Network Controllability-Based Prioritization of Candidates for SARS-CoV-2 Drug Repositioning

por Ackerman, Emily E., Shoemaker, Jason E.
Publicado 2020

Network perturbation analysis of gene transcriptional profiles reveals protein targets and mechanism of action of drugs and influenza A viral infection

por Noh, Heeju, Shoemaker, Jason E, Gunawan, Rudiyanto
Publicado 2018

Mathematical Modeling Finds Disparate Interferon Production Rates Drive Strain-Specific Immunodynamics during Deadly Influenza Infection

por Ackerman, Emily E., Weaver, Jordan J. A., Shoemaker, Jason E.
Publicado 2022

A dual controllability analysis of influenza virus-host protein-protein interaction networks for antiviral drug target discovery

por Ackerman, Emily E., Alcorn, John F., Hase, Takeshi, Shoemaker, Jason E.
Publicado 2019

DeltaNeTS+: elucidating the mechanism of drugs and diseases using gene expression and transcriptional regulatory networks

por Noh, Heeju, Hua, Ziyi, Chrysinas, Panagiotis, Shoemaker, Jason E., Gunawan, Rudiyanto
Publicado 2021

Identifying problematic drugs based on the characteristics of their targets

por Lopes, Tiago J. S., Shoemaker, Jason E., Matsuoka, Yukiko, Kawaoka, Yoshihiro, Kitano, Hiroaki
Publicado 2015

Confidence from uncertainty - A multi-target drug screening method from robust control theory

por Luni, Camilla, Shoemaker, Jason E, Sanft, Kevin R, Petzold, Linda R, Doyle, Francis J
Publicado 2010

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

por Shoemaker, Jason E, Lopes, Tiago JS, Ghosh, Samik, Matsuoka, Yukiko, Kawaoka, Yoshihiro, Kitano, Hiroaki
Publicado 2012

Multicellular spatial model of RNA virus replication and interferon responses reveals factors controlling plaque growth dynamics

por Aponte-Serrano, Josua O., Weaver, Jordan J. A., Sego, T. J., Glazier, James A., Shoemaker, Jason E.
Publicado 2021

Fathead minnow steroidogenesis: in silico analyses reveals tradeoffs between nominal target efficacy and robustness to cross-talk

por Shoemaker, Jason E, Gayen, Kalyan, Garcia-Reyero, Natàlia, Perkins, Edward J, Villeneuve, Daniel L, Liu, Li, Doyle, Francis J
Publicado 2010

Integrated network analysis reveals a novel role for the cell cycle in 2009 pandemic influenza virus-induced inflammation in macaque lungs

por Shoemaker, Jason E, Fukuyama, Satoshi, Eisfeld, Amie J, Muramoto, Yukiko, Watanabe, Shinji, Watanabe, Tokiko, Matsuoka, Yukiko, Kitano, Hiroaki, Kawaoka, Yoshihiro
Publicado 2012

Multi-spectral fluorescent reporter influenza viruses (Color-flu) as powerful tools for in vivo studies

por Fukuyama, Satoshi, Katsura, Hiroaki, Zhao, Dongming, Ozawa, Makoto, Ando, Tomomi, Shoemaker, Jason E., Ishikawa, Izumi, Yamada, Shinya, Neumann, Gabriele, Watanabe, Shinji, Kitano, Hiroaki, Kawaoka, Yoshihiro
Publicado 2015

Network-Guided Discovery of Influenza Virus Replication Host Factors

por Ackerman, Emily E., Kawakami, Eiryo, Katoh, Manami, Watanabe, Tokiko, Watanabe, Shinji, Tomita, Yuriko, Lopes, Tiago J., Matsuoka, Yukiko, Kitano, Hiroaki, Shoemaker, Jason E., Kawaoka, Yoshihiro
Publicado 2018

A comprehensive map of the influenza A virus replication cycle

por Matsuoka, Yukiko, Matsumae, Hiromi, Katoh, Manami, Eisfeld, Amie J, Neumann, Gabriele, Hase, Takeshi, Ghosh, Samik, Shoemaker, Jason E, Lopes, Tiago JS, Watanabe, Tokiko, Watanabe, Shinji, Fukuyama, Satoshi, Kitano, Hiroaki, Kawaoka, Yoshihiro
Publicado 2013

Blood Inflammatory Biomarkers Differentiate Inpatient and Outpatient Coronavirus Disease 2019 From Influenza

por Luciani, Lauren L, Miller, Leigh M, Zhai, Bo, Clarke, Karen, Hughes Kramer, Kailey, Schratz, Lucas J, Balasubramani, G K, Dauer, Klancie, Nowalk, M Patricia, Zimmerman, Richard K, Shoemaker, Jason E, Alcorn, John F
Publicado 2023

An Ultrasensitive Mechanism Regulates Influenza Virus-Induced Inflammation

por Shoemaker, Jason E., Fukuyama, Satoshi, Eisfeld, Amie J., Zhao, Dongming, Kawakami, Eiryo, Sakabe, Saori, Maemura, Tadashi, Gorai, Takeo, Katsura, Hiroaki, Muramoto, Yukiko, Watanabe, Shinji, Watanabe, Tokiko, Fuji, Ken, Matsuoka, Yukiko, Kitano, Hiroaki, Kawaoka, Yoshihiro
Publicado 2015

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions

por Schaefer, Martin H., Lopes, Tiago J. S., Mah, Nancy, Shoemaker, Jason E., Matsuoka, Yukiko, Fontaine, Jean-Fred, Louis-Jeune, Caroline, Eisfeld, Amie J., Neumann, Gabriele, Perez-Iratxeta, Carol, Kawaoka, Yoshihiro, Kitano, Hiroaki, Andrade-Navarro, Miguel A.
Publicado 2013

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

por Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, Devasahayam Arokia Balaya, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Wilighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2021

COVID‐19 Disease Map, a computational knowledge repository of virus‐host interaction mechanisms

por Ostaszewski, Marek, Niarakis, Anna, Mazein, Alexander, Kuperstein, Inna, Phair, Robert, Orta‐Resendiz, Aurelio, Singh, Vidisha, Aghamiri, Sara Sadat, Acencio, Marcio Luis, Glaab, Enrico, Ruepp, Andreas, Fobo, Gisela, Montrone, Corinna, Brauner, Barbara, Frishman, Goar, Monraz Gómez, Luis Cristóbal, Somers, Julia, Hoch, Matti, Kumar Gupta, Shailendra, Scheel, Julia, Borlinghaus, Hanna, Czauderna, Tobias, Schreiber, Falk, Montagud, Arnau, Ponce de Leon, Miguel, Funahashi, Akira, Hiki, Yusuke, Hiroi, Noriko, Yamada, Takahiro G, Dräger, Andreas, Renz, Alina, Naveez, Muhammad, Bocskei, Zsolt, Messina, Francesco, Börnigen, Daniela, Fergusson, Liam, Conti, Marta, Rameil, Marius, Nakonecnij, Vanessa, Vanhoefer, Jakob, Schmiester, Leonard, Wang, Muying, Ackerman, Emily E, Shoemaker, Jason E, Zucker, Jeremy, Oxford, Kristie, Teuton, Jeremy, Kocakaya, Ebru, Summak, Gökçe Yağmur, Hanspers, Kristina, Kutmon, Martina, Coort, Susan, Eijssen, Lars, Ehrhart, Friederike, Rex, D A B, Slenter, Denise, Martens, Marvin, Pham, Nhung, Haw, Robin, Jassal, Bijay, Matthews, Lisa, Orlic‐Milacic, Marija, Senff‐Ribeiro, Andrea, Rothfels, Karen, Shamovsky, Veronica, Stephan, Ralf, Sevilla, Cristoffer, Varusai, Thawfeek, Ravel, Jean‐Marie, Fraser, Rupsha, Ortseifen, Vera, Marchesi, Silvia, Gawron, Piotr, Smula, Ewa, Heirendt, Laurent, Satagopam, Venkata, Wu, Guanming, Riutta, Anders, Golebiewski, Martin, Owen, Stuart, Goble, Carole, Hu, Xiaoming, Overall, Rupert W, Maier, Dieter, Bauch, Angela, Gyori, Benjamin M, Bachman, John A, Vega, Carlos, Grouès, Valentin, Vazquez, Miguel, Porras, Pablo, Licata, Luana, Iannuccelli, Marta, Sacco, Francesca, Nesterova, Anastasia, Yuryev, Anton, de Waard, Anita, Turei, Denes, Luna, Augustin, Babur, Ozgun, Soliman, Sylvain, Valdeolivas, Alberto, Esteban‐Medina, Marina, Peña‐Chilet, Maria, Rian, Kinza, Helikar, Tomáš, Puniya, Bhanwar Lal, Modos, Dezso, Treveil, Agatha, Olbei, Marton, De Meulder, Bertrand, Ballereau, Stephane, Dugourd, Aurélien, Naldi, Aurélien, Noël, Vincent, Calzone, Laurence, Sander, Chris, Demir, Emek, Korcsmaros, Tamas, Freeman, Tom C, Augé, Franck, Beckmann, Jacques S, Hasenauer, Jan, Wolkenhauer, Olaf, Willighagen, Egon L, Pico, Alexander R, Evelo, Chris T, Gillespie, Marc E, Stein, Lincoln D, Hermjakob, Henning, D'Eustachio, Peter, Saez‐Rodriguez, Julio, Dopazo, Joaquin, Valencia, Alfonso, Kitano, Hiroaki, Barillot, Emmanuel, Auffray, Charles, Balling, Rudi, Schneider, Reinhard
Publicado 2021