Zhe Ji

Shanghai University of Engineering Science

Also affiliated with Fudan University, Tangshan People's Hospital, Anhui Normal University

Physics and AstronomyBiochemistry, Genetics and Molecular BiologyMedicine

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 25 papers. Top paper: “Noncanonical open reading frames encode functional proteins essential for cancer cell survival”.

Noncanonical open reading frames encode functional proteins essential for cancer cell survival

Nature Biotechnology(2021)10.1038/s41587-020-00806-2

N/A

4.5DataRank · unranked

198 citations

Oana M. Enache, Victor Luria, Karsten Krug, Karl R. Clauser, Joshua M. Dempster +21 more

Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Nature Methods(2018)10.1038/s41592-018-0014-2

N/A

4.3DataRank · unranked

141 citations

Adam L. Haber, Sean K. Simmons, Pradeep Natarajan, Zhe Ji, Michele A. Busby +8 more

Thousands of novel unannotated proteins expand the MHC I immunopeptidome in cancer

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.02.12.945840

N/A

1.7DataRank · unranked

45 citations

Travis Law, Karl R. Clauser, Susan Klaeger, Siranush Sarkizova, François Aguet +22 more

Deep learning of human polyadenylation sites at nucleotide resolution reveals molecular determinants of site usage and relevance in disease

Nature Communications(2023)10.1038/s41467-023-43266-3

N/A

1.1DataRank · unranked

43 citations

Zhe Ji, Emily K. Stroup

Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

eLife(2015)10.7554/elife.08890

N/A

0.960DataRank · unranked

599 citations

Ruisheng Song, Prisca Liberali, Kevin Struhl, Zhe Ji

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

Nature Biotechnology(2021)10.1038/s41587-021-01021-3

N/A

0.853DataRank · unranked

294 citations

Travis Law, Karl R. Clauser, Susan Klaeger, Siranush Sarkizova, François Aguet +24 more

Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers

Proceedings of the National Academy of Sciences(2019)10.1073/pnas.1821068116

N/A

0.815DataRank · unranked

228 citations

Lizhi He, Prisca Liberali, Kevin Struhl, Zhe Ji

Non-canonical open reading frames encode functional proteins essential for cancer cell survival

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.03.10.981001

N/A

0.686DataRank · unranked

12 citations

Oana M. Enache, Victor Luria, Karsten Krug, Karl R. Clauser, Joshua M. Dempster +21 more

Transcriptome-scale RNase-footprinting of RNA-protein complexes

Nature Biotechnology(2016)10.1038/nbt.3441

N/A

0.612DataRank · unranked

58 citations

Ruisheng Song, Hailiang Huang, Prisca Liberali, Kevin Struhl, Zhe Ji

Author Correction: Comprehensive comparative analysis of 5′-end RNA-sequencing methods

Nature Methods(2018)10.1038/s41592-018-0237-2

N/A

0.352DataRank · unranked

5 citations

Adam L. Haber, Sean K. Simmons, Pradeep Natarajan, Zhe Ji, Michele A. Busby +8 more

Author response: Many lncRNAs, 5’UTRs, and pseudogenes are translated and some are likely to express functional proteins

(2015)10.7554/elife.08890.029

N/A

0.194DataRank · unranked

2 citations

Ruisheng Song, Prisca Liberali, Kevin Struhl, Zhe Ji

The prolyl isomerase FKBP11 is a secretory translocon accessory factor

Molecular Biology of the Cell(2024)10.1091/mbc.e24-07-0305

N/A

0DataRank · unranked

2 citations

Ben Cheng, Frank Zhong, Roshan Jha, Yu Wan, Andrei Anghel +6 more

Delineating yeast cleavage and polyadenylation signals using deep learning

Genome Research(2024)10.1101/gr.278606.123

N/A

0DataRank · unranked

3 citations

Zhe Ji, Emily K. Stroup

Chromatin Organization Governs Transcriptional Response and Plasticity of Cancer Stem Cells

Advanced Science(2025)10.1002/advs.202407426

N/A

0DataRank · unranked

12 citations

Jane Frederick, Karla Medina, Elizabeth T. Bartom, Luay M. Almassalha, Yaqi Zhang +16 more

The Advances in Deep Learning Modeling of Polyadenylation Codes

Wiley Interdisciplinary Reviews - RNA(2025)10.1002/wrna.70017

N/A

0DataRank · unranked

0 citations

Tianjiao Sun, Qianru Li, John Carinato, Zhe Ji, Emily K. Stroup

Antibody targeting tumor-derived soluble NKG2D ligand sMIC reprograms NK cell homeostatic survival and function and enhances melanoma response to PDL1 blockade therapy

Journal of Hematology & Oncology(2020)10.1186/s13045-020-00896-0

N/A

0DataRank · unranked

42 citations

Payal Dhar, Xin Wang, Derek A. Wainwright, Bin Zhang, Jeffrey A. Sosman +3 more

Cell type- and stage-specific expression of Otx2 is regulated by multiple transcription factors and cis -regulatory modules in the retina

Development(2020)10.1242/dev.187922

N/A

0DataRank · unranked

41 citations

Nicolas Lonfat, Rong Zhao, Alexander E. Davis, Liang Li, Man-Ru Wu +5 more

CD95/Fas protects triple negative breast cancer from anti-tumor activity of NK cells

iScience(2021)10.1016/j.isci.2021.103348

N/A

0DataRank · unranked

20 citations

Jean‐Philippe Guégan, Christophe Ginestier, Assia Chaïbi, Alban Bessede, Emmanuelle Charafe‐Jauffret +14 more

Tumor-derived NKG2D ligand sMIC reprograms NK cells to an inflammatory phenotype through CBM signalosome activation

Communications Biology(2021)10.1038/s42003-021-02440-3

N/A

0DataRank · unranked

19 citations

Fahmin Basher, Zhe Ji, Lei Huang, Si Qin, Derek A. Wainwright +6 more

Spike-in normalization for single-cell RNA-seq reveals dynamic global transcriptional activity mediating anticancer drug response

NAR Genomics and Bioinformatics(2021)10.1093/nargab/lqab054

N/A

0DataRank · unranked

8 citations

Jane Frederick, Hongbin Wang, Hui Sheng, Vadim Backman, Zhe Ji +1 more

Low-input RNase footprinting for simultaneous quantification of cytosolic and mitochondrial translation

Genome Research(2022)10.1101/gr.276139.121

N/A

0DataRank · unranked

41 citations

Haiwang Yang, Emily K. Stroup, Hongbin Wang, Zhe Ji, Qianru Li

Rfoot‐seq: Transcriptomic RNase Footprinting for Mapping Stable RNA‐Protein Complexes and Rapid Ribosome Profiling

Current Protocols(2023)10.1002/cpz1.761

N/A

0DataRank · unranked

8 citations

Emily K. Stroup, Zhe Ji, Qianru Li

Delineating yeast cleavage and polyadenylation signals using deep learning

bioRxiv (Cold Spring Harbor Laboratory)(2023)10.1101/2023.10.10.561764

N/A

0DataRank · unranked

1 citations

Zhe Ji, Emily K. Stroup

Widespread stable noncanonical peptides identified by integrated analyses of ribosome profiling and ORF features

Nature Communications(2024)10.1038/s41467-024-46240-9

N/A

0DataRank · unranked

57 citations

Qianru Li, Emily K. Stroup, Sheng Wang, Zhe Ji, Haiwang Yang

Comparative analyses of gene networks mediating cancer metastatic potentials across lineage types

Briefings in Bioinformatics(2024)10.1093/bib/bbae357

N/A

0DataRank · unranked

2 citations

Emily K. Stroup, Ting-You Wang, Rendong Yang, Zhe Ji, Sheng Wang