Publications:

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HaploCoV: unsupervised classification and rapid detection of novel emerging variants of SARS-CoV-2.

Communications Biology

Chiara, Matteo M; Horner, David S DS; Ferrandi, Erika E; Gissi, Carmela C; Pesole, Graziano G

Publication Date: 2023-04-22

Variant appearance in text: TG: 83C>T

PubMed Link: 37087497

Variant Present in the following documents:

• 42003_2023_4784_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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MC38 colorectal tumor cell lines from two different sources display substantial differences in transcriptome, mutanome and neoantigen expression.

Frontiers In Immunology

Schrörs, Barbara B; Hos, Brett J BJ; Yildiz, Ikra G IG; Löwer, Martin M; Lang, Franziska F; Holtsträter, Christoph C; Becker, Julia J; Vormehr, Mathias M; Sahin, Ugur U; Ossendorp, Ferry F; Diken, Mustafa M

Publication Date: 2023

Variant appearance in text: TG: A28V

PubMed Link: 36969213

Variant Present in the following documents:

• Table_1.xlsx, sheet 1

View BVdb publication page

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Recapitulating thyroid cancer histotypes through engineering embryonic stem cells.

Nature Communications

Veschi, Veronica V; Turdo, Alice A; Modica, Chiara C; Verona, Francesco F; Di Franco, Simone S; Gaggianesi, Miriam M; Tirrò, Elena E; Di Bella, Sebastiano S; Iacono, Melania Lo ML; Pantina, Vincenzo Davide VD; Porcelli, Gaetana G; Mangiapane, Laura Rosa LR; Bianca, Paola P; Rizzo, Aroldo A; Sciacca, Elisabetta E; Pillitteri, Irene I; Vella, Veronica V; Belfiore, Antonino A; Bongiorno, Maria Rita MR; Pistone, Giuseppe G; Memeo, Lorenzo L; Colarossi, Lorenzo L; Giuffrida, Dario D; Colarossi, Cristina C; Vigneri, Paolo P; Todaro, Matilde M; Stassi, Giorgio G

Publication Date: 2023-03-11

Variant appearance in text: TG: A28V

PubMed Link: 36906579

Variant Present in the following documents:

• 41467_2023_36922_MOESM4_ESM.xls, sheet 2

View BVdb publication page

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Evolution of intra-tumoral heterogeneity across different pathological stages in papillary thyroid carcinoma.

Cancer Cell International

Affinito, Ornella O; Orlandella, Francesca Maria FM; Luciano, Neila N; Salvatore, Marco M; Salvatore, Giuliana G; Franzese, Monica M

Publication Date: 2022-08-22

Variant appearance in text: TG: A28V

PubMed Link: 35996174

Variant Present in the following documents:

• 12935_2022_2680_MOESM5_ESM.xlsx, sheet 4

View BVdb publication page

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Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes.

Nature Genetics

Zhou, Xueya X; Feliciano, Pamela P; Shu, Chang C; Wang, Tianyun T; Astrovskaya, Irina I; Hall, Jacob B JB; Obiajulu, Joseph U JU; Wright, Jessica R JR; Murali, Shwetha C SC; Xu, Simon Xuming SX; Brueggeman, Leo L; Thomas, Taylor R TR; Marchenko, Olena O; Fleisch, Christopher C; Barns, Sarah D SD; Snyder, LeeAnne Green LG; Han, Bing B; Chang, Timothy S TS; Turner, Tychele N TN; Harvey, William T WT; Nishida, Andrew A; O'Roak, Brian J BJ; Geschwind, Daniel H DH; , ; Michaelson, Jacob J JJ; Volfovsky, Natalia N; Eichler, Evan E EE; Shen, Yufeng Y; Chung, Wendy K WK

Publication Date: 2022-09

Variant appearance in text: TG: 83C>T

PubMed Link: 35982159

Variant Present in the following documents:

• 41588_2022_1148_MOESM7_ESM.xlsx, sheet 1
• 41588_2022_1148_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation.

Cell Stem Cell

Merkle, Florian T FT; Ghosh, Sulagna S; Genovese, Giulio G; Handsaker, Robert E RE; Kashin, Seva S; Meyer, Daniel D; Karczewski, Konrad J KJ; O'Dushlaine, Colm C; Pato, Carlos C; Pato, Michele M; MacArthur, Daniel G DG; McCarroll, Steven A SA; Eggan, Kevin K

Publication Date: 2022-03-03

Variant appearance in text: TG: 83C>T; Ala28Val; rs114543085

PubMed Link: 35176222

Variant Present in the following documents:

• mmc5.xlsx, sheet 1
• mmc5.xlsx, sheet 3

View BVdb publication page

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KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.

Plos One

Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW

Publication Date: 2022

Variant appearance in text: TG: A28V

PubMed Link: 35081118

Variant Present in the following documents:

• pone.0251286.s005.xlsx, sheet 8

View BVdb publication page

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KLF3 and PAX6 are candidate driver genes in late-stage, MSI-hypermutated endometrioid endometrial carcinomas.

Plos One

Rudd, Meghan L ML; Hansen, Nancy F NF; Zhang, Xiaolu X; Urick, Mary Ellen ME; Zhang, Suiyuan S; Merino, Maria J MJ; , ; Mullikin, James C JC; Brody, Lawrence C LC; Bell, Daphne W DW

Publication Date: 2022

Variant appearance in text: TG: A28V

PubMed Link: 35081118

Variant Present in the following documents:

• pone.0251286.s005.xlsx, sheet 8

View BVdb publication page

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Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function.

International Journal Of Biological Macromolecules

Hassan, Sk Sarif SS; Lundstrom, Kenneth K; Serrano-Aroca, Ángel Á; Adadi, Parise P; Aljabali, Alaa A A AAA; Redwan, Elrashdy M EM; Lal, Amos A; Kandimalla, Ramesh R; El-Aziz, Tarek Mohamed Abd TMA; Pal Choudhury, Pabitra P; Azad, Gajendra Kumar GK; Sherchan, Samendra P SP; Chauhan, Gaurav G; Tambuwala, Murtaza M; Takayama, Kazuo K; Barh, Debmalya D; Palu, Giorgio G; Basu, Pallab P; Uversky, Vladimir N VN

Publication Date: 2022-01-01

Variant appearance in text: TG: A28V

PubMed Link: 34863825

Variant Present in the following documents:

• Main text

View BVdb publication page

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Emergence of unique SARS-CoV-2 ORF10 variants and their impact on protein structure and function.

International Journal Of Biological Macromolecules

Hassan, Sk Sarif SS; Lundstrom, Kenneth K; Serrano-Aroca, Ángel Á; Adadi, Parise P; Aljabali, Alaa A A AAA; Redwan, Elrashdy M EM; Lal, Amos A; Kandimalla, Ramesh R; El-Aziz, Tarek Mohamed Abd TMA; Pal Choudhury, Pabitra P; Azad, Gajendra Kumar GK; Sherchan, Samendra P SP; Chauhan, Gaurav G; Tambuwala, Murtaza M; Takayama, Kazuo K; Barh, Debmalya D; Palu, Giorgio G; Basu, Pallab P; Uversky, Vladimir N VN

Publication Date: 2021-12-02

Variant appearance in text: TG: A28V

PubMed Link: 34863825

Variant Present in the following documents:

• Main text

View BVdb publication page

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Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.

Virus Research

Kumar, Sanjeet S; Bansal, Kanika K

Publication Date: 2022-01-15

Variant appearance in text: TG: A28V

PubMed Link: 34822953

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

View BVdb publication page

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Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2: A pan India study.

Virus Research

Kumar, Sanjeet S; Bansal, Kanika K

Publication Date: 2021-11-22

Variant appearance in text: TG: A28V

PubMed Link: 34822953

Variant Present in the following documents:

• mmc4.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: 2021-10-19

Variant appearance in text: TG: A28V

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 11

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: TG: A28V

PubMed Link: 34673281

Variant Present in the following documents:

• mmc2.xlsx, sheet 11

View BVdb publication page

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Large scale clinical exome sequencing uncovers the scope and severity of skin disorders associated with MC1R genetic variants.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Moore, Bryn S BS; Luo, Jonathan Z JZ; Stepanchick, Ann N AN; Mirshahi, Tooraj T

Publication Date: 2021-12

Variant appearance in text: TG: Ala28Val

PubMed Link: 34326492

Variant Present in the following documents:

• NIHMS1754145-supplement-Supplemental_Table_2.xlsx, sheet 1
• NIHMS1754145-supplement-Supplemental_Table_3.xlsx, sheet 1

View BVdb publication page

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Large scale clinical exome sequencing uncovers the scope and severity of skin disorders associated with MC1R genetic variants.

Genetics In Medicine : Official Journal Of The American College Of Medical Genetics

Moore, Bryn S BS; Luo, Jonathan Z JZ; Stepanchick, Ann N AN; Mirshahi, Tooraj T

Publication Date: 2021-12

Variant appearance in text: TG: Ala28Val

PubMed Link: 34326492

Variant Present in the following documents:

• NIHMS1754145-supplement-Supplemental_Table_3.xlsx, sheet 1
• NIHMS1754145-supplement-Supplemental_Table_2.xlsx, sheet 1

View BVdb publication page

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Permethrin resistance in Aedes aegypti: Genomic variants that confer knockdown resistance, recovery, and death.

Plos Genetics

Saavedra-Rodriguez, Karla K; Campbell, Corey L CL; Lozano, Saul S; Penilla-Navarro, Patricia P; Lopez-Solis, Alma A; Solis-Santoyo, Francisco F; Rodriguez, Americo D AD; Perera, Rushika R; Black Iv, William C WC

Publication Date: 2021-06

Variant appearance in text: TG: A28V

PubMed Link: 34138859

Variant Present in the following documents:

• pgen.1009606.s001.xlsx, sheet 1
• pgen.1009606.s002.xlsx, sheet 1

View BVdb publication page

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The mutational landscape of human olfactory G protein-coupled receptors.

Bmc Biology

Jimenez, Ramón Cierco RC; Casajuana-Martin, Nil N; García-Recio, Adrián A; Alcántara, Lidia L; Pardo, Leonardo L; Campillo, Mercedes M; Gonzalez, Angel A

Publication Date: 2021-02-05

Variant appearance in text: TG: 83C>T; Ala28Val

PubMed Link: 33546694

Variant Present in the following documents:

• 12915_2021_962_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

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Design of a companion bioinformatic tool to detect the emergence and geographical distribution of SARS-CoV-2 Spike protein genetic variants.

Journal Of Translational Medicine

Massacci, Alice A; Sperandio, Eleonora E; D'Ambrosio, Lorenzo L; Maffei, Mariano M; Palombo, Fabio F; Aurisicchio, Luigi L; Ciliberto, Gennaro G; Pallocca, Matteo M

Publication Date: 2020-12-30

Variant appearance in text: TG: 83C>T

PubMed Link: 33380328

Variant Present in the following documents:

• 12967_2020_2675_MOESM1_ESM.xlsx, sheet 1

View BVdb publication page

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Integrated molecular drivers coordinate biological and clinical states in melanoma.

Nature Genetics

Conway, Jake R JR; Dietlein, Felix F; Taylor-Weiner, Amaro A; AlDubayan, Saud S; Vokes, Natalie N; Keenan, Tanya T; Reardon, Brendan B; He, Meng Xiao MX; Margolis, Claire A CA; Weirather, Jason L JL; Haq, Rizwan R; Schilling, Bastian B; Stephen Hodi, F F; Schadendorf, Dirk D; Liu, David D; Van Allen, Eliezer M EM

Publication Date: 2020-12

Variant appearance in text: TG: 83C>T

PubMed Link: 33230298

Variant Present in the following documents:

• NIHMS1637640-supplement-SuppData1.xlsx, sheet 1

View BVdb publication page

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K-Ras-Activated Cells Can Develop into Lung Tumors When Runx3-Mediated Tumor Suppressor Pathways Are Abrogated.

Molecules And Cells

Lee, You-Soub YS; Lee, Ja-Yeol JY; Song, Soo-Hyun SH; Kim, Da-Mi DM; Lee, Jung-Won JW; Chi, Xin-Zi XZ; Ito, Yoshiaki Y; Bae, Suk-Chul SC

Publication Date: 2020-10-31

Variant appearance in text: TG: 83C>T; Ala28Val

PubMed Link: 33115981

Variant Present in the following documents:

• molce-43-889_Supple.xlsx, sheet 1

View BVdb publication page

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Precise allele-specific genome editing by spatiotemporal control of CRISPR-Cas9 via pronuclear transplantation.

Nature Communications

Li, Yanhe Y; Weng, Yuteng Y; Bai, Dandan D; Jia, Yanping Y; Liu, Yingdong Y; Zhang, Yalin Y; Kou, Xiaochen X; Zhao, Yanhong Y; Ruan, Jingling J; Chen, Jiayu J; Yin, Jiqing J; Wang, Hong H; Teng, Xiaoming X; Wang, Zuolin Z; Liu, Wenqiang W; Gao, Shaorong S

Publication Date: 2020-09-14

Variant appearance in text: TG: 83C>T

PubMed Link: 32929070

Variant Present in the following documents:

• 41467_2020_18391_MOESM5_ESM.xlsx, sheet 1

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: TG: 83C>T; Ala28Val

PubMed Link: 32433464

Variant Present in the following documents:

• 41467_2020_16399_MOESM5_ESM.xlsx, sheet 1

View BVdb publication page

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Comparative analysis of primary versus relapse/refractory DLBCL identifies shifts in mutation spectrum.

Oncotarget

Greenawalt, Danielle M DM; Liang, Winnie S WS; Saif, Sakina S; Johnson, Justin J; Todorov, Petar P; Dulak, Austin A; Enriquez, Daniel D; Halperin, Rebecca R; Ahmed, Ambar A; Saveliev, Vladislav V; Carpten, John J; Craig, David D; Barrett, J Carl JC; Dougherty, Brian B; Zinda, Michael M; Fawell, Stephen S; Dry, Jonathan R JR; Byth, Kate K

Publication Date: 2017-11-21

Variant appearance in text: TG: 83C>T

PubMed Link: 29245897

Variant Present in the following documents:

• oncotarget-08-99237-s002.xlsx, sheet 1
• oncotarget-08-99237-s003.xlsx, sheet 1

View BVdb publication page

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Landscape of genomic diversity and host adaptation in Fusarium graminearum.

Bmc Genomics

Laurent, Benoit B; Moinard, Magalie M; Spataro, Cathy C; Ponts, Nadia N; Barreau, Christian C; Foulongne-Oriol, Marie M

Publication Date: 2017-02-23

Variant appearance in text: TG: 83C>T

PubMed Link: 28231761

Variant Present in the following documents:

• 12864_2017_3524_MOESM3_ESM.xlsx, sheet 2

View BVdb publication page

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Variant discovery in the sheep milk transcriptome using RNA sequencing.

Bmc Genomics

Suárez-Vega, Aroa A; Gutiérrez-Gil, Beatriz B; Klopp, Christophe C; Tosser-Klopp, Gwenola G; Arranz, Juan José JJ

Publication Date: 2017-02-15

Variant appearance in text: TG: 83C>T

PubMed Link: 28202015

Variant Present in the following documents:

• 12864_2017_3581_MOESM1_ESM.xlsx, sheet 1

View BVdb publication page

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A Landscape of Pharmacogenomic Interactions in Cancer.

Cell

Iorio, Francesco F; Knijnenburg, Theo A TA; Vis, Daniel J DJ; Bignell, Graham R GR; Menden, Michael P MP; Schubert, Michael M; Aben, Nanne N; Gonçalves, Emanuel E; Barthorpe, Syd S; Lightfoot, Howard H; Cokelaer, Thomas T; Greninger, Patricia P; van Dyk, Ewald E; Chang, Han H; de Silva, Heshani H; Heyn, Holger H; Deng, Xianming X; Egan, Regina K RK; Liu, Qingsong Q; Mironenko, Tatiana T; Mitropoulos, Xeni X; Richardson, Laura L; Wang, Jinhua J; Zhang, Tinghu T; Moran, Sebastian S; Sayols, Sergi S; Soleimani, Maryam M; Tamborero, David D; Lopez-Bigas, Nuria N; Ross-Macdonald, Petra P; Esteller, Manel M; Gray, Nathanael S NS; Haber, Daniel A DA; Stratton, Michael R MR; Benes, Cyril H CH; Wessels, Lodewyk F A LFA; Saez-Rodriguez, Julio J; McDermott, Ultan U; Garnett, Mathew J MJ

Publication Date: 2016-07-28

Variant appearance in text: TG: 83C>T; A28V

PubMed Link: 27397505

Variant Present in the following documents:

• mmc3.xlsx, sheet 3

View BVdb publication page

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Simultaneous DNA and RNA Mapping of Somatic Mitochondrial Mutations across Diverse Human Cancers.

Plos Genetics

Stewart, James B JB; Alaei-Mahabadi, Babak B; Sabarinathan, Radhakrishnan R; Samuelsson, Tore T; Gorodkin, Jan J; Gustafsson, Claes M CM; Larsson, Erik E

Publication Date: 2015-06

Variant appearance in text: TG: A28V

PubMed Link: 26125550

Variant Present in the following documents:

• pgen.1005333.s008.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: TG: A28V; rs114543085

PubMed Link: 25032700

Variant Present in the following documents:

• pone.0101670.s004.xlsx, sheet 1

View BVdb publication page

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