Zhicheng Ji

MedicineBiochemistry, 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 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 52 papers. Top paper: “GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling”.

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

eLife(2020)10.7554/elife.50670

N/A

1.3DataRank · unranked

41 citations

Zhicheng Ji, Kristin N. Falkenstein, Weiqiang Zhou, Joanna L Henry, Hongkai Ji +2 more

Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

Nature(2021)10.1038/s41586-021-03752-4

N/A

0.948DataRank · unranked

555 citations

Jiajia Zhang, Zhicheng Ji, Ajay Vaghasia, Boyang Zhang, Emily Han-Chung Hsiue +50 more

Single-cell ATAC-seq signal extraction and enhancement with SCATE

Genome biology(2020)10.1186/s13059-020-02075-3

N/A

0DataRank · unranked

51 citations

Weiqiang Zhou, Wenpin Hou, Hongkai Ji, Zhicheng Ji

A Systematic Evaluation of Single-cell RNA-sequencing Imputation Methods

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.01.29.925974

N/A

0DataRank · unranked

31 citations

Zhicheng Ji, Hongkai Ji, Stephanie C. Hicks, Wenpin Hou

Single-cell transcriptomic reveals molecular diversity and developmental heterogeneity of human stem cell-derived oligodendrocyte lineage cells

Nature Communications(2021)10.1038/s41467-021-20892-3

N/A

0DataRank · unranked

108 citations

Alyssa Kallman, Weixiang Fang, Cynthia Berlinicke, Joseph Mertz, Prajwal Devkota +13 more

Global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

Journal of Neuroinflammation(2021)10.1186/s12974-021-02228-6

N/A

0DataRank · unranked

18 citations

Weiqiang Zhou, Zachary Renfro, Zhicheng Ji, Hongkai Ji, Yun Guan +2 more

A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.07.10.451910

N/A

0DataRank · unranked

16 citations

Zhicheng Ji, Zeyu Chen, E. John Wherry, Stephanie C. Hicks, Hongkai Ji +1 more

Tree-based Correlation Screen and Visualization for Exploring Phenotype-Cell Type Association in Multiple Sample Single-Cell RNA-Sequencing Experiments

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.10.27.466024

N/A

0DataRank · unranked

3 citations

Zhicheng Ji, Hongkai Ji, Boyang Zhang

Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.01.27.427793

N/A

0DataRank · unranked

0 citations

Weiqiang Zhou, Zachary Renfro, Zhicheng Ji, Hongkai Ji, Yun Guan +2 more

Discussion of “Exponential-Family Embedding With Application to Cell Developmental Trajectories for Single-Cell RNA-seq Data”

Journal of the American Statistical Association(2021)10.1080/01621459.2021.1880920

N/A

0DataRank · unranked

0 citations

Hongkai Ji, Zhicheng Ji

GLI transcriptional repression is inert prior to Hedgehog pathway activation

bioRxiv (Cold Spring Harbor Laboratory)(2021)10.1101/2021.06.29.450392

N/A

0DataRank · unranked

0 citations

Weiqiang Zhou, Zhicheng Ji, Kristin N. Falkenstein, Kaleigh E. Schuler, Kathryn E. Windsor +4 more

Unbiased visualization of single-cell genomic data with SCUBI

Cell Reports Methods(2022)10.1016/j.crmeth.2021.100135

N/A

0DataRank · unranked

12 citations

Zhicheng Ji, Wenpin Hou

Palo: spatially aware color palette optimization for single-cell and spatial data

Bioinformatics(2022)10.1093/bioinformatics/btac368

N/A

0DataRank · unranked

10 citations

Zhicheng Ji, Wenpin Hou

DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.21.521278

N/A

0DataRank · unranked

3 citations

Zhicheng Ji, Weiqiang Zhou, Jordi Abante, Michael A. Koldobskiy, Hongkai Ji +2 more

Decomposing spatial heterogeneity of cell trajectories with Paella

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.09.05.506682

N/A

0DataRank · unranked

1 citations

Zhicheng Ji, Wenpin Hou

Palo: Spatially-aware color palette optimization for single-cell and spatial data

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.13.484080

N/A

0DataRank · unranked

0 citations

Zhicheng Ji, Wenpin Hou

Controlling taxa abundance improves metatranscriptomics differential analysis

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.03.30.486415

N/A

0DataRank · unranked

0 citations

Li Ma, Zhicheng Ji

Controlling taxa abundance improves metatranscriptomics differential analysis

Research Square(2022)10.21203/rs.3.rs-1638292/v1

N/A

0DataRank · unranked

0 citations

Li Ma, Zhicheng Ji

Lung tumor-infiltrating T reg have divergent transcriptional profiles and function linked to checkpoint blockade response

bioRxiv (Cold Spring Harbor Laboratory)(2022)10.1101/2022.12.13.520329

N/A

0DataRank · unranked

0 citations

Jiajia Zhang, Boyang Zhang, Laurene S. Cheung, Zhen Zeng, Christopher Cherry +32 more

A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples

Nature Communications(2023)10.1038/s41467-023-42841-y

N/A

0DataRank · unranked

97 citations

Zhicheng Ji, Zeyu Chen, E. John Wherry, Stephanie C. Hicks, Hongkai Ji +1 more

Lung tumor–infiltrating Treghave divergent transcriptional profiles and function linked to checkpoint blockade response

Science Immunology(2023)10.1126/sciimmunol.adg1487

N/A

0DataRank · unranked

75 citations

Jiajia Zhang, Laurene S. Cheung, Sydney Connor, Boyang Zhang, Zhen Zeng +34 more

JAK-STAT activation contributes to cytotoxic T cell–mediated basal cell death in human chronic lung allograft dysfunction

JCI Insight(2023)10.1172/jci.insight.167082

N/A

0DataRank · unranked

29 citations

Jamie L. Todd, Fran L. Kelly, Andrew Nagler, Zhicheng Ji, Vaibhav Jain +4 more

DNA-initiated epigenetic cascades driven by C9orf72 hexanucleotide repeat

Neuron(2023)10.1016/j.neuron.2023.01.022

N/A

0DataRank · unranked

23 citations

Zhiyuan Huang, Honghe Liu, Zhicheng Ji, Amit Arora, Danfeng Cai +8 more

DNA methylation entropy is associated with DNA sequence features and developmental epigenetic divergence

Nucleic Acids Research(2023)10.1093/nar/gkad050

N/A

0DataRank · unranked

17 citations

Zhicheng Ji, Weiqiang Zhou, Jordi Abante, Michael A. Koldobskiy, Hongkai Ji +2 more

Nuclear PTEN Regulates Thymidylate Biosynthesis in Human Prostate Cancer Cell Lines

Metabolites(2023)10.3390/metabo13080939

N/A

0DataRank · unranked

4 citations

Mu‐En Wang, Changxin Wan, John M. Asara, Zhicheng Ji, Ming Chen +1 more

Controlling taxa abundance improves metatranscriptomics differential analysis

BMC Microbiology(2023)10.1186/s12866-023-02799-9

N/A

0DataRank · unranked

1 citations

Li Ma, Zhicheng Ji

Benchmarking large language models for genomic knowledge with GeneTuring

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.03.11.532238

N/A

0DataRank · unranked

42 citations

Xu Liao, Zhicheng Ji, Wenpin Hou, Xinyi Shang

Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.16.537094

N/A

0DataRank · unranked

38 citations

Zhicheng Ji, Wenpin Hou

Reference-free and cost-effective automated cell type annotation with GPT-4 in single-cell RNA-seq analysis

Research Square(2023)10.21203/rs.3.rs-2824971/v1

N/A

0DataRank · unranked

4 citations

Wenpin Hou, Zhicheng Ji

T cell transcriptional landscapes are shaped by TCR sequence similarity

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.11.27.568912

N/A

0DataRank · unranked

2 citations

Zhicheng Ji, Hao Wang

Integrating multiple single-cell multi-omics samples with Smmit

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.04.06.535857

N/A

0DataRank · unranked

0 citations

Zhicheng Ji, Changxin Wan

Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis

Nature Methods(2024)10.1038/s41592-024-02235-4

N/A

0DataRank · unranked

231 citations

Zhicheng Ji, Wenpin Hou

Comparing Large Language Models and Human Programmers for Generating Programming Code

Advanced Science(2024)10.1002/advs.202412279

N/A

0DataRank · unranked

39 citations

Zhicheng Ji, Wenpin Hou

A systematic evaluation of computational methods for cell segmentation

Briefings in Bioinformatics(2024)10.1093/bib/bbae407

N/A

0DataRank · unranked

29 citations

Junhan Zhao, Hongye Xu, Cheng Han, Zhiqiang Tao, Dawei Zhou +4 more

Divergent Clinical and Immunologic Outcomes Based on STK11 Co-mutation Status in Resectable KRAS- Mutant Lung Cancers Following Neoadjuvant Immune Checkpoint Blockade

Clinical Cancer Research(2024)10.1158/1078-0432.ccr-24-2983

N/A

0DataRank · unranked

14 citations

Sydney Connor, Khaled Sanber, Marianna Zahurak, Tianbei Zhang, Isha Gurumurthy +24 more

SifiNet: a robust and accurate method to identify feature gene sets and annotate cells

Nucleic Acids Research(2024)10.1093/nar/gkae307

N/A

0DataRank · unranked

5 citations

Zhicheng Ji, Liuyang Wang, Kouros Owzar, Qi-Jing Li, Cliburn Chan +2 more

Assessing large multimodal models for one-shot learning and interpretability in biomedical image classification

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2023.12.31.573796

N/A

0DataRank · unranked

12 citations

Yilong Qu, Huifang Ma, Zhicheng Ji, Wenpin Hou

A systematic evaluation of computational methods for cell segmentation

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.01.28.577670

N/A

0DataRank · unranked

1 citations

Junhan Zhao, Hongye Xu, Cheng Han, Zhiqiang Tao, Dawei Zhou +4 more

GPT-4V exhibits human-like performance in biomedical image classification

Research Square(2024)10.21203/rs.3.rs-3826740/v1

N/A

0DataRank · unranked

1 citations

Wenpin Hou, Zhicheng Ji

PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns

bioRxiv (Cold Spring Harbor Laboratory)(2024)10.1101/2024.03.20.585926

N/A

0DataRank · unranked

1 citations

Zhicheng Ji, Haotian Zhuang

Benchmarking large language models for genomic knowledge with GeneTuring

Briefings in Bioinformatics(2025)10.1093/bib/bbaf492

N/A

0DataRank · unranked

9 citations

Xu Liao, Zhicheng Ji, Wenpin Hou, Xinyi Shang

Single-cell and spatial detection of senescent cells using DeepScence

Cell Genomics(2025)10.1016/j.xgen.2025.101035

N/A

0DataRank · unranked

6 citations

Bing Ji, Runze Dong, Liangcai Gu, Cliburn Chan, Jichun Xie +5 more

Assessing Large Multimodal Models for One‐Shot Learning and Interpretability in Biomedical Image Classification

Advanced Intelligent Systems(2025)10.1002/aisy.202400947

N/A

0DataRank · unranked

4 citations

Qi Liu, Huifang Ma, Yilong Qu, Zhicheng Ji, Wenpin Hou

Vispro improves imaging analysis for Visium spatial transcriptomics

Genome biology(2025)10.1186/s13059-025-03648-w

N/A

0DataRank · unranked

3 citations

Xingyuan Zhang, Yilong Qu, Anru R. Zhang, Zhicheng Ji, Huifang Ma

Smmit: A pipeline for integrating multiple single-cell multi-omics samples

Computational and Structural Biotechnology Journal(2025)10.1016/j.csbj.2025.08.020

N/A

0DataRank · unranked

1 citations

Zhicheng Ji, Changxin Wan

Identifying cell-type-specific spatially variable genes with ctSVG

Genome biology(2025)10.1186/s13059-025-03870-6

N/A

0DataRank · unranked

1 citations

Xinyi Shang, Wenpin Hou, Zhicheng Ji, Haotian Zhuang

Comparative analysis of gene regulation in single cells using Compass

Cell Reports Methods(2025)10.1016/j.crmeth.2025.101035

N/A

0DataRank · unranked

1 citations

Yilong Qu, Zhiyou Ye, Tianbei Zhang, Hui-Fang Ma, Ming Chen +3 more

Transcriptome-wide association studies at cell state level using single-cell eQTL data

medRxiv(2025)10.1101/2025.03.17.25324128

N/A

0DataRank · unranked

1 citations

Eardi Lila, Zhicheng Ji, Ali Shojaie, Alexis Battle, Wei Sun +1 more

LLM-based cell type annotation harmonization across single-cell studies using GCTHarmony

Research Square(2025)10.21203/rs.3.rs-7151095/v1

N/A

0DataRank · unranked

0 citations

Zhicheng Ji, Xingyuan Zhang

A systematic evaluation of single-cell RNA-sequencing imputation methods

Genome biology(2020)10.1186/s13059-020-02132-x

N/A

0DataRank · unranked

328 citations

Zhicheng Ji, Hongkai Ji, Stephanie C. Hicks, Wenpin Hou

Pseudotimecascade visualizes gene expression cascade in pseudotime analysis

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.11.19.689263

N/A

0DataRank · unranked

0 citations

Bing Ji, Zhicheng Ji, Changxin Wan

Single cell transcriptomics of mouse kidney transplants reveals a myeloid cell pathway for transplant rejection

JCI Insight(2020)10.1172/jci.insight.141321

N/A

0DataRank · unranked

57 citations

Naveen Natesh, Irma Husain, Zhicheng Ji, Laura Barisoni, Jean Kwun +4 more