Publications:

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Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures.

Scientific Reports

Zheng, Weisheng W; Pu, Mengchen M; Li, Xiaorong X; Du, Zhaolan Z; Jin, Sutong S; Li, Xingshuai X; Zhou, Jielong J; Zhang, Yingsheng Y

Publication Date: 2023-05-30

Variant appearance in text: 225: A51X

PubMed Link: 37253775

Variant Present in the following documents:

• 41598_2023_35842_MOESM8_ESM.xlsx, sheet 1
• 41598_2023_35842_MOESM8_ESM.xlsx, sheet 3

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Integrated analysis of genomic and transcriptomic data for the discovery of splice-associated variants in cancer.

Nature Communications

Cotto, Kelsy C KC; Feng, Yang-Yang YY; Ramu, Avinash A; Richters, Megan M; Freshour, Sharon L SL; Skidmore, Zachary L ZL; Xia, Huiming H; McMichael, Joshua F JF; Kunisaki, Jason J; Campbell, Katie M KM; Chen, Timothy Hung-Po TH; Rozycki, Emily B EB; Adkins, Douglas D; Devarakonda, Siddhartha S; Sankararaman, Sumithra S; Lin, Yiing Y; Chapman, William C WC; Maher, Christopher A CA; Arora, Vivek V; Dunn, Gavin P GP; Uppaluri, Ravindra R; Govindan, Ramaswamy R; Griffith, Obi L OL; Griffith, Malachi M

Publication Date: 2023-03-22

Variant appearance in text: 225: A51X

PubMed Link: 36949070

Variant Present in the following documents:

• 41467_2023_37266_MOESM19_ESM.xlsx, sheet 18

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Persistent mutation burden drives sustained anti-tumor immune responses.

Nature Medicine

Niknafs, Noushin N; Balan, Archana A; Cherry, Christopher C; Hummelink, Karlijn K; Monkhorst, Kim K; Shao, Xiaoshan M XM; Belcaid, Zineb Z; Marrone, Kristen A KA; Murray, Joseph J; Smith, Kellie N KN; Levy, Benjamin B; Feliciano, Josephine J; Hann, Christine L CL; Lam, Vincent V; Pardoll, Drew M DM; Karchin, Rachel R; Seiwert, Tanguy Y TY; Brahmer, Julie R JR; Forde, Patrick M PM; Velculescu, Victor E VE; Anagnostou, Valsamo V

Publication Date: 2023-01-26

Variant appearance in text: 225: A51X

PubMed Link: 36702947

Variant Present in the following documents:

• 41591_2022_2163_MOESM3_ESM.xlsx, sheet 4

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Immune Infiltration-Related ceRNA Network Revealing Potential Biomarkers for Prognosis of Head and Neck Squamous Cell Carcinoma.

Disease Markers

Zhao, Shuai S; Peng, Mengle M; Wang, Zhongquan Z; Cao, Jingjing J; Zhang, Xinyu X; Yu, Ruijing R; Huang, Tao T; Lian, Wenping W

Publication Date: 2022

Variant appearance in text: 225: A51X

PubMed Link: 36097539

Variant Present in the following documents:

• 1014347.f2.pdf

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A hypoxia-related lncRNA model for prediction of head and neck squamous cell carcinoma prognosis.

Cancer Medicine

Xiang, Junwei J; He, Yaodong Y; Li, Yunshan Y; Wu, Kexuan K; Cheng, Mengxiang M; Wang, Yuanyin Y; Chen, Ran R

Publication Date: 2022-08-03

Variant appearance in text: 225: A51X

PubMed Link: 35920349

Variant Present in the following documents:

• CAM4-12-3773-s005.xlsx, sheet 1

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Pan-Cancer Analysis, Reveals COVID-19-Related BSG as a Novel Marker for Treatment and Identification of Multiple Human Cancers.

Frontiers In Cell And Developmental Biology

Huang, Tao T; He, Wei-Ying WY

Publication Date: 2022

Variant appearance in text: 225: A51X

PubMed Link: 35646943

Variant Present in the following documents:

• Table1.xlsx, sheet 5

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Frequent somatic gene conversion as a mechanism for loss of heterozygosity in tumor suppressor genes.

Genome Research

Takahashi, Kazuki K KK; Innan, Hideki H

Publication Date: 2022-06

Variant appearance in text: 225: A51X

PubMed Link: 35618418

Variant Present in the following documents:

• supp_gr.276617.122_Supplemental_Tables.xlsx, sheet 1

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Concurrent delivery of immune checkpoint blockade modulates T cell dynamics to enhance neoantigen vaccine-generated antitumor immunity.

Nature Cancer

Liu, Longchao L; Chen, Jiahui J; Zhang, Hongyi H; Ye, Jianfeng J; Moore, Casey C; Lu, Changzheng C; Fang, Yan Y; Fu, Yang-Xin YX; Li, Bo B

Publication Date: 2022-04

Variant appearance in text: 225: A51X

PubMed Link: 35393580

Variant Present in the following documents:

• NIHMS1784010-supplement-SourceData_Fig6.xlsx, sheet 8

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CDKN2A Deletion Leading to Hematogenous Metastasis of Human Gastric Carcinoma.

Frontiers In Oncology

Qiao, Juanli J; Tian, Yuan Y; Cheng, Xiaojing X; Liu, Zhaojun Z; Zhou, Jing J; Gu, Liankun L; Zhang, Baozhen B; Zhang, Lianhai L; Ji, Jiafu J; Xing, Rui R; Deng, Dajun D

Publication Date: 2021

Variant appearance in text: 225: A51X

PubMed Link: 35004325

Variant Present in the following documents:

• DataSheet_1.xlsx, sheet 2

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POLE/POLD1 mutation in non-exonuclease domain matters for predicting efficacy of immune-checkpoint-inhibitor therapy.

Clinical And Translational Medicine

Chen, Yan-Xing YX; Wang, Zi-Xian ZX; Yuan, Shu-Qiang SQ; Jiang, Teng-Jia TJ; Huang, You-Sheng YS; Xu, Rui-Hua RH; Wang, Feng F; Zhao, Qi Q

Publication Date: 2021-09

Variant appearance in text: 225: A51X

PubMed Link: 34586735

Variant Present in the following documents:

• CTM2-11-e524-s001.xlsx, sheet 4

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Long noncoding RNA SNHG1 promotes TERT expression by sponging miR-18b-5p in breast cancer.

Cell & Bioscience

Kang, Yujuan Y; Wan, Lin L; Wang, Qin Q; Yin, Yanling Y; Liu, Jiena J; Liu, Lei L; Wu, Hao H; Zhang, Lei L; Zhang, Xin X; Xu, Shouping S; Pang, Da D

Publication Date: 2021-08-31

Variant appearance in text: 225: A51X

PubMed Link: 34465388

Variant Present in the following documents:

• 13578_2021_675_MOESM4_ESM.pdf

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Immune-Inhibitory Gene Expression is Positively Correlated with Overall Immune Activity and Predicts Increased Survival Probability of Cervical and Head and Neck Cancer Patients.

Frontiers In Molecular Biosciences

Budhwani, Megha M; Turrell, Gavin G; Yu, Meihua M; Frazer, Ian H IH; Mehdi, Ahmed M AM; Chandra, Janin J

Publication Date: 2021

Variant appearance in text: 225: A51X

PubMed Link: 33834038

Variant Present in the following documents:

• table1.xlsx, sheet 5

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Genomic analysis of the prognostic effect of tumor-associated neutrophil-related genes across 15 solid cancer types: an immune perspective.

Annals Of Translational Medicine

Hao, Yuying Y; Hu, Pingping P; Zhang, Jiandong J

Publication Date: 2020-11

Variant appearance in text: 225: A51X

PubMed Link: 33313252

Variant Present in the following documents:

• atm-08-22-1507-supplementary.pdf

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High-risk lymph node ratio predicts worse prognosis in patients with locally advanced oral cancer.

Journal Of Oral Pathology & Medicine : Official Publication Of The International Association Of Oral Pathologists And The American Academy Of Oral Pathology

Zhao, Tong-Chao TC; Liang, Si-Yuan SY; Ju, Wu-Tong WT; Fu, Yong Y; Zhou, Zhi-Hang ZH; Wang, Li-Zhen LZ; Li, Jiang J; Zhang, Chen-Ping CP; Zhang, Zhi-Yuan ZY; Zhong, Lai-Ping LP

Publication Date: 2020-09

Variant appearance in text: 225: A51X

PubMed Link: 32449223

Variant Present in the following documents:

• JOP-49-787-s010.xlsx, sheet 1

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High expression of oxidative phosphorylation genes predicts improved survival in squamous cell carcinomas of the head and neck and lung.

Scientific Reports

Frederick, Mitchell M; Skinner, Heath D HD; Kazi, Sawad A SA; Sikora, Andrew G AG; Sandulache, Vlad C VC

Publication Date: 2020-04-14

Variant appearance in text: 225: A51X

PubMed Link: 32286489

Variant Present in the following documents:

• 41598_2020_63448_MOESM2_ESM.xlsx, sheet 6
• 41598_2020_63448_MOESM2_ESM.xlsx, sheet 13

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Interplay between DNA damage repair and apoptosis shapes cancer evolution through aneuploidy and microsatellite instability.

Nature Communications

Auslander, Noam N; Wolf, Yuri I YI; Koonin, Eugene V EV

Publication Date: 2020-03-06

Variant appearance in text: 225: A51X

PubMed Link: 32144251

Variant Present in the following documents:

• 41467_2020_15094_MOESM9_ESM.xlsx, sheet 1

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Mutation Clusters from Cancer Exome.

Genes

Kakushadze, Zura Z; Yu, Willie W

Publication Date: 2017-08-15

Variant appearance in text: 225: A51X

PubMed Link: 28809811

Variant Present in the following documents:

• Main text
• genes-08-00201.pdf

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Genome-wide DNA methylation profile identified a unique set of differentially methylated immune genes in oral squamous cell carcinoma patients in India.

Clinical Epigenetics

Basu, Baidehi B; Chakraborty, Joyeeta J; Chandra, Aditi A; Katarkar, Atul A; Baldevbhai, Jadav Ritesh Kumar JRK; Dhar Chowdhury, Debjit D; Ray, Jay Gopal JG; Chaudhuri, Keya K; Chatterjee, Raghunath R

Publication Date: 2017

Variant appearance in text: 225: A51X

PubMed Link: 28174608

Variant Present in the following documents:

• 13148_2017_314_MOESM3_ESM.xlsx, sheet 1

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Unique somatic and malignant expression patterns implicate PIWI-interacting RNAs in cancer-type specific biology.

Scientific Reports

Martinez, Victor D VD; Vucic, Emily A EA; Thu, Kelsie L KL; Hubaux, Roland R; Enfield, Katey S S KS; Pikor, Larissa A LA; Becker-Santos, Daiana D DD; Brown, Carolyn J CJ; Lam, Stephen S; Lam, Wan L WL

Publication Date: 2015-05-27

Variant appearance in text: 225: A51X

PubMed Link: 26013764

Variant Present in the following documents:

• srep10423-s3.xls, sheet 1

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