Jing Zhang

Publication Activity (10 Years)

Years Active: 2022-2024
Publications (10 Years): 22

Top Topics

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Top Venues

Science (New York, N.Y.)

Bioinformatics (Oxford, England)

Journal of computational biology : a journal of computational molecular cell biology

Science advances

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

Publications

Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Sophia C Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason J Liu, Gaoyuan Wang, Megan Spector, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, PsychENCODE Consortium, Jennifer R Moran, Jing Zhang, Donghoon Lee, Mark B Gerstein, Daniel H Geschwind, Kevin P White
Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq. bioRxiv : the preprint server for biology (2024)
Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min, Jing Zhang
Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. Bioinformatics (Oxford, England) 40 (6) (2024)
Sophia C Gaynor-Gillett, Lijun Cheng, Manman Shi, Jason J Liu, Gaoyuan Wang, Megan Spector, Mary Flaherty, Martha Wall, Ahyeon Hwang, Mengting Gu, Zhanlin Chen, Yuhang Chen, null null, Jennifer R Moran, Jing Zhang, Donghoon Lee, Mark B Gerstein, Daniel H Geschwind, Kevin P White
Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq. bioRxiv : the preprint server for biology (2024)
Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min, Jing Zhang
Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. Bioinformatics (Oxford, England) 40 (6) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Ziheng Duan, Dylan Riffle, Ren Li, Junhao Liu, Martin Renqiang Min, Jing Zhang
Impeller: a path-based heterogeneous graph learning method for spatial transcriptomic data imputation. Bioinformatics (Oxford, England) 40 (6) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Prashant S Emani, Jason J Liu, Declan Clarke, Matthew Jensen, Jonathan Warrell, Chirag Gupta, Ran Meng, Che Yu Lee, Siwei Xu, Cagatay Dursun, Shaoke Lou, Yuhang Chen, Zhiyuan Chu, Timur Galeev, Ahyeon Hwang, Yunyang Li, Zhengchang Su, Xiao Zhou, null null, Trygve E Bakken, Jaroslav Bendl, Lucy K Bicks, Tanima Chatterjee, Lijun Cheng, Yuyan Cheng, Yi Dai, Ziheng Duan, Mary Flaherty, John F Fullard, Michael Gancz, Diego Garrido-Martín, Sophia C Gaynor-Gillett, Jennifer Grundman, Natalie Hawken, Ella Henry, Gabriel E Hoffman, Ao Huang, Yunzhe Jiang, Ting Jin, Nikolas L Jorstad, Riki Kawaguchi, Saniya Khullar, Jianyin Liu, Junhao Liu, Shuang Liu, Shaojie Ma, Michael Margolis, Samantha Mazariegos, Jill E Moore, Jennifer R Moran, Eric Nguyen, Nishigandha Phalke, Milos Pjanic, Henry E Pratt, Diana Quintero, Ananya S Rajagopalan, Tiernon R Riesenmy, Nicole Shedd, Manman Shi, Megan Spector, Rosemarie Terwilliger, Kyle J Travaglini, Brie Wamsley, Gaoyuan Wang, Yan Xia, Shaohua Xiao, Andrew C Yang, Suchen Zheng, Michael J Gandal, Donghoon Lee, Ed S Lein, Panagiotis Roussos, Nenad Sestan, Nishigandha Phalke, Kevin P White, Hyejung Won, Matthew J Girgenti, Jing Zhang, Daifeng Wang, Daniel H Geschwind, Mark B Gerstein, null null
Single-cell genomics and regulatory networks for 388 human brains. Science (New York, N.Y.) 384 (6698) (2024)
Ziheng Duan, Yi Dai, Ahyeon Hwang, Cheyu Lee, Kaichi Xie, Chutong Xiao, Min Xu, Matthew J Girgenti, Jing Zhang
iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. PLoS computational biology 19 (9) (2023)
Ruiyi Zhang, Ziheng Duan, CheYu Lee, Dylan Riffle, Martin Renqiang Min, Jing Zhang
Turtling : a time-aware neural topic model on NIH grant data. Bioinformatics advances 3 (1) (2023)
Ruiyi Zhang, Ziheng Duan, CheYu Lee, Dylan Riffle, Martin Renqiang Min, Jing Zhang
Turtling : a time-aware neural topic model on NIH grant data. Bioinformatics advances 3 (1) (2023)
Xiangrui Zeng, Ziqian Lin, Mostofa Rafid Uddin, Bo Zhou, Chao Cheng, Jing Zhang, Zachary Freyberg, Min Xu
Structure Detection in Three-Dimensional Cellular Cryoelectron Tomograms by Reconstructing Two-Dimensional Annotated Tilt Series. Journal of computational biology : a journal of computational molecular cell biology 29 (8) (2022)
Siwei Xu, Mario Skarica, Ahyeon Hwang, Yi Dai, Cheyu Lee, Matthew J Girgenti, Jing Zhang
Translator: A Trans fer L earning Approach to Facilitate Single-Cell AT AC-Seq Data Analysis fr o m R eference Dataset. Journal of computational biology : a journal of computational molecular cell biology 29 (7) (2022)
Yanwen Gong, Shushrruth Sai Srinivasan, Ruiyi Zhang, Kai Kessenbrock, Jing Zhang
scEpiLock: A Weakly Supervised Learning Framework for cis -Regulatory Element Localization and Variant Impact Quantification for Single-Cell Epigenetic Data. Biomolecules 12 (7) (2022)
Shushrruth Sai Srinivasan, Yanwen Gong, Siwei Xu, Ahyeon Hwang, Min Xu, Matthew J Girgenti, Jing Zhang
InsuLock: A Weakly Supervised Learning Approach for Accurate Insulator Prediction, and Variant Impact Quantification. Genes 13 (4) (2022)
Lihua Zhang, Jing Zhang, Qing Nie
DIRECT-NET: An efficient method to discover cis-regulatory elements and construct regulatory networks from single-cell multiomics data. Science advances 8 (22) (2022)
Zhanlin Chen, William C King, Ahyeon Hwang, Mark B Gerstein, Jing Zhang
DeepVelo : Single-cell transcriptomic deep velocity field learning with neural ordinary differential equations. Science advances 8 (48) (2022)
Che Yu Lee, Yuhang Chen, Ziheng Duan, Min Xu, Matthew J Girgenti, Ke Xu, Mark Gerstein, Jing Zhang
Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. PLoS computational biology 18 (10) (2022)