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: TLR4: L498V

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

View BVdb publication page

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Somatic mutation distribution across tumour cohorts provides a signal for positive selection in cancer.

Nature Communications

Boström, Martin M; Larsson, Erik E

Publication Date: 2022-11-17

Variant appearance in text: TLR4: L498V

PubMed Link: 36396655

Variant Present in the following documents:

• 41467_2022_34746_MOESM10_ESM.xlsx, sheet 1
• 41467_2022_34746_MOESM1_ESM.pdf

View BVdb publication page

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mTOR Signaling and SREBP Activity Increase FADS2 Expression and Can Activate Sapienate Biosynthesis.

Cell Reports

Triki, Mouna M; Rinaldi, Gianmarco G; Planque, Melanie M; Broekaert, Dorien D; Winkelkotte, Alina M AM; Maier, Carina R CR; Janaki Raman, Sudha S; Vandekeere, Anke A; Van Elsen, Joke J; Orth, Martin F MF; Grünewald, Thomas G P TGP; Schulze, Almut A; Fendt, Sarah-Maria SM

Publication Date: 2020-06-23

Variant appearance in text: TLR4: L498V

PubMed Link: 32579932

Variant Present in the following documents:

• mmc5.xlsx, sheet 3

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Multi-omics characterization of molecular features of gastric cancer correlated with response to neoadjuvant chemotherapy.

Science Advances

Li, Ziyu Z; Gao, Xiangyu X; Peng, Xinxin X; May Chen, Mei-Ju MJ; Li, Zhe Z; Wei, Bin B; Wen, Xianzi X; Wei, Baoye B; Dong, Yu Y; Bu, Zhaode Z; Wu, Aiwen A; Wu, Qi Q; Tang, Lei L; Li, Zhongwu Z; Liu, Yiqiang Y; Zhang, Li L; Jia, Shuqin S; Zhang, Lianhai L; Shan, Fei F; Zhang, Ji J; Wu, Xiaojiang X; Ji, Xin X; Ji, Ke K; Wu, Xiaolong X; Shi, Jinyao J; Xing, Xiaofang X; Wu, Jianmin J; Lv, Guoqing G; Shen, Lin L; Ji, Xuwo X; Liang, Han H; Ji, Jiafu J

Publication Date: 2020-02

Variant appearance in text: TLR4: L498V

PubMed Link: 32133402

Variant Present in the following documents:

• aay4211_Table_S2.xlsx, sheet 1

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Identification of targeted therapy options for gastric adenocarcinoma by comprehensive analysis of genomic data.

Gastric Cancer : Official Journal Of The International Gastric Cancer Association And The Japanese Gastric Cancer Association

Hescheler, Daniel A DA; Plum, Patrick S PS; Zander, Thomas T; Quaas, Alexander A; Korenkov, Michael M; Gassa, Asmae A; Michel, Maximilian M; Bruns, Christiane J CJ; Alakus, Hakan H

Publication Date: 2020-07

Variant appearance in text: TLR4: L498V

PubMed Link: 32107691

Variant Present in the following documents:

• 10120_2020_1045_MOESM1_ESM.xlsx, sheet 2

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Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes.

Communications Biology

Dong, Xiaobao X; Huang, Dandan D; Yi, Xianfu X; Zhang, Shijie S; Wang, Zhao Z; Yan, Bin B; Chung Sham, Pak P; Chen, Kexin K; Jun Li, Mulin M

Publication Date: 2020-01-07

Variant appearance in text: TLR4: L498V

PubMed Link: 31925297

Variant Present in the following documents:

• 42003_2019_736_MOESM13_ESM.xlsx, sheet 1

View BVdb publication page

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A large peptidome dataset improves HLA class I epitope prediction across most of the human population.

Nature Biotechnology

Sarkizova, Siranush S; Klaeger, Susan S; Le, Phuong M PM; Li, Letitia W LW; Oliveira, Giacomo G; Keshishian, Hasmik H; Hartigan, Christina R CR; Zhang, Wandi W; Braun, David A DA; Ligon, Keith L KL; Bachireddy, Pavan P; Zervantonakis, Ioannis K IK; Rosenbluth, Jennifer M JM; Ouspenskaia, Tamara T; Law, Travis T; Justesen, Sune S; Stevens, Jonathan J; Lane, William J WJ; Eisenhaure, Thomas T; Lan Zhang, Guang G; Clauser, Karl R KR; Hacohen, Nir N; Carr, Steven A SA; Wu, Catherine J CJ; Keskin, Derin B DB

Publication Date: 2020-02

Variant appearance in text: TLR4: L498V

PubMed Link: 31844290

Variant Present in the following documents:

• NIHMS1541512-supplement-Sup_Data2.xlsx, sheet 4

View BVdb publication page

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Systematic analysis of the intersection of disease mutations with protein modifications.

Bmc Medical Genomics

Simpson, Claire M CM; Zhang, Bin B; Hornbeck, Peter V PV; Gnad, Florian F

Publication Date: 2019-07-25

Variant appearance in text: TLR4: L498V

PubMed Link: 31345222

Variant Present in the following documents:

• 12920_2019_543_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas.

Npj Genomic Medicine

Madubata, Chioma J CJ; Roshan-Ghias, Alireza A; Chu, Timothy T; Resnick, Samuel S; Zhao, Junfei J; Arnes, Luis L; Wang, Jiguang J; Rabadan, Raul R

Publication Date: 2017

Variant appearance in text: TLR4: L498V

PubMed Link: 29263839

Variant Present in the following documents:

• 41525_2017_32_MOESM8_ESM.xlsx, sheet 7

View BVdb publication page

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Impact of mutations in Toll-like receptor pathway genes on esophageal carcinogenesis.

Plos Genetics

Fels Elliott, Daffolyn Rachael DR; Perner, Juliane J; Li, Xiaodun X; Symmons, Martyn F MF; Verstak, Brett B; Eldridge, Matthew M; Bower, Lawrence L; O'Donovan, Maria M; Gay, Nick J NJ; , ; Fitzgerald, Rebecca C RC

Publication Date: 2017-05

Variant appearance in text: TLR4: L498V

PubMed Link: 28531216

Variant Present in the following documents:

• Main text
• pgen.1006808.s001.xlsx, sheet 1
• pgen.1006808.pdf
• pgen.1006808.s007.xlsx, sheet 1

View BVdb publication page

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A Landscape of Pharmacogenomic Interactions in Cancer.

Cell

Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ

Publication Date: 2016-07-28

Variant appearance in text: TLR4: 1492T>G; L498V

PubMed Link: 27397505

Variant Present in the following documents:

• mmc3.xlsx, sheet 2

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Age-related mutations associated with clonal hematopoietic expansion and malignancies.

Nature Medicine

Xie, Mingchao M; Lu, Charles C; Wang, Jiayin J; McLellan, Michael D MD; Johnson, Kimberly J KJ; Wendl, Michael C MC; McMichael, Joshua F JF; Schmidt, Heather K HK; Yellapantula, Venkata V; Miller, Christopher A CA; Ozenberger, Bradley A BA; Welch, John S JS; Link, Daniel C DC; Walter, Matthew J MJ; Mardis, Elaine R ER; Dipersio, John F JF; Chen, Feng F; Wilson, Richard K RK; Ley, Timothy J TJ; Ding, Li L

Publication Date: 2014-12

Variant appearance in text: TLR4: L498V

PubMed Link: 25326804

Variant Present in the following documents:

• NIHMS630249-supplement-6.xlsx, sheet 1
• NIHMS630249-supplement-5.xlsx, sheet 1
• NIHMS630249-supplement-7.xlsx, sheet 1

View BVdb publication page

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