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: MMUT: A499T

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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OpenCustomDB: Integration of Unannotated Open Reading Frames and Genetic Variants to Generate More Comprehensive Customized Protein Databases.

Journal Of Proteome Research

Guilloy, Noé N; Brunet, Marie A MA; Leblanc, Sébastien S; Jacques, Jean-François JF; Hardy, Marie-Pierre MP; Ehx, Grégory G; Lanoix, Joël J; Thibault, Pierre P; Perreault, Claude C; Roucou, Xavier X

Publication Date: 2023-03-24

Variant appearance in text: MUT: Ala499Thr

PubMed Link: 36961377

Variant Present in the following documents:

• pr3c00054_si_002.xlsx, sheet 2

View BVdb publication page

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Beneficial effects of mifepristone treatment in breast cancer patients selected by the progesterone receptor isoform ratio: Results from the MIPRA trial.

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

Elía, Andrés A; Saldain, Leo L; Vanzulli, Silvia I SI; Helguero, Luisa A LA; Lamb, Caroline A CA; Fabris, Victoria V; Pataccini, Gabriela G; Martínez-Vazquez, Paula P; Burruchaga, Javier J; Caillet-Bois, Ines I; Spengler, Eunice E; Acosta Haab, Gabriela G; Liguori, Marcos M; Castets, Alejandra A; Lovisi, Silvia S; Abascal, María F MF; Novaro, Virginia V; Sánchez, Jana J; Muñoz, Javier J; Belizán, Jose M JM; Abba, Martín C MC; Gass, Hugo H; Rojas, Paola P; Lanari, Claudia C

Publication Date: 2022-10-21

Variant appearance in text: MUT: 1495G>A; rs2229385

PubMed Link: 36269797

Variant Present in the following documents:

• ccr-22-2060_supplementary_table_s5_suppts5.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: MMUT: A499T

PubMed Link: 36241656

Variant Present in the following documents:

• 41598_2022_20939_MOESM2_ESM.xlsx, sheet 2
• 41598_2022_20939_MOESM15_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: MMUT: A499T

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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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: MUT: A499T; rs2229385

PubMed Link: 33791233

Variant Present in the following documents:

• Table_2.xlsx, sheet 1

View BVdb publication page

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Prioritization of candidate genes for a South African family with Parkinson's disease using in-silico tools.

Plos One

Sebate, Boiketlo B; Cuttler, Katelyn K; Cloete, Ruben R; Britz, Marcell M; Christoffels, Alan A; Williams, Monique M; Carr, Jonathan J; Bardien, Soraya S

Publication Date: 2021

Variant appearance in text: MUT: 1495G>A; rs2229385

PubMed Link: 33770142

Variant Present in the following documents:

• pone.0249324.s003.xlsx, sheet 2
• pone.0249324.s003.xlsx, sheet 1

View BVdb publication page

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Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy.

Cell

Krug, Karsten K; Jaehnig, Eric J EJ; Satpathy, Shankha S; Blumenberg, Lili L; Karpova, Alla A; Anurag, Meenakshi M; Miles, George G; Mertins, Philipp P; Geffen, Yifat Y; Tang, Lauren C LC; Heiman, David I DI; Cao, Song S; Maruvka, Yosef E YE; Lei, Jonathan T JT; Huang, Chen C; Kothadia, Ramani B RB; Colaprico, Antonio A; Birger, Chet C; Wang, Jarey J; Dou, Yongchao Y; Wen, Bo B; Shi, Zhiao Z; Liao, Yuxing Y; Wiznerowicz, Maciej M; Wyczalkowski, Matthew A MA; Chen, Xi Steven XS; Kennedy, Jacob J JJ; Paulovich, Amanda G AG; Thiagarajan, Mathangi M; Kinsinger, Christopher R CR; Hiltke, Tara T; Boja, Emily S ES; Mesri, Mehdi M; Robles, Ana I AI; Rodriguez, Henry H; Westbrook, Thomas F TF; Ding, Li L; Getz, Gad G; Clauser, Karl R KR; Fenyö, David D; Ruggles, Kelly V KV; Zhang, Bing B; Mani, D R DR; Carr, Steven A SA; Ellis, Matthew J MJ; Gillette, Michael A MA; ,

Publication Date: 2020-11-25

Variant appearance in text: MUT: A499T

PubMed Link: 33212010

Variant Present in the following documents:

• NIHMS1687926-supplement-Supplemental_Table_3.xlsx, sheet 5

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: MUT: A499T

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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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: MMUT: 1495G>A; Ala499Thr; rs2229385

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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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: MUT: A499T; rs2229385

PubMed Link: 31597922

Variant Present in the following documents:

• 41598_2019_50891_MOESM2_ESM.xlsx, sheet 1
• 41598_2019_50891_MOESM3_ESM.xlsx, sheet 1

View BVdb publication page

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Hyperammonemia after capecitabine associated with occult impairment of the urea cycle.

Cancer Medicine

Chu, Gilbert G; Salzman, Julia J

Publication Date: 2019-05

Variant appearance in text: MUT: A499T; rs2229385

PubMed Link: 30977266

Variant Present in the following documents:

• CAM4-8-1996-s001.pdf

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: MUT: 1495G>A

PubMed Link: 30937429

Variant Present in the following documents:

• famiglietti_supplementarytables1_rev_baz040.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: MUT: A499T; rs2229385

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 13
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 3

View BVdb publication page

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Organoids as a new model for improving regenerative medicine and cancer personalized therapy in renal diseases.

Cell Death & Disease

Grassi, Ludovica L; Alfonsi, Romina R; Francescangeli, Federica F; Signore, Michele M; De Angelis, Maria Laura ML; Addario, Antonio A; Costantini, Manuela M; Flex, Elisabetta E; Ciolfi, Andrea A; Pizzi, Simone S; Bruselles, Alessandro A; Pallocca, Matteo M; Simone, Giuseppe G; Haoui, Mustapha M; Falchi, Mario M; Milella, Michele M; Sentinelli, Steno S; Di Matteo, Paola P; Stellacci, Emilia E; Gallucci, Michele M; Muto, Giovanni G; Tartaglia, Marco M; De Maria, Ruggero R; Bonci, Désirée D

Publication Date: 2019-02-27

Variant appearance in text: MUT: 1495G>A; rs2229385

PubMed Link: 30814510

Variant Present in the following documents:

• 41419_2019_1453_MOESM27_ESM.xlsx, sheet 3
• 41419_2019_1453_MOESM27_ESM.xlsx, sheet 1

View BVdb publication page

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Genetic Evidence Supporting the Role of the Calcium Channel, CACNA1S, in Tooth Cusp and Root Patterning.

Frontiers In Physiology

Laugel-Haushalter, Virginie V; Morkmued, Supawich S; Stoetzel, Corinne C; Geoffroy, Véronique V; Muller, Jean J; Boland, Anne A; Deleuze, Jean-François JF; Chennen, Kirsley K; Pitiphat, Waranuch W; Dollfus, Hélène H; Niederreither, Karen K; Bloch-Zupan, Agnès A; Pungchanchaikul, Patimaporn P

Publication Date: 2018

Variant appearance in text: MUT: 1495G>A; rs2229385

PubMed Link: 30319441

Variant Present in the following documents:

• Table_7.xlsx, sheet 1
• Table_6.xlsx, sheet 1

View BVdb publication page

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Whole exome sequencing in three families segregating a pediatric case of sarcoidosis.

Bmc Medical Genomics

Calender, Alain A; Rollat Farnier, Pierre Antoine PA; Buisson, Adrien A; Pinson, Stéphane S; Bentaher, Abderrazzaq A; Lebecque, Serge S; Corvol, Harriet H; Abou Taam, Rola R; Houdouin, Véronique V; Bardel, Claire C; Roy, Pascal P; Devouassoux, Gilles G; Cottin, Vincent V; Seve, Pascal P; Bernaudin, Jean-François JF; Lim, Clarice X CX; Weichhart, Thomas T; Valeyre, Dominique D; Pacheco, Yves Y; Clement, Annick A; Nathan, Nadia N; ,

Publication Date: 2018-03-06

Variant appearance in text: MUT: 1495G>A; rs2229385

PubMed Link: 29510755

Variant Present in the following documents:

• 12920_2018_338_MOESM6_ESM.xlsx, sheet 3

View BVdb publication page

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Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Nature Communications

Zhu, Yafeng Y; Orre, Lukas M LM; Johansson, Henrik J HJ; Huss, Mikael M; Boekel, Jorrit J; Vesterlund, Mattias M; Fernandez-Woodbridge, Alejandro A; Branca, Rui M M RMM; Lehtiö, Janne J

Publication Date: 2018-03-02

Variant appearance in text: rs2229385

PubMed Link: 29500430

Variant Present in the following documents:

• 41467_2018_3311_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Whole-exome sequencing analysis of Waardenburg syndrome in a Chinese family.

Human Genome Variation

Chen, Dezhong D; Zhao, Na N; Wang, Jing J; Li, Zhuoyu Z; Wu, Changxin C; Fu, Jie J; Xiao, Han H

Publication Date: 2017

Variant appearance in text: rs2229385

PubMed Link: 28690861

Variant Present in the following documents:

• hgv201727-s1.xls, sheet 1

View BVdb publication page

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Exome sequencing deciphers a germline MET mutation in familial epidermal growth factor receptor-mutant lung cancer.

Cancer Science

Tode, Naoki N; Kikuchi, Toshiaki T; Sakakibara, Tomohiro T; Hirano, Taizou T; Inoue, Akira A; Ohkouchi, Shinya S; Tamada, Tsutomu T; Okazaki, Tatsuma T; Koarai, Akira A; Sugiura, Hisatoshi H; Niihori, Tetsuya T; Aoki, Yoko Y; Nakayama, Keiko K; Matsumoto, Kunio K; Matsubara, Yoichi Y; Yamamoto, Masayuki M; Watanabe, Akira A; Nukiwa, Toshihiro T; Ichinose, Masakazu M

Publication Date: 2017-06

Variant appearance in text: MUT: 1495G>A; rs2229385

PubMed Link: 28294470

Variant Present in the following documents:

• CAS-108-1263-s001.pdf

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: MUT: A499T; rs2229385

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: rs2229385

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: MUT: A499T

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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A mass-tolerant database search identifies a large proportion of unassigned spectra in shotgun proteomics as modified peptides.

Nature Biotechnology

Chick, Joel M JM; Kolippakkam, Deepak D; Nusinow, David P DP; Zhai, Bo B; Rad, Ramin R; Huttlin, Edward L EL; Gygi, Steven P SP

Publication Date: 2015-07

Variant appearance in text: rs2229385

PubMed Link: 26076430

Variant Present in the following documents:

• Main text
• nihms690171.pdf

View BVdb publication page

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Whole genome sequencing of an ethnic Pathan (Pakhtun) from the north-west of Pakistan.

Bmc Genomics

Ilyas, Muhammad M; Kim, Jong-Soo JS; Cooper, Jesse J; Shin, Young-Ah YA; Kim, Hak-Min HM; Cho, Yun Sung YS; Hwang, Seungwoo S; Kim, Hyunho H; Moon, Jaewoo J; Chung, Oksung O; Jun, JeHoon J; Rastogi, Achal A; Song, Sanghoon S; Ko, Junsu J; Manica, Andrea A; Rahman, Ziaur Z; Husnain, Tayyab T; Bhak, Jong J

Publication Date: 2015-03-12

Variant appearance in text: MUT: A499T; rs2229385

PubMed Link: 25887915

Variant Present in the following documents:

• 12864_2015_1290_MOESM7_ESM.xlsx, sheet 1

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: MUT: A499T; rs2229385

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: MUT: A499T; rs2229385

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: MUT: A499T; rs2229385

PubMed Link: 25352556

Variant Present in the following documents:

• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 19
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 9
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 20
• supp_gku1005_nar-01266-met-n-2014-File012.xlsx, sheet 23

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: MUT: A499T; rs2229385

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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