Publications:

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Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues.

Nature Communications

Abelin, Jennifer G JG; Bergstrom, Erik J EJ; Rivera, Keith D KD; Taylor, Hannah B HB; Klaeger, Susan S; Xu, Charles C; Verzani, Eva K EK; Jackson White, C C; Woldemichael, Hilina B HB; Virshup, Maya M; Olive, Meagan E ME; Maynard, Myranda M; Vartany, Stephanie A SA; Allen, Joseph D JD; Phulphagar, Kshiti K; Harry Kane, M M; Rachimi, Suzanna S; Mani, D R DR; Gillette, Michael A MA; Satpathy, Shankha S; Clauser, Karl R KR; Udeshi, Namrata D ND; Carr, Steven A SA

Publication Date: 2023-04-03

Variant appearance in text: p53: A86V

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

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CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.

Iscience

Zhou, Rong R; Tian, Kai K; Huang, Jie J; Duan, Wenjia W; Fu, Hongye H; Feng, Ying Y; Wang, Hui H; Jiang, Yongpeng Y; Li, Yuanjun Y; Wang, Rui R; Hu, Jiazhi J; Ma, Hanhui H; Qi, Zhi Z; Ji, Xiong X

Publication Date: 2022-09-16

Variant appearance in text: p53: 257C>T

PubMed Link: 36117989

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

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Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery.

Nature Communications

Havugimana, Pierre C PC; Goel, Raghuveera Kumar RK; Phanse, Sadhna S; Youssef, Ahmed A; Padhorny, Dzmitry D; Kotelnikov, Sergei S; Kozakov, Dima D; Emili, Andrew A

Publication Date: 2022-07-13

Variant appearance in text: TP53: A86V

PubMed Link: 35831314

Variant Present in the following documents:

• 41467_2022_31809_MOESM8_ESM.xlsx, sheet 3

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Clinical relevance of molecular characteristics in Burkitt lymphoma differs according to age.

Nature Communications

Burkhardt, Birgit B; Michgehl, Ulf U; Rohde, Jonas J; Erdmann, Tabea T; Berning, Philipp P; Reutter, Katrin K; Rohde, Marius M; Borkhardt, Arndt A; Burmeister, Thomas T; Dave, Sandeep S; Tzankov, Alexandar A; Dugas, Martin M; Sandmann, Sarah S; Fend, Falko F; Finger, Jasmin J; Mueller, Stephanie S; Gökbuget, Nicola N; Haferlach, Torsten T; Kern, Wolfgang W; Hartmann, Wolfgang W; Klapper, Wolfram W; Oschlies, Ilske I; Richter, Julia J; Kontny, Udo U; Lutz, Mathias M; Maecker-Kolhoff, Britta B; Ott, German G; Rosenwald, Andreas A; Siebert, Reiner R; von Stackelberg, Arend A; Strahm, Brigitte B; Woessmann, Wilhelm W; Zimmermann, Martin M; Zapukhlyak, Myroslav M; Grau, Michael M; Lenz, Georg G

Publication Date: 2022-07-06

Variant appearance in text: TP53: 257C>T

PubMed Link: 35794096

Variant Present in the following documents:

• 41467_2022_31355_MOESM5_ESM.xlsx, sheet 2

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Construction and validation of an immunoediting-based optimized neoantigen load (ioTNL) model to predict the response and prognosis of immune checkpoint therapy in various cancers.

Aging

Su, Xiaofan X; Jin, Haoxuan H; Wang, Jiaqian J; Lu, Huiping H; Gu, Tiantian T; Gao, Zhibo Z; Li, Manxiang M

Publication Date: 2022-05-25

Variant appearance in text: TP53: 257C>T

PubMed Link: 35613927

Variant Present in the following documents:

• aging-14-204101-s004.xlsx, sheet 1

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Proteogenomic characterization of 2002 human cancers reveals pan-cancer molecular subtypes and associated pathways.

Nature Communications

Zhang, Yiqun Y; Chen, Fengju F; Chandrashekar, Darshan S DS; Varambally, Sooryanarayana S; Creighton, Chad J CJ

Publication Date: 2022-05-13

Variant appearance in text: p53: A86V

PubMed Link: 35562349

Variant Present in the following documents:

• 41467_2022_30342_MOESM4_ESM.xlsx, sheet 1

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Genomic Correlates of Unfavorable Outcome in Locally Advanced Cervical Cancer Treated with Neoadjuvant Chemoradiation.

Cancer Research And Treatment

Wei, Yuchun Y; Wei, Chuqing C; Chen, Liang L; Liu, Ning N; Ou, Qiuxiang Q; Yin, Jiani C JC; Pang, Jiaohui J; Fang, Zhenhao Z; Wu, Xue X; Wang, Xiaonan X; Mu, Dianbin D; Shao, Yang Y; Yu, Jinming J; Yuan, Shuanghu S

Publication Date: 2022-10

Variant appearance in text: TP53: A86V

PubMed Link: 35038823

Variant Present in the following documents:

• crt-2021-963.pdf

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PD-L1 targeting and subclonal immune escape mediated by PD-L1 mutations in metastatic colorectal cancer.

Journal For Immunotherapy Of Cancer

Stein, Alexander A; Simnica, Donjete D; Schultheiß, Christoph C; Scholz, Rebekka R; Tintelnot, Joseph J; Gökkurt, Eray E; von Wenserski, Lisa L; Willscher, Edith E; Paschold, Lisa L; Sauer, Markus M; Lorenzen, Sylvie S; Riera-Knorrenschild, Jorge J; Depenbusch, Reinhard R; Ettrich, Thomas J TJ; Dörfel, Steffen S; Al-Batran, Salah-Eddin SE; Karthaus, Meinolf M; Pelzer, Uwe U; Waberer, Lisa L; Hinke, Axel A; Bauer, Marcus M; Massa, Chiara C; Seliger, Barbara B; Wickenhauser, Claudia C; Bokemeyer, Carsten C; Hegewisch-Becker, Susanna S; Binder, Mascha M

Publication Date: 2021-07

Variant appearance in text: TP53: 257C>T; Ala86Val

PubMed Link: 34315821

Variant Present in the following documents:

• jitc-2021-002844supp002.xlsx, sheet 1

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Circulating Tumor DNA Analyses Predict Disease Recurrence in Non-Muscle-Invasive Bladder Cancer.

Frontiers In Oncology

Zhang, Jinghua J; Dai, Daofeng D; Tian, Junqiang J; Li, Lifeng L; Bai, Jing J; Xu, Yaping Y; Wang, Zhiping Z; Tang, Aifa A

Publication Date: 2021

Variant appearance in text: TP53: 257C>T

PubMed Link: 33996580

Variant Present in the following documents:

• Table_1.xlsx, sheet 1
• Table_2.xlsx, sheet 1

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Significance of gene mutations in the Wnt signaling pathway in traditional serrated adenomas of the colon and rectum.

Plos One

Nakanishi, Hiroyoshi H; Sawada, Takeshi T; Kaizaki, Yasuharu Y; Ota, Ryosuke R; Suzuki, Hiromu H; Yamamoto, Eiichiro E; Aoki, Hironori H; Eizuka, Makoto M; Hasatani, Kenkei K; Takahashi, Naoki N; Inagaki, Satoko S; Ebi, Masahide M; Kato, Hiroyuki H; Kubota, Eiji E; Kataoka, Hiromi H; Takahashi, Satoru S; Tokino, Takashi T; Minamoto, Toshinari T; Sugai, Tamotsu T; Sasaki, Yasushi Y

Publication Date: 2020

Variant appearance in text: TP53: Ala86Val

PubMed Link: 32092099

Variant Present in the following documents:

• pone.0229262.s007.xlsx, sheet 1

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Decoding Somatic Driver Gene Mutations and Affected Signaling Pathways in Human Medulloblastoma Subgroups.

Journal Of Cancer

Robbins, Charles J CJ; Bou-Dargham, Mayassa J MJ; Sanchez, Kevin K; Rosen, Matthew C MC; Sang, Qing-Xiang Amy QA

Publication Date: 2018

Variant appearance in text: TP53: 257C>T

PubMed Link: 30588243

Variant Present in the following documents:

• jcav09p4596s2.xlsx, sheet 1

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Pan-urologic cancer genomic subtypes that transcend tissue of origin.

Nature Communications

Chen, Fengju F; Zhang, Yiqun Y; Bossé, Dominick D; Lalani, Aly-Khan A AA; Hakimi, A Ari AA; Hsieh, James J JJ; Choueiri, Toni K TK; Gibbons, Don L DL; Ittmann, Michael M; Creighton, Chad J CJ

Publication Date: 2017-08-04

Variant appearance in text: TP53: A86V

PubMed Link: 28775315

Variant Present in the following documents:

• 41467_2017_289_MOESM7_ESM.xlsx, sheet 1

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iFish: predicting the pathogenicity of human nonsynonymous variants using gene-specific/family-specific attributes and classifiers.

Scientific Reports

Wang, Meng M; Wei, Liping L

Publication Date: 2016-08-16

Variant appearance in text: TP53: A86V

PubMed Link: 27527004

Variant Present in the following documents:

• srep31321-s5.xls, sheet 1

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Genetic alterations of triple negative breast cancer by targeted next-generation sequencing and correlation with tumor morphology.

Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc

Weisman, Paul S PS; Ng, Charlotte K Y CK; Brogi, Edi E; Eisenberg, Rachel E RE; Won, Helen H HH; Piscuoglio, Salvatore S; De Filippo, Maria R MR; Ioris, Rafael R; Akram, Muzaffar M; Norton, Larry L; Weigelt, Britta B; Berger, Michael F MF; Reis-Filho, Jorge S JS; Wen, Hannah Y HY

Publication Date: 2016-05

Variant appearance in text: TP53: A86V

PubMed Link: 26939876

Variant Present in the following documents:

• NIHMS752475-supplement-3.xlsx, sheet 1

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GESPA: classifying nsSNPs to predict disease association.

Bmc Bioinformatics

Khurana, Jay K JK; Reeder, Jay E JE; Shrimpton, Antony E AE; Thakar, Juilee J

Publication Date: 2015-07-25

Variant appearance in text: TP53: A86V

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 1

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

Variant appearance in text: TP53: A86V

PubMed Link: 25348012

Variant Present in the following documents:

• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

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Codon 104 variation of p53 gene provides adaptive apoptotic responses to extreme environments in mammals of the Tibet plateau.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Zhao, Yang Y; Ren, Ji-Long JL; Wang, Ming-Yang MY; Zhang, Sheng-Ting ST; Liu, Yu Y; Li, Min M; Cao, Yi-Bin YB; Zu, Hu-Yue HY; Chen, Xiao-Cheng XC; Wu, Chung-I CI; Nevo, Eviatar E; Chen, Xue-Qun XQ; Du, Ji-Zeng JZ

Publication Date: 2013-12-17

Variant appearance in text: p53: A86V

PubMed Link: 24297887

Variant Present in the following documents:

• Main text

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Predicting the functional impact of protein mutations: application to cancer genomics.

Nucleic Acids Research

Reva, Boris B; Antipin, Yevgeniy Y; Sander, Chris C

Publication Date: 2011-09-01

Variant appearance in text: TP53: A86V

PubMed Link: 21727090

Variant Present in the following documents:

• supp_gkr407_Supplement2_Table_SM1_COSMIC_mutations.xls, sheet 1

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