Jian Ma

ORCID

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 52

Top Venues

Nature genetics

Nature methods

bioRxiv : the preprint server for biology

Nature communications

Carnegie Mellon University

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

Affiliation History

Carnegie Mellon University Jan 01 2016

United States

Associate Professor :: School of Computer Science

University of Illinois at Urbana-Champaign Aug 01 2015 - Dec 31 2015

United States

Associate Professor

University of Illinois at Urbana-Champaign Aug 16 2009 - Jul 31 2015

United States

Assistant Professor

Publications

Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods (2024)
Omid Gholamalamdari, Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang, Gabriela A Hernandez Gonzalez, Athanasios E Vouzas, Peiyao A Zhao, David M Gilbert, Jian Ma, Bas van Steensel, Andrew S Belmont
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function. bioRxiv : the preprint server for biology (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods 21 (5) (2024)
Nikki Bialy, Frank Alber, Brenda J Andrews, Michael Angelo, Brian J Beliveau, Lacramioara Bintu, Alistair Nicol Boettiger, Ulrike Boehm, Claire M Brown, Mahmoud Bukar Maina, James J Chambers, Beth A Cimini, Kevin W Eliceiri, Rachel Errington, Orestis Faklaris, Nathalie Gaudreault, Ronald N Germain, Wojtek J Goscinski, David Grünwald, Michael Halter, Dorit Hanein, John W Hickey, Judith Lacoste, Alex Laude, Emma Lundberg, Jian Ma, Leonel Malacrida, Josh Moore, Glyn Nelson, Elizabeth Kathleen Neumann, Roland Nitschke, Shuichi Onami, Jaime A Pimentel, Anne L Plant, Andrea J Radtke, Bikash Sabata, Denis Schapiro, Johannes Schöneberg, Jeffrey M Spraggins, Damir Sudar, Wouter-Michiel Vierdag, Niels Volkmann, Carolina Wählby, Siyuan Steven Wang, Ziv Rafael Yaniv, Caterina Strambio-De-Castilla
Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ArXiv (2024)
Pradeep Kumar, Omid Gholamalamdari, Yang Zhang, Liguo Zhang, Anastassiia Vertii, Tom van Schaik, Daan Peric-Hupkes, Takayo Sasaki, David M Gilbert, Bas van Steensel, Jian Ma, Paul D Kaufman, Andrew S Belmont
Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types. Communications biology 7 (1) (2024)
Valerie Chen, Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. Nature methods 21 (8) (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
Author Correction: scGHOST: identifying single-cell 3D genome subcompartments. Nature methods (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics (2024)
Valerie Chen, Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. Nature methods 21 (8) (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics 56 (8) (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics 56 (8) (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics 56 (8) (2024)
Valerie Chen, Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. Nature methods 21 (8) (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods 21 (5) (2024)
Valerie Chen, Muyu Yang, Wenbo Cui, Joon Sik Kim, Ameet Talwalkar, Jian Ma
Applying interpretable machine learning in computational biology-pitfalls, recommendations and opportunities for new developments. Nature methods 21 (8) (2024)
DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A Logsdon, Steven Jared Solar, Dmitry Antipov, Brandon D Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M Storer, Jiadong Lin, Abigail N Sequeira, Riley J Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R Beck, Arjun Biddanda, Matthew Borchers, Gerard G Bouffard, Emry Brannan, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Yongwook Choi, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H Garcia, Luciana de Gennaro, David M Gilbert, Richard E Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S Harris, Gabrielle A Hartley, William T Harvey, Michael Hiller, Kendra Hoekzema, Marlys L Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William D Lees, Alexandra P Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F I Martinez, Patrick Masterson, Rajiv C McCoy, Barbara McGrath, Sean McKinney, Britta S Meyer, Karen H Miga, Saswat Kumar Mohanty, Katherine M Munson, Karol Pal, Matthew W Pennell, Pavel A Pevzner, David Porubsky, Tamara Potapova, Francisca R Ringeling, Joana L Rocha, Oliver A Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C Schatz, Nicholas J Schork, Cole Shanks, Linnéa Smeds, Dongmin R Son, Cynthia Steiner, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A Zhao, Yixin Zhu, Erich D Jarvis, Jennifer L Gerton, Iker Rivas-González, Benedict Paten, Zachary Alfano Szpiech, Christian D Huber, Tobias L Lenz, Miriam K Konkel, Soojin V Yi, Stefan Canzar, Corey T Watson, Peter H Sudmant, Erin K Molloy, Erik Garrison, Craig B Lowe, Mario Ventura, Rachel J O'Neill, Sergey Koren, Kateryna D Makova, Adam M Phillippy, Evan E Eichler
Complete sequencing of ape genomes. bioRxiv : the preprint server for biology (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods 21 (5) (2024)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
GAGE-seq concurrently profiles multiscale 3D genome organization and gene expression in single cells. Nature genetics 56 (8) (2024)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: identifying single-cell 3D genome subcompartments. Nature methods 21 (5) (2024)
DongAhn Yoo, Arang Rhie, Prajna Hebbar, Francesca Antonacci, Glennis A Logsdon, Steven Jared Solar, Dmitry Antipov, Brandon D Pickett, Yana Safonova, Francesco Montinaro, Yanting Luo, Joanna Malukiewicz, Jessica M Storer, Jiadong Lin, Abigail N Sequeira, Riley J Mangan, Glenn Hickey, Graciela Monfort Anez, Parithi Balachandran, Anton Bankevich, Christine R Beck, Arjun Biddanda, Matthew Borchers, Gerard G Bouffard, Emry Brannan, Shelise Y Brooks, Lucia Carbone, Laura Carrel, Yongwook Choi, Juyun Crawford, Mark Diekhans, Eric Engelbrecht, Cedric Feschotte, Giulio Formenti, Gage H Garcia, Luciana de Gennaro, David M Gilbert, Richard E Green, Andrea Guarracino, Ishaan Gupta, Diana Haddad, Junmin Han, Robert S Harris, Gabrielle A Hartley, William T Harvey, Michael Hiller, Kendra Hoekzema, Marlys L Houck, Hyeonsoo Jeong, Kaivan Kamali, Manolis Kellis, Bryce Kille, Chul Lee, Youngho Lee, William D Lees, Alexandra P Lewis, Qiuhui Li, Mark Loftus, Yong Hwee Eddie Loh, Hailey Loucks, Jian Ma, Yafei Mao, Juan F I Martinez, Patrick Masterson, Rajiv C McCoy, Barbara McGrath, Sean McKinney, Britta S Meyer, Karen H Miga, Saswat Kumar Mohanty, Katherine M Munson, Karol Pal, Matthew W Pennell, Pavel A Pevzner, David Porubsky, Tamara Potapova, Francisca R Ringeling, Joana L Rocha, Oliver A Ryder, Samuel Sacco, Swati Saha, Takayo Sasaki, Michael C Schatz, Nicholas J Schork, Cole Shanks, Linnéa Smeds, Dongmin R Son, Cynthia Steiner, Alexander P Sweeten, Michael G Tassia, Françoise Thibaud-Nissen, Edmundo Torres-González, Mihir Trivedi, Wenjie Wei, Julie Wertz, Muyu Yang, Panpan Zhang, Shilong Zhang, Yang Zhang, Zhenmiao Zhang, Sarah A Zhao, Yixin Zhu, Erich D Jarvis, Jennifer L Gerton, Iker Rivas-González, Benedict Paten, Zachary Alfano Szpiech, Christian D Huber, Tobias L Lenz, Miriam K Konkel, Soojin V Yi, Stefan Canzar, Corey T Watson, Peter H Sudmant, Erin K Molloy, Erik Garrison, Craig B Lowe, Mario Ventura, Rachel J O'Neill, Sergey Koren, Kateryna D Makova, Adam M Phillippy, Evan E Eichler
Complete sequencing of ape genomes. bioRxiv : the preprint server for biology (2024)
Omid Gholamalamdari, Tom van Schaik, Yuchuan Wang, Pradeep Kumar, Liguo Zhang, Yang Zhang, Gabriela A Hernandez Gonzalez, Athanasios E Vouzas, Peiyao A Zhao, David M Gilbert, Jian Ma, Bas van Steensel, Andrew S Belmont
Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function. bioRxiv : the preprint server for biology (2024)
Yang Zhang, Lorenzo Boninsegna, Muyu Yang, Tom Misteli, Frank Alber, Jian Ma
Computational methods for analysing multiscale 3D genome organization. Nature reviews. Genetics (2023)
Pradeep Kumar, Omid Gholamalamdari, Yang Zhang, Liguo Zhang, Anastassiia Vertii, Tom van Schaik, Daan Peric-Hupkes, Takayo Sasaki, David M Gilbert, Bas van Steensel, Jian Ma, Paul D Kaufman, Andrew S Belmont
Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types. bioRxiv : the preprint server for biology (2023)
Kyle Xiong, Ruochi Zhang, Jian Ma
scGHOST: Identifying single-cell 3D genome subcompartments. bioRxiv : the preprint server for biology (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics (2023)
Riccardo Calandrelli, Xingzhao Wen, John Lalith Charles Richard, Zhifei Luo, Tri C Nguyen, Chien-Ju Chen, Zhijie Qi, Shuanghong Xue, Weizhong Chen, Zhangming Yan, Weixin Wu, Kathia Zaleta-Rivera, Rong Hu, Miao Yu, Yuchuan Wang, Wenbo Li, Jian Ma, Bing Ren, Sheng Zhong
Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells. Nature communications 14 (1) (2023)
Tianming Zhou, Ruochi Zhang, Deyong Jia, Raymond T Doty, Adam D Munday, Daniel Gao, Li Xin, Janis L Abkowitz, Zhijun Duan, Jian Ma
Concurrent profiling of multiscale 3D genome organization and gene expression in single mammalian cells. bioRxiv : the preprint server for biology (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics 55 (1) (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics 55 (1) (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics 55 (1) (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics 55 (1) (2023)
Benjamin Chidester, Tianming Zhou, Shahul Alam, Jian Ma
SPICEMIX enables integrative single-cell spatial modeling of cell identity. Nature genetics 55 (1) (2023)
Yihe Deng, Ruochi Zhang, Pan Xu, Jian Ma, Quanquan Gu
PhyGCN: Pre-trained Hypergraph Convolutional Neural Networks with Self-supervised Learning. bioRxiv : the preprint server for biology (2023)
Sunmi Seok, Young-Chae Kim, Yang Zhang, Bo Kong, Grace Guo, Jian Ma, Byron Kemper, Jongsook Kim Kemper
Feeding activates FGF15-SHP-TFEB-mediated lipophagy in the gut. The EMBO journal 41 (17) (2022)
Xiaopeng Zhu, Yang Zhang, Yuchuan Wang, Dechao Tian, Andrew S Belmont, Jason R Swedlow, Jian Ma
Nucleome Browser: an integrative and multimodal data navigation platform for 4D Nucleome. Nature methods 19 (8) (2022)
Anat Melamed, Tomas W Fitzgerald, Yuchuan Wang, Jian Ma, Ewan Birney, Charles R M Bangham
Selective clonal persistence of human retroviruses in vivo: Radial chromatin organization, integration site, and host transcription. Science advances 8 (17) (2022)
Ruochi Zhang, Tianming Zhou, Jian Ma
Multiscale and integrative single-cell Hi-C analysis with Higashi. Nature biotechnology (2021)
Yifeng Tao, Ashok Rajaraman, Xiaoyue Cui, Ziyi Cui, Haoran Chen, Yuanqi Zhao, Jesse Eaton, Hannah Kim, Jian Ma, Russell Schwartz
Assessing the contribution of tumor mutational phenotypes to cancer progression risk. PLoS computational biology 17 (3) (2021)
Sangwon Byun, Sunmi Seok, Young-Chae Kim, Yang Zhang, Peter Yau, Naoki Iwamori, H Eric Xu, Jian Ma, Byron Kemper, Jongsook Kim Kemper
Fasting-induced FGF21 signaling activates hepatic autophagy and lipid degradation via JMJD3 histone demethylase. Nature communications 11 (1) (2020)
Cicera R Lazzarotto, Nikolay L Malinin, Yichao Li, Ruochi Zhang, Yang Yang, GaHyun Lee, Eleanor Cowley, Yanghua He, Xin Lan, Kasey Jividen, Varun Katta, Natalia G Kolmakova, Christopher T Petersen, Qian Qi, Evgheni Strelcov, Samantha Maragh, Giedre Krenciute, Jian Ma, Yong Cheng, Shengdar Q Tsai
CHANGE-seq reveals genetic and epigenetic effects on CRISPR-Cas9 genome-wide activity. Nature biotechnology 38 (11) (2020)
Dechao Tian, Ruochi Zhang, Yang Zhang, Xiaopeng Zhu, Jian Ma
MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome. Genome research 30 (2) (2020)
Young-Chae Kim, Sunmi Seok, Yang Zhang, Jian Ma, Bo Kong, Grace Guo, Byron Kemper, Jongsook Kim Kemper
Intestinal FGF15/19 physiologically repress hepatic lipogenesis in the late fed-state by activating SHP and DNMT3A. Nature communications 11 (1) (2020)
Liguo Zhang, Yang Zhang, Yu Chen, Omid Gholamalamdari, Yuchuan Wang, Jian Ma, Andrew S Belmont
TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes. Genome research (2020)
Kyle Xiong, Jian Ma
Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions. Nature communications 10 (1) (2019)
Kavya Kannan, Molly Shook, Yang Li, Gene E Robinson, Jian Ma
Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera. G3 (Bethesda, Md.) 9 (4) (2019)
Sai Ma, Yuan-Pang Hsieh, Jian Ma, Chang Lu
Low-input and multiplexed microfluidic assay reveals epigenomic variation across cerebellum and prefrontal cortex. Science advances 4 (4) (2018)

Jian Ma.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Jian Ma