Publications:

---

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.

Proteins

Lubin, Joseph H JH; Zardecki, Christine C; Dolan, Elliott M EM; Lu, Changpeng C; Shen, Zhuofan Z; Dutta, Shuchismita S; Westbrook, John D JD; Hudson, Brian P BP; Goodsell, David S DS; Williams, Jonathan K JK; Voigt, Maria M; Sarma, Vidur V; Xie, Lingjun L; Venkatachalam, Thejasvi T; Arnold, Steven S; Alfaro Alvarado, Luz Helena LH; Catalfano, Kevin K; Khan, Aaliyah A; McCarthy, Erika E; Staggers, Sophia S; Tinsley, Brea B; Trudeau, Alan A; Singh, Jitendra J; Whitmore, Lindsey L; Zheng, Helen H; Benedek, Matthew M; Currier, Jenna J; Dresel, Mark M; Duvvuru, Ashish A; Dyszel, Britney B; Fingar, Emily E; Hennen, Elizabeth M EM; Kirsch, Michael M; Khan, Ali A AA; Labrie-Cleary, Charlotte C; Laporte, Stephanie S; Lenkeit, Evan E; Martin, Kailey K; Orellana, Marilyn M; Ortiz-Alvarez de la Campa, Melanie M; Paredes, Isaac I; Wheeler, Baleigh B; Rupert, Allison A; Sam, Andrew A; See, Katherine K; Soto Zapata, Santiago S; Craig, Paul A PA; Hall, Bonnie L BL; Jiang, Jennifer J; Koeppe, Julia R JR; Mills, Stephen A SA; Pikaart, Michael J MJ; Roberts, Rebecca R; Bromberg, Yana Y; Hoyer, J Steen JS; Duffy, Siobain S; Tischfield, Jay J; Ruiz, Francesc X FX; Arnold, Eddy E; Baum, Jean J; Sandberg, Jesse J; Brannigan, Grace G; Khare, Sagar D SD; Burley, Stephen K SK

Publication Date: 2021-09-27

Variant appearance in text: 225: S301P

PubMed Link: 34580920

Variant Present in the following documents:

• Main text
• PROT-9999-0.pdf

View BVdb publication page

---

Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic.

Proteins

Lubin, Joseph H JH; Zardecki, Christine C; Dolan, Elliott M EM; Lu, Changpeng C; Shen, Zhuofan Z; Dutta, Shuchismita S; Westbrook, John D JD; Hudson, Brian P BP; Goodsell, David S DS; Williams, Jonathan K JK; Voigt, Maria M; Sarma, Vidur V; Xie, Lingjun L; Venkatachalam, Thejasvi T; Arnold, Steven S; Alfaro Alvarado, Luz Helena LH; Catalfano, Kevin K; Khan, Aaliyah A; McCarthy, Erika E; Staggers, Sophia S; Tinsley, Brea B; Trudeau, Alan A; Singh, Jitendra J; Whitmore, Lindsey L; Zheng, Helen H; Benedek, Matthew M; Currier, Jenna J; Dresel, Mark M; Duvvuru, Ashish A; Dyszel, Britney B; Fingar, Emily E; Hennen, Elizabeth M EM; Kirsch, Michael M; Khan, Ali A AA; Labrie-Cleary, Charlotte C; Laporte, Stephanie S; Lenkeit, Evan E; Martin, Kailey K; Orellana, Marilyn M; Ortiz-Alvarez de la Campa, Melanie M; Paredes, Isaac I; Wheeler, Baleigh B; Rupert, Allison A; Sam, Andrew A; See, Katherine K; Soto Zapata, Santiago S; Craig, Paul A PA; Hall, Bonnie L BL; Jiang, Jennifer J; Koeppe, Julia R JR; Mills, Stephen A SA; Pikaart, Michael J MJ; Roberts, Rebecca R; Bromberg, Yana Y; Hoyer, J Steen JS; Duffy, Siobain S; Tischfield, Jay J; Ruiz, Francesc X FX; Arnold, Eddy E; Baum, Jean J; Sandberg, Jesse J; Brannigan, Grace G; Khare, Sagar D SD; Burley, Stephen K SK

Publication Date: 2022-05

Variant appearance in text: 225: S301P

PubMed Link: 34580920

Variant Present in the following documents:

• Main text
• PROT-9999-0.pdf

View BVdb publication page

---

Secondary resistance to anti-EGFR therapy by transcriptional reprogramming in patient-derived colorectal cancer models.

Genome Medicine

Vangala, Deepak D; Ladigan, Swetlana S; Liffers, Sven T ST; Noseir, Soha S; Maghnouj, Abdelouahid A; Götze, Tina-Maria TM; Verdoodt, Berlinda B; Klein-Scory, Susanne S; Godfrey, Laura L; Zowada, Martina K MK; Huerta, Mario M; Edelstein, Daniel L DL; de Villarreal, Jaime Martinez JM; Marqués, Miriam M; Kumbrink, Jörg J; Jung, Andreas A; Schiergens, Tobias T; Werner, Jens J; Heinemann, Volker V; Stintzing, Sebastian S; Lindoerfer, Doris D; Mansmann, Ulrich U; Pohl, Michael M; Teschendorf, Christian C; Bernhardt, Christiane C; Wolters, Heiner H; Stern, Josef J; Usta, Selami S; Viebahn, Richard R; Admard, Jacob J; Casadei, Nicolas N; Fröhling, Stefan S; Ball, Claudia R CR; Siveke, Jens T JT; Glimm, Hanno H; Tannapfel, Andrea A; Schmiegel, Wolff W; Hahn, Stephan A SA

Publication Date: 2021-07-16

Variant appearance in text: 225: 901T>C

PubMed Link: 34271981

Variant Present in the following documents:

• 13073_2021_926_MOESM5_ESM.xlsx, sheet 31

View BVdb publication page

---

The evolving proteome of SARS-CoV-2 predominantly uses mutation combination strategy for survival.

Computational And Structural Biotechnology Journal

Patro, L Ponoop Prasad LPP; Sathyaseelan, Chakkarai C; Uttamrao, Patil Pranita PP; Rathinavelan, Thenmalarchelvi T

Publication Date: 2021

Variant appearance in text: 225: S301P

PubMed Link: 34109017

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

View BVdb publication page

---

A Multipronged Approach Establishes Covalent Modification of β-Tubulin as the Mode of Action of Benzamide Anti-cancer Toxins.

Journal Of Medicinal Chemistry

Povedano, Juan Manuel JM; Rallabandi, Rameshu R; Bai, Xin X; Ye, Xuecheng X; Liou, Joel J; Chen, Hong H; Kim, Jiwoong J; Xie, Yang Y; Posner, Bruce B; Rice, Luke L; De Brabander, Jef K JK; McFadden, David G DG

Publication Date: 2020-11-25

Variant appearance in text: 225: 901T>C

PubMed Link: 33180487

Variant Present in the following documents:

• jm0c01482_si_002.xlsx, sheet 1

View BVdb publication page

---

RNA editing of BFP, a point mutant of GFP, using artificial APOBEC1 deaminase to restore the genetic code.

Scientific Reports

Bhakta, Sonali S; Sakari, Matomo M; Tsukahara, Toshifumi T

Publication Date: 2020-10-14

Variant appearance in text: 225: 901T>C

PubMed Link: 33057101

Variant Present in the following documents:

• 41598_2020_74374_MOESM4_ESM.xlsx, sheet 1

View BVdb publication page

---

High-density genetic linkage-map construction of hawthorn and QTL mapping for important fruit traits.

Plos One

Zhao, Yuhui Y; Zhao, Yidi Y; Guo, Yinshan Y; Su, Kai K; Shi, Xiaochang X; Liu, Di D; Zhang, Jijun J

Publication Date: 2020

Variant appearance in text: 225: 901T>C

PubMed Link: 32045463

Variant Present in the following documents:

• pone.0229020.s004.xlsx, sheet 1

View BVdb publication page

---

Identification of Single Nucleotide Polymorphism in Red Clover (Trifolium pratense L.) Using Targeted Genomic Amplicon Sequencing and RNA-seq.

Frontiers In Plant Science

Li, Wenli W; Riday, Heathcliffe H; Riehle, Christina C; Edwards, Andrea A; Dinkins, Randy R

Publication Date: 2019

Variant appearance in text: 225: 901T>C

PubMed Link: 31708937

Variant Present in the following documents:

• DataSheet_2.xlsx, sheet 1

View BVdb publication page

---

Targeting DDR2 enhances tumor response to anti-PD-1 immunotherapy.

Science Advances

Tu, Megan M MM; Lee, Francis Y F FYF; Jones, Robert T RT; Kimball, Abigail K AK; Saravia, Elizabeth E; Graziano, Robert F RF; Coleman, Brianne B; Menard, Krista K; Yan, Jun J; Michaud, Erin E; Chang, Han H; Abdel-Hafiz, Hany A HA; Rozhok, Andrii I AI; Duex, Jason E JE; Agarwal, Neeraj N; Chauca-Diaz, Ana A; Johnson, Linda K LK; Ng, Terry L TL; Cambier, John C JC; Clambey, Eric T ET; Costello, James C JC; Korman, Alan J AJ; Theodorescu, Dan D

Publication Date: 2019-02

Variant appearance in text: 225: 901T>C

PubMed Link: 30801016

Variant Present in the following documents:

• aav2437_Table_S1.xlsx, sheet 1

View BVdb publication page

---

Revisiting aneuploidy profile of surgically retrieved spermatozoa by whole exome sequencing molecular karyotype.

Plos One

Cheung, Stephanie S; Schlegel, Peter N PN; Rosenwaks, Zev Z; Palermo, Gianpiero D GD

Publication Date: 2019

Variant appearance in text: 225: 901T>C

PubMed Link: 30608972

Variant Present in the following documents:

• pone.0210079.s007.xlsx, sheet 3

View BVdb publication page

---

Integrated genomic and metabolomic profiling of ISC1, an emerging Leishmania donovani population in the Indian subcontinent.

Infection, Genetics And Evolution : Journal Of Molecular Epidemiology And Evolutionary Genetics In Infectious Diseases

Cuypers, Bart B; Berg, Maya M; Imamura, Hideo H; Dumetz, Franck F; De Muylder, Géraldine G; Domagalska, Malgorzata A MA; Rijal, Suman S; Bhattarai, Narayan Raj NR; Maes, Ilse I; Sanders, Mandy M; Cotton, James A JA; Meysman, Pieter P; Laukens, Kris K; Dujardin, Jean-Claude JC

Publication Date: 2018-08

Variant appearance in text: 225: 901T>C

PubMed Link: 29679745

Variant Present in the following documents:

• mmc3.xlsx, sheet 1

View BVdb publication page

---