Yufeng Shen

Publication Activity (10 Years)

Years Active: 2019-2024
Publications (10 Years): 39

Top Topics

Dna Methylation

Congenital Heart Disease

Top Venues

Circulation. Genomic and precision medicine

Nature genetics

Genome research

medRxiv : the preprint server for health sciences

This page only lists publications with an associated author ORCID identifier.

Publications

Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research 34 (7) (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research 34 (7) (2024)
Giangela Stokes, Zhuowei Li, Nicole Talaba, William Genthe, Maria B Brix, Betty Pham, Mark D Wienhold, Gracia Sandok, Rebecca Hernan, Julia Wynn, Haiyang Tang, Diana M Tabima, Allison Rodgers, Timothy A Hacker, Naomi C Chesler, Pan Zhang, Rabi Murad, Jason X-J Yuan, Yufeng Shen, Wendy K Chung, David J McCulley
Rescuing lung development through embryonic inhibition of histone acetylation. Science translational medicine 16 (732) (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research (2024)
Giangela Stokes, Zhuowei Li, Nicole Talaba, William Genthe, Maria B Brix, Betty Pham, Mark D Wienhold, Gracia Sandok, Rebecca Hernan, Julia Wynn, Haiyang Tang, Diana M Tabima, Allison Rodgers, Timothy A Hacker, Naomi C Chesler, Pan Zhang, Rabi Murad, Jason X-J Yuan, Yufeng Shen, Wendy K Chung, David J McCulley
Rescuing lung development through embryonic inhibition of histone acetylation. Science translational medicine 16 (732) (2024)
Feng Xiao, Xiaoran Zhang, Sarah U Morton, Seong Won Kim, Youfei Fan, Joshua M Gorham, Huan Zhang, Paul J Berkson, Neil Mazumdar, Yangpo Cao, Jian Chen, Jacob Hagen, Xujie Liu, Pingzhu Zhou, Felix Richter, Yufeng Shen, Tarsha Ward, Bruce D Gelb, Jonathan G Seidman, Christine E Seidman, William T Pu
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature genetics 56 (3) (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research (2024)
Feng Xiao, Xiaoran Zhang, Sarah U Morton, Seong Won Kim, Youfei Fan, Joshua M Gorham, Huan Zhang, Paul J Berkson, Neil Mazumdar, Yangpo Cao, Jian Chen, Jacob Hagen, Xujie Liu, Pingzhu Zhou, Felix Richter, Yufeng Shen, Tarsha Ward, Bruce D Gelb, Jonathan G Seidman, Christine E Seidman, William T Pu
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature genetics 56 (3) (2024)
Feng Xiao, Xiaoran Zhang, Sarah U Morton, Seong Won Kim, Youfei Fan, Joshua M Gorham, Huan Zhang, Paul J Berkson, Neil Mazumdar, Yangpo Cao, Jian Chen, Jacob Hagen, Xujie Liu, Pingzhu Zhou, Felix Richter, Yufeng Shen, Tarsha Ward, Bruce D Gelb, Jonathan G Seidman, Christine E Seidman, William T Pu
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature genetics 56 (3) (2024)
Guojie Zhong, Yige Zhao, Demi Zhuang, Wendy K Chung, Yufeng Shen
PreMode predicts mode-of-action of missense variants by deep graph representation learning of protein sequence and structural context. bioRxiv : the preprint server for biology (2024)
Feng Xiao, Xiaoran Zhang, Sarah U Morton, Seong Won Kim, Youfei Fan, Joshua M Gorham, Huan Zhang, Paul J Berkson, Neil Mazumdar, Yangpo Cao, Jian Chen, Jacob Hagen, Xujie Liu, Pingzhu Zhou, Felix Richter, Yufeng Shen, Tarsha Ward, Bruce D Gelb, Jonathan G Seidman, Christine E Seidman, William T Pu
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature genetics 56 (3) (2024)
Chencheng Xu, Suying Bao, Ye Wang, Wenxing Li, Hao Chen, Yufeng Shen, Tao Jiang, Chaolin Zhang
Reference-informed prediction of alternative splicing and splicing-altering mutations from sequences. Genome research (2024)
Feng Xiao, Xiaoran Zhang, Sarah U Morton, Seong Won Kim, Youfei Fan, Joshua M Gorham, Huan Zhang, Paul J Berkson, Neil Mazumdar, Yangpo Cao, Jian Chen, Jacob Hagen, Xujie Liu, Pingzhu Zhou, Felix Richter, Yufeng Shen, Tarsha Ward, Bruce D Gelb, Jonathan G Seidman, Christine E Seidman, William T Pu
Functional dissection of human cardiac enhancers and noncoding de novo variants in congenital heart disease. Nature genetics (2024)
Yige Zhao, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy K Chung, Yufeng Shen
A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data. medRxiv : the preprint server for health sciences (2023)
Guojie Zhong, Yoolim A Choi, Yufeng Shen
VBASS enables integration of single cell gene expression data in Bayesian association analysis of rare variants. Communications biology 6 (1) (2023)
Yige Zhao, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy K Chung, Yufeng Shen
A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data. medRxiv : the preprint server for health sciences (2023)
Jianing Fu, Zicheng Wang, Mercedes Martinez, Aleksandar Z Obradovic, Wenyu Jiao, Kristjana Frangaj, Rebecca T L Jones, Xinzheng V Guo, Ya Zhang, Wan-I Kuo, Huaibin Mabel Ko, Alina Iuga, Constanza Bay Muntnich, Adriana Prada Rey, Kortney Rogers, Julien Zuber, Wenji Ma, Michelle Miron, Donna L Farber, Joshua I Weiner, Tomoaki Kato, Yufeng Shen, Megan Sykes
Plasticity of intragraft alloreactive T cell clones in human gut correlates with transplant outcomes. The Journal of experimental medicine 221 (1) (2023)
Emily L Griffin, Shannon N Nees, Sarah U Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie M Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa L Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen C King, James F Cnota, Richard W Kim, George A Porter, Martina Brueckner, Christine E Seidman, Yufeng Shen, Bruce D Gelb, Elizabeth Goldmuntz, Jane W Newburger, Amy E Roberts, Wendy K Chung
Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circulation. Genomic and precision medicine (2023)
Yige Zhao, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy K Chung, Yufeng Shen
A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data. medRxiv : the preprint server for health sciences (2023)
Na Zhu, Charles A LeDuc, Ilene Fennoy, Blandine Laferrère, Claudia A Doege, Yufeng Shen, Wendy K Chung, Rudolph L Leibel
Predicted loss of function alleles in Bassoon (BSN) are associated with obesity. medRxiv : the preprint server for health sciences (2023)
Min Young Jang, Parth N Patel, Alexandre C Pereira, Jon A L Willcox, Alireza Haghighi, Angela C Tai, Shefali S Verma, Sarah U Morton, Joshua M Gorham, David M McKean, Steven R DePalma, Daniel Bernstein, Martina Brueckner, Wendy K Chung, Alessandro Giardini, Elizabeth Goldmuntz, Jonathan R Kaltman, Richard W Kim, Jane W Newburger, Yufeng Shen, Deepak Srivastava, Martin Tristani-Firouzi, Bruce D Gelb, George A Porter, Christine E Seidman, Jonathan G Seidman
Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease. Circulation. Genomic and precision medicine (2023)
Na Zhu, Charles A LeDuc, Ilene Fennoy, Blandine Laferrère, Claudia A Doege, Yufeng Shen, Wendy K Chung, Rudolph L Leibel
Rare predicted loss of function alleles in Bassoon (BSN) are associated with obesity. NPJ genomic medicine 8 (1) (2023)
Emily L Griffin, Shannon N Nees, Sarah U Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie M Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa L Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen C King, James F Cnota, Richard W Kim, George A Porter, Martina Brueckner, Christine E Seidman, Yufeng Shen, Bruce D Gelb, Elizabeth Goldmuntz, Jane W Newburger, Amy E Roberts, Wendy K Chung
Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circulation. Genomic and precision medicine (2023)
Min Young Jang, Parth N Patel, Alexandre C Pereira, Jon A L Willcox, Alireza Haghighi, Angela C Tai, Shefali S Verma, Sarah U Morton, Joshua M Gorham, David M McKean, Steven R DePalma, Daniel Bernstein, Martina Brueckner, Wendy K Chung, Alessandro Giardini, Elizabeth Goldmuntz, Jonathan R Kaltman, Richard W Kim, Jane W Newburger, Yufeng Shen, Deepak Srivastava, Martin Tristani-Firouzi, Bruce D Gelb, George A Porter, Christine E Seidman, Jonathan G Seidman
Contribution of Previously Unrecognized RNA Splice-Altering Variants to Congenital Heart Disease. Circulation. Genomic and precision medicine (2023)
Yige Zhao, Guojie Zhong, Jake Hagen, Hongbing Pan, Wendy K Chung, Yufeng Shen
A probabilistic graphical model for estimating selection coefficient of missense variants from human population sequence data. medRxiv : the preprint server for health sciences (2023)
Matthew J Lewis, Alexander Hsieh, Lu Qiao, Renjie Tan, Brigitte Kazzi, Alexandra Channing, Emily L Griffin, Vaidehi Jobanputra, Jennifer Su, Chowdhury Shahryar, Lazaros K Kochilas, William Gaynor, Teresa Lee, Elizabeth Goldmuntz, Mark W Russell, Seema Mital, Martin Tristani-Firouzi, Martina Brueckner, Jane W Newburger, Yufeng Shen, Wendy K Chung
Association of Predicted Damaging De Novo Variants on Ventricular Function in Individuals With Congenital Heart Disease. Circulation. Genomic and precision medicine (2023)
Emily L Griffin, Shannon N Nees, Sarah U Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie M Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa L Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen C King, James F Cnota, Richard W Kim, George A Porter, Martina Brueckner, Christine E Seidman, Yufeng Shen, Bruce D Gelb, Elizabeth Goldmuntz, Jane W Newburger, Amy E Roberts, Wendy K Chung
Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circulation. Genomic and precision medicine (2023)
Emily L Griffin, Shannon N Nees, Sarah U Morton, Julia Wynn, Nihir Patel, Vaidehi Jobanputra, Scott Robinson, Stephanie M Kochav, Alice Tao, Carli Andrews, Nancy Cross, Judith Geva, Kristen Lanzilotta, Alyssa L Ritter, Eileen Taillie, Alexandra Thompson, Chris Meyer, Rachel Akers, Eileen C King, James F Cnota, Richard W Kim, George A Porter, Martina Brueckner, Christine E Seidman, Yufeng Shen, Bruce D Gelb, Elizabeth Goldmuntz, Jane W Newburger, Amy E Roberts, Wendy K Chung
Evidence-Based Assessment of Congenital Heart Disease Genes to Enable Returning Results in a Genomic Study. Circulation. Genomic and precision medicine (2023)
Xueya Zhou, Pamela Feliciano, Chang Shu, Tianyun Wang, Irina Astrovskaya, Jacob B Hall, Joseph U Obiajulu, Jessica R Wright, Shwetha C Murali, Simon Xuming Xu, Leo Brueggeman, Taylor R Thomas, Olena Marchenko, Christopher Fleisch, Sarah D Barns, LeeAnne Green Snyder, Bing Han, Timothy S Chang, Tychele N Turner, William T Harvey, Andrew Nishida, Brian J O'Roak, Daniel H Geschwind, null null, Jacob J Michaelson, Natalia Volfovsky, Evan E Eichler, Yufeng Shen, Wendy K Chung
Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes. Nature genetics 54 (9) (2022)
Sarah U Morton, Alexandre da Costa Pereira, Daniel Quiat, Felix Richter, Alexander Kitaygorodsky, Jacob Hagen, Daniel Bernstein, Martina Brueckner, Elizabeth Goldmuntz, Richard W Kim, Richard P Lifton, George A Porter, Martin Tristani-Firouzi, Wendy K Chung, Amy E Roberts, Bruce D Gelb, Yufeng Shen, Jane W Newburger, Jonathan G Seidman, Christine E Seidman
Genome-Wide De Novo Variants in Congenital Heart Disease Are Not Associated With Maternal Diabetes or Obesity. Circulation. Genomic and precision medicine 15 (2) (2022)
Renjie Tan, Yufeng Shen
Accurate in silico confirmation of rare copy number variant calls from exome sequencing data using transfer learning. Nucleic acids research (2022)
Bryan J González, Haoquan Zhao, Jacqueline Niu, Damian J Williams, Jaeyop Lee, Chris N Goulbourne, Yuan Xing, Yong Wang, Jose Oberholzer, Maria H Blumenkrantz, Xiaojuan Chen, Charles A LeDuc, Wendy K Chung, Henry M Colecraft, Jesper Gromada, Yufeng Shen, Robin S Goland, Rudolph L Leibel, Dieter Egli
Reduced calcium levels and accumulation of abnormal insulin granules in stem cell models of HNF1A deficiency. Communications biology 5 (1) (2022)
Haicang Zhang, Michelle S Xu, Xiao Fan, Wendy K Chung, Yufeng Shen
Predicting functional effect of missense variants using graph attention neural networks. Nature machine intelligence 4 (11) (2022)
Xiao Fan, Julia Wynn, Ning Shang, Cong Liu, Alexander Fedotov, Miranda L G Hallquist, Adam H Buchanan, Marc S Williams, Maureen E Smith, Christin Hoell, Laura J F Rasmussen-Torvik, Josh F Peterson, Georgia L Wiesner, Andrea M Murad, Gail P Jarvik, Adam S Gordon, Elisabeth A Rosenthal, Ian B Stanaway, David R Crosslin, Eric B Larson, Kathleen A Leppig, Nora B Henrikson, Janet L Williams, Rongling Li, Scott Hebbring, Chunhua Weng, Yufeng Shen, Katherine D Crew, Wendy K Chung
Penetrance of Breast Cancer Susceptibility Genes From the eMERGE III Network. JNCI cancer spectrum 5 (4) (2021)
Hongjian Qi, Haicang Zhang, Yige Zhao, Chen Chen, John J Long, Wendy K Chung, Yongtao Guan, Yufeng Shen
MVP predicts the pathogenicity of missense variants by deep learning. Nature communications 12 (1) (2021)
Felix Richter, Sarah U Morton, Seong Won Kim, Alexander Kitaygorodsky, Lauren K Wasson, Kathleen M Chen, Jian Zhou, Hongjian Qi, Nihir Patel, Steven R DePalma, Michael Parfenov, Jason Homsy, Joshua M Gorham, Kathryn B Manheimer, Matthew Velinder, Andrew Farrell, Gabor T Marth, Eric E Schadt, Jonathan R Kaltman, Jane W Newburger, Alessandro Giardini, Elizabeth Goldmuntz, Martina Brueckner, Richard Kim, George A Porter, Daniel Bernstein, Wendy K Chung, Deepak Srivastava, Martin Tristani-Firouzi, Olga G Troyanskaya, Diane E Dickel, Yufeng Shen, Jonathan G Seidman, Christine E Seidman, Bruce D Gelb
Genomic analyses implicate noncoding de novo variants in congenital heart disease. Nature genetics 52 (8) (2020)
Pamela Feliciano, Xueya Zhou, Irina Astrovskaya, Tychele N Turner, Tianyun Wang, Leo Brueggeman, Rebecca Barnard, Alexander Hsieh, LeeAnne Green Snyder, Donna M Muzny, Aniko Sabo, null null, Richard A Gibbs, Evan E Eichler, Brian J O'Roak, Jacob J Michaelson, Natalia Volfovsky, Yufeng Shen, Wendy K Chung
Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes. NPJ genomic medicine 4 (2019)
Wenji Ma, Jaeyop Lee, Daniel Backenroth, Yu Jerry Zhou, Erin Bush, Peter Sims, Kang Liu, Yufeng Shen
Single cell RNA-Seq reveals pre-cDCs fate determined by transcription factor combinatorial dose. BMC molecular and cell biology 20 (1) (2019)