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1.

Dissecting the treatment-naive ecosystem of human melanoma brain metastasis.

Biermann, Jana; Melms, Johannes C; Amin, Amit Dipak; Wang, Yiping; Caprio, Lindsay A; Karz, Alcida; Tagore, Somnath; Barrera, Irving; Ibarra-Arellano, Miguel A; Andreatta, Massimo; Fullerton, Benjamin T; Gretarsson, Kristjan H; Sahu, Varun; Mangipudy, Vaibhav S; Nguyen, Trang T T; Nair, Ajay; Rogava, Meri; Ho, Patricia; Koch, Peter D; Banu, Matei; Humala, Nelson; Mahajan, Aayushi; Walsh, Zachary H; Shah, Shivem B; Vaccaro, Daniel H; Caldwell, Blake; Mu, Michael; Wünnemann, Florian; Chazotte, Margot; Berhe, Simon; Luoma, Adrienne M; Driver, Joseph; Ingham, Matthew; Khan, Shaheer A; Rapisuwon, Suthee; Slingluff, Craig L; Eigentler, Thomas; Röcken, Martin; Carvajal, Richard; Atkins, Michael B; Davies, Michael A; Agustinus, Albert; Bakhoum, Samuel F; Azizi, Elham; Siegelin, Markus; Lu, Chao; Carmona, Santiago J; Hibshoosh, Hanina; Ribas, Antoni; Canoll, Peter.

Cell ; 185(14): 2591-2608.e30, 2022 07 07.

Artículo en Inglés | MEDLINE | ID: mdl-35803246

2.

A modular master regulator landscape controls cancer transcriptional identity.

Paull, Evan O; Aytes, Alvaro; Jones, Sunny J; Subramaniam, Prem S; Giorgi, Federico M; Douglass, Eugene F; Tagore, Somnath; Chu, Brennan; Vasciaveo, Alessandro; Zheng, Siyuan; Verhaak, Roel; Abate-Shen, Cory; Alvarez, Mariano J; Califano, Andrea.

Cell ; 184(2): 334-351.e20, 2021 01 21.

Artículo en Inglés | MEDLINE | ID: mdl-33434495

3.

A molecular single-cell lung atlas of lethal COVID-19.

Melms, Johannes C; Biermann, Jana; Huang, Huachao; Wang, Yiping; Nair, Ajay; Tagore, Somnath; Katsyv, Igor; Rendeiro, André F; Amin, Amit Dipak; Schapiro, Denis; Frangieh, Chris J; Luoma, Adrienne M; Filliol, Aveline; Fang, Yinshan; Ravichandran, Hiranmayi; Clausi, Mariano G; Alba, George A; Rogava, Meri; Chen, Sean W; Ho, Patricia; Montoro, Daniel T; Kornberg, Adam E; Han, Arnold S; Bakhoum, Mathieu F; Anandasabapathy, Niroshana; Suárez-Fariñas, Mayte; Bakhoum, Samuel F; Bram, Yaron; Borczuk, Alain; Guo, Xinzheng V; Lefkowitch, Jay H; Marboe, Charles; Lagana, Stephen M; Del Portillo, Armando; Tsai, Emily J; Zorn, Emmanuel; Markowitz, Glen S; Schwabe, Robert F; Schwartz, Robert E; Elemento, Olivier; Saqi, Anjali; Hibshoosh, Hanina; Que, Jianwen; Izar, Benjamin.

Nature ; 595(7865): 114-119, 2021 07.

Artículo en Inglés | MEDLINE | ID: mdl-33915568

4.

Author Correction: A molecular single-cell lung atlas of lethal COVID-19.

Melms, Johannes C; Biermann, Jana; Huang, Huachao; Wang, Yiping; Nair, Ajay; Tagore, Somnath; Katsyv, Igor; Rendeiro, André F; Amin, Amit Dipak; Schapiro, Denis; Frangieh, Chris J; Luoma, Adrienne M; Filliol, Aveline; Fang, Yinshan; Ravichandran, Hiranmayi; Clausi, Mariano G; Alba, George A; Rogava, Meri; Chen, Sean W; Ho, Patricia; Montoro, Daniel T; Kornberg, Adam E; Han, Arnold S; Bakhoum, Mathieu F; Anandasabapathy, Niroshana; Suárez-Fariñas, Mayte; Bakhoum, Samuel F; Bram, Yaron; Borczuk, Alain; Guo, Xinzheng V; Lefkowitch, Jay H; Marboe, Charles; Lagana, Stephen M; Del Portillo, Armando; Tsai, Emily J; Zorn, Emmanuel; Markowitz, Glen S; Schwabe, Robert F; Schwartz, Robert E; Elemento, Olivier; Saqi, Anjali; Hibshoosh, Hanina; Que, Jianwen; Izar, Benjamin.

Nature ; 598(7882): E2, 2021 Oct.

Artículo en Inglés | MEDLINE | ID: mdl-34625743

5.

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.

Tagore, Somnath; Gorohovski, Alessandro; Jensen, Lars Juhl; Frenkel-Morgenstern, Milana.

PLoS Comput Biol ; 15(8): e1007239, 2019 08.

Artículo en Inglés | MEDLINE | ID: mdl-31437145

6.

ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.

Frenkel-Morgenstern, Milana; Gorohovski, Alessandro; Tagore, Somnath; Sekar, Vaishnovi; Vazquez, Miguel; Valencia, Alfonso.

Nucleic Acids Res ; 45(12): 7094-7105, 2017 Jul 07.

Artículo en Inglés | MEDLINE | ID: mdl-28549153

7.

ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.

Gorohovski, Alessandro; Tagore, Somnath; Palande, Vikrant; Malka, Assaf; Raviv-Shay, Dorith; Frenkel-Morgenstern, Milana.

Nucleic Acids Res ; 45(D1): D790-D795, 2017 01 04.

Artículo en Inglés | MEDLINE | ID: mdl-27899596

8.

Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.

Rogava, Meri; Aprati, Tyler J; Chi, Wei-Yu; Melms, Johannes C; Hug, Clemens; Davis, Stephanie H; Earlie, Ethan M; Chung, Charlie; Deshmukh, Sachin K; Wu, Sharon; Sledge, George; Tang, Stephen; Ho, Patricia; Amin, Amit Dipak; Caprio, Lindsay; Gurjao, Carino; Tagore, Somnath; Ngo, Bryan; Lee, Michael J; Zanetti, Giorgia; Wang, Yiping; Chen, Sean; Ge, William; Melo, Luiza Martins Nascentes; Allies, Gabriele; Rösler, Jonas; Gibney, Goeffrey T; Schmitz, Oliver J; Sykes, Megan; Creusot, Rémi J; Tüting, Thomas; Schadendorf, Dirk; Röcken, Martin; Eigentler, Thomas K; Molotkov, Andrei; Mintz, Akiva; Bakhoum, Samuel F; Beyaz, Semir; Cantley, Lewis C; Sorger, Peter K; Meckelmann, Sven W; Tasdogan, Alpaslan; Liu, David; Laughney, Ashley M; Izar, Benjamin.

Nat Cancer ; 5(3): 433-447, 2024 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-38286827

9.

Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations.

Tagore, Somnath; Tsang, Samuel; Mills, Gordon B; Califano, Andrea.

bioRxiv ; 2023 May 02.

Artículo en Inglés | MEDLINE | ID: mdl-37205498

10.

KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response.

Ager, Casey R; Zhang, Mingxuan; Chaimowitz, Matthew; Bansal, Shruti; Tagore, Somnath; Obradovic, Aleksandar; Jugler, Collin; Rogava, Meri; Melms, Johannes C; McCann, Patrick; Spina, Catherine; Drake, Charles G; Dallos, Matthew C; Izar, Benjamin.

J Immunother Cancer ; 11(9)2023 09.

Artículo en Inglés | MEDLINE | ID: mdl-37657842

11.

Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens.

Wang, Yiping; Fan, Joy Linyue; Melms, Johannes C; Amin, Amit Dipak; Georgis, Yohanna; Barrera, Irving; Ho, Patricia; Tagore, Somnath; Abril-Rodríguez, Gabriel; He, Siyu; Jin, Yinuo; Biermann, Jana; Hofree, Matan; Caprio, Lindsay; Berhe, Simon; Khan, Shaheer A; Henick, Brian S; Ribas, Antoni; Macosko, Evan Z; Chen, Fei; Taylor, Alison M; Schwartz, Gary K; Carvajal, Richard D; Azizi, Elham; Izar, Benjamin.

Nat Genet ; 55(1): 19-25, 2023 01.

Artículo en Inglés | MEDLINE | ID: mdl-36624340

12.

tRNA methylation resolves codon usage bias at the limit of cell viability.

Masuda, Isao; Yamaki, Yuka; Detroja, Rajesh; Tagore, Somnath; Moore, Henry; Maharjan, Sunita; Nakano, Yuko; Christian, Thomas; Matsubara, Ryuma; Lowe, Todd M; Frenkel-Morgenstern, Milana; Hou, Ya-Ming.

Cell Rep ; 41(4): 111539, 2022 10 25.

Artículo en Inglés | MEDLINE | ID: mdl-36288695

13.

A multi-organ chip with matured tissue niches linked by vascular flow.

Ronaldson-Bouchard, Kacey; Teles, Diogo; Yeager, Keith; Tavakol, Daniel Naveed; Zhao, Yimu; Chramiec, Alan; Tagore, Somnath; Summers, Max; Stylianos, Sophia; Tamargo, Manuel; Lee, Busub Marcus; Halligan, Susan P; Abaci, Erbil Hasan; Guo, Zongyou; Jacków, Joanna; Pappalardo, Alberto; Shih, Jerry; Soni, Rajesh K; Sonar, Shivam; German, Carrie; Christiano, Angela M; Califano, Andrea; Hirschi, Karen K; Chen, Christopher S; Przekwas, Andrzej; Vunjak-Novakovic, Gordana.

Nat Biomed Eng ; 6(4): 351-371, 2022 04.

Artículo en Inglés | MEDLINE | ID: mdl-35478225

14.

Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.

Broyde, Joshua; Simpson, David R; Murray, Diana; Paull, Evan O; Chu, Brennan W; Tagore, Somnath; Jones, Sunny J; Griffin, Aaron T; Giorgi, Federico M; Lachmann, Alexander; Jackson, Peter; Sweet-Cordero, E Alejandro; Honig, Barry; Califano, Andrea.

Nat Biotechnol ; 39(2): 215-224, 2021 02.

Artículo en Inglés | MEDLINE | ID: mdl-32929263

15.

ASAPP: Architectural Similarity-Based Automated Pathway Prediction System and Its Application in Host-Pathogen Interactions.

Sen, Rishika; Tagore, Somnath; De, Rajat K.

IEEE/ACM Trans Comput Biol Bioinform ; 17(2): 506-515, 2020.

Artículo en Inglés | MEDLINE | ID: mdl-30281472

16.

Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks.

Carmi, Gon; Tagore, Somnath; Gorohovski, Alessandro; Sivan, Aviad; Raviv-Shay, Dorith; Frenkel-Morgenstern, Milana.

Sci Rep ; 10(1): 15628, 2020 09 24.

Artículo en Inglés | MEDLINE | ID: mdl-32973219

17.

Cluster Quality based Non-Reductional (CQNR) oversampling technique and effector protein predictor based on 3D structure (EPP3D) of proteins.

Sen, Rishika; Tagore, Somnath; De, Rajat K.

Comput Biol Med ; 112: 103374, 2019 09.

Artículo en Inglés | MEDLINE | ID: mdl-31419629

18.

Species scaling and extrapolation.

Gomase, Virendra S; Tagore, Somnath.

Curr Drug Metab ; 9(3): 193-8, 2008 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-18336221

19.

Epigenomics.

Gomase, Virendra S; Tagore, Somnath.

Curr Drug Metab ; 9(3): 232-7, 2008 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-18336226

20.

Blood stage parasites: sufficient to induce protective immunity.

Gomase, Virendra S; Tagore, Somnath.

Curr Drug Metab ; 9(3): 238-40, 2008 Mar.

Artículo en Inglés | MEDLINE | ID: mdl-18336227

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Dissecting the treatment-naive ecosystem of human melanoma brain metastasis.

A modular master regulator landscape controls cancer transcriptional identity.

A molecular single-cell lung atlas of lethal COVID-19.

Author Correction: A molecular single-cell lung atlas of lethal COVID-19.

ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.

ChiPPI: a novel method for mapping chimeric protein-protein interactions uncovers selection principles of protein fusion events in cancer.

ChiTaRS-3.1-the enhanced chimeric transcripts and RNA-seq database matched with protein-protein interactions.

Loss of Pip4k2c confers liver-metastatic organotropism through insulin-dependent PI3K-AKT pathway activation.

Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations.

KLRG1 marks tumor-infiltrating CD4 T cell subsets associated with tumor progression and immunotherapy response.

Multimodal single-cell and whole-genome sequencing of small, frozen clinical specimens.

tRNA methylation resolves codon usage bias at the limit of cell viability.

A multi-organ chip with matured tissue niches linked by vascular flow.

Oncoprotein-specific molecular interaction maps (SigMaps) for cancer network analyses.

ASAPP: Architectural Similarity-Based Automated Pathway Prediction System and Its Application in Host-Pathogen Interactions.

Design principles of gene evolution for niche adaptation through changes in protein-protein interaction networks.

Cluster Quality based Non-Reductional (CQNR) oversampling technique and effector protein predictor based on 3D structure (EPP3D) of proteins.

Species scaling and extrapolation.

Epigenomics.

Blood stage parasites: sufficient to induce protective immunity.