Publications:

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Beyond Structural Bioinformatics for Genomics with Dynamics Characterization of an Expanded KRAS Mutational Landscape.

Biorxiv : The Preprint Server For Biology

Ratnasinghe, Brian D BD; Haque, Neshatul N; Wagenknecht, Jessica B JB; Jensen, Davin R DR; Esparza, Guadalupe V GV; Leverence, Elise N EN; De Assuncao, Thiago Milech TM; Mathison, Angela J AJ; Lomberk, Gwen G; Smith, Brian C BC; Volkman, Brian F BF; Urrutia, Raul R; Zimmermann, Michael T MT

Publication Date: 2023-04-28

Variant appearance in text: KRAS: T35A

PubMed Link: 37207265

Variant Present in the following documents:

• Main text
• nihpp-2023.04.28.536249v1.pdf

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The Importance of Mg2+ -Free State in Nucleotide Exchange of Oncogenic K-Ras Mutants.

Chemistry (Weinheim An Der Bergstrasse, Germany)

Pálfy, Gyula G; Menyhárd, Dóra K DK; Ákontz-Kiss, Hanna H; Vida, István I; Batta, Gyula G; Tőke, Orsolya O; Perczel, András A

Publication Date: 2022-10-21

Variant appearance in text: K-Ras4B: T35A

PubMed Link: 35781716

Variant Present in the following documents:

• CHEM-28-0.pdf

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Understanding the influence of AMG 510 on the structure of KRASG12C empowered by molecular dynamics simulation.

Computational And Structural Biotechnology Journal

Li, Yu Y; Han, Lei L; Zhang, Ziding Z

Publication Date: 2022

Variant appearance in text: KRAS: T35A

PubMed Link: 35284050

Variant Present in the following documents:

• Main text
• main.pdf

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A structural model of a Ras-Raf signalosome.

Nature Structural & Molecular Biology

Mysore, Venkatesh P VP; Zhou, Zhi-Wei ZW; Ambrogio, Chiara C; Li, Lianbo L; Kapp, Jonas N JN; Lu, Chunya C; Wang, Qi Q; Tucker, Maxwell R MR; Okoro, Jeffrey J JJ; Nagy-Davidescu, Gabriela G; Bai, Xiaochen X; Plückthun, Andreas A; Jänne, Pasi A PA; Westover, Kenneth D KD; Shan, Yibing Y; Shaw, David E DE

Publication Date: 2021-10

Variant appearance in text: KRAS: T35A

PubMed Link: 34625747

Variant Present in the following documents:

• Main text

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BET proteolysis targeted chimera-based therapy of novel models of Richter Transformation-diffuse large B-cell lymphoma.

Leukemia

Fiskus, Warren W; Mill, Christopher P CP; Perera, Dimuthu D; Birdwell, Christine C; Deng, Qing Q; Yang, Haopeng H; Lara, Bernardo H BH; Jain, Nitin N; Burger, Jan J; Ferrajoli, Alessandra A; Davis, John A JA; Saenz, Dyana T DT; Jin, Wendy W; Coarfa, Cristian C; Crews, Craig M CM; Green, Michael R MR; Khoury, Joseph D JD; Bhalla, Kapil N KN

Publication Date: 2021-09

Variant appearance in text: KRAS: T35A

PubMed Link: 33654205

Variant Present in the following documents:

• 41375_2021_1181_MOESM1_ESM.pdf

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Dynamically encoded reactivity of Ras enzymes: opening new frontiers for drug discovery.

Cancer Metastasis Reviews

Pálfy, Gyula G; Menyhárd, Dóra K DK; Perczel, András A

Publication Date: 2020-12

Variant appearance in text: K-Ras4B: Thr35Ala

PubMed Link: 32815102

Variant Present in the following documents:

• Main text
• 10555_2020_Article_9917.pdf

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Identification of relevant genetic alterations in cancer using topological data analysis.

Nature Communications

Rabadán, Raúl R; Mohamedi, Yamina Y; Rubin, Udi U; Chu, Tim T; Alghalith, Adam N AN; Elliott, Oliver O; Arnés, Luis L; Cal, Santiago S; Obaya, Álvaro J ÁJ; Levine, Arnold J AJ; Cámara, Pablo G PG

Publication Date: 2020-07-30

Variant appearance in text: KRAS: T35A

PubMed Link: 32732999

Variant Present in the following documents:

• 41467_2020_17659_MOESM3_ESM.xls, sheet 1

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Dissection of major cancer gene variants in subsets of circulating tumor cells in advanced breast cancer.

Scientific Reports

D'Oronzo, Stella S; Lovero, Domenica D; Palmirotta, Raffaele R; Stucci, Luigia Stefania LS; Tucci, Marco M; Felici, Claudia C; Cascardi, Eliano E; Giardina, Carmela C; Cafforio, Paola P; Silvestris, Franco F

Publication Date: 2019-11-21

Variant appearance in text: KRAS: 103A>G; T35A

PubMed Link: 31754145

Variant Present in the following documents:

• 41598_2019_Article_53660.pdf
• 41598_2019_53660_MOESM1_ESM.pdf

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Circulating Tumor DNA Sequencing Analysis of Gastroesophageal Adenocarcinoma.

Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research

Maron, Steven B SB; Chase, Leah M LM; Lomnicki, Samantha S; Kochanny, Sara S; Moore, Kelly L KL; Joshi, Smita S SS; Landron, Stacie S; Johnson, Julie J; Kiedrowski, Lesli A LA; Nagy, Rebecca J RJ; Lanman, Richard B RB; Kim, Seung Tae ST; Lee, Jeeyun J; Catenacci, Daniel V T DVT

Publication Date: 2019-12-01

Variant appearance in text: KRAS: T35A

PubMed Link: 31427281

Variant Present in the following documents:

• Main text

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Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.

Plos One

Prentice, Leah M LM; Miller, Ruth R RR; Knaggs, Jeff J; Mazloomian, Alborz A; Aguirre Hernandez, Rosalia R; Franchini, Patrick P; Parsa, Kourosh K; Tessier-Cloutier, Basile B; Lapuk, Anna A; Huntsman, David D; Schaeffer, David F DF; Sheffield, Brandon S BS

Publication Date: 2018

Variant appearance in text: KRAS: T35A

PubMed Link: 29698444

Variant Present in the following documents:

• pone.0196434.s001.xlsx, sheet 1
• pone.0196434.s001.xlsx, sheet 3
• pone.0196434.s001.xlsx, sheet 2

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Comprehensive genomic analysis of Oesophageal Squamous Cell Carcinoma reveals clinical relevance.

Scientific Reports

Du, Peina P; Huang, Peide P; Huang, Xuanlin X; Li, Xiangchun X; Feng, Zhimin Z; Li, Fengyu F; Liang, Shaoguang S; Song, Yongmei Y; Stenvang, Jan J; Brünner, Nils N; Yang, Huanming H; Ou, Yunwei Y; Gao, Qiang Q; Li, Lin L

Publication Date: 2017-11-10

Variant appearance in text: KRAS: 103A>G; T35A

PubMed Link: 29127303

Variant Present in the following documents:

• 41598_2017_14909_MOESM4_ESM.xlsx, sheet 1

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Genomic analyses reveal FAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma.

Gigascience

Cheng, Caixia C; Cui, Heyang H; Zhang, Ling L; Jia, Zhiwu Z; Song, Bin B; Wang, Fang F; Li, Yaoping Y; Liu, Jing J; Kong, Pengzhou P; Shi, Ruyi R; Bi, Yanghui Y; Yang, Bin B; Wang, Juan J; Zhao, Zhenxiang Z; Zhang, Yanyan Y; Hu, Xiaoling X; Yang, Jie J; He, Chanting C; Zhao, Zhiping Z; Wang, Jinfen J; Xi, Yanfeng Y; Xu, Enwei E; Li, Guodong G; Guo, Shiping S; Chen, Yunqing Y; Yang, Xiaofeng X; Chen, Xing X; Liang, Jianfang J; Guo, Jiansheng J; Cheng, Xiaolong X; Wang, Chuangui C; Zhan, Qimin Q; Cui, Yongping Y

Publication Date: 2016

Variant appearance in text: KRAS: 103A>G; T35A

PubMed Link: 26759717

Variant Present in the following documents:

• 13742_2015_107_MOESM11_ESM.xlsx, sheet 1

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Genomic analyses reveal mutational signatures and frequently altered genes in esophageal squamous cell carcinoma.

American Journal Of Human Genetics

Zhang, Ling L; Zhou, Yong Y; Cheng, Caixia C; Cui, Heyang H; Cheng, Le L; Kong, Pengzhou P; Wang, Jiaqian J; Li, Yin Y; Chen, Wenliang W; Song, Bin B; Wang, Fang F; Jia, Zhiwu Z; Li, Lin L; Li, Yaoping Y; Yang, Bin B; Liu, Jing J; Shi, Ruyi R; Bi, Yanghui Y; Zhang, Yanyan Y; Wang, Juan J; Zhao, Zhenxiang Z; Hu, Xiaoling X; Yang, Jie J; Li, Hongyi H; Gao, Zhibo Z; Chen, Gang G; Huang, Xuanlin X; Yang, Xukui X; Wan, Shengqing S; Chen, Chao C; Li, Bin B; Tan, Yongkai Y; Chen, Longyun L; He, Minghui M; Xie, Sha S; Li, Xiangchun X; Zhuang, Xuehan X; Wang, Mengyao M; Xia, Zhi Z; Luo, Longhai L; Ma, Jie J; Dong, Bing B; Zhao, Jiuzhou J; Song, Yongmei Y; Ou, Yunwei Y; Li, Enming E; Xu, Liyan L; Wang, Jinfen J; Xi, Yanfeng Y; Li, Guodong G; Xu, Enwei E; Liang, Jianfang J; Yang, Xiaofeng X; Guo, Jiansheng J; Chen, Xing X; Zhang, Yanbo Y; Li, Qingshan Q; Liu, Lixin L; Li, Yingrui Y; Zhang, Xiuqing X; Yang, Huanming H; Lin, Dongxin D; Cheng, Xiaolong X; Guo, Yongjun Y; Wang, Jun J; Zhan, Qimin Q; Cui, Yongping Y

Publication Date: 2015-04-02

Variant appearance in text: KRAS: 103A>G; T35A

PubMed Link: 25839328

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

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Ubiquitination of K-Ras enhances activation and facilitates binding to select downstream effectors.

Science Signaling

Sasaki, Atsuo T AT; Carracedo, Arkaitz A; Locasale, Jason W JW; Anastasiou, Dimitrios D; Takeuchi, Koh K; Kahoud, Emily Rose ER; Haviv, Sasson S; Asara, John M JM; Pandolfi, Pier Paolo PP; Cantley, Lewis C LC

Publication Date: 2011-03-08

Variant appearance in text: KRAS: T35A

PubMed Link: 21386094

Variant Present in the following documents:

• Main text

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