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: SKIV2L: A1071V

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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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: SKIV2L: A1071V; rs449643

PubMed Link: 36991000

Variant Present in the following documents:

• 41467_2023_37221_MOESM5_ESM.xlsx, sheet 3

View BVdb publication page

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Circulating messenger RNA variants as a potential biomarker for surveillance of hepatocellular carcinoma.

Frontiers In Oncology

Block, Timothy T; Zezulinski, Daniel D; Kaplan, David E DE; Lu, Jingqiao J; Zanine, Samantha S; Zhan, Tingting T; Doria, Cataldo C; Sayeed, Aejaz A

Publication Date: 2022

Variant appearance in text: rs449643

PubMed Link: 36582804

Variant Present in the following documents:

• Table_6.xlsx, sheet 1

View BVdb publication page

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Establishment and characterization of a new mantle cell lymphoma cell line with a NOTCH2 mutation, Arbo.

Ejhaem

Safa, Firas F; Rasmussen, Terri T; Lobelle-Rich, Patricia P; Collier, Stephanie S; Milligan, Nicholas N; Schmeig, John J; Schmid, Janet J; Wiewiorowski, Carol C; Totaro, Denise D; Brown, Theresa C TC; Satyavarapu, Ishwarya I; Badoo, Melody M; Ungerleider, Nathan N; Flemington, Erik K EK; Safah, Hana H; Saba, Nakhle S NS

Publication Date: 2022-11

Variant appearance in text: rs449643

PubMed Link: 36467812

Variant Present in the following documents:

• JHA2-3-1326-s001.xlsx, sheet 1

View BVdb publication page

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Next-generation whole exome sequencing to delineate the genetic basis of primary congenital glaucoma.

Scientific Reports

Rauf, Bushra B; Khan, Shahid Y SY; Jiao, Xiaodong X; Irum, Bushra B; Ashfaq, Ramla R; Zehra, Mubashra M; Khan, Asma A AA; Naeem, Muhammad Asif MA; Shahzad, Mohsin M; Riazuddin, Sheikh S; Hejtmancik, J Fielding JF; Riazuddin, S Amer SA

Publication Date: 2022-10-14

Variant appearance in text: SKIV2L: A1071V

PubMed Link: 36241656

Variant Present in the following documents:

• 41598_2022_20939_MOESM12_ESM.xlsx, sheet 2
• 41598_2022_20939_MOESM13_ESM.xlsx, sheet 2
• 41598_2022_20939_MOESM9_ESM.xlsx, sheet 2

View BVdb publication page

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A genomic deletion encompassing CRYBB2-CRYBB2P1 is responsible for autosomal recessive congenital cataracts.

Human Genome Variation

Irum, Bushra B; Kabir, Firoz F; Shoshany, Nadav N; Khan, Shahid Y SY; Rauf, Bushra B; Naeem, Muhammad Asif MA; Qaiser, Tanveer A TA; Riazuddin, Sheikh S; Hejtmancik, J Fielding JF; Riazuddin, S Amer SA

Publication Date: 2022-09-08

Variant appearance in text: SKIV2L: A1071V

PubMed Link: 36075891

Variant Present in the following documents:

• 41439_2022_208_MOESM4_ESM.xlsx, sheet 2

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: SKIV2L: A1071V

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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Synergistic insights into human health from aptamer- and antibody-based proteomic profiling.

Nature Communications

Pietzner, Maik M; Wheeler, Eleanor E; Carrasco-Zanini, Julia J; Kerrison, Nicola D ND; Oerton, Erin E; Koprulu, Mine M; Luan, Jian'an J; Hingorani, Aroon D AD; Williams, Steve A SA; Wareham, Nicholas J NJ; Langenberg, Claudia C

Publication Date: 2021-11-24

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 34819519

Variant Present in the following documents:

• 41467_2021_27164_MOESM1_ESM.pdf

View BVdb publication page

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Synergistic insights into human health from aptamer- and antibody-based proteomic profiling.

Nature Communications

Pietzner, Maik M; Wheeler, Eleanor E; Carrasco-Zanini, Julia J; Kerrison, Nicola D ND; Oerton, Erin E; Koprulu, Mine M; Luan, Jian'an J; Hingorani, Aroon D AD; Williams, Steve A SA; Wareham, Nicholas J NJ; Langenberg, Claudia C

Publication Date: 2021-11-24

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 34819519

Variant Present in the following documents:

• 41467_2021_27164_MOESM1_ESM.pdf

View BVdb publication page

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Disseminated Talaromyces marneffei Infection in a Non-HIV Infant With a Homozygous Private Variant of RELB.

Frontiers In Cellular And Infection Microbiology

Ding, Xiaofang X; Huang, Han H; Zhong, Lili L; Chen, Min M; Peng, Fang F; Zhang, Bing B; Cui, Xinyu X; Yang, Xiu-An XA

Publication Date: 2021

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 33791233

Variant Present in the following documents:

• Table_2.xlsx, sheet 1

View BVdb publication page

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The Biological Significance of Multi-copy Regions and Their Impact on Variant Discovery.

Genomics, Proteomics & Bioinformatics

Sun, Jing J; Zhang, Yanfang Y; Wang, Minhui M; Guan, Qian Q; Yang, Xiujia X; Ou, Jin Xia JX; Yan, Mingchen M; Wang, Chengrui C; Zhang, Yan Y; Li, Zhi-Hao ZH; Lan, Chunhong C; Mao, Chen C; Zhou, Hong-Wei HW; Hao, Bingtao B; Zhang, Zhenhai Z

Publication Date: 2020-10

Variant appearance in text: SKIV2L: 3212C>T; Ala1071Val

PubMed Link: 32827758

Variant Present in the following documents:

• mmc12.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: SKIV2L: A1071V

PubMed Link: 32273506

Variant Present in the following documents:

• 41467_2020_15456_MOESM6_ESM.xlsx, sheet 1

View BVdb publication page

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The role of myoglobin in epithelial cancers: Insights from transcriptomics.

International Journal Of Molecular Medicine

Bicker, Anne A; Nauth, Theresa T; Gerst, Daniela D; Aboouf, Mostafa Ahmed MA; Fandrey, Joachim J; Kristiansen, Glen G; Gorr, Thomas Alexander TA; Hankeln, Thomas T

Publication Date: 2020-02

Variant appearance in text: SKIV2L: 3212C>T; Ala1071Val

PubMed Link: 31894249

Variant Present in the following documents:

• Supplementary_Data2.xlsx, sheet 8
• Supplementary_Data2.xlsx, sheet 2
• Supplementary_Data2.xlsx, sheet 3
• Supplementary_Data2.xlsx, sheet 4
• Supplementary_Data2.xlsx, sheet 7
• Supplementary_Data2.xlsx, sheet 1
• Supplementary_Data2.xlsx, sheet 6

View BVdb publication page

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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: SKIV2L: 3212C>T; Ala1071Val; rs449643

PubMed Link: 31640808

Variant Present in the following documents:

• 13059_2019_1838_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar.

Database : The Journal Of Biological Databases And Curation

Famiglietti, M L ML; Estreicher, A A; Breuza, L L; Poux, S S; Redaschi, N N; Xenarios, I I; Bridge, A A; ,

Publication Date: 2019-01-01

Variant appearance in text: SKIV2L: 3212C>T; Ala1071Val

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.xlsx, sheet 1

View BVdb publication page

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Fine-mapping of HLA class I and class II genes identified two independent novel variants associated with nasopharyngeal carcinoma susceptibility.

Cancer Medicine

Wang, Tong-Min TM; Zhou, Ting T; He, Yong-Qiao YQ; Xue, Wen-Qiong WQ; Zhang, Jiang-Bo JB; Zheng, Xiao-Hui XH; Li, Xi-Zhao XZ; Zhang, Shao-Dan SD; Zeng, Yi-Xin YX; Jia, Wei-Hua WH

Publication Date: 2018-12

Variant appearance in text: rs449643

PubMed Link: 30378292

Variant Present in the following documents:

• CAM4-7-6308-s006.xlsx, sheet 1

View BVdb publication page

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A likely pathogenic variant putatively affecting splicing of PIGA identified in a multiple congenital anomalies hypotonia-seizures syndrome 2 (MCAHS2) family pedigree via whole-exome sequencing.

Molecular Genetics & Genomic Medicine

Yang, Junli J; Wang, Qiong Q; Zhuo, Qingcui Q; Tian, Huiling H; Li, Wen W; Luo, Fang F; Zhang, Jinghui J; Bi, Dan D; Peng, Jing J; Zhou, Dong D; Xin, Huawei H

Publication Date: 2018-09

Variant appearance in text: SKIV2L: 3212C>T; A1071V; rs449643

PubMed Link: 29974678

Variant Present in the following documents:

• MGG3-6-739-s002.xlsx, sheet 6
• MGG3-6-739-s002.xlsx, sheet 2

View BVdb publication page

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Fine mapping genetic associations between the HLA region and extremely high intelligence.

Scientific Reports

Zabaneh, Delilah D; Krapohl, Eva E; Simpson, Michael A MA; Miller, Mike B MB; Iacono, William G WG; McGue, Matt M; Putallaz, Martha M; Lubinski, David D; Plomin, Robert R; Breen, Gerome G

Publication Date: 2017-01-24

Variant appearance in text: rs449643

PubMed Link: 28117369

Variant Present in the following documents:

• srep41182.pdf

View BVdb publication page

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Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model.

The Journal Of Pathology

Maguire, Sarah L SL; Peck, Barrie B; Wai, Patty T PT; Campbell, James J; Barker, Holly H; Gulati, Aditi A; Daley, Frances F; Vyse, Simon S; Huang, Paul P; Lord, Christopher J CJ; Farnie, Gillian G; Brennan, Keith K; Natrajan, Rachael R

Publication Date: 2016-11

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 27512948

Variant Present in the following documents:

• PATH-240-315-s015.xlsx, sheet 1

View BVdb publication page

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Impact of polymorphisms in microRNA biogenesis genes on colon cancer risk and microRNA expression levels: a population-based, case-control study.

Bmc Medical Genomics

Mullany, Lila E LE; Herrick, Jennifer S JS; Wolff, Roger K RK; Buas, Matthew F MF; Slattery, Martha L ML

Publication Date: 2016-04-23

Variant appearance in text: rs449643

PubMed Link: 27107574

Variant Present in the following documents:

• Main text
• 12920_2016_Article_181.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: rs449643

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: SKIV2L: A1071V

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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Proteogenomic analysis reveals exosomes are more oncogenic than ectosomes.

Oncotarget

Keerthikumar, Shivakumar S; Gangoda, Lahiru L; Liem, Michael M; Fonseka, Pamali P; Atukorala, Ishara I; Ozcitti, Cemil C; Mechler, Adam A; Adda, Christopher G CG; Ang, Ching-Seng CS; Mathivanan, Suresh S

Publication Date: 2015-06-20

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 25944692

Variant Present in the following documents:

• oncotarget-06-15375-s005.xlsx, sheet 2

View BVdb publication page

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Whole-exome sequencing of pancreatic cancer defines genetic diversity and therapeutic targets.

Nature Communications

Witkiewicz, Agnieszka K AK; McMillan, Elizabeth A EA; Balaji, Uthra U; Baek, GuemHee G; Lin, Wan-Chi WC; Mansour, John J; Mollaee, Mehri M; Wagner, Kay-Uwe KU; Koduru, Prasad P; Yopp, Adam A; Choti, Michael A MA; Yeo, Charles J CJ; McCue, Peter P; White, Michael A MA; Knudsen, Erik S ES

Publication Date: 2015-04-09

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 25855536

Variant Present in the following documents:

• ncomms7744-s2.xlsx, 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: SKIV2L: A1071V; rs449643

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: SKIV2L: A1071V

PubMed Link: 25352556

Variant Present in the following documents:

• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 24

View BVdb publication page

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Host genetics and immune control of HIV-1 infection: fine mapping for the extended human MHC region in an African cohort.

Genes And Immunity

Prentice, H A HA; Pajewski, N M NM; He, D D; Zhang, K K; Brown, E E EE; Kilembe, W W; Allen, S S; Hunter, E E; Kaslow, R A RA; Tang, J J

Publication Date: 2014

Variant appearance in text: SKIV2L: A1071V; rs449643

PubMed Link: 24784026

Variant Present in the following documents:

• NIHMS580846-supplement-1.xlsx, sheet 3
• NIHMS580846-supplement-1.xlsx, sheet 2

View BVdb publication page

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Haplotype-based search for SNPs associated with differential type 1 diabetes risk among chromosomes carrying a specific HLA DRB1-DQA1-DQB1 haplotype.

Diabetes, Obesity & Metabolism

McGinnis, R R; McLaren, W W; Ranganath, V V; Whittaker, P P; Hunt, S S; Deloukas, P P; ,

Publication Date: 2009-02

Variant appearance in text: rs449643

PubMed Link: 19143810

Variant Present in the following documents:

• Main text

View BVdb publication page

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The joint allele-frequency spectrum in closely related species.

Genetics

Chen, Hua H; Green, Richard E RE; Pääbo, Svante S; Slatkin, Montgomery M

Publication Date: 2007-09

Variant appearance in text: rs449643

PubMed Link: 17603120

Variant Present in the following documents:

• Main text

View BVdb publication page

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