Pesquisa | BVS Doenças Infecciosas e Parasitárias

1.

WeSME: uncovering mutual exclusivity of cancer drivers and beyond.

Kim, Yoo-Ah; Madan, Sanna; Przytycka, Teresa M.

Bioinformatics ; 33(6): 814-821, 2017 03 15.

Artigo em Inglês | MEDLINE | ID: mdl-27153670

2.

BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions.

Dao, Phuong; Kim, Yoo-Ah; Wojtowicz, Damian; Madan, Sanna; Sharan, Roded; Przytycka, Teresa M.

PLoS Comput Biol ; 13(10): e1005695, 2017 Oct.

Artigo em Inglês | MEDLINE | ID: mdl-29023534

3.

Comparative validation of the D. melanogaster modENCODE transcriptome annotation.

Chen, Zhen-Xia; Sturgill, David; Qu, Jiaxin; Jiang, Huaiyang; Park, Soo; Boley, Nathan; Suzuki, Ana Maria; Fletcher, Anthony R; Plachetzki, David C; FitzGerald, Peter C; Artieri, Carlo G; Atallah, Joel; Barmina, Olga; Brown, James B; Blankenburg, Kerstin P; Clough, Emily; Dasgupta, Abhijit; Gubbala, Sai; Han, Yi; Jayaseelan, Joy C; Kalra, Divya; Kim, Yoo-Ah; Kovar, Christie L; Lee, Sandra L; Li, Mingmei; Malley, James D; Malone, John H; Mathew, Tittu; Mattiuzzo, Nicolas R; Munidasa, Mala; Muzny, Donna M; Ongeri, Fiona; Perales, Lora; Przytycka, Teresa M; Pu, Ling-Ling; Robinson, Garrett; Thornton, Rebecca L; Saada, Nehad; Scherer, Steven E; Smith, Harold E; Vinson, Charles; Warner, Crystal B; Worley, Kim C; Wu, Yuan-Qing; Zou, Xiaoyan; Cherbas, Peter; Kellis, Manolis; Eisen, Michael B; Piano, Fabio; Kionte, Karin.

Genome Res ; 24(7): 1209-23, 2014 Jul.

Artigo em Inglês | MEDLINE | ID: mdl-24985915

4.

Understanding Genotype-Phenotype Effects in Cancer via Network Approaches.

Kim, Yoo-Ah; Cho, Dong-Yeon; Przytycka, Teresa M.

PLoS Comput Biol ; 12(3): e1004747, 2016 Mar.

Artigo em Inglês | MEDLINE | ID: mdl-26963104

5.

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types.

Kim, Yoo-Ah; Cho, Dong-Yeon; Dao, Phuong; Przytycka, Teresa M.

Bioinformatics ; 31(12): i284-92, 2015 Jun 15.

Artigo em Inglês | MEDLINE | ID: mdl-26072494

6.

Computational design of mRNA vaccines.

Kim, Yoo-Ah; Mousavi, Kambiz; Yazdi, Amirali; Zwierzyna, Magda; Cardinali, Marco; Fox, Dillion; Peel, Thomas; Coller, Jeff; Aggarwal, Kunal; Maruggi, Giulietta.

Vaccine ; 42(7): 1831-1840, 2024 Mar 07.

Artigo em Inglês | MEDLINE | ID: mdl-37479613

7.

Chapter 5: Network biology approach to complex diseases.

Cho, Dong-Yeon; Kim, Yoo-Ah; Przytycka, Teresa M.

PLoS Comput Biol ; 8(12): e1002820, 2012.

Artigo em Inglês | MEDLINE | ID: mdl-23300411

8.

Influence network model uncovers relations between biological processes and mutational signatures.

Amgalan, Bayarbaatar; Wojtowicz, Damian; Kim, Yoo-Ah; Przytycka, Teresa M.

Genome Med ; 15(1): 15, 2023 03 06.

Artigo em Inglês | MEDLINE | ID: mdl-36879282

9.

Identifying causal genes and dysregulated pathways in complex diseases.

Kim, Yoo-Ah; Wuchty, Stefan; Przytycka, Teresa M.

PLoS Comput Biol ; 7(3): e1001095, 2011 Mar.

Artigo em Inglês | MEDLINE | ID: mdl-21390271

10.

Mutational Signatures as Sensors of Environmental Exposures: Analysis of Smoking-Induced Lung Tissue Remodeling.

Kim, Yoo-Ah; Hodzic, Ermin; Amgalan, Bayarbaatar; Saslafsky, Ariella; Wojtowicz, Damian; Przytycka, Teresa M.

Biomolecules ; 12(10)2022 09 27.

Artigo em Inglês | MEDLINE | ID: mdl-36291592

11.

Modeling information flow in biological networks.

Kim, Yoo-Ah; Przytycki, Jozef H; Wuchty, Stefan; Przytycka, Teresa M.

Phys Biol ; 8(3): 035012, 2011 Jun.

Artigo em Inglês | MEDLINE | ID: mdl-21572171

12.

Network integration meets network dynamics.

Przytycka, Teresa M; Kim, Yoo-Ah.

BMC Biol ; 8: 48, 2010 Apr 28.

Artigo em Inglês | MEDLINE | ID: mdl-20513250

13.

RepairSig: Deconvolution of DNA damage and repair contributions to the mutational landscape of cancer.

Wojtowicz, Damian; Hoinka, Jan; Amgalan, Bayarbaatar; Kim, Yoo-Ah; Przytycka, Teresa M.

Cell Syst ; 12(10): 994-1003.e4, 2021 10 20.

Artigo em Inglês | MEDLINE | ID: mdl-34375586

14.

Mutational Signatures: From Methods to Mechanisms.

Kim, Yoo-Ah; Leiserson, Mark D M; Moorjani, Priya; Sharan, Roded; Wojtowicz, Damian; Przytycka, Teresa M.

Annu Rev Biomed Data Sci ; 4: 189-206, 2021 07 20.

Artigo em Inglês | MEDLINE | ID: mdl-34465178

15.

Identifying Drug Sensitivity Subnetworks with NETPHIX.

Kim, Yoo-Ah; Sarto Basso, Rebecca; Wojtowicz, Damian; Liu, Amanda S; Hochbaum, Dorit S; Vandin, Fabio; Przytycka, Teresa M.

iScience ; 23(10): 101619, 2020 Oct 23.

Artigo em Inglês | MEDLINE | ID: mdl-33089107

16.

Network-based approaches elucidate differences within APOBEC and clock-like signatures in breast cancer.

Kim, Yoo-Ah; Wojtowicz, Damian; Sarto Basso, Rebecca; Sason, Itay; Robinson, Welles; Hochbaum, Dorit S; Leiserson, Mark D M; Sharan, Roded; Vadin, Fabio; Przytycka, Teresa M.

Genome Med ; 12(1): 52, 2020 05 29.

Artigo em Inglês | MEDLINE | ID: mdl-32471470

17.

Hidden Markov models lead to higher resolution maps of mutation signature activity in cancer.

Wojtowicz, Damian; Sason, Itay; Huang, Xiaoqing; Kim, Yoo-Ah; Leiserson, Mark D M; Przytycka, Teresa M; Sharan, Roded.

Genome Med ; 11(1): 49, 2019 07 26.

Artigo em Inglês | MEDLINE | ID: mdl-31349863

18.

The language of a virus.

Kim, Yoo-Ah; Przytycka, Teresa M.

Science ; 371(6526): 233-234, 2021 01 15.

Artigo em Inglês | MEDLINE | ID: mdl-33446542

19.

Sex- and tissue-specific functions of Drosophila doublesex transcription factor target genes.

Clough, Emily; Jimenez, Erin; Kim, Yoo-Ah; Whitworth, Cale; Neville, Megan C; Hempel, Leonie U; Pavlou, Hania J; Chen, Zhen-Xia; Sturgill, David; Dale, Ryan K; Smith, Harold E; Przytycka, Teresa M; Goodwin, Stephen F; Van Doren, Mark; Oliver, Brian.

Dev Cell ; 31(6): 761-73, 2014 Dec 22.

Artigo em Inglês | MEDLINE | ID: mdl-25535918

20.

Module cover - a new approach to genotype-phenotype studies.

Kim, Yoo-Ah; Salari, Raheleh; Wuchty, Stefan; Przytycka, Teresa M.

Pac Symp Biocomput ; : 135-46, 2013.

Artigo em Inglês | MEDLINE | ID: mdl-23424119

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