Nichols
Published 2019-11-01

De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes

by W. Scott Watkins, E. Javier Hernandez, Sergiusz Wesolowski, Brent W. Bisgrove, Ryan T. Sunderland, Edwin Lin, Gordon Lemmon, Bradley L. Demarest, Thomas A. Miller, Daniel Bernstein, Martina Brueckner, Wendy K. Chung, Bruce D. Gelb, Elizabeth Goldmuntz, Jane W. Newburger, Christine E. Seidman, Yufeng Shen, H. Joseph Yost, Mark Yandell, Martin Tristani-Firouzi
Published 2019-10-01

Loss of RNA expression and allele-specific expression associated with congenital heart disease

by David M. McKean, Jason Homsy, Hiroko Wakimoto, Neil Patel, Joshua Gorham, Steven R. DePalma, James S. Ware, Samir Zaidi, Wenji Ma, Nihir Patel, Richard P. Lifton, Wendy K. Chung, Richard Kim, Yufeng Shen, Martina Brueckner, Elizabeth Goldmuntz, Andrew J. Sharp, Christine E. Seidman, Bruce D. Gelb, J. G. Seidman
Published 2016-09-01

Rare variants in SOX17 are associated with pulmonary arterial hypertension with congenital heart disease

by Na Zhu, Carrie L. Welch, Jiayao Wang, Philip M. Allen, Claudia Gonzaga-Jauregui, Lijiang Ma, Alejandra K. King, Usha Krishnan, Erika B. Rosenzweig, D. Dunbar Ivy, Eric D. Austin, Rizwan Hamid, Michael W. Pauciulo, Katie A. Lutz, William C. Nichols, Jeffrey G. Reid, John D. Overton, Aris Baras, Frederick E. Dewey, Yufeng Shen, Wendy K. Chung
Published 2018-07-01