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: PABPC1: P414S

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 3
• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 2

View BVdb publication page

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A Phase II Trial of Guadecitabine plus Atezolizumab in Metastatic Urothelial Carcinoma Progressing after Initial Immune Checkpoint Inhibitor Therapy.

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

Jang, H Josh HJ; Hostetter, Galen G; MacFarlane, Alexander W AW; Madaj, Zachary Z; Ross, Eric A EA; Hinoue, Toshinori T; Kulchycki, Justin R JR; Burgos, Ryan S RS; Tafseer, Mahvish M; Alpaugh, R Katherine RK; Schwebel, Candice L CL; Kokate, Rutika R; Geynisman, Daniel M DM; Zibelman, Matthew R MR; Ghatalia, Pooja P; Nichols, Peter W PW; Chung, Woonbok W; Madzo, Jozef J; Hahn, Noah M NM; Quinn, David I DI; Issa, Jean-Pierre J JJ; Topper, Michael J MJ; Baylin, Stephen B SB; Shen, Hui H; Campbell, Kerry S KS; Jones, Peter A PA; Plimack, Elizabeth R ER

Publication Date: 2023-03-16

Variant appearance in text: PABPC1: P414S

PubMed Link: 36928921

Variant Present in the following documents:

• ccr-22-3642_supplementary_tables_1_suppts1.xlsx, sheet 3

View BVdb publication page

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Integrative proteomic characterization of adenocarcinoma of esophagogastric junction.

Nature Communications

Li, Shengli S; Yuan, Li L; Xu, Zhi-Yuan ZY; Xu, Jing-Li JL; Chen, Gui-Ping GP; Guan, Xiaoqing X; Pan, Guang-Zhao GZ; Hu, Can C; Dong, Jinyun J; Du, Yi-An YA; Yang, Li-Tao LT; Ni, Mao-Wei MW; Jiang, Rui-Bin RB; Zhu, Xiu X; Lv, Hang H; Xu, Han-Dong HD; Zhang, Sheng-Jie SJ; Qin, Jiang-Jiang JJ; Cheng, Xiang-Dong XD

Publication Date: 2023-02-11

Variant appearance in text: PABPC1: 1240C>T; P414S; rs796192778

PubMed Link: 36774361

Variant Present in the following documents:

• 41467_2023_36462_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Genetic variants in African-American and Hispanic patients with breast cancer.

Oncology Letters

Dutta, Pranabananda P; Keung, Man Y MY; Wu, Yanyuan Y; Vadgama, Jaydutt V JV

Publication Date: 2023-02

Variant appearance in text: PABPC1: 1240C>T; P414S

PubMed Link: 36644153

Variant Present in the following documents:

• Supplementary_Data5.xlsx, sheet 2
• Supplementary_Data5.xlsx, sheet 1

View BVdb publication page

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Whole exome sequencing identified a novel POT1 variant as a candidate pathogenic allele underlying a Li-Fraumeni-like family.

Frontiers In Oncology

Li, Yuping Y; Xie, Yupeng Y; Wang, Di D; Xu, Hanyan H; Ye, Junru J; Yin, Jiani C JC; Chen, Junjie J; Yan, Junrong J; Ye, Bin B; Chen, Chengshui C

Publication Date: 2022

Variant appearance in text: PABPC1: 1240C>T; P414S

PubMed Link: 36387164

Variant Present in the following documents:

• Table_1.xlsx, sheet 1

View BVdb publication page

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Integrated proteogenomic characterization across major histological types of pituitary neuroendocrine tumors.

Cell Research

Zhang, Fan F; Zhang, Qilin Q; Zhu, Jiajun J; Yao, Boyuan B; Ma, Chi C; Qiao, Nidan N; He, Shiman S; Ye, Zhao Z; Wang, Yunzhi Y; Han, Rui R; Feng, Jinwen J; Wang, Yongfei Y; Qin, Zhaoyu Z; Ma, Zengyi Z; Li, Kai K; Zhang, Yichao Y; Tian, Sha S; Chen, Zhengyuan Z; Tan, Subei S; Wu, Yue Y; Ran, Peng P; Wang, Ye Y; Ding, Chen C; Zhao, Yao Y

Publication Date: 2022-12

Variant appearance in text: PABPC1: 1240C>T; P414S; rs796192778

PubMed Link: 36307579

Variant Present in the following documents:

• 41422_2022_736_MOESM10_ESM.xlsx, sheet 3

View BVdb publication page

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Whole-exome sequencing of epithelial ovarian carcinomas differing in resistance to platinum therapy.

Life Science Alliance

Hlaváč, Viktor V; Holý, Petr P; Václavíková, Radka R; Rob, Lukáš L; Hruda, Martin M; Mrhalová, Marcela M; Černaj, Petr P; Bouda, Jiří J; Souček, Pavel P

Publication Date: 2022-10-13

Variant appearance in text: PABPC1: Pro414Ser

PubMed Link: 36229065

Variant Present in the following documents:

• LSA-2022-01551_TableS16.xlsx, sheet 1

View BVdb publication page

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Tracking Clonal Evolution of Multiple Myeloma Using Targeted Next-Generation DNA Sequencing.

Biomedicines

Salomon-Perzyński, Aleksander A; Barankiewicz, Joanna J; Machnicki, Marcin M; Misiewicz-Krzemińska, Irena I; Pawlak, Michał M; Radomska, Sylwia S; Krzywdzińska, Agnieszka A; Bluszcz, Aleksandra A; Stawiński, Piotr P; Rydzanicz, Małgorzata M; Jakacka, Natalia N; Solarska, Iwona I; Borg, Katarzyna K; Spyra-Górny, Zofia Z; Szpila, Tomasz T; Puła, Bartosz B; Grosicki, Sebastian S; Stokłosa, Tomasz T; Płoski, Rafał R; Lech-Marańda, Ewa E; Jakubikova, Jana J; Jamroziak, Krzysztof K

Publication Date: 2022-07-12

Variant appearance in text: PABPC1: 1240C>T

PubMed Link: 35884979

Variant Present in the following documents:

• Main text
• biomedicines-10-01674.pdf

View BVdb publication page

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Mutations of MSH5 in nonobstructive azoospermia (NOA) and rescued via in vivo gene editing.

Signal Transduction And Targeted Therapy

Chen, Min M; Yao, Chencheng C; Qin, Yingying Y; Cui, Xiuhong X; Li, Peng P; Ji, Zhiyong Z; Lin, Limei L; Wu, Haowei H; Zhou, Zhi Z; Gui, Yaoting Y; Li, Zheng Z; Gao, Fei F

Publication Date: 2022-01-03

Variant appearance in text: PABPC1: 1240C>T; Pro414Ser; rs796192778

PubMed Link: 34980881

Variant Present in the following documents:

• 41392_2021_710_MOESM2_ESM.xlsx, sheet 2
• 41392_2021_710_MOESM2_ESM.xlsx, sheet 3

View BVdb publication page

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Mutations of MSH5 in nonobstructive azoospermia (NOA) and rescued via in vivo gene editing.

Signal Transduction And Targeted Therapy

Chen, Min M; Yao, Chencheng C; Qin, Yingying Y; Cui, Xiuhong X; Li, Peng P; Ji, Zhiyong Z; Lin, Limei L; Wu, Haowei H; Zhou, Zhi Z; Gui, Yaoting Y; Li, Zheng Z; Gao, Fei F

Publication Date: 2022-01-03

Variant appearance in text: PABPC1: 1240C>T; Pro414Ser; rs796192778

PubMed Link: 34980881

Variant Present in the following documents:

• 41392_2021_710_MOESM2_ESM.xlsx, sheet 3
• 41392_2021_710_MOESM2_ESM.xlsx, sheet 2

View BVdb publication page

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A renal cell carcinoma tumorgraft platform to advance precision medicine.

Cell Reports

Elias, Roy R; Tcheuyap, Vanina T VT; Kaushik, Akash K AK; Singla, Nirmish N; Gao, Ming M; Reig Torras, Oscar O; Christie, Alana A; Mulgaonkar, Aditi A; Woolford, Layton L; Stevens, Christina C; Kettimuthu, Kavitha Priya KP; Pavia-Jimenez, Andrea A; Boroughs, Lindsey K LK; Joyce, Allison A; Dakanali, Marianna M; Notgrass, Hollis H; Margulis, Vitaly V; Cadeddu, Jeffrey A JA; Pedrosa, Ivan I; Williams, Noelle S NS; Sun, Xiankai X; DeBerardinis, Ralph J RJ; Öz, Orhan K OK; Zhong, Hua H; Seshagiri, Somasekar S; Modrusan, Zora Z; Cantarel, Brandi L BL; Kapur, Payal P; Brugarolas, James J

Publication Date: 2021-11-23

Variant appearance in text: PABPC1: 1240C>T; P414S; rs796192778

PubMed Link: 34818533

Variant Present in the following documents:

• NIHMS1761779-supplement-Table_S8.xlsx, sheet 1

View BVdb publication page

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A renal cell carcinoma tumorgraft platform to advance precision medicine.

Cell Reports

Elias, Roy R; Tcheuyap, Vanina T VT; Kaushik, Akash K AK; Singla, Nirmish N; Gao, Ming M; Reig Torras, Oscar O; Christie, Alana A; Mulgaonkar, Aditi A; Woolford, Layton L; Stevens, Christina C; Kettimuthu, Kavitha Priya KP; Pavia-Jimenez, Andrea A; Boroughs, Lindsey K LK; Joyce, Allison A; Dakanali, Marianna M; Notgrass, Hollis H; Margulis, Vitaly V; Cadeddu, Jeffrey A JA; Pedrosa, Ivan I; Williams, Noelle S NS; Sun, Xiankai X; DeBerardinis, Ralph J RJ; Öz, Orhan K OK; Zhong, Hua H; Seshagiri, Somasekar S; Modrusan, Zora Z; Cantarel, Brandi L BL; Kapur, Payal P; Brugarolas, James J

Publication Date: 2021-11-23

Variant appearance in text: PABPC1: 1240C>T; P414S; rs796192778

PubMed Link: 34818533

Variant Present in the following documents:

• NIHMS1761779-supplement-Table_S8.xlsx, sheet 1

View BVdb publication page

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Natural and cryptic peptides dominate the immunopeptidome of atypical teratoid rhabdoid tumors.

Journal For Immunotherapy Of Cancer

Marcu, Ana A; Schlosser, Andreas A; Keupp, Anne A; Trautwein, Nico N; Johann, Pascal P; Wölfl, Matthias M; Lager, Johanna J; Monoranu, Camelia Maria CM; Walz, Juliane S JS; Henkel, Lisa M LM; Krauß, Jürgen J; Ebinger, Martin M; Schuhmann, Martin M; Thomale, Ulrich Wilhelm UW; Pietsch, Torsten T; Klinker, Erdwine E; Schlegel, Paul G PG; Oyen, Florian F; Reisner, Yair Y; Rammensee, Hans-Georg HG; Eyrich, Matthias M

Publication Date: 2021-10

Variant appearance in text: PABPC1: P414S

PubMed Link: 34599019

Variant Present in the following documents:

• jitc-2021-003404supp008.pdf

View BVdb publication page

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Sequencing of a central nervous system tumor demonstrates cancer transmission in an organ transplant.

Life Science Alliance

Gingras, Marie-Claude MC; Sabo, Aniko A; Cardenas, Maria M; Rana, Abbas A; Dhingra, Sadhna S; Meng, Qingchang Q; Hu, Jianhong J; Muzny, Donna M DM; Doddapaneni, Harshavardhan H; Perez, Lesette L; Korchina, Viktoriya V; Nessner, Caitlin C; Liu, Xiuping X; Chao, Hsu H; Goss, John J; Gibbs, Richard A RA

Publication Date: 2021-09

Variant appearance in text: PABPC1: P414S

PubMed Link: 34301805

Variant Present in the following documents:

• LSA-2020-00941_TableS4.xlsx, sheet 1

View BVdb publication page

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Identification of KRAS G12V associated clonal neoantigens and immune microenvironment in long-term survival of pancreatic adenocarcinoma.

Cancer Immunology, Immunotherapy : Cii

Wang, Chao C; Shi, Min M; Zhang, Lei L; Ji, Jun J; Xie, Ruyan R; Wu, Chao C; Guo, Xianchao X; Yang, Ying Y; Zhou, Wei W; Peng, Chenhong C; Zhang, Henghui H; Yuan, Fei F; Zhang, Jun J

Publication Date: 2021-07-13

Variant appearance in text: PABPC1: 1240C>T; P414S

PubMed Link: 34255132

Variant Present in the following documents:

• 262_2021_3012_MOESM1_ESM.xlsx, sheet 2

View BVdb publication page

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Identification of KRAS G12V associated clonal neoantigens and immune microenvironment in long-term survival of pancreatic adenocarcinoma.

Cancer Immunology, Immunotherapy : Cii

Wang, Chao C; Shi, Min M; Zhang, Lei L; Ji, Jun J; Xie, Ruyan R; Wu, Chao C; Guo, Xianchao X; Yang, Ying Y; Zhou, Wei W; Peng, Chenhong C; Zhang, Henghui H; Yuan, Fei F; Zhang, Jun J

Publication Date: 2022-02

Variant appearance in text: PABPC1: 1240C>T; P414S

PubMed Link: 34255132

Variant Present in the following documents:

• 262_2021_3012_MOESM1_ESM.xlsx, sheet 2

View BVdb publication page

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Dynamics of genomic and immune responses during primary immunotherapy resistance in mismatch repair-deficient tumors.

Cold Spring Harbor Molecular Case Studies

Takahashi, Nobuyuki N; Rajapakse, Vinodh N VN; Pongor, Lorinc L; Kumar, Suresh S; Tlemsani, Camille C; Erwin-Cohen, Rebecca R; Young, Howard A HA; Hewitt, Stephen S; Wei, Jun S JS; Khan, Javed J; Villarino, Alejandro V AV; Trepel, Jane B JB; Thomas, Anish A

Publication Date: 2020-10

Variant appearance in text: PABPC1: Pro414Ser

PubMed Link: 33028646

Variant Present in the following documents:

• supp_mcs.a005678_Supplemental_Tables_.xlsx, sheet 2

View BVdb publication page

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Identification of a nonsense mutation in TNNI3K associated with cardiac conduction disease.

Journal Of Clinical Laboratory Analysis

Liu, Jiang J; Liu, Da D; Li, Muzheng M; Wu, Keke K; Liu, Na N; Zhao, Chenyu C; Shi, Xiaoliu X; Liu, Qiming Q

Publication Date: 2020-09

Variant appearance in text: PABPC1: P414S

PubMed Link: 32529721

Variant Present in the following documents:

• JCLA-34-e23418-s003.xls, sheet 1

View BVdb publication page

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YAP1 mediates survival of ALK-rearranged lung cancer cells treated with alectinib via pro-apoptotic protein regulation.

Nature Communications

Tsuji, Takahiro T; Ozasa, Hiroaki H; Aoki, Wataru W; Aburaya, Shunsuke S; Yamamoto Funazo, Tomoko T; Furugaki, Koh K; Yoshimura, Yasushi Y; Yamazoe, Masatoshi M; Ajimizu, Hitomi H; Yasuda, Yuto Y; Nomizo, Takashi T; Yoshida, Hironori H; Sakamori, Yuichi Y; Wake, Hiroaki H; Ueda, Mitsuyoshi M; Kim, Young Hak YH; Hirai, Toyohiro T

Publication Date: 2020-01-03

Variant appearance in text: PABPC1: P414S

PubMed Link: 31900393

Variant Present in the following documents:

• 41467_2019_13771_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome.

Nature Communications

Davies, Helen R HR; Hodgson, Kirsty K; Schwalbe, Edward E; Coxhead, Jonathan J; Sinclair, Naomi N; Zou, Xueqing X; Cockell, Simon S; Husain, Akhtar A; Nik-Zainal, Serena S; Rajan, Neil N

Publication Date: 2019-10-17

Variant appearance in text: PABPC1: 1240C>T; P414S

PubMed Link: 31624251

Variant Present in the following documents:

• 41467_2019_12746_MOESM4_ESM.xlsx, sheet 4

View BVdb publication page

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Novel NOG (p.P42S) mutation causes proximal symphalangism in a four-generation Chinese family.

Bmc Medical Genetics

Sha, Yanwei Y; Ma, Ding D; Zhang, Ning N; Wei, Xiaoli X; Liu, Wensheng W; Wang, Xiong X

Publication Date: 2019-08-01

Variant appearance in text: PABPC1: P414S; rs796192778

PubMed Link: 31370824

Variant Present in the following documents:

• 12881_2019_864_MOESM2_ESM.xlsx, sheet 1

View BVdb publication page

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Establishment and genomic characterization of gingivobuccal carcinoma cell lines with smokeless tobacco associated genetic alterations and oncogenic PIK3CA mutation.

Scientific Reports

Pansare, Kshama K; Gardi, Nilesh N; Kamat, Sayee S; Dange, Prerana P; Previn, Rahul R; Gera, Poonam P; Kowtal, Pradnya P; Amin, Kishore K; Sarin, Rajiv R

Publication Date: 2019-06-04

Variant appearance in text: PABPC1: P414S; rs796192778

PubMed Link: 31164688

Variant Present in the following documents:

• 41598_2019_44143_MOESM2_ESM.xls, sheet 1

View BVdb publication page

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PRIMA-1MET-induced neuroblastoma cell death is modulated by p53 and mycn through glutathione level.

Journal Of Experimental & Clinical Cancer Research : Cr

Mlakar, Vid V; Jurkovic Mlakar, Simona S; Lesne, Laurence L; Marino, Denis D; Rathi, Komal S KS; Maris, John M JM; Ansari, Marc M; Gumy-Pause, Fabienne F

Publication Date: 2019-02-12

Variant appearance in text: PABPC1: P414S

PubMed Link: 30755224

Variant Present in the following documents:

• 13046_2019_1066_MOESM1_ESM.xlsx, sheet 8
• 13046_2019_1066_MOESM1_ESM.xlsx, sheet 5
• 13046_2019_1066_MOESM1_ESM.xlsx, sheet 7

View BVdb publication page

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Revisiting aneuploidy profile of surgically retrieved spermatozoa by whole exome sequencing molecular karyotype.

Plos One

Cheung, Stephanie S; Schlegel, Peter N PN; Rosenwaks, Zev Z; Palermo, Gianpiero D GD

Publication Date: 2019

Variant appearance in text: PABPC1: 1240C>T; Pro414Ser

PubMed Link: 30608972

Variant Present in the following documents:

• pone.0210079.s007.xlsx, sheet 19
• pone.0210079.s007.xlsx, sheet 18
• pone.0210079.s007.xlsx, sheet 21
• pone.0210079.s007.xlsx, sheet 4
• pone.0210079.s007.xlsx, sheet 20
• pone.0210079.s007.xlsx, sheet 22

View BVdb publication page

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Immunogenomic Landscape Contributes to Hyperprogressive Disease after Anti-PD-1 Immunotherapy for Cancer.

Iscience

Xiong, Donghai D; Wang, Yian Y; Singavi, Arun K AK; Mackinnon, Alexander C AC; George, Ben B; You, Ming M

Publication Date: 2018-11-30

Variant appearance in text: PABPC1: P414S

PubMed Link: 30439581

Variant Present in the following documents:

• mmc2.xlsx, sheet 4

View BVdb publication page

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Comparative analysis of primary versus relapse/refractory DLBCL identifies shifts in mutation spectrum.

Oncotarget

Greenawalt, Danielle M DM; Liang, Winnie S WS; Saif, Sakina S; Johnson, Justin J; Todorov, Petar P; Dulak, Austin A; Enriquez, Daniel D; Halperin, Rebecca R; Ahmed, Ambar A; Saveliev, Vladislav V; Carpten, John J; Craig, David D; Barrett, J Carl JC; Dougherty, Brian B; Zinda, Michael M; Fawell, Stephen S; Dry, Jonathan R JR; Byth, Kate K

Publication Date: 2017-11-21

Variant appearance in text: PABPC1: 1240C>T; P414S; rs796192778

PubMed Link: 29245897

Variant Present in the following documents:

• oncotarget-08-99237-s002.xlsx, sheet 1

View BVdb publication page

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Mutational heterogeneity in non-serous ovarian cancers.

Scientific Reports

Teer, Jamie K JK; Yoder, Sean S; Gjyshi, Anxhela A; Nicosia, Santo V SV; Zhang, Chaomei C; Monteiro, Alvaro N A ANA

Publication Date: 2017-08-29

Variant appearance in text: PABPC1: P414S

PubMed Link: 28852190

Variant Present in the following documents:

• 41598_2017_10432_MOESM2_ESM.xlsx, sheet 10

View BVdb publication page

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