Yaping Liu

Publication Activity (10 Years)

Years Active: 2021-2024
Publications (10 Years): 32

Top Topics

Embryonic Stem Cells

Dna Methylation

High Fat Diet Induced

Top Venues

Journal of the American Society of Nephrology : JASN

bioRxiv : the preprint server for biology

Nature communications

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

Publications

Kouki Abe, Brian Maunze, Pedro-Avila Lopez, Jessica Xu, Nefertiti Muhammad, Guang-Yu Yang, David W Katz, Yaping Liu, Shannon M Lauberth
Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome. Science advances 10 (27) (2024)
James W Li, Ravi Bandaru, Yaping Liu
FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. bioRxiv : the preprint server for biology (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel S Freeman, David W Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature communications 15 (1) (2024)
James W Li, Ravi Bandaru, Yaping Liu
FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. bioRxiv : the preprint server for biology (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN 35 (5) (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel Freeman, David Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. bioRxiv : the preprint server for biology (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN 35 (5) (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN 35 (5) (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel S Freeman, David W Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature communications 15 (1) (2024)
James W Li, Ravi Bandaru, Yaping Liu
FinaleToolkit: Accelerating Cell-Free DNA Fragmentation Analysis with a High-Speed Computational Toolkit. bioRxiv : the preprint server for biology (2024)
Hao Tian, Pengfei Luan, Yaping Liu, Guoqiang Li
Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic acids research 52 (7) (2024)
Hao Tian, Pengfei Luan, Yaping Liu, Guoqiang Li
Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic acids research (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel Freeman, David Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. bioRxiv : the preprint server for biology (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN 35 (5) (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel S Freeman, David W Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature communications 15 (1) (2024)
Hao Tian, Pengfei Luan, Yaping Liu, Guoqiang Li
Tet-mediated DNA methylation dynamics affect chromosome organization. Nucleic acids research 52 (7) (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN 35 (5) (2024)
Kouki Abe, Brian Maunze, Pedro-Avila Lopez, Jessica Xu, Nefertiti Muhammad, Guang-Yu Yang, David W Katz, Yaping Liu, Shannon M Lauberth
Downstream-of-gene (DoG) transcripts contribute to an imbalance in the cancer cell transcriptome. Science advances 10 (27) (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel Freeman, David Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. bioRxiv : the preprint server for biology (2024)
Yaping Liu, Sarah C Reed, Christopher Lo, Atish D Choudhury, Heather A Parsons, Daniel G Stover, Gavin Ha, Gregory Gydush, Justin Rhoades, Denisse Rotem, Samuel S Freeman, David W Katz, Ravi Bandaru, Haizi Zheng, Hailu Fu, Viktor A Adalsteinsson, Manolis Kellis
FinaleMe: Predicting DNA methylation by the fragmentation patterns of plasma cell-free DNA. Nature communications 15 (1) (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN 35 (5) (2024)
Alison J Perl, Han Liu, Matthew R Hass, Nirpesh Adhikari, Praneet Chaturvedi, Yueh-Chiang Hu, Rulang Jiang, Yaping Liu, Raphael Kopan
Reduced Nephron Endowment in Six2-TGCtg Mice Is Due to Six3 Misexpression by Aberrant Enhancer-Promoter Interactions in the Transgene. Journal of the American Society of Nephrology : JASN (2024)
Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T Weirauch, Louis J Muglia, Li Wang, Yaping Liu
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome biology 24 (1) (2023)
Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T Weirauch, Louis J Muglia, Li Wang, Yaping Liu
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome biology 24 (1) (2023)
Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T Weirauch, Louis J Muglia, Li Wang, Yaping Liu
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome biology 24 (1) (2023)
Hailu Fu, Haizi Zheng, Xiaoting Chen, Matthew T Weirauch, Louis J Muglia, Li Wang, Yaping Liu
NOMe-HiC: joint profiling of genetic variant, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule. Genome biology 24 (1) (2023)
Xionghui Zhou, Haizi Zheng, Hailu Fu, Kelsey L Dillehay McKillip, Susan M Pinney, Yaping Liu
CRAG: de novo characterization of cell-free DNA fragmentation hotspots in plasma whole-genome sequencing. Genome medicine 14 (1) (2022)
Haizi Zheng, Michelle S Zhu, Yaping Liu
FinaleDB: a browser and database of cell-free DNA fragmentation patterns. Bioinformatics (Oxford, England) 37 (16) (2021)
Yaping Liu
At the dawn: cell-free DNA fragmentomics and gene regulation. British journal of cancer (2021)