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: A90C

PubMed Link: 37253775

Variant Present in the following documents:

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

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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: A90C

PubMed Link: 36949070

Variant Present in the following documents:

• 41467_2023_37266_MOESM19_ESM.xlsx, sheet 12
• 41467_2023_37266_MOESM19_ESM.xlsx, sheet 15

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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: A90C

PubMed Link: 36702947

Variant Present in the following documents:

• 41591_2022_2163_MOESM3_ESM.xlsx, sheet 3

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Comprehensive analyses of PDHA1 that serves as a predictive biomarker for immunotherapy response in cancer.

Frontiers In Pharmacology

Deng, Langmei L; Jiang, Anqi A; Zeng, Hanqing H; Peng, Xiaoji X; Song, Liying L

Publication Date: 2022

Variant appearance in text: 225: A90C

PubMed Link: 36003495

Variant Present in the following documents:

• table4.xlsx, sheet 1

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The Long Non-Coding RNA FAM222A-AS1 Negatively Modulates MiR-Let-7f to Promote Colorectal Cancer Progression.

Frontiers In Oncology

Song, Mengmeng M; Li, Ye Y; Chen, Zhewen Z; Zhang, Jie J; Yang, Liuqing L; Zhang, Fan F; Song, Chunhua C; Miao, Mingyong M; Chang, Wenjun W; Shi, Hanping H

Publication Date: 2022

Variant appearance in text: 225: a90c

PubMed Link: 35646686

Variant Present in the following documents:

• Table_12.xlsx, sheet 2

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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: A90C

PubMed Link: 35618418

Variant Present in the following documents:

• supp_gr.276617.122_Supplemental_Tables.xlsx, sheet 1

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Characterization of Pyroptosis-Related Subtypes via RNA-Seq and ScRNA-Seq to Predict Chemo-Immunotherapy Response in Triple-Negative Breast Cancer.

Frontiers In Genetics

Li, Chenlu C; Pan, Jingjing J; Jiang, Yinyan Y; Wu, Yanzhi Y; Jin, Zhenlin Z; Chen, Xupeng X

Publication Date: 2022

Variant appearance in text: 225: a90c

PubMed Link: 35386285

Variant Present in the following documents:

• DataSheet3.xlsx, sheet 4

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KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.

Plos One

Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW

Publication Date: 2022

Variant appearance in text: 225: A90C

PubMed Link: 35081118

Variant Present in the following documents:

• pone.0251286.s005.xlsx, sheet 8

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KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.

Plos One

Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW

Publication Date: 2022

Variant appearance in text: 225: A90C

PubMed Link: 35081118

Variant Present in the following documents:

• pone.0251286.s005.xlsx, sheet 8

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A chemoresistance lncRNA signature for recurrence risk stratification of colon cancer patients with chemotherapy.

Molecular Therapy. Nucleic Acids

Wang, Hao H; Gao, Yuzhen Y; Vafaei, Somayeh S; Yu, Qiaoyan Q; Zhang, Jun J; Wang, Liangjing L

Publication Date: 2022-03-08

Variant appearance in text: 225: A90C

PubMed Link: 35036055

Variant Present in the following documents:

• mmc1.pdf
• mmc2.pdf

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Toward a Natural Classification of Botryosphaeriaceae: A Study of the Type Specimens of Botryosphaeria sensu lato.

Frontiers In Microbiology

Zhang, Ying Y; Zhou, Yupei Y; Sun, Wei W; Zhao, Lili L; Pavlic-Zupanc, D D; Crous, Pedro W PW; Slippers, Bernard B; Dai, Yucheng Y

Publication Date: 2021

Variant appearance in text: 225: A90C

PubMed Link: 34803952

Variant Present in the following documents:

• Main text

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Short-term amino acid, clinicopathologic, and echocardiographic findings in healthy dogs fed a commercial plant-based diet.

Plos One

Cavanaugh, Sarah M SM; Cavanaugh, Ryan P RP; Gilbert, Gregory E GE; Leavitt, Elena L EL; Ketzis, Jennifer K JK; Vieira, Aline B AB

Publication Date: 2021

Variant appearance in text: 225: A90C

PubMed Link: 34637461

Variant Present in the following documents:

• Main text

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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: A90C

PubMed Link: 34465388

Variant Present in the following documents:

• 13578_2021_675_MOESM4_ESM.pdf

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Chloroplast acquisition without the gene transfer in kleptoplastic sea slugs, Plakobranchus ocellatus.

Elife

Maeda, Taro T; Takahashi, Shunichi S; Yoshida, Takao T; Shimamura, Shigeru S; Takaki, Yoshihiro Y; Nagai, Yukiko Y; Toyoda, Atsushi A; Suzuki, Yutaka Y; Arimoto, Asuka A; Ishii, Hisaki H; Satoh, Nori N; Nishiyama, Tomoaki T; Hasebe, Mitsuyasu M; Maruyama, Tadashi T; Minagawa, Jun J; Obokata, Junichi J; Shigenobu, Shuji S

Publication Date: 2021-04-27

Variant appearance in text: 225: A90C

PubMed Link: 33902812

Variant Present in the following documents:

• Main text

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MYBL2-Driven Transcriptional Programs Link Replication Stress and Error-prone DNA Repair With Genomic Instability in Lung Adenocarcinoma.

Frontiers In Oncology

Morris, Benjamin B BB; Wages, Nolan A NA; Grant, Patrick A PA; Stukenberg, P Todd PT; Gentzler, Ryan D RD; Hall, Richard D RD; Akerley, Wallace L WL; Varghese, Thomas K TK; Arnold, Susanne M SM; Williams, Terence M TM; Coppola, Vincenzo V; Jones, David R DR; Auble, David T DT; Mayo, Marty W MW

Publication Date: 2020

Variant appearance in text: 225: a90c

PubMed Link: 33489883

Variant Present in the following documents:

• DataSheet_5.xlsx, sheet 1

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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: A90C

PubMed Link: 33313252

Variant Present in the following documents:

• atm-08-22-1507-supplementary.pdf

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Novel oral anticoagulant vs. warfarin in elderly atrial fibrillation patients with normal, mid-range, and reduced left ventricular ejection fraction.

Esc Heart Failure

Wu, Victor Chien-Chia VC; Wang, Chun-Li CL; Lee, Cheng-Hung CH; Chen, Yu-Ling YL; Tu, Hui-Tzu HT; Wu, Michael M; Kuo, Chang-Fu CF; Chen, Shao-Wei SW; Huang, Yu-Tung YT; Wen, Ming-Shien MS; Chang, Shang-Hung SH

Publication Date: 2020-10

Variant appearance in text: 225: A90C

PubMed Link: 32677373

Variant Present in the following documents:

• Main text

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Comprehensive analysis of indels in whole-genome microsatellite regions and microsatellite instability across 21 cancer types.

Genome Research

Fujimoto, Akihiro A; Fujita, Masashi M; Hasegawa, Takanori T; Wong, Jing Hao JH; Maejima, Kazuhiro K; Oku-Sasaki, Aya A; Nakano, Kaoru K; Shiraishi, Yuichi Y; Miyano, Satoru S; Yamamoto, Go G; Akagi, Kiwamu K; Imoto, Seiya S; Nakagawa, Hidewaki H

Publication Date: 2020-03-24

Variant appearance in text: 225: a90c

PubMed Link: 32209592

Variant Present in the following documents:

• supp_gr.255026.119_Supplemental_Tables.xlsx, sheet 3

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The asymmetry and cooperativity of tandem glycine riboswitch aptamers.

Rna (New York, N.Y.)

Torgerson, Chad D CD; Hiller, David A DA; Strobel, Scott A SA

Publication Date: 2020-05

Variant appearance in text: 225: A90C

PubMed Link: 31992591

Variant Present in the following documents:

• supp_073577.119_Supplemental_SMARTT_Data.xlsx, sheet 4

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CNApp, a tool for the quantification of copy number alterations and integrative analysis revealing clinical implications.

Elife

Franch-Expósito, Sebastià S; Bassaganyas, Laia L; Vila-Casadesús, Maria M; Hernández-Illán, Eva E; Esteban-Fabró, Roger R; Díaz-Gay, Marcos M; Lozano, Juan José JJ; Castells, Antoni A; Llovet, Josep Maria JM; Castellví-Bel, Sergi S; Camps, Jordi J

Publication Date: 2020-01-15

Variant appearance in text: 225: A90C

PubMed Link: 31939734

Variant Present in the following documents:

• elife-50267-fig1-figsupp1-data1.xlsx, sheet 1

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Predicting the success of an invader: Niche shift versus niche conservatism.

Ecology And Evolution

Sherpa, Stéphanie S; Guéguen, Maya M; Renaud, Julien J; Blum, Michael G B MGB; Gaude, Thierry T; Laporte, Frédéric F; Akiner, Mustafa M; Alten, Bulent B; Aranda, Carles C; Barre-Cardi, Hélène H; Bellini, Romeo R; Bengoa Paulis, Mikel M; Chen, Xiao-Guang XG; Eritja, Roger R; Flacio, Eleonora E; Foxi, Cipriano C; Ishak, Intan H IH; Kalan, Katja K; Kasai, Shinji S; Montarsi, Fabrizio F; Pajović, Igor I; Petrić, Dušan D; Termine, Rosa R; Turić, Nataša N; Vazquez-Prokopec, Gonzalo M GM; Velo, Enkelejda E; Vignjević, Goran G; Zhou, Xiaohong X; Després, Laurence L

Publication Date: 2019-11

Variant appearance in text: 225: A90C

PubMed Link: 31788205

Variant Present in the following documents:

• Main text

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Lack of detectable neoantigen depletion signals in the untreated cancer genome.

Nature Genetics

Van den Eynden, Jimmy J; Jiménez-Sánchez, Alejandro A; Miller, Martin L ML; Larsson, Erik E

Publication Date: 2019-12

Variant appearance in text: 225: A90C

PubMed Link: 31768072

Variant Present in the following documents:

• EMS84665-supplement-Suppl__table_2.xlsx, sheet 2

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Identification of 12 cancer types through genome deep learning.

Scientific Reports

Sun, Yingshuai Y; Zhu, Sitao S; Ma, Kailong K; Liu, Weiqing W; Yue, Yao Y; Hu, Gang G; Lu, Huifang H; Chen, Wenbin W

Publication Date: 2019-11-21

Variant appearance in text: EGR1: a90c

PubMed Link: 31754222

Variant Present in the following documents:

• 41598_2019_53989_MOESM4_ESM.xlsx, sheet 9

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Cancer-associated mutations in DICER1 RNase IIIa and IIIb domains exert similar effects on miRNA biogenesis.

Nature Communications

Vedanayagam, Jeffrey J; Chatila, Walid K WK; Aksoy, Bülent Arman BA; Majumdar, Sonali S; Skanderup, Anders Jacobsen AJ; Demir, Emek E; Schultz, Nikolaus N; Sander, Chris C; Lai, Eric C EC

Publication Date: 2019-08-15

Variant appearance in text: 225: A90C

PubMed Link: 31417090

Variant Present in the following documents:

• 41467_2019_11610_MOESM10_ESM.xlsx, sheet 3

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A genetic selection reveals functional metastable structures embedded in a toxin-encoding mRNA.

Elife

Masachis, Sara S; Tourasse, Nicolas J NJ; Lays, Claire C; Faucher, Marion M; Chabas, Sandrine S; Iost, Isabelle I; Darfeuille, Fabien F

Publication Date: 2019-08-14

Variant appearance in text: 225: A90C

PubMed Link: 31411564

Variant Present in the following documents:

• Main text

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Analysis of adult cerebral cortex and hippocampus transcriptomes reveals unique molecular changes in the Ts1Cje mouse model of down syndrome.

Brain Pathology (Zurich, Switzerland)

Guedj, Faycal F; Pennings, Jeroen L A JL; Wick, Heather C HC; Bianchi, Diana W DW

Publication Date: 2015-01

Variant appearance in text: 225: A90C

PubMed Link: 24916381

Variant Present in the following documents:

• Main text

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Phospholipase C in living cells: activation, inhibition, Ca2+ requirement, and regulation of M current.

The Journal Of General Physiology

Horowitz, Lisa F LF; Hirdes, Wiebke W; Suh, Byung-Chang BC; Hilgemann, Donald W DW; Mackie, Ken K; Hille, Bertil B

Publication Date: 2005-09

Variant appearance in text: 225: A90C

PubMed Link: 16129772

Variant Present in the following documents:

• Main text

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