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: EPHA7: I138V

PubMed Link: 37012232

Variant Present in the following documents:

• 41467_2023_37547_MOESM12_ESM.xlsx, sheet 3

View BVdb publication page

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Comprehensive Assessment of Indian Variations in the Druggable Kinome Landscape Highlights Distinct Insights at the Sequence, Structure and Pharmacogenomic Stratum.

Frontiers In Pharmacology

Panda, Gayatri G; Mishra, Neha N; Sharma, Disha D; Kutum, Rintu R; Bhoyar, Rahul C RC; Jain, Abhinav A; Imran, Mohamed M; Senthilvel, Vigneshwar V; Divakar, Mohit Kumar MK; Mishra, Anushree A; Garg, Parth P; Banerjee, Priyanka P; Sivasubbu, Sridhar S; Scaria, Vinod V; Ray, Arjun A

Publication Date: 2022

Variant appearance in text: EPHA7: I138V; rs2278107

PubMed Link: 35865963

Variant Present in the following documents:

• DataSheet1.pdf
• Table12.xlsx, sheet 1

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: EPHA7: I138V

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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Multiomics Landscape Uncovers the Molecular Mechanism of the Malignant Evolution of Lung Adenocarcinoma Cells to Chronic Low Dose Cadmium Exposure.

Frontiers In Oncology

Dai, Shun-Dong SD; Wang, Shuang S; Qin, Ya-Nan YN; Zhu, Jin-Chao JC

Publication Date: 2021

Variant appearance in text: EPHA7: I138V

PubMed Link: 34858801

Variant Present in the following documents:

• Table_1.xls, sheet 1

View BVdb publication page

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Genomic and evolutionary portraits of disease relapse in acute myeloid leukemia.

Leukemia

Rapaport, Franck F; Neelamraju, Yaseswini Y; Baslan, Timour T; Hassane, Duane D; Gruszczynska, Agata A; Robert de Massy, Marc M; Farnoud, Noushin N; Haddox, Samuel S; Lee, Tak T; Medina-Martinez, Juan J; Sheridan, Caroline C; Thurmond, Alexis A; Becker, Michael M; Bekiranov, Stefan S; Carroll, Martin M; Moses Murdock, Heardly H; Valk, Peter J M PJM; Bullinger, Lars L; D'Andrea, Richard R; Lowe, Scott W SW; Neuberg, Donna D; Levine, Ross L RL; Melnick, Ari A; Garrett-Bakelman, Francine E FE

Publication Date: 2021-09

Variant appearance in text: EPHA7: Ile138Val

PubMed Link: 33580203

Variant Present in the following documents:

• 41375_2021_1153_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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RNF213 gene mutation in circulating tumor DNA detected by targeted next-generation sequencing in the assisted discrimination of early-stage lung cancer from pulmonary nodules.

Thoracic Cancer

Jiang, Ning N; Zhou, Jie J; Zhang, Wenhao W; Li, Peichao P; Liu, Yu Y; Shi, Hubo H; Zhang, Chengke C; Wang, Yunshan Y; Zhou, Chengjun C; Peng, Chuanliang C; Zhang, Weiquan W; Hao, Yingtao Y; Sun, Qifeng Q; Li, Yuliang Y; Zhao, Xiaogang X

Publication Date: 2021-01

Variant appearance in text: EPHA7: I138V; rs2278107

PubMed Link: 33200540

Variant Present in the following documents:

• TCA-12-181-s002.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: EPHA7: I138V

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: EPHA7: 412A>G; Ile138Val

PubMed Link: 31894249

Variant Present in the following documents:

• Supplementary_Data2.xlsx, sheet 7

View BVdb publication page

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Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors.

Cell Reports

Vigilante, Alessandra A; Laddach, Anna A; Moens, Nathalie N; Meleckyte, Ruta R; Leha, Andreas A; Ghahramani, Arsham A; Culley, Oliver J OJ; Kathuria, Annie A; Hurling, Chloe C; Vickers, Alice A; Wiseman, Erika E; Tewary, Mukul M; Zandstra, Peter W PW; , ; Durbin, Richard R; Fraternali, Franca F; Stegle, Oliver O; Birney, Ewan E; Luscombe, Nicholas M NM; Danovi, Davide D; Watt, Fiona M FM

Publication Date: 2019-02-19

Variant appearance in text: EPHA7: I138V

PubMed Link: 30784590

Variant Present in the following documents:

• mmc6.xlsx, sheet 1

View BVdb publication page

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Systematic screening of isogenic cancer cells identifies DUSP6 as context-specific synthetic lethal target in melanoma.

Oncotarget

Wittig-Blaich, Stephanie S; Wittig, Rainer R; Schmidt, Steffen S; Lyer, Stefan S; Bewerunge-Hudler, Melanie M; Gronert-Sum, Sabine S; Strobel-Freidekind, Olga O; Müller, Carolin C; List, Markus M; Jaskot, Aleksandra A; Christiansen, Helle H; Hafner, Mathias M; Schadendorf, Dirk D; Block, Ines I; Mollenhauer, Jan J

Publication Date: 2017-04-04

Variant appearance in text: EPHA7: I138V; rs2278107

PubMed Link: 28423600

Variant Present in the following documents:

• oncotarget-08-23760-s002.xlsx, sheet 1

View BVdb publication page

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Tobacco habituated and non-habituated subjects exhibit different mutational spectrums in head and neck squamous cell carcinoma.

3 Biotech

Rawal, Rakesh M RM; Joshi, Madhvi N MN; Bhargava, Poonam P; Shaikh, Inayat I; Pandit, Aanal S AS; Patel, Riddhi P RP; Patel, Shanaya S; Kothari, Kiran K; Shah, Manoj M; Saxena, Akshay A; Bagatharia, Snehal B SB

Publication Date: 2015-10

Variant appearance in text: EPHA7: I138V

PubMed Link: 28324520

Variant Present in the following documents:

• 13205_2014_267_MOESM1_ESM.xlsx, sheet 1

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: EPHA7: I138V; rs2278107

PubMed Link: 27512948

Variant Present in the following documents:

• PATH-240-315-s015.xlsx, sheet 1

View BVdb publication page

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Deleterious coding variants in multi-case families with non-syndromic cleft lip and/or palate phenotypes.

Scientific Reports

Pengelly, Reuben J RJ; Arias, Liliana L; Martínez, Julio J; Upstill-Goddard, Rosanna R; Seaby, Eleanor G EG; Gibson, Jane J; Ennis, Sarah S; Collins, Andrew A; Briceño, Ignacio I

Publication Date: 2016-07-26

Variant appearance in text: EPHA7: I138V; rs2278107

PubMed Link: 27456059

Variant Present in the following documents:

• srep30457-s2.xls, sheet 2
• srep30457-s2.xls, sheet 1

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: rs2278107

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: EPHA7: I138V

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 4

View BVdb publication page

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Sporadic hemangioblastomas are characterized by cryptic VHL inactivation.

Acta Neuropathologica Communications

Shankar, Ganesh M GM; Taylor-Weiner, Amaro A; Lelic, Nina N; Jones, Robert T RT; Kim, James C JC; Francis, Joshua M JM; Abedalthagafi, Malak M; Borges, Lawrence F LF; Coumans, Jean-Valery JV; Curry, William T WT; Nahed, Brian V BV; Shin, John H JH; Paek, Sun Ha SH; Park, Sung-Hye SH; Stewart, Chip C; Lawrence, Michael S MS; Cibulskis, Kristian K; Thorner, Aaron R AR; Van Hummelen, Paul P; Stemmer-Rachamimov, Anat O AO; Batchelor, Tracy T TT; Carter, Scott L SL; Hoang, Mai P MP; Santagata, Sandro S; Louis, David N DN; Barker, Fred G FG; Meyerson, Matthew M; Getz, Gad G; Brastianos, Priscilla K PK; Cahill, Daniel P DP

Publication Date: 2014-12-24

Variant appearance in text: EPHA7: 412A>G; I138V; rs2278107

PubMed Link: 25589003

Variant Present in the following documents:

• 40478_2014_167_MOESM1_ESM.xlsx, sheet 6

View BVdb publication page

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Recent applications of chemosensitivity tests for colorectal cancer treatment.

World Journal Of Gastroenterology

Yoon, Yong Sik YS; Kim, Jin Cheon JC

Publication Date: 2014-11-28

Variant appearance in text: rs2278107

PubMed Link: 25469008

Variant Present in the following documents:

• Main text

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: EPHA7: I138V; rs2278107

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: EPHA7: I138V; rs2278107

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: EPHA7: I138V; rs2278107

PubMed Link: 24219164

Variant Present in the following documents:

• cas0105-0202-SD3.xlsx, sheet 1

View BVdb publication page

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Absolute pitch exhibits phenotypic and genetic overlap with synesthesia.

Human Molecular Genetics

Gregersen, Peter K PK; Kowalsky, Elena E; Lee, Annette A; Baron-Cohen, Simon S; Fisher, Simon E SE; Asher, Julian E JE; Ballard, David D; Freudenberg, Jan J; Li, Wentian W

Publication Date: 2013-05-15

Variant appearance in text: rs2278107

PubMed Link: 23406871

Variant Present in the following documents:

• Main text

View BVdb publication page

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EPH-EPHRIN in human gastrointestinal cancers.

World Journal Of Gastrointestinal Oncology

Sugimura, Haruhiko H; Wang, Jian-Dong JD; Mori, Hiroki H; Tsuboi, Masaru M; Nagura, Kiyoko K; Igarashi, Hisaki H; Tao, Hong H; Nakamura, Ritsuko R; Natsume, Hiroko H; Kahyo, Tomoaki T; Shinmura, Kazuya K; Konno, Hiroyuki H; Hamaya, Yasushi Y; Kanaoka, Shigeru S; Kataoka, Hideki H; Zhou, Xiao-Jun XJ

Publication Date: 2010-12-15

Variant appearance in text: rs2278107

PubMed Link: 21191536

Variant Present in the following documents:

• Main text

View BVdb publication page

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Whole genome survey of coding SNPs reveals a reproducible pathway determinant of Parkinson disease.

Human Mutation

Srinivasan, Balaji S BS; Doostzadeh, Jaleh J; Absalan, Farnaz F; Mohandessi, Sharareh S; Jalili, Roxana R; Bigdeli, Saharnaz S; Wang, Justin J; Mahadevan, Jaydev J; Lee, Caroline L G CL; Davis, Ronald W RW; William Langston, J J; Ronaghi, Mostafa M

Publication Date: 2009-02

Variant appearance in text: rs2278107

PubMed Link: 18853455

Variant Present in the following documents:

• Main text
• humu0030-0228.pdf

View BVdb publication page

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