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: HELZ: V74M

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: HELZ: V74M; rs8080100

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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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: HELZ: V74M; rs8080100

PubMed Link: 36467812

Variant Present in the following documents:

• JHA2-3-1326-s001.xlsx, sheet 1

View BVdb publication page

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Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.

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

Wang, Tianyun T; Kim, Chang N CN; Bakken, Trygve E TE; Gillentine, Madelyn A MA; Henning, Barbara B; Mao, Yafei Y; Gilissen, Christian C; , ; Nowakowski, Tomasz J TJ; Eichler, Evan E EE

Publication Date: 2022-11-15

Variant appearance in text: HELZ: 220G>A; Val74Met

PubMed Link: 36350923

Variant Present in the following documents:

• pnas.2203491119.sd01.xlsx, sheet 1

View BVdb publication page

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Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition.

Molecular & Cellular Proteomics : Mcp

Schmitt, Marisa M; Sinnberg, Tobias T; Bratl, Katrin K; Zittlau, Katharina K; Garbe, Claus C; Macek, Boris B; Nalpas, Nicolas C NC

Publication Date: 2021

Variant appearance in text: HELZ: V74M; rs8080100

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 11
• mmc2.xlsx, sheet 3
• mmc2.xlsx, sheet 4
• mmc2.xlsx, sheet 6
• mmc2.xlsx, sheet 9

View BVdb publication page

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Proteogenomics Reveals Perturbed Signaling Networks in Malignant Melanoma Cells Resistant to BRAF Inhibition.

Molecular & Cellular Proteomics : Mcp

Schmitt, Marisa M; Sinnberg, Tobias T; Bratl, Katrin K; Zittlau, Katharina K; Garbe, Claus C; Macek, Boris B; Nalpas, Nicolas C NC

Publication Date: 2021-10-19

Variant appearance in text: HELZ: V74M; rs8080100

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 6
• mmc2.xlsx, sheet 11
• mmc2.xlsx, sheet 3
• mmc2.xlsx, sheet 4
• mmc2.xlsx, sheet 9

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: HELZ: Val74Met; rs8080100

PubMed Link: 33791233

Variant Present in the following documents:

• Table_2.xlsx, sheet 1

View BVdb publication page

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Identification of a nonsense mutation in TNNI3K associated with cardiac conduction disease.

Journal Of Clinical Laboratory Analysis

Liu, Jiang J; Liu, Da D; Li, Muzheng M; Wu, Keke K; Liu, Na N; Zhao, Chenyu C; Shi, Xiaoliu X; Liu, Qiming Q

Publication Date: 2020-09

Variant appearance in text: HELZ: V74M; rs8080100

PubMed Link: 32529721

Variant Present in the following documents:

• JCLA-34-e23418-s003.xls, 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: HELZ: 220G>A; Val74Met

PubMed Link: 31894249

Variant Present in the following documents:

• Supplementary_Data2.xlsx, sheet 5
• Supplementary_Data2.xlsx, sheet 7
• Supplementary_Data2.xlsx, sheet 6

View BVdb publication page

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DNA methylation loss promotes immune evasion of tumours with high mutation and copy number load.

Nature Communications

Jung, Hyunchul H; Kim, Hong Sook HS; Kim, Jeong Yeon JY; Sun, Jong-Mu JM; Ahn, Jin Seok JS; Ahn, Myung-Ju MJ; Park, Keunchil K; Esteller, Manel M; Lee, Se-Hoon SH; Choi, Jung Kyoon JK

Publication Date: 2019-09-19

Variant appearance in text: HELZ: V74M

PubMed Link: 31537801

Variant Present in the following documents:

• 41467_2019_12159_MOESM8_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: HELZ: V74M; rs8080100

PubMed Link: 30894629

Variant Present in the following documents:

• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 9
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 6
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 10
• 41598_2019_41277_MOESM4_ESM.xlsx, sheet 7

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: rs8080100

PubMed Link: 30814510

Variant Present in the following documents:

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

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: HELZ: 220G>A; Val74Met; rs8080100

PubMed Link: 30319441

Variant Present in the following documents:

• Table_7.xlsx, sheet 1
• Table_5.xlsx, sheet 1

View BVdb publication page

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Multi-OMICS analyses unveil STAT1 as a potential modifier gene in mevalonate kinase deficiency.

Annals Of The Rheumatic Diseases

Carapito, Raphael R; Carapito, Christine C; Morlon, Aurore A; Paul, Nicodème N; Vaca Jacome, Alvaro Sebastian AS; Alsaleh, Ghada G; Rolli, Véronique V; Tahar, Ouria O; Aouadi, Ismail I; Rompais, Magali M; Delalande, François F; Pichot, Angélique A; Georgel, Philippe P; Messer, Laurent L; Sibilia, Jean J; Cianferani, Sarah S; Van Dorsselaer, Alain A; Bahram, Seiamak S

Publication Date: 2018-11

Variant appearance in text: HELZ: V74M; rs8080100

PubMed Link: 30030262

Variant Present in the following documents:

• annrheumdis-2018-213524supp002.xlsx, sheet 1

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: rs8080100

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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Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

Oncotarget

Ma, Shiyong S; Menon, Ranjeeta R; Poulos, Rebecca C RC; Wong, Jason W H JWH

Publication Date: 2017-11-10

Variant appearance in text: HELZ: V74M; rs8080100

PubMed Link: 29221171

Variant Present in the following documents:

• oncotarget-08-95841-s002.xlsx, sheet 1
• oncotarget-08-95841-s002.xlsx, sheet 4

View BVdb publication page

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Whole-genome sequencing in multiplex families with psychoses reveals mutations in the SHANK2 and SMARCA1 genes segregating with illness.

Molecular Psychiatry

Homann, O R OR; Misura, K K; Lamas, E E; Sandrock, R W RW; Nelson, P P; McDonough, S I SI; DeLisi, L E LE

Publication Date: 2016-12

Variant appearance in text: HELZ: V74M

PubMed Link: 27001614

Variant Present in the following documents:

• NIHMS753666-supplement-2.xlsx, sheet 6

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: rs8080100

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: HELZ: V74M

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 2

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: HELZ: V74M; rs8080100

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 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: HELZ: V74M; rs8080100

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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Whole exome sequencing of a single osteosarcoma case--integrative analysis with whole transcriptome RNA-seq data.

Human Genomics

Reimann, Ene E; Kõks, Sulev S; Ho, Xuan Dung XD; Maasalu, Katre K; Märtson, Aare A

Publication Date: 2014-12-11

Variant appearance in text: HELZ: V74M

PubMed Link: 25496518

Variant Present in the following documents:

• 40246_2014_20_MOESM1_ESM.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: HELZ: V74M; rs8080100

PubMed Link: 25390934

Variant Present in the following documents:

• pone.0112430.s004.xlsx, sheet 1

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: HELZ: V74M; rs8080100

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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Effect of a poly(ADP-ribose) polymerase-1 inhibitor against esophageal squamous cell carcinoma cell lines.

Cancer Science

Nasuno, Tomomitsu T; Mimaki, Sachiyo S; Okamoto, Makito M; Esumi, Hiroyasu H; Tsuchihara, Katsuya K

Publication Date: 2014-02

Variant appearance in text: HELZ: V74M; rs8080100

PubMed Link: 24219164

Variant Present in the following documents:

• cas0105-0202-SD3.xlsx, sheet 1

View BVdb publication page

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