Publications:

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Rational design of phase separating peptides based on phase separating protein sequence of p53.

Scientific Reports

Kamagata, Kiyoto K; Hando, Atsumi A; Ariefai, Maulana M; Iwaki, Nanako N; Kanbayashi, Saori S; Koike, Ryotaro R; Ikeda, Keisuke K

Publication Date: 2023-04-06

Variant appearance in text: p53: Y234F

PubMed Link: 37024567

Variant Present in the following documents:

• Main text
• 41598_2023_Article_32632.pdf

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CTCF DNA-binding domain undergoes dynamic and selective protein-protein interactions.

Iscience

Zhou, Rong R; Tian, Kai K; Huang, Jie J; Duan, Wenjia W; Fu, Hongye H; Feng, Ying Y; Wang, Hui H; Jiang, Yongpeng Y; Li, Yuanjun Y; Wang, Rui R; Hu, Jiazhi J; Ma, Hanhui H; Qi, Zhi Z; Ji, Xiong X

Publication Date: 2022-09-16

Variant appearance in text: p53: 701A>T

PubMed Link: 36117989

Variant Present in the following documents:

• mmc4.xlsx, sheet 1

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Rational peptide design for regulating liquid-liquid phase separation on the basis of residue-residue contact energy.

Scientific Reports

Kamagata, Kiyoto K; Ariefai, Maulana M; Takahashi, Hiroto H; Hando, Atsumi A; Subekti, Dwiky Rendra Graha DRG; Ikeda, Keisuke K; Hirano, Atsushi A; Kameda, Tomoshi T

Publication Date: 2022-08-12

Variant appearance in text: p53: Y234F

PubMed Link: 35962177

Variant Present in the following documents:

• Main text
• 41598_2022_Article_17829.pdf

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Structure-dependent recruitment and diffusion of guest proteins in liquid droplets of FUS.

Scientific Reports

Kamagata, Kiyoto K; Iwaki, Nanako N; Kanbayashi, Saori S; Banerjee, Trishit T; Chiba, Rika R; Gaudon, Virginie V; Castaing, Bertrand B; Sakomoto, Seiji S

Publication Date: 2022-05-02

Variant appearance in text: p53: Y234F

PubMed Link: 35501371

Variant Present in the following documents:

• Main text
• 41598_2022_Article_11177.pdf

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Molecular principles of recruitment and dynamics of guest proteins in liquid droplets.

Scientific Reports

Kamagata, Kiyoto K; Iwaki, Nanako N; Hazra, Milan Kumar MK; Kanbayashi, Saori S; Banerjee, Trishit T; Chiba, Rika R; Sakomoto, Seiji S; Gaudon, Virginie V; Castaing, Bertrand B; Takahashi, Hiroto H; Kimura, Michiko M; Oikawa, Hiroyuki H; Takahashi, Satoshi S; Levy, Yaakov Y

Publication Date: 2021-09-29

Variant appearance in text: p53: Y234F

PubMed Link: 34588591

Variant Present in the following documents:

• Main text
• 41598_2021_Article_98955.pdf

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Transient binding and jumping dynamics of p53 along DNA revealed by sub-millisecond resolved single-molecule fluorescence tracking.

Scientific Reports

Subekti, Dwiky Rendra Graha DRG; Murata, Agato A; Itoh, Yuji Y; Takahashi, Satoshi S; Kamagata, Kiyoto K

Publication Date: 2020-08-13

Variant appearance in text: p53: Y234F

PubMed Link: 32792545

Variant Present in the following documents:

• Main text
• 41598_2020_Article_70763.pdf

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White blood cell and cell-free DNA analyses for detection of residual disease in gastric cancer.

Nature Communications

Leal, Alessandro A; van Grieken, Nicole C T NCT; Palsgrove, Doreen N DN; Phallen, Jillian J; Medina, Jamie E JE; Hruban, Carolyn C; Broeckaert, Mark A M MAM; Anagnostou, Valsamo V; Adleff, Vilmos V; Bruhm, Daniel C DC; Canzoniero, Jenna V JV; Fiksel, Jacob J; Nordsmark, Marianne M; Warmerdam, Fabienne A R M FARM; Verheul, Henk M W HMW; van Spronsen, Dick Johan DJ; Beerepoot, Laurens V LV; Geenen, Maud M MM; Portielje, Johanneke E A JEA; Jansen, Edwin P M EPM; van Sandick, Johanna J; Meershoek-Klein Kranenbarg, Elma E; van Laarhoven, Hanneke W M HWM; van der Peet, Donald L DL; van de Velde, Cornelis J H CJH; Verheij, Marcel M; Fijneman, Remond R; Scharpf, Robert B RB; Meijer, Gerrit A GA; Cats, Annemieke A; Velculescu, Victor E VE

Publication Date: 2020-01-27

Variant appearance in text: TP53: Y234F

PubMed Link: 31988276

Variant Present in the following documents:

• 41467_2020_14310_MOESM6_ESM.xlsx, sheet 6
• 41467_2020_14310_MOESM8_ESM.xlsx, sheet 1
• 41467_2020_14310_MOESM6_ESM.xlsx, sheet 7
• 41467_2020_14310_MOESM6_ESM.xlsx, sheet 8
• 41467_2020_14310_MOESM10_ESM.xlsx, sheet 1
• 41467_2020_14310_MOESM9_ESM.xlsx, sheet 1

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Liquid-like droplet formation by tumor suppressor p53 induced by multivalent electrostatic interactions between two disordered domains.

Scientific Reports

Kamagata, Kiyoto K; Kanbayashi, Saori S; Honda, Masaya M; Itoh, Yuji Y; Takahashi, Hiroto H; Kameda, Tomoshi T; Nagatsugi, Fumi F; Takahashi, Satoshi S

Publication Date: 2020-01-17

Variant appearance in text: p53: Y234F

PubMed Link: 31953488

Variant Present in the following documents:

• Main text
• 41598_2020_Article_57521.pdf

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Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p53.

Scientific Reports

Kamagata, Kiyoto K; Mano, Eriko E; Itoh, Yuji Y; Wakamoto, Takuro T; Kitahara, Ryo R; Kanbayashi, Saori S; Takahashi, Hiroto H; Murata, Agato A; Kameda, Tomoshi T

Publication Date: 2019-06-28

Variant appearance in text: p53: Y234F

PubMed Link: 31253862

Variant Present in the following documents:

• Main text
• 41598_2019_Article_44688.pdf

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Finding driver mutations in cancer: Elucidating the role of background mutational processes.

Plos Computational Biology

Brown, Anna-Leigh AL; Li, Minghui M; Goncearenco, Alexander A; Panchenko, Anna R AR

Publication Date: 2019-04

Variant appearance in text: TP53: Y234F

PubMed Link: 31034466

Variant Present in the following documents:

• pcbi.1006981.s010.xlsx, sheet 1

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One-Dimensional Search Dynamics of Tumor Suppressor p53 Regulated by a Disordered C-Terminal Domain.

Biophysical Journal

Murata, Agato A; Itoh, Yuji Y; Mano, Eriko E; Kanbayashi, Saori S; Igarashi, Chihiro C; Takahashi, Hiroto H; Takahashi, Satoshi S; Kamagata, Kiyoto K

Publication Date: 2017-06-06

Variant appearance in text: p53: Y234F

PubMed Link: 28591603

Variant Present in the following documents:

• Main text

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p53 Proteoforms and Intrinsic Disorder: An Illustration of the Protein Structure-Function Continuum Concept.

International Journal Of Molecular Sciences

Uversky, Vladimir N VN

Publication Date: 2016-11-10

Variant appearance in text: p53: Y234F

PubMed Link: 27834926

Variant Present in the following documents:

• ijms-17-01874-s001.pdf

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iFish: predicting the pathogenicity of human nonsynonymous variants using gene-specific/family-specific attributes and classifiers.

Scientific Reports

Wang, Meng M; Wei, Liping L

Publication Date: 2016-08-16

Variant appearance in text: TP53: Y234F

PubMed Link: 27527004

Variant Present in the following documents:

• srep31321-s5.xls, sheet 1

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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: TP53: Y234F

PubMed Link: 26206375

Variant Present in the following documents:

• 12859_2015_673_MOESM1_ESM.xls, sheet 1

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Smyd1 facilitates heart development by antagonizing oxidative and ER stress responses.

Plos One

Rasmussen, Tara L TL; Ma, Yanlin Y; Park, Chong Yon CY; Harriss, June J; Pierce, Stephanie A SA; Dekker, Joseph D JD; Valenzuela, Nicolas N; Srivastava, Deepak D; Schwartz, Robert J RJ; Stewart, M David MD; Tucker, Haley O HO

Publication Date: 2015

Variant appearance in text: p53: Y234F

PubMed Link: 25803368

Variant Present in the following documents:

• Main text
• pone.0121765.pdf

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Benchmarking mutation effect prediction algorithms using functionally validated cancer-related missense mutations.

Genome Biology

Martelotto, Luciano G LG; Ng, Charlotte Ky CK; De Filippo, Maria R MR; Zhang, Yan Y; Piscuoglio, Salvatore S; Lim, Raymond S RS; Shen, Ronglai R; Norton, Larry L; Reis-Filho, Jorge S JS; Weigelt, Britta B

Publication Date: 2014-10-28

Variant appearance in text: TP53: Y234F

PubMed Link: 25348012

Variant Present in the following documents:

• 13059_2014_484_MOESM2_ESM.xlsx, sheet 1

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Predicting the functional impact of protein mutations: application to cancer genomics.

Nucleic Acids Research

Reva, Boris B; Antipin, Yevgeniy Y; Sander, Chris C

Publication Date: 2011-09-01

Variant appearance in text: TP53: Y234F

PubMed Link: 21727090

Variant Present in the following documents:

• supp_gkr407_Supplement2_Table_SM1_COSMIC_mutations.xls, sheet 1

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