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: CACNA1A: G1104S

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 3

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Comprehensive proteogenomic characterization of early duodenal cancer reveals the carcinogenesis tracks of different subtypes.

Nature Communications

Li, Lingling L; Jiang, Dongxian D; Liu, Hui H; Guo, Chunmei C; Zhao, Rui R; Zhang, Qiao Q; Xu, Chen C; Qin, Zhaoyu Z; Feng, Jinwen J; Liu, Yang Y; Wang, Haixing H; Chen, Weijie W; Zhang, Xue X; Li, Bin B; Bai, Lin L; Tian, Sha S; Tan, Subei S; Yu, Zixiang Z; Chen, Lingli L; Huang, Jie J; Zhao, Jian-Yuan JY; Hou, Yingyong Y; Ding, Chen C

Publication Date: 2023-03-29

Variant appearance in text: rs16027

PubMed Link: 36991000

Variant Present in the following documents:

• 41467_2023_37221_MOESM5_ESM.xlsx, sheet 3

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Integrative proteogenomic characterization of early esophageal cancer.

Nature Communications

Li, Lingling L; Jiang, Dongxian D; Zhang, Qiao Q; Liu, Hui H; Xu, Fujiang F; Guo, Chunmei C; Qin, Zhaoyu Z; Wang, Haixing H; Feng, Jinwen J; Liu, Yang Y; Chen, Weijie W; Zhang, Xue X; Bai, Lin L; Tian, Sha S; Tan, Subei S; Xu, Chen C; Song, Qi Q; Liu, Yalan Y; Zhong, Yunshi Y; Chen, Tianyin T; Zhou, Pinghong P; Zhao, Jian-Yuan JY; Hou, Yingyong Y; Ding, Chen C

Publication Date: 2023-03-25

Variant appearance in text: rs16027

PubMed Link: 36966136

Variant Present in the following documents:

• 41467_2023_37440_MOESM4_ESM.xlsx, sheet 2

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Whole Exome Sequencing of Hemiplegic Migraine Patients Shows an Increased Burden of Missense Variants in CACNA1H and CACNA1I Genes.

Molecular Neurobiology

Maksemous, Neven N; Harder, Aster V E AVE; Ibrahim, Omar O; Vijfhuizen, Lisanne S LS; Sutherland, Heidi H; Pelzer, Nadine N; de Boer, Irene I; Terwindt, Gisela M GM; Lea, Rodney A RA; van den Maagdenberg, Arn M J M AMJM; Griffiths, Lyn R LR

Publication Date: 2023-02-14

Variant appearance in text: rs16027

PubMed Link: 36786913

Variant Present in the following documents:

• 12035_2023_3255_MOESM1_ESM.xlsx, sheet 1

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Genomic, transcriptomic, and metabolomic profiles of hiPSC-derived dopamine neurons from clinically discordant brothers with identical PRKN deletions.

Npj Parkinson'S Disease

Cukier, Holly N HN; Kim, Hyunjin H; Griswold, Anthony J AJ; Codreanu, Simona G SG; Prince, Lisa M LM; Sherrod, Stacy D SD; McLean, John A JA; Dykxhoorn, Derek M DM; Ess, Kevin C KC; Hedera, Peter P; Bowman, Aaron B AB; Neely, M Diana MD

Publication Date: 2022-06-29

Variant appearance in text: rs16027

PubMed Link: 35768426

Variant Present in the following documents:

• 41531_2022_346_MOESM2_ESM.xlsx, sheet 1

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Integrated DNA and RNA Sequencing Reveals Drivers of Endocrine Resistance in Estrogen Receptor-Positive Breast Cancer.

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

Xia, Youli Y; He, Xiaping X; Renshaw, Lorna L; Martinez-Perez, Carlos C; Kay, Charlene C; Gray, Mark M; Meehan, James J; Parker, Joel S JS; Perou, Charles M CM; Carey, Lisa A LA; Dixon, J Michael JM; Turnbull, Arran A

Publication Date: 2022-08-15

Variant appearance in text: rs16027

PubMed Link: 35653148

Variant Present in the following documents:

• ccr-21-3189_supplementary_tables_ts1-9_suppts1-9.xlsx, sheet 5

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A stop-gain mutation in GXYLT1 promotes metastasis of colorectal cancer via the MAPK pathway.

Cell Death & Disease

Peng, Lin L; Zhao, Min M; Liu, Tianqi T; Chen, Jiangbo J; Gao, Pin P; Chen, Lei L; Xing, Pu P; Wang, Zaozao Z; Di, Jiabo J; Xu, Qiang Q; Qu, Hong H; Jiang, Beihai B; Su, Xiangqian X

Publication Date: 2022-04-22

Variant appearance in text: CACNA1A: G1104S

PubMed Link: 35459861

Variant Present in the following documents:

• 41419_2022_4844_MOESM4_ESM.xlsx, sheet 3

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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: CACNA1A: G1104S

PubMed Link: 31900393

Variant Present in the following documents:

• 41467_2019_13771_MOESM5_ESM.xlsx, sheet 1

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PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations.

Genome Biology

Zhang, Chao C; Gao, Yang Y; Ning, Zhilin Z; Lu, Yan Y; Zhang, Xiaoxi X; Liu, Jiaojiao J; Xie, Bo B; Xue, Zhe Z; Wang, Xiaoji X; Yuan, Kai K; Ge, Xueling X; Pan, Yuwen Y; Liu, Chang C; Tian, Lei L; Wang, Yuchen Y; Lu, Dongsheng D; Hoh, Boon-Peng BP; Xu, Shuhua S

Publication Date: 2019-10-22

Variant appearance in text: rs16027

PubMed Link: 31640808

Variant Present in the following documents:

• 13059_2019_1838_MOESM3_ESM.xlsx, sheet 1

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Distinctive mutational spectrum and karyotype disruption in long-term cisplatin-treated urothelial carcinoma cell lines.

Scientific Reports

Skowron, Margaretha A MA; Petzsch, Patrick P; Hardt, Karin K; Wagner, Nicholas N; Beier, Manfred M; Stepanow, Stefanie S; Drechsler, Matthias M; Rieder, Harald H; Köhrer, Karl K; Niegisch, Günter G; Hoffmann, Michèle J MJ; Schulz, Wolfgang A WA

Publication Date: 2019-10-09

Variant appearance in text: CACNA1A: G1104S; rs16027

PubMed Link: 31597922

Variant Present in the following documents:

• 41598_2019_50891_MOESM2_ESM.xlsx, sheet 1

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Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

Cell Reports

Vigilante, Alessandra A; Laddach, Anna A; Moens, Nathalie N; Meleckyte, Ruta R; Leha, Andreas A; Ghahramani, Arsham A; Culley, Oliver J OJ; Kathuria, Annie A; Hurling, Chloe C; Vickers, Alice A; Wiseman, Erika E; Tewary, Mukul M; Zandstra, Peter W PW; , ; Durbin, Richard R; Fraternali, Franca F; Stegle, Oliver O; Birney, Ewan E; Luscombe, Nicholas M NM; Danovi, Davide D; Watt, Fiona M FM

Publication Date: 2019-02-19

Variant appearance in text: CACNA1A: G1104S

PubMed Link: 30784590

Variant Present in the following documents:

• mmc6.xlsx, sheet 1

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X-linked ADGRG2 mutation and obstructive azoospermia in a large Pakistani family.

Scientific Reports

Khan, Muhammad Jaseem MJ; Pollock, Nijole N; Jiang, Huaiyang H; Castro, Carlos C; Nazli, Rubina R; Ahmed, Jawad J; Basit, Sulman S; Rajkovic, Aleksandar A; Yatsenko, Alexander N AN

Publication Date: 2018-11-02

Variant appearance in text: CACNA1A: G1104S; rs16027

PubMed Link: 30389958

Variant Present in the following documents:

• 41598_2018_34262_MOESM2_ESM.xlsx, sheet 2

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A high-throughput sequence analysis of Japanese patients revealed 11 candidate genes associated with type 1 autoimmune pancreatitis susceptibility.

Biochemistry And Biophysics Reports

Fujibayashi, Shugo S; Sasajima, Junpei J; Goto, Takuma T; Tanaka, Hiroki H; Kawabata, Hidemasa H; Fujii, Tsuneshi T; Nakamura, Kazumasa K; Chiba, Atsushi A; Yanagawa, Nobuyuki N; Moriichi, Kentaro K; Fujiya, Mikihiro M; Kohgo, Yutaka Y

Publication Date: 2016-07

Variant appearance in text: rs16027

PubMed Link: 28955865

Variant Present in the following documents:

• Main text
• main.pdf

View BVdb publication page

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Reproducible Analysis of Post-Translational Modifications in Proteomes--Application to Human Mutations.

Plos One

Holehouse, Alex S AS; Naegle, Kristen M KM

Publication Date: 2015

Variant appearance in text: rs16027

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

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Dependable and Efficient Clinical Molecular Diagnosis of Chinese RP Patient with Targeted Exon Sequencing.

Plos One

Yang, Liping L; Cui, Hui H; Yin, Xiaobei X; Dou, Hongliang H; Zhao, Lin L; Chen, Ningning N; Zhang, Jinlu J; Zhang, Huirong H; Li, Genlin G; Ma, Zhizhong Z

Publication Date: 2015

Variant appearance in text: CACNA1A: 3310G>A; G1104S; rs16027

PubMed Link: 26496393

Variant Present in the following documents:

• pone.0140684.s004.xlsx, sheet 4
• pone.0140684.s004.xlsx, sheet 5
• pone.0140684.s004.xlsx, sheet 2

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Population genomic analysis of 962 whole genome sequences of humans reveals natural selection in non-coding regions.

Plos One

Yu, Fuli F; Lu, Jian J; Liu, Xiaoming X; Gazave, Elodie E; Chang, Diana D; Raj, Srilakshmi S; Hunter-Zinck, Haley H; Blekhman, Ran R; Arbiza, Leonardo L; Van Hout, Cris C; Morrison, Alanna A; Johnson, Andrew D AD; Bis, Joshua J; Cupples, L Adrienne LA; Psaty, Bruce M BM; Muzny, Donna D; Yu, Jin J; Gibbs, Richard A RA; Keinan, Alon A; Clark, Andrew G AG; Boerwinkle, Eric E

Publication Date: 2015

Variant appearance in text: rs16027

PubMed Link: 25807536

Variant Present in the following documents:

• pone.0121644.s002.xls, sheet 1

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Exome sequencing of case-unaffected-parents trios reveals recessive and de novo genetic variants in sporadic ALS.

Scientific Reports

Steinberg, Karyn Meltz KM; Yu, Bing B; Koboldt, Daniel C DC; Mardis, Elaine R ER; Pamphlett, Roger R

Publication Date: 2015-03-16

Variant appearance in text: CACNA1A: G1104S; rs16027

PubMed Link: 25773295

Variant Present in the following documents:

• srep09124-s2.xls, sheet 1

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Whole-genome sequencing of the world's oldest people.

Plos One

Gierman, Hinco J HJ; Fortney, Kristen K; Roach, Jared C JC; Coles, Natalie S NS; Li, Hong H; Glusman, Gustavo G; Markov, Glenn J GJ; Smith, Justin D JD; Hood, Leroy L; Coles, L Stephen LS; Kim, Stuart K SK

Publication Date: 2014

Variant appearance in text: CACNA1A: G1104S; rs16027

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

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Association of single nucleotide polymorphisms of CACNA1A gene in migraine.

Indian Journal Of Human Genetics

Bashir, Aadil A; Saleem, Shiekh S; Wani, Maqbool M; Rasool, Roohi R; Wani, Irfan Yousuf IY; Gulnar, Azhara A; Verma, Sawan S

Publication Date: 2014-01

Variant appearance in text: rs16027

PubMed Link: 24959015

Variant Present in the following documents:

• Main text

View BVdb publication page

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Integrating EMR-linked and in vivo functional genetic data to identify new genotype-phenotype associations.

Plos One

Mosley, Jonathan D JD; Van Driest, Sara L SL; Weeke, Peter E PE; Delaney, Jessica T JT; Wells, Quinn S QS; Bastarache, Lisa L; Roden, Dan M DM; Denny, Josh C JC

Publication Date: 2014

Variant appearance in text: rs16027

PubMed Link: 24949630

Variant Present in the following documents:

• Main text
• pone.0100322.pdf

View BVdb publication page

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Gamma-aminobutyric acid system genes--no evidence for a role in alcohol use and abuse in a community-based sample.

Alcoholism, Clinical And Experimental Research

Irons, Daniel E DE; Iacono, William G WG; Oetting, William S WS; Kirkpatrick, Robert M RM; Vrieze, Scott I SI; Miller, Michael B MB; McGue, Matt M

Publication Date: 2014-04

Variant appearance in text: rs16027

PubMed Link: 24460875

Variant Present in the following documents:

• Main text

View BVdb publication page

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Genetic and functional characterisation of the P/Q calcium channel in episodic ataxia with epilepsy.

The Journal Of Physiology

Rajakulendran, Sanjeev S; Graves, Tracey D TD; Labrum, Robyn W RW; Kotzadimitriou, Dimitrios D; Eunson, Louise L; Davis, Mary B MB; Davies, Rosalyn R; Wood, Nicholas W NW; Kullmann, Dimitri M DM; Hanna, Michael G MG; Schorge, Stephanie S

Publication Date: 2010-06-01

Variant appearance in text: rs16027

PubMed Link: 20156848

Variant Present in the following documents:

• Main text

View BVdb publication page

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Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases.

Nucleic Acids Research

Ryu, Gil-Mi GM; Song, Pamela P; Kim, Kyu-Won KW; Oh, Kyung-Soo KS; Park, Keun-Joon KJ; Kim, Jong Hun JH

Publication Date: 2009-03

Variant appearance in text: rs16027

PubMed Link: 19139070

Variant Present in the following documents:

• gkn1008_nar-01723-s-2008-File011.xls, sheet 2
• gkn1008_nar-01723-s-2008-File009.xls, sheet 2

View BVdb publication page

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