Publications:

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Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures.

Scientific Reports

Zheng, Weisheng W; Pu, Mengchen M; Li, Xiaorong X; Du, Zhaolan Z; Jin, Sutong S; Li, Xingshuai X; Zhou, Jielong J; Zhang, Yingsheng Y

Publication Date: 2023-05-30

Variant appearance in text: 225: A52S

PubMed Link: 37253775

Variant Present in the following documents:

• 41598_2023_35842_MOESM8_ESM.xlsx, sheet 3
• 41598_2023_35842_MOESM8_ESM.xlsx, sheet 1

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Persistent mutation burden drives sustained anti-tumor immune responses.

Nature Medicine

Niknafs, Noushin N; Balan, Archana A; Cherry, Christopher C; Hummelink, Karlijn K; Monkhorst, Kim K; Shao, Xiaoshan M XM; Belcaid, Zineb Z; Marrone, Kristen A KA; Murray, Joseph J; Smith, Kellie N KN; Levy, Benjamin B; Feliciano, Josephine J; Hann, Christine L CL; Lam, Vincent V; Pardoll, Drew M DM; Karchin, Rachel R; Seiwert, Tanguy Y TY; Brahmer, Julie R JR; Forde, Patrick M PM; Velculescu, Victor E VE; Anagnostou, Valsamo V

Publication Date: 2023-01-26

Variant appearance in text: 225: A52S

PubMed Link: 36702947

Variant Present in the following documents:

• 41591_2022_2163_MOESM3_ESM.xlsx, sheet 4

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Glutathione peroxidase 2 is a metabolic driver of the tumor immune microenvironment and immune checkpoint inhibitor response.

Journal For Immunotherapy Of Cancer

Ahmed, Kazi Mokim KM; Veeramachaneni, Ratna R; Deng, Defeng D; Putluri, Nagireddy N; Putluri, Vasanta V; Cardenas, Maria F MF; Wheeler, David A DA; Decker, William K WK; Frederick, Andy I AI; Kazi, Sawad S; Sikora, Andrew G AG; Sandulache, Vlad C VC; Frederick, Mitchell J MJ

Publication Date: 2022-08

Variant appearance in text: 225: A52S

PubMed Link: 36002187

Variant Present in the following documents:

• jitc-2022-004752supp001.xlsx, sheet 3
• jitc-2022-004752supp001.xlsx, sheet 2

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Frequent somatic gene conversion as a mechanism for loss of heterozygosity in tumor suppressor genes.

Genome Research

Takahashi, Kazuki K KK; Innan, Hideki H

Publication Date: 2022-06

Variant appearance in text: 225: A52S

PubMed Link: 35618418

Variant Present in the following documents:

• supp_gr.276617.122_Supplemental_Tables.xlsx, sheet 9

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A platform for oncogenomic reporting and interpretation.

Nature Communications

Reisle, Caralyn C; Williamson, Laura M LM; Pleasance, Erin E; Davies, Anna A; Pellegrini, Brayden B; Bleile, Dustin W DW; Mungall, Karen L KL; Chuah, Eric E; Jones, Martin R MR; Ma, Yussanne Y; Lewis, Eleanor E; Beckie, Isaac I; Pham, David D; Matiello Pletz, Raphael R; Muhammadzadeh, Amir A; Pierce, Brandon M BM; Li, Jacky J; Stevenson, Ross R; Wong, Hansen H; Bailey, Lance L; Reisle, Abbey A; Douglas, Matthew M; Bonakdar, Melika M; Nelson, Jessica M T JMT; Grisdale, Cameron J CJ; Krzywinski, Martin M; Fisic, Ana A; Mitchell, Teresa T; Renouf, Daniel J DJ; Yip, Stephen S; Laskin, Janessa J; Marra, Marco A MA; Jones, Steven J M SJM

Publication Date: 2022-02-09

Variant appearance in text: 225: A52S

PubMed Link: 35140225

Variant Present in the following documents:

• 41467_2022_28348_MOESM4_ESM.xlsx, sheet 9

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Allele-specific genomic data elucidate the role of somatic gain and copy-number neutral loss of heterozygosity in cancer.

Cell Systems

Ciani, Yari Y; Fedrizzi, Tarcisio T; Prandi, Davide D; Lorenzin, Francesca F; Locallo, Alessio A; Gasperini, Paola P; Franceschini, Gian Marco GM; Benelli, Matteo M; Elemento, Olivier O; Fava, Luca L LL; Inga, Alberto A; Demichelis, Francesca F

Publication Date: 2022-02-16

Variant appearance in text: 225: A52S

PubMed Link: 34731645

Variant Present in the following documents:

• mmc2.xlsx, sheet 1

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Long noncoding RNA SNHG1 promotes TERT expression by sponging miR-18b-5p in breast cancer.

Cell & Bioscience

Kang, Yujuan Y; Wan, Lin L; Wang, Qin Q; Yin, Yanling Y; Liu, Jiena J; Liu, Lei L; Wu, Hao H; Zhang, Lei L; Zhang, Xin X; Xu, Shouping S; Pang, Da D

Publication Date: 2021-08-31

Variant appearance in text: 225: A52S

PubMed Link: 34465388

Variant Present in the following documents:

• 13578_2021_675_MOESM4_ESM.pdf

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Fast mutual exclusivity algorithm nominates potential synthetic lethal gene pairs through brute force matrix product computations.

Computational And Structural Biotechnology Journal

Fedrizzi, Tarcisio T; Ciani, Yari Y; Lorenzin, Francesca F; Cantore, Thomas T; Gasperini, Paola P; Demichelis, Francesca F

Publication Date: 2021

Variant appearance in text: 225: A52S

PubMed Link: 34429855

Variant Present in the following documents:

• mmc2.xlsx, sheet 2

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Targeting natural splicing plasticity of APOBEC3B restricts its expression and mutagenic activity.

Communications Biology

Rouf Banday, A A; Onabajo, Olusegun O OO; Lin, Seraph Han-Yin SH; Obajemu, Adeola A; Vargas, Joselin M JM; Delviks-Frankenberry, Krista A KA; Lamy, Philippe P; Bayanjargal, Ariunaa A; Zettelmeyer, Clara C; Florez-Vargas, Oscar O; Pathak, Vinay K VK; Dyrskjøt, Lars L; Prokunina-Olsson, Ludmila L

Publication Date: 2021-03-22

Variant appearance in text: 225: A52S

PubMed Link: 33753867

Variant Present in the following documents:

• 42003_2021_1844_MOESM3_ESM.xlsx, sheet 2

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DNA mismatch repair promotes APOBEC3-mediated diffuse hypermutation in human cancers.

Nature Genetics

Mas-Ponte, David D; Supek, Fran F

Publication Date: 2020-09

Variant appearance in text: 225: A52S

PubMed Link: 32747826

Variant Present in the following documents:

• EMS118039-supplement-Supplementary_Tables_1_10.xlsx, sheet 5

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High expression of oxidative phosphorylation genes predicts improved survival in squamous cell carcinomas of the head and neck and lung.

Scientific Reports

Frederick, Mitchell M; Skinner, Heath D HD; Kazi, Sawad A SA; Sikora, Andrew G AG; Sandulache, Vlad C VC

Publication Date: 2020-04-14

Variant appearance in text: 225: A52S

PubMed Link: 32286489

Variant Present in the following documents:

• 41598_2020_63448_MOESM2_ESM.xlsx, sheet 14
• 41598_2020_63448_MOESM2_ESM.xlsx, sheet 7

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NOTCH target gene HES5 mediates oncogenic and tumor suppressive functions in hepatocarcinogenesis.

Oncogene

Luiken, Sarah S; Fraas, Angelika A; Bieg, Matthias M; Sugiyanto, Raisatun R; Goeppert, Benjamin B; Singer, Stephan S; Ploeger, Carolin C; Warsow, Gregor G; Marquardt, Jens U JU; Sticht, Carsten C; De La Torre, Carolina C; Pusch, Stefan S; Mehrabi, Arianeb A; Gretz, Norbert N; Schlesner, Matthias M; Eils, Roland R; Schirmacher, Peter P; Longerich, Thomas T; Roessler, Stephanie S

Publication Date: 2020-04

Variant appearance in text: 225: 154G>T

PubMed Link: 32055024

Variant Present in the following documents:

• 41388_2020_1198_MOESM2_ESM.xlsx, sheet 1

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Integrative and comparative genomic analyses identify clinically relevant pulmonary carcinoid groups and unveil the supra-carcinoids.

Nature Communications

Alcala, N N; Leblay, N N; Gabriel, A A G AAG; Mangiante, L L; Hervas, D D; Giffon, T T; Sertier, A S AS; Ferrari, A A; Derks, J J; Ghantous, A A; Delhomme, T M TM; Chabrier, A A; Cuenin, C C; Abedi-Ardekani, B B; Boland, A A; Olaso, R R; Meyer, V V; Altmuller, J J; Le Calvez-Kelm, F F; Durand, G G; Voegele, C C; Boyault, S S; Moonen, L L; Lemaitre, N N; Lorimier, P P; Toffart, A C AC; Soltermann, A A; Clement, J H JH; Saenger, J J; Field, J K JK; Brevet, M M; Blanc-Fournier, C C; Galateau-Salle, F F; Le Stang, N N; Russell, P A PA; Wright, G G; Sozzi, G G; Pastorino, U U; Lacomme, S S; Vignaud, J M JM; Hofman, V V; Hofman, P P; Brustugun, O T OT; Lund-Iversen, M M; Thomas de Montpreville, V V; Muscarella, L A LA; Graziano, P P; Popper, H H; Stojsic, J J; Deleuze, J F JF; Herceg, Z Z; Viari, A A; Nuernberg, P P; Pelosi, G G; Dingemans, A M C AMC; Milione, M M; Roz, L L; Brcic, L L; Volante, M M; Papotti, M G MG; Caux, C C; Sandoval, J J; Hernandez-Vargas, H H; Brambilla, E E; Speel, E J M EJM; Girard, N N; Lantuejoul, S S; McKay, J D JD; Foll, M M; Fernandez-Cuesta, L L

Publication Date: 2019-08-20

Variant appearance in text: 225: A52S

PubMed Link: 31431620

Variant Present in the following documents:

• 41467_2019_11276_MOESM7_ESM.xlsx, sheet 1

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Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max).

Bmc Plant Biology

Jaiswal, Sarika S; Jadhav, Pravin V PV; Jasrotia, Rahul Singh RS; Kale, Prashant B PB; Kad, Snehal K SK; Moharil, Mangesh P MP; Dudhare, Mahendra S MS; Kheni, Jashminkumar J; Deshmukh, Amit G AG; Mane, Shyamsundar S SS; Nandanwar, Ravindra S RS; Penna, Suprasanna S; Manjaya, Joy G JG; Iquebal, Mir Asif MA; Tomar, Rukam Singh RS; Kawar, Prashant G PG; Rai, Anil A; Kumar, Dinesh D

Publication Date: 2019-01-15

Variant appearance in text: 225: 154G>T

PubMed Link: 30646861

Variant Present in the following documents:

• 12870_2018_1601_MOESM7_ESM.xlsx, sheet 1

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Genomic Features of Response to Combination Immunotherapy in Patients with Advanced Non-Small-Cell Lung Cancer.

Cancer Cell

Hellmann, Matthew D MD; Nathanson, Tavi T; Rizvi, Hira H; Creelan, Benjamin C BC; Sanchez-Vega, Francisco F; Ahuja, Arun A; Ni, Ai A; Novik, Jacki B JB; Mangarin, Levi M B LMB; Abu-Akeel, Mohsen M; Liu, Cailian C; Sauter, Jennifer L JL; Rekhtman, Natasha N; Chang, Eliza E; Callahan, Margaret K MK; Chaft, Jamie E JE; Voss, Martin H MH; Tenet, Megan M; Li, Xue-Mei XM; Covello, Kelly K; Renninger, Andrea A; Vitazka, Patrik P; Geese, William J WJ; Borghaei, Hossein H; Rudin, Charles M CM; Antonia, Scott J SJ; Swanton, Charles C; Hammerbacher, Jeff J; Merghoub, Taha T; McGranahan, Nicholas N; Snyder, Alexandra A; Wolchok, Jedd D JD

Publication Date: 2018-05-14

Variant appearance in text: 225: A52S

PubMed Link: 29657128

Variant Present in the following documents:

• mmc3.xlsx, sheet 3

View BVdb publication page

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