Jianlin Cheng

ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 104

Top Venues

bioRxiv : the preprint server for biology

Proteins

Bioinformatics (Oxford, England)

BMC bioinformatics

University of Missouri Columbia

University of California Irvine (PHD)

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

Affiliation History

University of Missouri Columbia Jan 01 2018

United States

Professor :: Department of Electrical Engineering and Computer Science

University of Missouri Columbia Sep 01 2016 - Dec 31 2017

United States

Professor :: Department of Computer Science

University of Missouri Columbia - Aug 31 2016

United States

Associate Professor :: Computer Science

University of Missouri Columbia

United States

Assistant Professor :: Computer Science

Education History

University of California Irvine

United States

PHD :: Computer Science

Publications

Nabin Giri, Jianlin Cheng
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. Nature communications 15 (1) (2024)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net. Briefings in bioinformatics 25 (4) (2024)
Nabin Giri, Jianlin Cheng
De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model. bioRxiv : the preprint server for biology (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore Pintilie, Stephen Burley, Jiri Cerny, Vincent Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis Rohou, Bohdan Schneider, Benjamin Sellers, Chenghua Chao, Elizabeth Sourial, Chris Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel Moriarty, Andrew Muenks, Garib Murshudov, Robert Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar Pothula, Christopher Rowley, Daipayan Sarkar, Luisa Schäfer, Christopher Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea Vaiana, Sundeep Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Alex Morehead, Jian Liu, Jianlin Cheng
Protein structure accuracy estimation using geometry-complete perceptron networks. Protein science : a publication of the Protein Society 33 (3) (2024)
Nabin Giri, Liguo Wang, Jianlin Cheng
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Scientific data 11 (1) (2024)
Nabin Giri, Jianlin Cheng
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. Nature communications 15 (1) (2024)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net. Briefings in bioinformatics 25 (4) (2024)
Xiao Chen, Jian Liu, Nolan Park, Jianlin Cheng
A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models. Biomolecules 14 (5) (2024)
Alex Morehead, Jianlin Cheng
Geometry-complete diffusion for 3D molecule generation and optimization. Communications chemistry 7 (1) (2024)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net. Briefings in bioinformatics 25 (4) (2024)
Nabin Giri, Jianlin Cheng
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. Nature communications 15 (1) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods 21 (7) (2024)
Nabin Giri, Liguo Wang, Jianlin Cheng
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Scientific data 11 (1) (2024)
Alex Morehead, Jian Liu, Jianlin Cheng
Protein structure accuracy estimation using geometry-complete perceptron networks. Protein science : a publication of the Protein Society 33 (3) (2024)
Frimpong Boadu, Ahhyun Lee, Jianlin Cheng
Deep learning methods for protein function prediction. Proteomics (2024)
Ryan M Finnerty, Daniel J Carulli, Akshata Hegde, Yanli Wang, Frimpong Baodu, Sarayut Winuthayanon, Jianlin Cheng, Wipawee Winuthayanon
Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos. bioRxiv : the preprint server for biology (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Alex Morehead, Jian Liu, Jianlin Cheng
Protein structure accuracy estimation using geometry-complete perceptron networks. Protein science : a publication of the Protein Society 33 (3) (2024)
Nabin Giri, Jianlin Cheng
De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model. bioRxiv : the preprint server for biology (2024)
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs. Bioinformatics (Oxford, England) 40 (3) (2024)
Xiao Chen, Jian Liu, Nolan Park, Jianlin Cheng
A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models. Biomolecules 14 (5) (2024)
Xiao Chen, Jian Liu, Nolan Park, Jianlin Cheng
A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models. Biomolecules 14 (5) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods 21 (7) (2024)
Yanli Wang, Jianlin Cheng
HiCDiff: single-cell Hi-C data denoising with diffusion models. Briefings in bioinformatics 25 (4) (2024)
Alex Morehead, Jian Liu, Jianlin Cheng
Protein structure accuracy estimation using geometry-complete perceptron networks. Protein science : a publication of the Protein Society 33 (3) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods (2024)
Alex Morehead, Jianlin Cheng
Geometry-complete diffusion for 3D molecule generation and optimization. Communications chemistry 7 (1) (2024)
Alex Morehead, Jianlin Cheng
Geometry-complete diffusion for 3D molecule generation and optimization. Communications chemistry 7 (1) (2024)
Nabin Giri, Jianlin Cheng
De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM. Nature communications 15 (1) (2024)
Alex Morehead, Jianlin Cheng
Geometry-complete diffusion for 3D molecule generation and optimization. Communications chemistry 7 (1) (2024)
Yanli Wang, Jianlin Cheng
HiCDiff: single-cell Hi-C data denoising with diffusion models. Briefings in bioinformatics 25 (4) (2024)
Nabin Giri, Liguo Wang, Jianlin Cheng
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Scientific data 11 (1) (2024)
Alex Morehead, Jianlin Cheng
Geometry-complete perceptron networks for 3D molecular graphs. Bioinformatics (Oxford, England) 40 (2) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net. Briefings in bioinformatics 25 (4) (2024)
Ryan M Finnerty, Daniel J Carulli, Akshata Hegde, Yanli Wang, Frimpong Baodu, Sarayut Winuthayanon, Jianlin Cheng, Wipawee Winuthayanon
Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos. bioRxiv : the preprint server for biology (2024)
Alex Morehead, Jianlin Cheng
Geometry-complete perceptron networks for 3D molecular graphs. Bioinformatics (Oxford, England) 40 (2) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore Pintilie, Stephen Burley, Jiri Cerny, Vincent Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis Rohou, Bohdan Schneider, Benjamin Sellers, Chenghua Chao, Elizabeth Sourial, Chris Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel Moriarty, Andrew Muenks, Garib Murshudov, Robert Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar Pothula, Christopher Rowley, Daipayan Sarkar, Luisa Schäfer, Christopher Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea Vaiana, Sundeep Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods 21 (7) (2024)
Nabin Giri, Jianlin Cheng
De Novo Atomic Protein Structure Modeling for Cryo-EM Density Maps Using 3D Transformer and Hidden Markov Model. bioRxiv : the preprint server for biology (2024)
Nabin Giri, Liguo Wang, Jianlin Cheng
Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Scientific data 11 (1) (2024)
Frimpong Boadu, Jianlin Cheng
Improving protein function prediction by learning and integrating representations of protein sequences and function labels. Bioinformatics advances 4 (1) (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge. Research square (2024)
Catherine L Lawson, Andriy Kryshtafovych, Grigore D Pintilie, Stephen K Burley, Jiri Cerny, Vincent B Chen, Paul Emsley, Alberto Gobbi, Andrzej Joachimiak, Sigrid Noreng, Michael G Prisant, Randy J Read, Jane S Richardson, Alexis L Rohou, Bohdan Schneider, Benjamin D Sellers, Chenghua Shao, Elizabeth Sourial, Chris I Williams, Christopher J Williams, Ying Yang, Venkat Abbaraju, Pavel V Afonine, Matthew L Baker, Paul S Bond, Thomas L Blundell, Tom Burnley, Arthur Campbell, Renzhi Cao, Jianlin Cheng, Grzegorz Chojnowski, Kathryn D Cowtan, Frank Dimaio, Reza Esmaeeli, Nabin Giri, Helmut Grubmüller, Soon Wen Hoh, Jie Hou, Corey F Hryc, Carola Hunte, Maxim Igaev, Agnel-Praveen Joseph, Wei-Chun Kao, Daisuke Kihara, Dilip Kumar, Lijun Lang, Sean Lin, Sai Raghavendra Maddhuri Venkata Subramaniya, Sumit Mittal, Arup Mondal, Nigel W Moriarty, Andrew Muenks, Garib N Murshudov, Robert A Nicholls, Mateusz Olek, Colin M Palmer, Alberto Perez, Emmi Pohjolainen, Karunakar R Pothula, Christopher N Rowley, Daipayan Sarkar, Luisa U Schäfer, Christopher J Schlicksup, Gunnar F Schröder, Mrinal Shekhar, Dong Si, Abhishek Singharoy, Oleg V Sobolev, Genki Terashi, Andrea C Vaiana, Sundeep C Vedithi, Jacob Verburgt, Xiao Wang, Rangana Warshamanage, Martyn David Winn, Simone Weyand, Keitaro Yamashita, Minglei Zhao, Michael F Schmid, Helen M Berman, Wah Chiu
Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature methods (2024)
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs. Bioinformatics (Oxford, England) 40 (3) (2024)
Jian Liu, Zhiye Guo, Tianqi Wu, Raj S Roy, Chen Chen, Jianlin Cheng
Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15. Communications chemistry 6 (1) (2023)
Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng
3D-equivariant graph neural networks for protein model quality assessment. Bioinformatics (Oxford, England) 39 (1) (2023)
Nabin Giri, Jianlin Cheng
Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge. Biomolecules 13 (1) (2023)
Frimpong Boadu, Hongyuan Cao, Jianlin Cheng
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. Bioinformatics (Oxford, England) 39 (39 Suppl 1) (2023)
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking. bioRxiv : the preprint server for biology (2023)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking. bioRxiv : the preprint server for biology (2023)
Zhiye Guo, Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu, Jianlin Cheng
Diffusion models in bioinformatics and computational biology. Nature reviews bioengineering 2 (2) (2023)
Jian Liu, Zhiye Guo, Tianqi Wu, Raj Shekhor Roy, Farhan Quadir, Chen Chen, Jianlin Cheng
Enhancing AlphaFold-Multimer-based Protein Complex Structure Prediction with MULTICOM in CASP15. bioRxiv : the preprint server for biology (2023)
Jianlin Cheng, Raj Shekhor Roy, Jian Liu, Nabin Giri, Zhiye Guo
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15. bioRxiv : the preprint server for biology (2023)
Raj S Roy, Jian Liu, Nabin Giri, Zhiye Guo, Jianlin Cheng
Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15. Proteins (2023)
Nabin Giri, Jianlin Cheng
Cryo2Struct : A Large Labeled Cryo-EM Density Map Dataset for AI-based Reconstruction of Protein Structures. bioRxiv : the preprint server for biology (2023)
Chen Chen, Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng
3D-equivariant graph neural networks for protein model quality assessment. Bioinformatics (Oxford, England) 39 (1) (2023)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking. bioRxiv : the preprint server for biology (2023)
Alex Morehead, Chen Chen, Ada Sedova, Jianlin Cheng
DIPS-Plus: The enhanced database of interacting protein structures for interface prediction. Scientific data 10 (1) (2023)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking. bioRxiv : the preprint server for biology (2023)
Nabin Giri, Jianlin Cheng
Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge. Biomolecules 13 (1) (2023)
Cole E McKay, Jianlin Cheng, John J Tanner
Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold. Scientific reports 13 (1) (2023)
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
CryoPPP: A Large Expert-Labelled Cryo-EM Image Dataset for Machine Learning Protein Particle Picking. bioRxiv : the preprint server for biology (2023)
Zhiye Guo, Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu, Jianlin Cheng
Diffusion models in bioinformatics and computational biology. Nature reviews bioengineering 2 (2) (2023)
Frimpong Boadu, Hongyuan Cao, Jianlin Cheng
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. bioRxiv : the preprint server for biology (2023)
Xiao Chen, Alex Morehead, Jian Liu, Jianlin Cheng
A gated graph transformer for protein complex structure quality assessment and its performance in CASP15. Bioinformatics (Oxford, England) 39 (39 Suppl 1) (2023)
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
A large expert-curated cryo-EM image dataset for machine learning protein particle picking. Scientific data 10 (1) (2023)
Jian Liu, Zhiye Guo, Tianqi Wu, Raj S Roy, Farhan Quadir, Chen Chen, Jianlin Cheng
Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15. Communications biology 6 (1) (2023)
Marc F Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A Bates, Marco Giulini, Rodrigo V Honorato, Charlotte van Noort, Joao M C Teixeira, Alexandre M J J Bonvin, Ren Kong, Hang Shi, Xufeng Lu, Shan Chang, Jian Liu, Zhiye Guo, Xiao Chen, Alex Morehead, Raj S Roy, Tianqi Wu, Nabin Giri, Farhan Quadir, Chen Chen, Jianlin Cheng, Carlos A Del Carpio, Eichiro Ichiishi, Luis A Rodriguez-Lumbreras, Juan Fernandez-Recio, Ameya Harmalkar, Lee-Shin Chu, Sam Canner, Rituparna Smanta, Jeffrey J Gray, Hao Li, Peicong Lin, Jiahua He, Huanyu Tao, Sheng-You Huang, Jorge Roel-Touris, Brian Jimenez-Garcia, Charles W Christoffer, Anika J Jain, Yuki Kagaya, Harini Kannan, Tsukasa Nakamura, Genki Terashi, Jacob C Verburgt, Yuanyuan Zhang, Zicong Zhang, Hayato Fujuta, Masakazu Sekijima, Daisuke Kihara, Omeir Khan, Sergei Kotelnikov, Usman Ghani, Dzmitry Padhorny, Dmitri Beglov, Sandor Vajda, Dima Kozakov, Surendra S Negi, Tiziana Ricciardelli, Didier Barradas-Bautista, Zhen Cao, Mohit Chawla, Luigi Cavallo, Romina Oliva, Rui Yin, Melyssa Cheung, Johnathan D Guest, Jessica Lee, Brian G Pierce, Ben Shor, Tomer Cohen, Matan Halfon, Dina Schneidman-Duhovny, Shaowen Zhu, Rujie Yin, Yuanfei Sun, Yang Shen, Martyna Maszota-Zieleniak, Krzysztof K Bojarski, Emilia A Lubecka, Mateusz Marcisz, Annemarie Danielsson, Lukasz Dziadek, Margrethe Gaardlos, Artur Gieldon, Adam Liwo, Sergey A Samsonov, Rafal Slusarz, Karolina Zieba, Adam K Sieradzan, Cezary Czaplewski, Shinpei Kobayashi, Yuta Miyakawa, Yasuomi Kiyota, Mayuko Takeda-Shitaka, Kliment Olechnovič, Lukas Valancauskas, Justas Dapkunas, Ceslovas Venclovas, Björn Wallner, Lin Yang, Chengyu Hou, Xiaodong He, Shuai Guo, Shenda Jiang, Xiaoliang Ma, Rui Duan, Liming Qui, Xianjin Xu, Xiaoqin Zou, Sameer Velankar, Shoshana J Wodak
Impact of AlphaFold on structure prediction of protein complexes: The CASP15-CAPRI experiment. Proteins (2023)
Nabin Giri, Jianlin Cheng
Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge. Biomolecules 13 (1) (2023)
Yahan Li, Ping Xiao, Frimpong Boadu, Anna K Goldkamp, Snehal Nirgude, Jianlin Cheng, Darren Erich Hagen, Jennifer M Kalish, Rocío Melissa Rivera
The counterpart congenital overgrowth syndromes Beckwith-Wiedemann Syndrome in human and large offspring syndrome in bovine involve alterations in DNA methylation, transcription, and chromatin configuration. medRxiv : the preprint server for health sciences (2023)
Zhiye Guo, Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu, Jianlin Cheng
Diffusion models in bioinformatics and computational biology. Nature reviews bioengineering 2 (2) (2023)
Frimpong Boadu, Hongyuan Cao, Jianlin Cheng
Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. bioRxiv : the preprint server for biology (2023)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
Accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net. bioRxiv : the preprint server for biology (2023)
Sajid Mahmud, Alex Morehead, Jianlin Cheng
Accurate prediction of protein tertiary structural changes induced by single-site mutations with equivariant graph neural networks. bioRxiv : the preprint server for biology (2023)
Rajan Gyawali, Ashwin Dhakal, Liguo Wang, Jianlin Cheng
CryoVirusDB: A Labeled Cryo-EM Image Dataset for AI-Driven Virus Particle Picking. bioRxiv : the preprint server for biology (2023)
Nabin Giri, Jianlin Cheng
Improving Protein-Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge. Biomolecules 13 (1) (2023)
Ashwin Dhakal, Rajan Gyawali, Liguo Wang, Jianlin Cheng
CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM Micrographs. bioRxiv : the preprint server for biology (2023)
Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
Correction to: Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. BMC bioinformatics 23 (1) (2022)
Zhiye Guo, Jian Liu, Jeffrey Skolnick, Jianlin Cheng
Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks. Nature communications 13 (1) (2022)
Raj S Roy, Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng
A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers. Bioinformatics (Oxford, England) 38 (7) (2022)
Xiao Chen, Jianlin Cheng
DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network. BMC bioinformatics 23 (Suppl 3) (2022)
Justin B Hackett, Hua Yang, Chen Chen, Jie Hou, Tieming Ji, Jianlin Cheng, James A Birchler
Dosage-sensitive miRNAs trigger modulation of gene expression during genomic imbalance in maize. Nature communications 13 (1) (2022)
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
DeepDist: real-value inter-residue distance prediction with deep residual convolutional network. BMC bioinformatics 22 (1) (2021)
Hua Yang, Justin B Hackett, Chen Chen, Jie Hou, Rocío Melissa Rivera, Jianlin Cheng, James A Birchler
Predominantly inverse modulation of gene expression in genomically unbalanced disomic haploid maize. The Plant cell 33 (4) (2021)
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A Birchler, Jianlin Cheng
DeepGRN: prediction of transcription factor binding site across cell-types using attention-based deep neural networks. BMC bioinformatics 22 (1) (2021)
Justin B Hackett, Hua Yang, Chen Chen, Jie Hou, Katherine M Hanson, Patrice S Albert, Rocío Melissa Rivera, Jianlin Cheng, James A Birchler
Genomic imbalance determines positive and negative modulation of gene expression in diploid maize. The Plant cell 33 (4) (2021)
Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
Correction to: DeepDist: real‑value inter‑residue distance prediction with deep residual convolutional network. BMC bioinformatics 22 (1) (2021)
Chen Chen, Tianqi Wu, Zhiye Guo, Jianlin Cheng
Combination of deep neural network with attention mechanism enhances the explainability of protein contact prediction. Proteins 89 (6) (2021)
Ashwin Dhakal, Cole McKay, John J Tanner, Jianlin Cheng
Artificial intelligence in the prediction of protein-ligand interactions: recent advances and future directions. Briefings in bioinformatics (2021)
Chen Chen, Jie Hou, Xiaowen Shi, Hua Yang, James A Birchler, Jianlin Cheng
GNET2: an R package for constructing gene regulatory networks from transcriptomic data. Bioinformatics (Oxford, England) 37 (14) (2021)
Jian Liu, Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng
Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14. Proteins (2021)
Elham Soltanikazemi, Farhan Quadir, Raj S Roy, Zhiye Guo, Jianlin Cheng
Distance-based reconstruction of protein quaternary structures from inter-chain contacts. Proteins (2021)
Oluwatosin Oluwadare, Max Highsmith, Douglass Turner, Erez Lieberman Aiden, Jianlin Cheng
GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data. BMC molecular and cell biology 21 (1) (2020)
Zhiye Guo, Jie Hou, Jianlin Cheng
DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures. Proteins 89 (2) (2020)
Adil Al-Azzawi, Anes Ouadou, Highsmith Max, Ye Duan, John J Tanner, Jianlin Cheng
DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM. BMC bioinformatics 21 (1) (2020)
Adil Al-Azzawi, Anes Ouadou, Ye Duan, Jianlin Cheng
Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction. BMC bioinformatics 21 (Suppl 21) (2020)
Adil Al-Azzawi, Anes Ouadou, John J Tanner, Jianlin Cheng
AutoCryoPicker: an unsupervised learning approach for fully automated single particle picking in Cryo-EM images. BMC bioinformatics 20 (1) (2019)
Jianlin Cheng, Myong-Ho Choe, Arne Elofsson, Kun-Sop Han, Jie Hou, Ali H A Maghrabi, Liam James McGuffin, David Menéndez-Hurtado, Kliment Olechnovič, Torsten Schwede, Gabriel Studer, Karolis Uziela, Česlovas Venclovas, Björn Wallner
Estimation of model accuracy in CASP13. Proteins 87 (12) (2019)

Jianlin Cheng.css-eqlu8i{font-size:small;padding-left:4px;}

Publication Activity (10 Years)

Top Topics

Top Venues

Jianlin Cheng