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: HSPG2: V1967I

PubMed Link: 37012232

Variant Present in the following documents:

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

View BVdb publication page

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SMAP is a pipeline for sample matching in proteogenomics.

Nature Communications

Li, Ling L; Niu, Mingming M; Erickson, Alyssa A; Luo, Jie J; Rowbotham, Kincaid K; Guo, Kai K; Huang, He H; Li, Yuxin Y; Jiang, Yi Y; Hur, Junguk J; Liu, Chunyu C; Peng, Junmin J; Wang, Xusheng X

Publication Date: 2022-02-08

Variant appearance in text: HSPG2: V1967I

PubMed Link: 35136070

Variant Present in the following documents:

• 41467_2022_28411_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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Cancer neoantigen prioritization through sensitive and reliable proteogenomics analysis.

Nature Communications

Wen, Bo B; Li, Kai K; Zhang, Yun Y; Zhang, Bing B

Publication Date: 2020-04-09

Variant appearance in text: HSPG2: V1967I

PubMed Link: 32273506

Variant Present in the following documents:

• 41467_2020_15456_MOESM6_ESM.xlsx, sheet 1
• 41467_2020_15456_MOESM5_ESM.xlsx, sheet 1
• 41467_2020_15456_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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A reference collection of patient-derived cell line and xenograft models of proneural, classical and mesenchymal glioblastoma.

Scientific Reports

Stringer, Brett W BW; Day, Bryan W BW; D'Souza, Rochelle C J RCJ; Jamieson, Paul R PR; Ensbey, Kathleen S KS; Bruce, Zara C ZC; Lim, Yi Chieh YC; Goasdoué, Kate K; Offenhäuser, Carolin C; Akgül, Seçkin S; Allan, Suzanne S; Robertson, Thomas T; Lucas, Peter P; Tollesson, Gert G; Campbell, Scott S; Winter, Craig C; Do, Hongdo H; Dobrovic, Alexander A; Inglis, Po-Ling PL; Jeffree, Rosalind L RL; Johns, Terrance G TG; Boyd, Andrew W AW

Publication Date: 2019-03-20

Variant appearance in text: HSPG2: V1967I; rs2229475

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 10
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 7
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 8

View BVdb publication page

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Proteogenomics connects somatic mutations to signalling in breast cancer.

Nature

Mertins, Philipp P; Mani, D R DR; Ruggles, Kelly V KV; Gillette, Michael A MA; Clauser, Karl R KR; Wang, Pei P; Wang, Xianlong X; Qiao, Jana W JW; Cao, Song S; Petralia, Francesca F; Kawaler, Emily E; Mundt, Filip F; Krug, Karsten K; Tu, Zhidong Z; Lei, Jonathan T JT; Gatza, Michael L ML; Wilkerson, Matthew M; Perou, Charles M CM; Yellapantula, Venkata V; Huang, Kuan-lin KL; Lin, Chenwei C; McLellan, Michael D MD; Yan, Ping P; Davies, Sherri R SR; Townsend, R Reid RR; Skates, Steven J SJ; Wang, Jing J; Zhang, Bing B; Kinsinger, Christopher R CR; Mesri, Mehdi M; Rodriguez, Henry H; Ding, Li L; Paulovich, Amanda G AG; Fenyö, David D; Ellis, Matthew J MJ; Carr, Steven A SA; ,

Publication Date: 2016-06-02

Variant appearance in text: HSPG2: V1967I; rs2229475

PubMed Link: 27251275

Variant Present in the following documents:

• NIHMS778057-supplement-supp_table5.xlsx, sheet 2

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: rs2229475

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

View BVdb publication page

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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: HSPG2: V1967I

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 3

View BVdb publication page

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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: HSPG2: V1967I; rs2229475

PubMed Link: 25773295

Variant Present in the following documents:

• srep09124-s3.xls, sheet 1

View BVdb publication page

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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: HSPG2: V1967I; rs2229475

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

View BVdb publication page

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The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.

Nucleic Acids Research

Tang, Xiaojia X; Baheti, Saurabh S; Shameer, Khader K; Thompson, Kevin J KJ; Wills, Quin Q; Niu, Nifang N; Holcomb, Ilona N IN; Boutet, Stephane C SC; Ramakrishnan, Ramesh R; Kachergus, Jennifer M JM; Kocher, Jean-Pierre A JP; Weinshilboum, Richard M RM; Wang, Liewei L; Thompson, E Aubrey EA; Kalari, Krishna R KR

Publication Date: 2014-12-16

Variant appearance in text: HSPG2: V1967I; rs2229475

PubMed Link: 25352556

Variant Present in the following documents:

• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 22
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 13
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 14
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 11

View BVdb publication page

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NCI-60 whole exome sequencing and pharmacological CellMiner analyses.

Plos One

Reinhold, William C WC; Varma, Sudhir S; Sousa, Fabricio F; Sunshine, Margot M; Abaan, Ogan D OD; Davis, Sean R SR; Reinhold, Spencer W SW; Kohn, Kurt W KW; Morris, Joel J; Meltzer, Paul S PS; Doroshow, James H JH; Pommier, Yves Y

Publication Date: 2014

Variant appearance in text: HSPG2: V1967I; rs2229475

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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Association of the HSPG2 gene with neuroleptic-induced tardive dyskinesia.

Neuropsychopharmacology : Official Publication Of The American College Of Neuropsychopharmacology

Syu, Aoi A; Ishiguro, Hiroki H; Inada, Toshiya T; Horiuchi, Yasue Y; Tanaka, Syunsuke S; Ishikawa, Maya M; Arai, Makoto M; Itokawa, Masanari M; Niizato, Kazuhiro K; Iritani, Shuji S; Ozaki, Norio N; Takahashi, Makoto M; Kakita, Akiyoshi A; Takahashi, Hitoshi H; Nawa, Hiroyuki H; Keino-Masu, Kazuko K; Arikawa-Hirasawa, Eri E; Arinami, Tadao T

Publication Date: 2010-04

Variant appearance in text: rs2229475

PubMed Link: 20072119

Variant Present in the following documents:

• Main text

View BVdb publication page

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