Anti-correlated feature selection prevents false discovery of subpopulations in scRNAseq
Tyler, Scott R, Lozano-Ojalvo, Daniel, Guccione, Ernesto, Schadt, Eric E
Published in Nature communications (24.01.2024)
Published in Nature communications (24.01.2024)
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Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children
Beckmann, Noam D, Comella, Phillip H, Cheng, Esther, Lepow, Lauren, Beckmann, Aviva G, Tyler, Scott R, Mouskas, Konstantinos, Simons, Nicole W, Hoffman, Gabriel E, Francoeur, Nancy J, Del Valle, Diane Marie, Kang, Gurpawan, Do, Anh, Moya, Emily, Wilkins, Lillian, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Yi, Nancy, Yu, Alex, Chung, Jonathan, Hartnett, Matthew, Eaton, Melody, Hatem, Sandra, Jamal, Hajra, Akyatan, Alara, Tabachnikova, Alexandra, Liharska, Lora E, Cotter, Liam, Fennessy, Brian, Vaid, Akhil, Barturen, Guillermo, Shah, Hardik, Wang, Ying-Chih, Sridhar, Shwetha Hara, Soto, Juan, Bose, Swaroop, Madrid, Kent, Ellis, Ethan, Merzier, Elyze, Vlachos, Konstantinos, Fishman, Nataly, Tin, Manying, Smith, Melissa, Xie, Hui, Patel, Manishkumar, Nie, Kai, Argueta, Kimberly, Harris, Jocelyn, Karekar, Neha, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Tuballes, Kevin, Scott, Ieisha, Kumar, Arvind, Jaladanki, Suraj, Agashe, Charuta, Thompson, Ryan, Clark, Evan, Losic, Bojan, Peters, Lauren, Roussos, Panagiotis, Zhu, Jun, Wang, Wenhui, Kasarskis, Andrew, Glicksberg, Benjamin S, Nadkarni, Girish, Bogunovic, Dusan, Elaiho, Cordelia, Gangadharan, Sandeep, Ofori-Amanfo, George, Alesso-Carra, Kasey, Onel, Kenan, Wilson, Karen M, Argmann, Carmen, Bunyavanich, Supinda, Alarcón-Riquelme, Marta E, Marron, Thomas U, Rahman, Adeeb, Kim-Schulze, Seunghee, Gnjatic, Sacha, Gelb, Bruce D, Merad, Miriam, Sebra, Robert, Schadt, Eric E, Charney, Alexander W
Published in Nature communications (11.08.2021)
Published in Nature communications (11.08.2021)
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Journal Article
Redox-dependent Igfbp2 signaling controls Brca1 DNA damage response to govern neural stem cell fate
Shahin, Weam S, Ebed, Shima O, Tyler, Scott R, Miljkovic, Branko, Choi, Soon H, Zhang, Yulong, Zhou, Weihong, Evans, Idil A, Yeaman, Charles, Engelhardt, John F
Published in Nature communications (27.01.2023)
Published in Nature communications (27.01.2023)
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Journal Article
Depletion of Airway Submucosal Glands and TP63 + KRT5 + Basal Cells in Obliterative Bronchiolitis
Swatek, Anthony M, Lynch, Thomas J, Crooke, Adrianne K, Anderson, Preston J, Tyler, Scott R, Brooks, Leonard, Ivanovic, Marina, Klesney-Tait, Julia A, Eberlein, Michael, Pena, Tahuanty, Meyerholz, David K, Engelhardt, John F, Parekh, Kalpaj R
Published in American journal of respiratory and critical care medicine (15.04.2018)
Published in American journal of respiratory and critical care medicine (15.04.2018)
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Journal Article
PyMINEr Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq
Tyler, Scott R., Rotti, Pavana G., Sun, Xingshen, Yi, Yaling, Xie, Weiliang, Winter, Michael C., Flamme-Wiese, Miles J., Tucker, Budd A., Mullins, Robert F., Norris, Andrew W., Engelhardt, John F.
Published in Cell reports (Cambridge) (12.02.2019)
Published in Cell reports (Cambridge) (12.02.2019)
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Journal Article
Merged Affinity Network Association Clustering: Joint multi-omic/clinical clustering to identify disease endotypes
Tyler, Scott R., Chun, Yoojin, Ribeiro, Victoria M., Grishina, Galina, Grishin, Alexander, Hoffman, Gabriel E., Do, Anh N., Bunyavanich, Supinda
Published in Cell reports (Cambridge) (13.04.2021)
Published in Cell reports (Cambridge) (13.04.2021)
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Journal Article
The draft genome sequence of the ferret (Mustela putorius furo) facilitates study of human respiratory disease
Peng, Xinxia, Alföldi, Jessica, Gori, Kevin, Eisfeld, Amie J, Tyler, Scott R, Tisoncik-Go, Jennifer, Brawand, David, Law, G Lynn, Skunca, Nives, Hatta, Masato, Gasper, David J, Kelly, Sara M, Chang, Jean, Thomas, Matthew J, Johnson, Jeremy, Berlin, Aaron M, Lara, Marcia, Russell, Pamela, Swofford, Ross, Turner-Maier, Jason, Young, Sarah, Hourlier, Thibaut, Aken, Bronwen, Searle, Steve, Sun, Xingshen, Yi, Yaling, Suresh, M, Tumpey, Terrence M, Siepel, Adam, Wisely, Samantha M, Dessimoz, Christophe, Kawaoka, Yoshihiro, Birren, Bruce W, Lindblad-Toh, Kerstin, Di Palma, Federica, Engelhardt, John F, Palermo, Robert E, Katze, Michael G
Published in Nature biotechnology (01.12.2014)
Published in Nature biotechnology (01.12.2014)
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Journal Article
Highly Efficient Transgenesis in Ferrets Using CRISPR/Cas9-Mediated Homology-Independent Insertion at the ROSA26 Locus
Yu, Miao, Sun, Xingshen, Tyler, Scott R, Liang, Bo, Swatek, Anthony M, Lynch, Thomas J, He, Nan, Yuan, Feng, Feng, Zehua, Rotti, Pavana G, Choi, Soon H, Shahin, Weam, Liu, Xiaoming, Yan, Ziying, Engelhardt, John F
Published in Scientific reports (13.02.2019)
Published in Scientific reports (13.02.2019)
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Journal Article
Wnt Signaling Regulates Airway Epithelial Stem Cells in Adult Murine Submucosal Glands
Lynch, Thomas J., Anderson, Preston J., Xie, Weiliang, Crooke, Adrianne K., Liu, Xiaoming, Tyler, Scott R., Luo, Meihui, Kusner, David M., Zhang, Yulong, Neff, Traci, Burnette, Daniel C., Walters, Katherine S., Goodheart, Michael J., Parekh, Kalpaj R., Engelhardt, John F.
Published in Stem cells (Dayton, Ohio) (01.11.2016)
Published in Stem cells (Dayton, Ohio) (01.11.2016)
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Journal Article
Leveraging -omics for asthma endotyping
Tyler, Scott R., Bunyavanich, Supinda
Published in Journal of allergy and clinical immunology (01.07.2019)
Published in Journal of allergy and clinical immunology (01.07.2019)
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Journal Article
Real-Time Monitoring of Insulin Using a Graphene Field-Effect Transistor Aptameric Nanosensor
Hao, Zhuang, Zhu, Yibo, Wang, Xuejun, Rotti, Pavana G, DiMarco, Christopher, Tyler, Scott R, Zhao, Xuezeng, Engelhardt, John F, Hone, James, Lin, Qiao
Published in ACS applied materials & interfaces (23.08.2017)
Published in ACS applied materials & interfaces (23.08.2017)
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Journal Article
Infection Is Not Required for Mucoinflammatory Lung Disease in CFTR-Knockout Ferrets
Rosen, Bradley H, Evans, T Idil Apak, Moll, Shashanna R, Gray, Jaimie S, Liang, Bo, Sun, Xingshen, Zhang, Yulong, Jensen-Cody, Chandler W, Swatek, Anthony M, Zhou, Weihong, He, Nan, Rotti, Pavana G, Tyler, Scott R, Keiser, Nicholas W, Anderson, Preston J, Brooks, Leonard, Li, Yalan, Pope, R Marshall, Rajput, Maheen, Hoffman, Eric A, Wang, Kai, Harris, J Kirk, Parekh, Kalpaj R, Gibson-Corley, Katherine N, Engelhardt, John F
Published in American journal of respiratory and critical care medicine (15.05.2018)
Published in American journal of respiratory and critical care medicine (15.05.2018)
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Journal Article
Is the plasticity of the Th17 subset a key source of allergenic Th2 responses?
Lozano‐Ojalvo, Daniel, Tyler, Scott R., Berin, M. Cecilia
Published in Allergy (Copenhagen) (01.10.2021)
Published in Allergy (Copenhagen) (01.10.2021)
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Journal Article
Submucosal Gland Myoepithelial Cells Are Reserve Stem Cells That Can Regenerate Mouse Tracheal Epithelium
Lynch, Thomas J., Anderson, Preston J., Rotti, Pavana G., Tyler, Scott R., Crooke, Adrianne K., Choi, Soon H., Montoro, Daniel T., Silverman, Carolyn L., Shahin, Weam, Zhao, Rui, Jensen-Cody, Chandler W., Adamcakova-Dodd, Andrea, Evans, T. Idil Apak, Xie, Weiliang, Zhang, Yulong, Mou, Hongmei, Herring, B. Paul, Thorne, Peter S., Rajagopal, Jayaraj, Yeaman, Charles, Parekh, Kalpaj R., Engelhardt, John F.
Published in Cell stem cell (03.05.2018)
Published in Cell stem cell (03.05.2018)
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Journal Article
Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae
Thompson, Ryan C, Simons, Nicole W, Wilkins, Lillian, Cheng, Esther, Del Valle, Diane Marie, Hoffman, Gabriel E, Cervia, Carlo, Fennessy, Brian, Mouskas, Konstantinos, Francoeur, Nancy J, Johnson, Jessica S, Lepow, Lauren, Le Berichel, Jessica, Chang, Christie, Beckmann, Aviva G, Wang, Ying-Chih, Nie, Kai, Zaki, Nicholas, Tuballes, Kevin, Barcessat, Vanessa, Cedillo, Mario A, Yuan, Dan, Huckins, Laura, Roussos, Panos, Marron, Thomas U, Glicksberg, Benjamin S, Nadkarni, Girish, Heath, James R, Gonzalez-Kozlova, Edgar, Boyman, Onur, Kim-Schulze, Seunghee, Sebra, Robert, Merad, Miriam, Gnjatic, Sacha, Schadt, Eric E, Charney, Alexander W, Beckmann, Noam D
Published in Nature medicine (01.01.2023)
Published in Nature medicine (01.01.2023)
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Journal Article
Allergen recognition by specific effector Th2 cells enables IL‐2‐dependent activation of regulatory T‐cell responses in humans
Lozano‐Ojalvo, Daniel, Tyler, Scott R., Aranda, Carlos J., Wang, Julie, Sicherer, Scott, Sampson, Hugh A., Wood, Robert A., Burks, A. Wesley, Jones, Stacie M., Leung, Donald Y. M., Lafaille, Maria Curotto, Berin, M. Cecilia
Published in Allergy (Copenhagen) (01.03.2023)
Published in Allergy (Copenhagen) (01.03.2023)
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Journal Article
Defective innate immunity and hyperinflammation in newborn cystic fibrosis transmembrane conductance regulator-knockout ferret lungs
Keiser, Nicholas W, Birket, Susan E, Evans, Idil A, Tyler, Scott R, Crooke, Adrianne K, Sun, Xingshen, Zhou, Weihong, Nellis, Joseph R, Stroebele, Elizabeth K, Chu, Kengyeh K, Tearney, Guillermo J, Stevens, Mark J, Harris, J Kirk, Rowe, Steven M, Engelhardt, John F
Published in American journal of respiratory cell and molecular biology (01.06.2015)
Published in American journal of respiratory cell and molecular biology (01.06.2015)
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Acetate supplementation rescues social deficits and alters transcriptional regulation in prefrontal cortex of Shank3 deficient mice
Osman, Aya, Mervosh, Nicholas L., Strat, Ana N., Euston, Tanner J., Zipursky, Gillian, Pollak, Rebecca M., Meckel, Katherine R., Tyler, Scott R., Chan, Kenny L., Buxbaum Grice, Ariela, Drapeau, Elodie, Litichevskiy, Lev, Gill, Jasleen, Zeldin, Sharon M., Thaiss, Christoph A., Buxbaum, Joseph.D., Breen, Michael S., Kiraly, Drew D.
Published in Brain, behavior, and immunity (01.11.2023)
Published in Brain, behavior, and immunity (01.11.2023)
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Journal Article
Lung phenotype of juvenile and adult cystic fibrosis transmembrane conductance regulator-knockout ferrets
Sun, Xingshen, Olivier, Alicia K, Liang, Bo, Yi, Yaling, Sui, Hongshu, Evans, Turan I A, Zhang, Yulong, Zhou, Weihong, Tyler, Scott R, Fisher, John T, Keiser, Nicholas W, Liu, Xiaoming, Yan, Ziying, Song, Yi, Goeken, J Adam, Kinyon, Joann M, Fligg, Danielle, Wang, Xiaoyan, Xie, Weiliang, Lynch, Thomas J, Kaminsky, Paul M, Stewart, Zoe A, Pope, R Marshall, Frana, Timothy, Meyerholz, David K, Parekh, Kalpaj, Engelhardt, John F
Published in American journal of respiratory cell and molecular biology (01.03.2014)
Published in American journal of respiratory cell and molecular biology (01.03.2014)
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Journal Article
Pancreatic and Islet Remodeling in Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) Knockout Ferrets
Rotti, Pavana G., Xie, Weiliang, Poudel, Ananta, Yi, Yaling, Sun, Xingshen, Tyler, Scott R., Uc, Aliye, Norris, Andrew W., Hara, Manami, Engelhardt, John F., Gibson-Corley, Katherine N.
Published in The American journal of pathology (01.04.2018)
Published in The American journal of pathology (01.04.2018)
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