Jianlin Cheng

Also affiliated with University of Missouri

Biochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 1%percentile

8.2Author DataRank

Indexed papers

11in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Why this DataRank?

An author's DataRank is the sum of the DataRanks of all 11 indexed papers attributed to them. A prolific author with many moderate-impact papers can outrank one with a single high-impact paper.

Author scores recompute whenever paper DataRanks are refreshed, so this number lags the underlying paper scores by at most one batch run.

Read the full methodology →

The highest-impact dataset this researcher has shared, ranked by DataRank — the single contribution doing the most to lift their data-sharing standing.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222

Top 9%

2.3DataRank

Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Papers

Driven by 103 papers — median percentile 65. Top paper: “Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment”.

Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26222

Top 9%

2.3DataRank

Top 9%127 citations

Guillaume Brysbaert, Théo Mauri, Nurul Nadzirin, Sameer Velankar, Raphaël A. G. Chaleil +95 more

Impact of AlphaFold on structure prediction of protein complexes: The CASP15‐CAPRI experiment

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26609

Top 11%

1.9DataRank

Top 11%81 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

Scientific Data(2023)10.1038/s41597-023-02409-3

Top 23%

0.879DataRank

Top 23%25 citations

Chen Chen, Ada Sedova, Jianlin Cheng, Alex Morehead

Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge

Nature Methods(2024)10.1038/s41592-024-02321-7

Top 23%

0.871DataRank

Top 23%18 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent B. Chen +76 more

Deep learning for reconstructing protein structures from cryo-EM density maps: Recent advances and future directions

Current Opinion in Structural Biology(2023)10.1016/j.sbi.2023.102536

N/A

0.637DataRank · unranked

69 citations

Raj S. Roy, Jianlin Cheng, Nabin Giri

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

Bioinformatics(2022)10.1093/bioinformatics/btac063

N/A

0.596DataRank · unranked

52 citations

Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng, Raj S. Roy

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

Scientific Data(2024)10.1038/s41597-024-03299-9

Top 34%

0.571DataRank

Top 34%19 citations

Liguo Wang, Jianlin Cheng, Nabin Giri

Geometry-complete perceptron networks for 3D molecular graphs

Bioinformatics(2024)10.1093/bioinformatics/btae087

N/A

0.558DataRank · unranked

18 citations

Jianlin Cheng, Alex Morehead

Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment

Utrecht University Repository (Utrecht University)(2023)10.22541/au.168888815.53957253/v1

Top 36%

0.540DataRank

Top 36%17 citations

Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato +95 more

A gated graph transformer for protein complex structure quality assessment and its performance in CASP15

Bioinformatics(2023)10.1093/bioinformatics/btad203

N/A

0.494DataRank · unranked

26 citations

Alex Morehead, Jian Liu, Jianlin Cheng, Xiao Chen

Pigs: Large Animal Preclinical Cancer Models

World Journal of Oncology(2024)10.14740/wjon1763

N/A

0.483DataRank · unranked

24 citations

Tejas Katam, Akshata Hegde, Jianlin Cheng, Randall S. Prather, Kristin M. Whitworth +7 more

Evaluating representation learning on the protein structure universe

PubMed(2024)10.48550/arxiv.2406.13864

Top 43%

0.435DataRank

Top 43%6 citations

Alex Morehead, Chaitanya K Joshi, Zuobai Zhang, Kieran Didi, Simon V. Mathis +6 more

Quantitative Proteomics Reveals Docosahexaenoic Acid-Mediated Neuroprotective Effects in Lipopolysaccharide-Stimulated Microglial Cells

Journal of Proteome Research(2020)10.1021/acs.jproteome.9b00792

N/A

0.425DataRank · unranked

16 citations

Runting Li, Pei N. Liu, Xue Geng, Brian Mooney, Chen Chen +7 more

Diffusion Models in Bioinformatics: A New Wave of Deep Learning Revolution in Action

arXiv (Cornell University)(2023)10.48550/arxiv.2302.10907

N/A

0.385DataRank · unranked

12 citations

Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu +2 more

Outcomes of the 2019 EMDataResource model challenge: validation of cryo-EM models at near-atomic resolution

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.12.147033

Top 48%

0.375DataRank

Top 48%7 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

Multi-head attention-based U-Nets for predicting protein domain boundaries using 1D sequence features and 2D distance maps

BMC Bioinformatics(2022)10.1186/s12859-022-04829-1

N/A

0.345DataRank · unranked

9 citations

Zhiye Guo, Farhan Quadir, Jian Liu, Jianlin Cheng, Sajid Mahmud

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

10.22541/au.161733097.71126646/v1

N/A

0.345DataRank · unranked

9 citations

Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng, Jian Liu

CryoTransformer: A Transformer Model for Picking Protein Particles from Cryo-EM Micrographs

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.19.563155

N/A

0.330DataRank · unranked

8 citations

Rajan Gyawali, Liguo Wang, Jianlin Cheng, Ashwin Dhakal

Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs

(2024)10.1109/medai62885.2024.00009

N/A

0.312DataRank · unranked

7 citations

Zhiyuan Yang, Mingyue Gao, Biplab Poudel, Newgin Sam Ebin Sam Dhas, Rajan Gyawali +4 more

3D-equivariant graph neural networks for protein model quality assessment

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.12.488060

N/A

0.312DataRank · unranked

7 citations

Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng, Chen Chen

Adapting Segment Anything Model (SAM) through Prompt-based Learning for Enhanced Protein Identification in Cryo-EM Micrographs

arXiv (Cornell University)(2023)10.48550/arxiv.2311.16140

N/A

0.241DataRank · unranked

4 citations

Zhiyuan Yang, Mingyue Gao, Biplab Poudel, Newgin Sam Ebin Sam Dhas, Rajan Gyawali +4 more

Boosting AlphaFold protein tertiary structure prediction through MSA engineering and extensive model sampling and ranking in CASP16

Communications Biology(2025)10.1038/s42003-025-08960-6

N/A

0.208DataRank · unranked

3 citations

Pawan Neupane, Jianlin Cheng, Jian Liu

Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.06.14.545024

Top 67%

0.171DataRank

Top 67%2 citations

Liguo Wang, Jianlin Cheng, Nabin Giri

How to go with the flow: flow matching in bioinformatics and computational biology

(2025)10.22541/au.175382408.89466370/v3

N/A

0.165DataRank · unranked

2 citations

Lazar Atanackovic, Akshata Hegde, Yanli Wang, Frimpong Boadu, Joel Selvaraj +4 more

Improving AlphaFold2-based Protein Tertiary Structure Prediction with MULTICOM in CASP15

Research Square(2023)10.21203/rs.3.rs-2962687/v1

N/A

0.165DataRank · unranked

2 citations

Zhiye Guo, Tianqi Wu, Raj S. Roy, Chen Chen, Jianlin Cheng +1 more

High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green Alga Chlamydomonas reinhardtii

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.07.13.499508

N/A

0.104DataRank · unranked

1 citations

William McHargue, Catherine E. Bailey, Ningning Zhang, Chen Chen, James Eckhardt +8 more

Biochemical, structural, and computational analyses of two new clinically identified missense mutations of ALDH7A1

Chemico-Biological Interactions(2024)10.1016/j.cbi.2024.110993

N/A

0.104DataRank · unranked

1 citations

David P. Buckley, Alessandra Palpacelli, Ida Cursio, Elisabetta Cesaroni, Jianlin Cheng +2 more

A labeled dataset for AI-based cryo-EM map enhancement

Computational and Structural Biotechnology Journal(2025)10.1016/j.csbj.2025.06.041

Top 78%

0.104DataRank

Top 78%1 citations

Xiao Chen, Liguo Wang, Jianlin Cheng, Nabin Giri

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Nature Communications(2022)10.1038/s41467-022-34600-2

N/A

0DataRank · unranked

56 citations

Jian Liu, Jeffrey Skolnick, Jianlin Cheng, Zhiye Guo

DNCON2_Inter: Predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Research Square(2021)10.21203/rs.3.rs-228041/v1

N/A

0DataRank · unranked

2 citations

Raj S. Roy, Randal Halfmann, Jianlin Cheng, Farhan Quadir

Traumatic brain injury recapitulates developmental changes of axons

Progress in Neurobiology(2022)10.1016/j.pneurobio.2022.102332

N/A

0DataRank · unranked

23 citations

Chen Chen, Brian J. Kelley, Alexandra Tomasevich, Hyoungjoo Lee, Jean-Pierre Dollé +5 more

Protein Model Accuracy Estimation Empowered by Deep Learning and Inter-residue Distance Prediction in CASP14

Research Square(2021)10.21203/rs.3.rs-228012/v1

N/A

0DataRank · unranked

3 citations

Jian Liu, Zhiye Guo, Tianqi Wu, Jie Hou, Jianlin Cheng +1 more

High‐throughput identification of novel heat tolerance genes via genome‐wide pooled mutant screens in the model green alga Chlamydomonas reinhardtii

Plant Cell & Environment(2022)10.1111/pce.14507

N/A

0DataRank · unranked

8 citations

William McHargue, Catherine E. Bailey, Ningning Zhang, Chen Chen, James Eckhardt +8 more

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

BMC Bioinformatics(2022)10.1186/s12859-022-04683-1

N/A

0DataRank · unranked

6 citations

Jianlin Cheng, Xiao Chen

Distance-based Reconstruction of Protein Quaternary Structures from Inter-Chain Contacts

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.24.445503

N/A

0DataRank · unranked

3 citations

Farhan Quadir, Raj S. Roy, Jianlin Cheng, Elham Soltanikazemi

A Gated Graph Transformer for Protein Complex Structure Quality Assessment and its Performance in CASP15

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.05.19.492741

N/A

0DataRank · unranked

7 citations

Alex Morehead, Jian Liu, Jianlin Cheng, Xiao Chen

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.06.19.496734

N/A

0DataRank · unranked

7 citations

Jian Liu, Jeffrey Skolnick, Jianlin Cheng, Zhiye Guo

Prediction of inter-chain distance maps of protein complexes with 2D attention-based deep neural networks

Research Square(2022)10.21203/rs.3.rs-1658872/v1

N/A

0DataRank · unranked

5 citations

Jian Liu, Jeffrey Skolnick, Jianlin Cheng, Zhiye Guo

Multi-Head Attention-based U-Nets for Predicting Protein Domain Boundaries Using 1D Sequence Features and 2D Distance Maps

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.04.08.487689

N/A

0DataRank · unranked

1 citations

Zhiye Guo, Farhan Quadir, Jian Liu, Jianlin Cheng, Sajid Mahmud

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

International Journal of Molecular Sciences(2020)10.3390/ijms21082873

N/A

0DataRank · unranked

280 citations

Jie Hou, John J. Tanner, Jianlin Cheng, Chen Chen

Diffusion models in bioinformatics and computational biology

Nature Reviews Bioengineering(2023)10.1038/s44222-023-00114-9

N/A

0DataRank · unranked

130 citations

Jian Liu, Yanli Wang, Mengrui Chen, Duolin Wang, Dong Xu +2 more

Improving protein tertiary structure prediction by deep learning and distance prediction in CASP14

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.28.428706

N/A

0DataRank · unranked

3 citations

Tianqi Wu, Zhiye Guo, Jie Hou, Jianlin Cheng, Jian Liu

Enhancing alphafold-multimer-based protein complex structure prediction with MULTICOM in CASP15

Communications Biology(2023)10.1038/s42003-023-05525-3

N/A

0DataRank · unranked

76 citations

Zhiye Guo, Tianqi Wu, Raj S. Roy, Farhan Quadir, Chen Chen +2 more

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

Bioinformatics(2023)10.1093/bioinformatics/btad208

N/A

0DataRank · unranked

74 citations

Hongyuan Cao, Jianlin Cheng, Frimpong Boadu

A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.09.19.460941

N/A

0DataRank · unranked

6 citations

Farhan Quadir, Elham Soltanikazemi, Jianlin Cheng, Raj S. Roy

Improving AlphaFold2-based protein tertiary structure prediction with MULTICOM in CASP15

Communications Chemistry(2023)10.1038/s42004-023-00991-6

N/A

0DataRank · unranked

31 citations

Zhiye Guo, Tianqi Wu, Raj S. Roy, Chen Chen, Jianlin Cheng +1 more

Dissection of a Down syndrome-associated trisomy to separate the gene dosage-dependent and -independent effects of an extra chromosome

Human Molecular Genetics(2023)10.1093/hmg/ddad056

N/A

0DataRank · unranked

21 citations

Yichen Li, Eduardo Cortes-Gomez, Xiaoling Jiang, Shuang Gao, Annie Pao +16 more

3D-equivariant graph neural networks for protein model quality assessment

Bioinformatics(2023)10.1093/bioinformatics/btad030

N/A

0DataRank · unranked

33 citations

Xiao Chen, Alex Morehead, Tianqi Wu, Jianlin Cheng, Chen Chen

High-Performance Deep Learning Toolbox for Genome-Scale Prediction of Protein Structure and Function

PubMed(2021)10.1109/mlhpc54614.2021.00010

N/A

0DataRank · unranked

13 citations

Peik K. Lund-Andersen, Alex Morehead, Sajid Mahmud, Chen Chen, Xiao Chen +12 more

Atomic protein structure refinement using all-atom graph representations and SE(3)-equivariant graph transformer

Bioinformatics(2023)10.1093/bioinformatics/btad298

N/A

0DataRank · unranked

24 citations

Zhiye Guo, Jianlin Cheng, Tianqi Wu

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15

Proteins Structure Function and Bioinformatics(2023)10.1002/prot.26542

N/A

0DataRank · unranked

23 citations

Jian Liu, Nabin Giri, Zhiye Guo, Jianlin Cheng, Raj S. Roy

MULTICOM2 open-source protein structure prediction system powered by deep learning and distance prediction

Scientific Reports(2021)10.1038/s41598-021-92395-6

N/A

0DataRank · unranked

4 citations

Jian Liu, Zhiye Guo, Jie Hou, Jianlin Cheng, Tianqi Wu

Four-Dimensional Chromosome Structure Prediction

International Journal of Molecular Sciences(2021)10.3390/ijms22189785

N/A

0DataRank · unranked

9 citations

Jianlin Cheng, Max Highsmith

Enhancing AlphaFold-Multimer-based Protein Complex Structure Prediction with MULTICOM in CASP15

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.05.16.541055

N/A

0DataRank · unranked

16 citations

Zhiye Guo, Tianqi Wu, Raj S. Roy, Farhan Quadir, Chen Chen +2 more

Protein model accuracy estimation empowered by deep learning and inter-residue distance prediction in CASP14

Scientific Reports(2021)10.1038/s41598-021-90303-6

N/A

0DataRank · unranked

12 citations

Jian Liu, Zhiye Guo, Tianqi Wu, Jie Hou, Jianlin Cheng +1 more

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.01.17.524477

N/A

0DataRank · unranked

11 citations

Hongyuan Cao, Jianlin Cheng, Frimpong Boadu

Accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and specialized U-Net

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.02.560572

N/A

0DataRank · unranked

11 citations

Ashwin Dhakal, Liguo Wang, Jianlin Cheng, Rajan Gyawali

Distance‐based reconstruction of protein quaternary structures from inter‐chain contacts

Proteins Structure Function and Bioinformatics(2021)10.1002/prot.26269

N/A

0DataRank · unranked

13 citations

Farhan Quadir, Raj S. Roy, Zhiye Guo, Jianlin Cheng, Elham Soltanikazemi

Geometry-Complete Diffusion for 3D Molecule Generation and Optimization

arXiv (Cornell University)(2023)10.48550/arxiv.2302.04313

N/A

0DataRank · unranked

7 citations

Jianlin Cheng, Alex Morehead

Improving deep learning-based protein distance prediction in CASP14

Bioinformatics(2021)10.1093/bioinformatics/btab355

N/A

0DataRank · unranked

20 citations

Tianqi Wu, Jian Liu, Jie Hou, Jianlin Cheng, Zhiye Guo

Enhancing AlphaFold-Multimer-based Protein Complex Structure Prediction with MULTICOM in CASP15

Research Square(2023)10.21203/rs.3.rs-2963209/v1

N/A

0DataRank · unranked

3 citations

Zhiye Guo, Tianqi Wu, Raj S. Roy, Farhan Quadir, Chen Chen +2 more

DeepComplex: A Web Server of Predicting Protein Complex Structures by Deep Learning Inter-chain Contact Prediction and Distance-Based Modelling

Frontiers in Molecular Biosciences(2021)10.3389/fmolb.2021.716973

N/A

0DataRank · unranked

25 citations

Raj S. Roy, Elham Soltanikazemi, Jianlin Cheng, Farhan Quadir

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Scientific Reports(2021)10.1038/s41598-021-91827-7

N/A

0DataRank · unranked

27 citations

Raj S. Roy, Randal Halfmann, Jianlin Cheng, Farhan Quadir

Combining pairwise structural similarity and deep learning interface contact prediction to estimate protein complex model accuracy in CASP15

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.08.531814

N/A

0DataRank · unranked

1 citations

Raj S. Roy, Jian Liu, Nabin Giri, Zhiye Guo, Jianlin Cheng

Semi-Supervised Graph Learning Meets Dimensionality Reduction

(2023)10.1109/icmla58977.2023.00303

N/A

0DataRank · unranked

1 citations

Watchanan Chantapakul, Jianlin Cheng, Alex Morehead

Crystal structure of domain of unknown function 507 (DUF507) reveals a new protein fold

Scientific Reports(2023)10.1038/s41598-023-40558-y

N/A

0DataRank · unranked

0 citations

Jianlin Cheng, John J. Tanner, Cole McKay

Geometry-complete diffusion for 3D molecule generation and optimization

Communications Chemistry(2024)10.1038/s42004-024-01233-z

N/A

0DataRank · unranked

65 citations

Jianlin Cheng, Alex Morehead

Deep learning methods for protein function prediction

PROTEOMICS(2024)10.1002/pmic.202300471

N/A

0DataRank · unranked

46 citations

Ahhyun Lee, Jianlin Cheng, Frimpong Boadu

De novo atomic protein structure modeling for cryoEM density maps using 3D transformer and HMM

Nature Communications(2024)10.1038/s41467-024-49647-6

N/A

0DataRank · unranked

45 citations

Jianlin Cheng, Nabin Giri

CryoTransformer: a transformer model for picking protein particles from cryo-EM micrographs

Bioinformatics(2024)10.1093/bioinformatics/btae109

N/A

0DataRank · unranked

42 citations

Rajan Gyawali, Liguo Wang, Jianlin Cheng, Ashwin Dhakal

CryoSegNet: accurate cryo-EM protein particle picking by integrating the foundational AI image segmentation model and attention-gated U-Net

Briefings in Bioinformatics(2024)10.1093/bib/bbae282

N/A

0DataRank · unranked

40 citations

Ashwin Dhakal, Liguo Wang, Jianlin Cheng, Rajan Gyawali

Artificial intelligence in cryo-EM protein particle picking: recent advances and remaining challenges

Briefings in Bioinformatics(2024)10.1093/bib/bbaf011

N/A

0DataRank · unranked

28 citations

Rajan Gyawali, Liguo Wang, Jianlin Cheng, Ashwin Dhakal

VEHiCLE: a Variationally Encoded Hi-C Loss Enhancement algorithm for improving and generating Hi-C data

Scientific Reports(2021)10.1038/s41598-021-88115-9

N/A

0DataRank · unranked

39 citations

Jianlin Cheng, Max Highsmith

DeepDist: real-value inter-residue distance prediction with deep residual convolutional network

BMC Bioinformatics(2021)10.1186/s12859-021-03960-9

N/A

0DataRank · unranked

53 citations

Zhiye Guo, Jie Hou, Jianlin Cheng, Tianqi Wu

Cryo-EM model validation recommendations based on outcomes of the 2019 EMDataResource challenge

Nature Methods(2021)10.1038/s41592-020-01051-w

N/A

0DataRank · unranked

119 citations

Andriy Kryshtafovych, Paul D. Adams, Pavel V. Afonine, Matthew L. Baker, Benjamin A. Barad +49 more

Protein structure accuracy estimation using geometry‐complete perceptron networks

Protein Science(2024)10.1002/pro.4932

N/A

0DataRank · unranked

9 citations

Jian Liu, Jianlin Cheng, Alex Morehead

Estimating protein complex model accuracy using graph transformers and pairwise similarity graphs

Bioinformatics Advances(2024)10.1093/bioadv/vbaf180

N/A

0DataRank · unranked

3 citations

Pawan Neupane, Jianlin Cheng, Jian Liu

A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models

Biomolecules(2024)10.3390/biom14050574

N/A

0DataRank · unranked

2 citations

Jian Liu, Nolan Park, Jianlin Cheng, Xiao Chen

Flow matching for generative modeling in bioinformatics and computational biology

(2025)10.22541/au.175382408.89466370/v4

N/A

0DataRank · unranked

0 citations

Lazar Atanackovic, Akshata Hegde, Yanli Wang, Frimpong Boadu, Joel Selvaraj +4 more

DNSS2: improved ab initio protein secondary structure prediction using advanced deep learning architectures

Authorea(2020)10.22541/au.158379414.46257409

N/A

0DataRank · unranked

5 citations

Jie Hou, Jianlin Cheng, Zhiye Guo

Predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.11.09.373878

N/A

0DataRank · unranked

7 citations

Raj S. Roy, Randal Halfmann, Jianlin Cheng, Farhan Quadir

Auto3DCryoMap: an automated particle alignment approach for 3D cryo-EM density map reconstruction

BMC Bioinformatics(2020)10.1186/s12859-020-03885-9

N/A

0DataRank · unranked

5 citations

Anes Ouadou, Ye Duan, Jianlin Cheng, Adil Al-Azzawi

Outcomes of the EMDataResource Cryo-EM Ligand Modeling Challenge

Research Square(2024)10.21203/rs.3.rs-3864137/v1

N/A

0DataRank · unranked

2 citations

Andriy Kryshtafovych, Grigore Pintilie, S.K. Burley, Jiri Cerny, Vincent Chen +76 more

A Survey of Deep Learning Methods for Estimating the Accuracy of Protein Quaternary Structure Models

Preprints.org(2024)10.20944/preprints202403.0063.v1

N/A

0DataRank · unranked

0 citations

Jian Liu, Nolan Park, Jianlin Cheng, Xiao Chen

Reviewer #1 (Public review): Multi-omics analyses and machine learning prediction of oviductal responses in the presence of gametes and embryos

(2024)10.7554/elife.100705.1.sa2

N/A

0DataRank · unranked

0 citations

Daniel J Carulli, Akshata Hegde, Yanli Wang, Frimpong Baodu, Sarayut Winuthayanon +3 more

Assessing the potential of deep learning for protein–ligand docking

Nature Machine Intelligence(2025)10.1038/s42256-025-01160-1

N/A

0DataRank · unranked

11 citations

Nabin Giri, Jian LIU, Pawan Neupane, Jianlin Cheng, Alex Morehead

FlowDock: Geometric flow matching for generative protein–ligand docking and affinity prediction

Bioinformatics(2025)10.1093/bioinformatics/btaf187

N/A

0DataRank · unranked

12 citations

Jianlin Cheng, Alex Morehead

Improving AlphaFold2 ‐ and AlphaFold3 ‐Based Protein Complex Structure Prediction With MULTICOM4 in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.26850

N/A

0DataRank · unranked

10 citations

Pawan Neupane, Jianlin Cheng, Jian Liu

CryoTEN: efficiently enhancing cryo-EM density maps using transformers

Bioinformatics(2025)10.1093/bioinformatics/btaf092

N/A

0DataRank · unranked

9 citations

Liguo Wang, Jianlin Cheng, Joel Selvaraj

Enhancer Rewiring Orchestrates Inflammation and Loss of Cell Identity During Muscle Stem Cell Aging

Aging Cell(2025)10.1111/acel.70289

N/A

0DataRank · unranked

4 citations

Na Yang, Evelyn Pizano, Lin Wang, James R. Occean, Chang‐Yi Cui +13 more

Heme oxygenase promotes B‐Raf‐dependent melanosphere formation

Pigment Cell & Melanoma Research(2020)10.1111/pcmr.12905

N/A

0DataRank · unranked

10 citations

Jie Hou, Philip Mannino, Jianlin Cheng, Mark Hannink, Kimberly J. Jasmer

Protein‐Ligand Structure and Affinity Prediction in CASP16 Using a Geometric Deep Learning Ensemble and Flow Matching

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.26827

N/A

0DataRank · unranked

4 citations

Jian Liu, Pawan Neupane, Nabin Giri, Jianlin Cheng, Alex Morehead

Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

Scientific Reports(2020)10.1038/s41598-020-60598-y

N/A

0DataRank · unranked

110 citations

Spencer A. Moritz, Jonas Pfab, Jie Hou, Renzhi Cao, Liguo Wang +3 more

Highlights of Model Quality Assessment in CASP16

Proteins Structure Function and Bioinformatics(2025)10.1002/prot.70035

N/A

0DataRank · unranked

1 citations

Recep Adiyaman, Shaima N Alhaddad, Bijan Behzadi, Jianlin Cheng, Xinyue Cui +19 more

Accurate Prediction of Protein Complex Stoichiometry by Integrating AlphaFold3 and Template Information

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.01.12.632663

N/A

0DataRank · unranked

8 citations

Pawan Neupane, Jianlin Cheng, Jian Liu

Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.07.03.663071

N/A

0DataRank · unranked

4 citations

Ashwin Dhakal, Jianlin Cheng, Rajan Gyawali

Protein-ligand structure and affinity prediction in CASP16 using a geometric deep learning ensemble and flow matching

(2025)10.22541/au.173812699.96369139/v1

N/A

0DataRank · unranked

2 citations

Jian Liu, Pawan Neupane, Nabin Giri, Jianlin Cheng, Alex Morehead

Improving AlphaFold2 and 3-based protein complex structure prediction with MULTICOM4 in CASP16

(2025)10.22541/au.174164605.55561866/v1

N/A

0DataRank · unranked

2 citations

Pawan Neupane, Jianlin Cheng, Jian Liu

DeepCryoPicker: fully automated deep neural network for single protein particle picking in cryo-EM

BMC Bioinformatics(2020)10.1186/s12859-020-03809-7

N/A

0DataRank · unranked

71 citations

Anes Ouadou, Highsmith Max, Ye Duan, John J. Tanner, Jianlin Cheng +1 more

Multimodal deep learning integration of cryo-EM and AlphaFold3 for high-accuracy protein structure determination

Research Square(2025)10.21203/rs.3.rs-7055373/v1

N/A

0DataRank · unranked

0 citations

Rajan Gyawali, Ashwin Dhakal, Jianlin Cheng

ETSAM: Effectively Segmenting Cell Membranes in cryo-Electron Tomograms

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.23.689996

N/A

0DataRank · unranked

0 citations

Jianlin Cheng, Joel Selvaraj

DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.03.29.437573

N/A

0DataRank · unranked

0 citations

Jianlin Cheng, Xiao Chen

TAPIOCA: Topological Attention and Predictive Inference of Chromatin Arrangement Using Epigenetic Features

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.05.16.444378

N/A

0DataRank · unranked

0 citations

Jianlin Cheng, Max Highsmith

Jianlin Cheng

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