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: BUD13: P148L

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: BUD13: P148L; rs11820589

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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Expanding the prostate cancer cell line repertoire with ACRJ-PC28, an AR-negative neuroendocrine cell line derived from an African-Caribbean patient.

Cancer Research Communications

Valentine, Henkel H; Aiken, William W; Morrison, Belinda B; Zhao, Ziran Z; Fowle, Holly H; Wasserman, Jason S JS; Thompson, Elon E; Chin, Warren W; Young, Mark M; Clarke, Shannique S; Gibbs, Denise D; Harrison, Sharon S; McLaughlin, Wayne W; Kwok, Tim T; Jin, Fang F; Campbell, Kerry S KS; Horvath, Anelia A; Thompson, Rory R; Lee, Norman H NH; Zhou, Yan Y; Graña, Xavier X; Ragin, Camille C; Badal, Simone S

Publication Date: 2022-11

Variant appearance in text: BUD13: P148L; rs11820589

PubMed Link: 36643868

Variant Present in the following documents:

• crc-22-0245-s07.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: BUD13: P148L

PubMed Link: 36241656

Variant Present in the following documents:

• 41598_2022_20939_MOESM8_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: BUD13: P148L; rs11820589

PubMed Link: 36075891

Variant Present in the following documents:

• 41439_2022_208_MOESM4_ESM.xlsx, sheet 2
• 41439_2022_208_MOESM3_ESM.xlsx, sheet 2

View BVdb publication page

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Exome Sequencing Data Analysis and a Case-Control Study in Mexican Population Reveals Lipid Trait Associations of New and Known Genetic Variants in Dyslipidemia-Associated Loci.

Frontiers In Genetics

Jurado-Camacho, Pedro A PA; Cid-Soto, Miguel A MA; Barajas-Olmos, Francisco F; García-Ortíz, Humberto H; Baca-Peynado, Paulina P; Martínez-Hernández, Angélica A; Centeno-Cruz, Federico F; Contreras-Cubas, Cecilia C; González-Villalpando, María Elena ME; Saldaña-Álvarez, Yolanda Y; Salas-Martinez, Guadalupe G; Mendoza-Caamal, Elvia C EC; González-Villalpando, Clicerio C; Córdova, Emilio J EJ; Orozco, Lorena L

Publication Date: 2022

Variant appearance in text: rs11820589

PubMed Link: 35669185

Variant Present in the following documents:

• Main text
• fgene-13-807381.pdf

View BVdb publication page

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Loss of heterozygosity of essential genes represents a widespread class of potential cancer vulnerabilities.

Nature Communications

Nichols, Caitlin A CA; Gibson, William J WJ; Brown, Meredith S MS; Kosmicki, Jack A JA; Busanovich, John P JP; Wei, Hope H; Urbanski, Laura M LM; Curimjee, Naomi N; Berger, Ashton C AC; Gao, Galen F GF; Cherniack, Andrew D AD; Dhe-Paganon, Sirano S; Paolella, Brenton R BR; Beroukhim, Rameen R

Publication Date: 2020-05-20

Variant appearance in text: BUD13: 443C>T; Pro148Leu; rs11820589

PubMed Link: 32433464

Variant Present in the following documents:

• 41467_2020_16399_MOESM7_ESM.xlsx, sheet 1
• 41467_2020_16399_MOESM5_ESM.xlsx, 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: BUD13: P148L

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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Association of Genetically Predicted Lipid Levels With the Extent of Coronary Atherosclerosis in Icelandic Adults.

Jama Cardiology

Björnsson, Eythór E; Thorleifsson, Guðmar G; Helgadóttir, Anna A; Guðnason, Thórarinn T; Guðbjartsson, Tómas T; Andersen, Karl K; Grétarsdóttir, Sólveig S; Ólafsson, Ísleifur Í; Tragante, Vinicius V; Ólafsson, Ólafur Hreiðar ÓH; Jónsdóttir, Birna B; Eyjólfsson, Guðmundur I GI; Sigurðardóttir, Ólöf Ó; Thorgeirsson, Guðmundur G; Guðbjartsson, Daníel F DF; Thorsteinsdóttir, Unnur U; Hólm, Hilma H; Stefánsson, Kári K

Publication Date: 2020-01-01

Variant appearance in text: rs11820589

PubMed Link: 31746962

Variant Present in the following documents:

• jamacardiol-5-13-s001.pdf

View BVdb publication page

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The transferability of lipid loci across African, Asian and European cohorts.

Nature Communications

Kuchenbaecker, Karoline K; Telkar, Nikita N; Reiker, Theresa T; Walters, Robin G RG; Lin, Kuang K; Eriksson, Anders A; Gurdasani, Deepti D; Gilly, Arthur A; Southam, Lorraine L; Tsafantakis, Emmanouil E; Karaleftheri, Maria M; Seeley, Janet J; Kamali, Anatoli A; Asiki, Gershim G; Millwood, Iona Y IY; Holmes, Michael M; Du, Huaidong H; Guo, Yu Y; Kumari, Meena M; Dedoussis, George G; Li, Liming L; Chen, Zhengming Z; Sandhu, Manjinder S MS; Zeggini, Eleftheria E; ,

Publication Date: 2019-09-24

Variant appearance in text: rs11820589

PubMed Link: 31551420

Variant Present in the following documents:

• Main text
• 41467_2019_Article_12026.pdf
• 41467_2019_12026_MOESM1_ESM.pdf

View BVdb publication page

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Extensive disruption of protein interactions by genetic variants across the allele frequency spectrum in human populations.

Nature Communications

Fragoza, Robert R; Das, Jishnu J; Wierbowski, Shayne D SD; Liang, Jin J; Tran, Tina N TN; Liang, Siqi S; Beltran, Juan F JF; Rivera-Erick, Christen A CA; Ye, Kaixiong K; Wang, Ting-Yi TY; Yao, Li L; Mort, Matthew M; Stenson, Peter D PD; Cooper, David N DN; Wei, Xiaomu X; Keinan, Alon A; Schimenti, John C JC; Clark, Andrew G AG; Yu, Haiyuan H

Publication Date: 2019-09-12

Variant appearance in text: rs11820589

PubMed Link: 31515488

Variant Present in the following documents:

• 41467_2019_11959_MOESM11_ESM.xlsx, sheet 1
• 41467_2019_11959_MOESM6_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: BUD13: P148L; rs11820589

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 5

View BVdb publication page

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An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies.

Genome Medicine

Zhao, Junfei J; Cheng, Feixiong F; Jia, Peilin P; Cox, Nancy N; Denny, Joshua C JC; Zhao, Zhongming Z

Publication Date: 2018-01-29

Variant appearance in text: BUD13: P148L; rs11820589

PubMed Link: 29378629

Variant Present in the following documents:

• 13073_2018_513_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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Transforming growth factor-β signaling pathway-associated genes SMAD2 and TGFBR2 are implicated in metabolic syndrome in a Taiwanese population.

Scientific Reports

Lin, Eugene E; Kuo, Po-Hsiu PH; Liu, Yu-Li YL; Yang, Albert C AC; Tsai, Shih-Jen SJ

Publication Date: 2017-10-19

Variant appearance in text: rs11820589

PubMed Link: 29051557

Variant Present in the following documents:

• Main text
• 41598_2017_Article_14025.pdf

View BVdb publication page

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Distinct Patterns of Association of Variants at 11q23.3 Chromosomal Region with Coronary Artery Disease and Dyslipidemia in the Population of Andhra Pradesh, India.

Plos One

Pranav Chand, Rayabarapu R; Kumar, Arramraju Sreenivas AS; Anuj, Kapadia K; Vishnupriya, Satti S; Mohan Reddy, Battini B

Publication Date: 2016

Variant appearance in text: rs11820589

PubMed Link: 27257688

Variant Present in the following documents:

• Main text
• pone.0153720.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: rs11820589

PubMed Link: 26659599

Variant Present in the following documents:

• pone.0144692.s002.xlsx, sheet 1

View BVdb publication page

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Kuwaiti population subgroup of nomadic Bedouin ancestry-Whole genome sequence and analysis.

Genomics Data

John, Sumi Elsa SE; Thareja, Gaurav G; Hebbar, Prashantha P; Behbehani, Kazem K; Thanaraj, Thangavel Alphonse TA; Alsmadi, Osama O

Publication Date: 2015-03

Variant appearance in text: rs11820589

PubMed Link: 26484159

Variant Present in the following documents:

• Main text
• main.pdf

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: BUD13: P148L

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 5

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: BUD13: P148L; rs11820589

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: BUD13: P148L; rs11820589

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 25
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 10

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: BUD13: P148L; rs11820589

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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Amerindian-specific regions under positive selection harbour new lipid variants in Latinos.

Nature Communications

Ko, Arthur A; Cantor, Rita M RM; Weissglas-Volkov, Daphna D; Nikkola, Elina E; Reddy, Prasad M V Linga PM; Sinsheimer, Janet S JS; Pasaniuc, Bogdan B; Brown, Robert R; Alvarez, Marcus M; Rodriguez, Alejandra A; Rodriguez-Guillen, Rosario R; Bautista, Ivette C IC; Arellano-Campos, Olimpia O; Muñoz-Hernández, Linda L LL; Salomaa, Veikko V; Kaprio, Jaakko J; Jula, Antti A; Jauhiainen, Matti M; Heliövaara, Markku M; Raitakari, Olli O; Lehtimäki, Terho T; Eriksson, Johan G JG; Perola, Markus M; Lohmueller, Kirk E KE; Matikainen, Niina N; Taskinen, Marja-Riitta MR; Rodriguez-Torres, Maribel M; Riba, Laura L; Tusie-Luna, Teresa T; Aguilar-Salinas, Carlos A CA; Pajukanta, Päivi P

Publication Date: 2014-06-02

Variant appearance in text: rs11820589

PubMed Link: 24886709

Variant Present in the following documents:

• Main text
• ncomms4983.pdf

View BVdb publication page

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Systematic evaluation of coding variation identifies a candidate causal variant in TM6SF2 influencing total cholesterol and myocardial infarction risk.

Nature Genetics

Holmen, Oddgeir L OL; Zhang, He H; Fan, Yanbo Y; Hovelson, Daniel H DH; Schmidt, Ellen M EM; Zhou, Wei W; Guo, Yanhong Y; Zhang, Ji J; Langhammer, Arnulf A; Løchen, Maja-Lisa ML; Ganesh, Santhi K SK; Vatten, Lars L; Skorpen, Frank F; Dalen, Håvard H; Zhang, Jifeng J; Pennathur, Subramaniam S; Chen, Jin J; Platou, Carl C; Mathiesen, Ellisiv B EB; Wilsgaard, Tom T; Njølstad, Inger I; Boehnke, Michael M; Chen, Y Eugene YE; Abecasis, Gonçalo R GR; Hveem, Kristian K; Willer, Cristen J CJ

Publication Date: 2014-04

Variant appearance in text: BUD13: Pro148Leu; rs11820589

PubMed Link: 24633158

Variant Present in the following documents:

• NIHMS570373-supplement-1.pdf

View BVdb publication page

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Investigation of gene-by-sex interactions for lipid traits in diverse populations from the population architecture using genomics and epidemiology study.

Bmc Genetics

Taylor, Kira C KC; Carty, Cara L CL; Dumitrescu, Logan L; Bůžková, Petra P; Cole, Shelley A SA; Hindorff, Lucia L; Schumacher, Fred R FR; Wilkens, Lynne R LR; Shohet, Ralph V RV; Quibrera, P Miguel PM; Johnson, Karen C KC; Henderson, Brian E BE; Haessler, Jeff J; Franceschini, Nora N; Eaton, Charles B CB; Duggan, David J DJ; Cochran, Barbara B; Cheng, Iona I; Carlson, Chris S CS; Brown-Gentry, Kristin K; Anderson, Garnet G; Ambite, Jose Luis JL; Haiman, Christopher C; Le Marchand, Loïc L; Kooperberg, Charles C; Crawford, Dana C DC; Buyske, Steven S; North, Kari E KE; Fornage, Myriam M; ,

Publication Date: 2013-05-01

Variant appearance in text: rs11820589

PubMed Link: 23634756

Variant Present in the following documents:

• Main text
• 1471-2156-14-33.pdf

View BVdb publication page

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A bivariate genome-wide approach to metabolic syndrome: STAMPEED consortium.

Diabetes

Kraja, Aldi T AT; Vaidya, Dhananjay D; Pankow, James S JS; Goodarzi, Mark O MO; Assimes, Themistocles L TL; Kullo, Iftikhar J IJ; Sovio, Ulla U; Mathias, Rasika A RA; Sun, Yan V YV; Franceschini, Nora N; Absher, Devin D; Li, Guo G; Zhang, Qunyuan Q; Feitosa, Mary F MF; Glazer, Nicole L NL; Haritunians, Talin T; Hartikainen, Anna-Liisa AL; Knowles, Joshua W JW; North, Kari E KE; Iribarren, Carlos C; Kral, Brian B; Yanek, Lisa L; O'Reilly, Paul F PF; McCarthy, Mark I MI; Jaquish, Cashell C; Couper, David J DJ; Chakravarti, Aravinda A; Psaty, Bruce M BM; Becker, Lewis C LC; Province, Michael A MA; Boerwinkle, Eric E; Quertermous, Thomas T; Palotie, Leena L; Jarvelin, Marjo-Riitta MR; Becker, Diane M DM; Kardia, Sharon L R SL; Rotter, Jerome I JI; Chen, Yii-Der Ida YD; Borecki, Ingrid B IB

Publication Date: 2011-04

Variant appearance in text: rs11820589

PubMed Link: 21386085

Variant Present in the following documents:

• Main text
• 1329.pdf

View BVdb publication page

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Genome-wide association study of Lp-PLA(2) activity and mass in the Framingham Heart Study.

Plos Genetics

Suchindran, Sunil S; Rivedal, David D; Guyton, John R JR; Milledge, Tom T; Gao, Xiaoyi X; Benjamin, Ashlee A; Rowell, Jennifer J; Ginsburg, Geoffrey S GS; McCarthy, Jeanette J JJ

Publication Date: 2010-04-29

Variant appearance in text: rs11820589

PubMed Link: 20442857

Variant Present in the following documents:

• Main text
• pgen.1000928.pdf

View BVdb publication page

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Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Proceedings Of The National Academy Of Sciences Of The United States Of America

Hindorff, Lucia A LA; Sethupathy, Praveen P; Junkins, Heather A HA; Ramos, Erin M EM; Mehta, Jayashri P JP; Collins, Francis S FS; Manolio, Teri A TA

Publication Date: 2009-06-09

Variant appearance in text: BUD13: P148L; rs11820589

PubMed Link: 19474294

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: BUD13: P148L; rs11820589

PubMed Link: 19139070

Variant Present in the following documents:

• gkn1008_nar-01723-s-2008-File008.xls, sheet 5

View BVdb publication page

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