Multi-study inference of regulatory networks for more accurate models of gene regulation

por Castro, Dayanne M., de Veaux, Nicholas R., Miraldi, Emily R., Bonneau, Richard
Publicado 2019

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

por Kurtz, Zachary D., Müller, Christian L., Miraldi, Emily R., Littman, Dan R., Blaser, Martin J., Bonneau, Richard A.
Publicado 2015

Elevated CD153 Expression on Aged T Follicular Helper Cells is Vital for B cell Responses

por Thomas, Alyssa L., Wayman, Joseph A., Almanan, Maha, Bejjani, Anthony T., Miraldi, Emily R., Chougnet, Claire A., Hildeman, David A.
Publicado 2023

Analysis of 3D genomic interactions identifies candidate host genes that transposable elements potentially regulate

por Raviram, Ramya, Rocha, Pedro P., Luo, Vincent M., Swanzey, Emily, Miraldi, Emily R., Chuong, Edward B., Feschotte, Cédric, Bonneau, Richard, Skok, Jane A.
Publicado 2018

CX(3)CR1(+) mononuclear phagocytes support colitis-associated innate lymphoid cell production of IL-22

por Longman, Randy S., Diehl, Gretchen E., Victorio, Daniel A., Huh, Jun R., Galan, Carolina, Miraldi, Emily R., Swaminath, Arun, Bonneau, Richard, Scherl, Ellen J., Littman, Dan R.
Publicado 2014

4C-ker: A Method to Reproducibly Identify Genome-Wide Interactions Captured by 4C-Seq Experiments

por Raviram, Ramya, Rocha, Pedro P., Müller, Christian L., Miraldi, Emily R., Badri, Sana, Fu, Yi, Swanzey, Emily, Proudhon, Charlotte, Snetkova, Valentina, Bonneau, Richard, Skok, Jane A.
Publicado 2016

Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells

por Miraldi, Emily R., Pokrovskii, Maria, Watters, Aaron, Castro, Dayanne M., De Veaux, Nicholas, Hall, Jason A., Lee, June-Yong, Ciofani, Maria, Madar, Aviv, Carriero, Nick, Littman, Dan R., Bonneau, Richard
Publicado 2019

A Damage-Independent Role for 53BP1 that Impacts Break Order and Igh Architecture during Class Switch Recombination

por Rocha, Pedro P., Raviram, Ramya, Fu, Yi, Kim, JungHyun, Luo, Vincent M., Aljoufi, Arafat, Swanzey, Emily, Pasquarella, Alessandra, Balestrini, Alessia, Miraldi, Emily R., Bonneau, Richard, Petrini, John, Schotta, Gunnar, Skok, Jane A.
Publicado 2016

maxATAC: Genome-scale transcription-factor binding prediction from ATAC-seq with deep neural networks

por Cazares, Tareian A., Rizvi, Faiz W., Iyer, Balaji, Chen, Xiaoting, Kotliar, Michael, Bejjani, Anthony T., Wayman, Joseph A., Donmez, Omer, Wronowski, Benjamin, Parameswaran, Sreeja, Kottyan, Leah C., Barski, Artem, Weirauch, Matthew T., Prasath, V. B. Surya, Miraldi, Emily R.
Publicado 2023

Global discovery of lupus genetic risk variant allelic enhancer activity

por Lu, Xiaoming, Chen, Xiaoting, Forney, Carmy, Donmez, Omer, Miller, Daniel, Parameswaran, Sreeja, Hong, Ted, Huang, Yongbo, Pujato, Mario, Cazares, Tareian, Miraldi, Emily R., Ray, John P., de Boer, Carl G., Harley, John B., Weirauch, Matthew T., Kottyan, Leah C.
Publicado 2021

High-performance single-cell gene regulatory network inference at scale: the Inferelator 3.0

por Skok Gibbs, Claudia, Jackson, Christopher A, Saldi, Giuseppe-Antonio, Tjärnberg, Andreas, Shah, Aashna, Watters, Aaron, De Veaux, Nicholas, Tchourine, Konstantine, Yi, Ren, Hamamsy, Tymor, Castro, Dayanne M, Carriero, Nicholas, Gorissen, Bram L, Gresham, David, Miraldi, Emily R, Bonneau, Richard
Publicado 2022

DDX5 and its associated lncRNA Rmrp modulate Th17 cell effector functions

por Huang, Wendy, Thomas, Benjamin, Flynn, Ryan A., Gavzy, Samuel J., Wu, Lin, Kim, Sangwon V., Hall, Jason A., Miraldi, Emily R., Ng, Charles P., Rigo, Frank, Meadows, Sarah, Montoya, Nina R., Herrera, Natalia G., Domingos, Ana I., Rastinejad, Fraydoon, Myers, Richard M., Fuller-Pace, Frances V., Bonneau, Richard, Chang, Howard Y., Acuto, Oreste, Littman, Dan R.
Publicado 2015

Hybrid Gene Origination Creates Human-Virus Chimeric Proteins during Infection

por Ho, Jessica Sook Yuin, Angel, Matthew, Ma, Yixuan, Sloan, Elizabeth, Wang, Guojun, Martinez-Romero, Carles, Alenquer, Marta, Roudko, Vladimir, Chung, Liliane, Zheng, Simin, Chang, Max, Fstkchyan, Yesai, Clohisey, Sara, Dinan, Adam M., Gibbs, James, Gifford, Robert, Shen, Rong, Gu, Quan, Irigoyen, Nerea, Campisi, Laura, Huang, Cheng, Zhao, Nan, Jones, Joshua D., van Knippenberg, Ingeborg, Zhu, Zeyu, Moshkina, Natasha, Meyer, Léa, Noel, Justine, Peralta, Zuleyma, Rezelj, Veronica, Kaake, Robyn, Rosenberg, Brad, Wang, Bo, Wei, Jiajie, Paessler, Slobodan, Wise, Helen M., Johnson, Jeffrey, Vannini, Alessandro, Amorim, Maria João, Baillie, J. Kenneth, Miraldi, Emily R., Benner, Christopher, Brierley, Ian, Digard, Paul, Łuksza, Marta, Firth, Andrew E., Krogan, Nevan, Greenbaum, Benjamin D., MacLeod, Megan K., van Bakel, Harm, Garcìa-Sastre, Adolfo, Yewdell, Jonathan W., Hutchinson, Edward, Marazzi, Ivan
Publicado 2020

TOP1 inhibition therapy protects against SARS-CoV-2-induced lethal inflammation

por Ho, Jessica Sook Yuin, Mok, Bobo Wing-Yee, Campisi, Laura, Jordan, Tristan, Yildiz, Soner, Parameswaran, Sreeja, Wayman, Joseph A., Gaudreault, Natasha N., Meekins, David A., Indran, Sabarish V., Morozov, Igor, Trujillo, Jessie D., Fstkchyan, Yesai S., Rathnasinghe, Raveen, Zhu, Zeyu, Zheng, Simin, Zhao, Nan, White, Kris, Ray-Jones, Helen, Malysheva, Valeriya, Thiecke, Michiel J., Lau, Siu-Ying, Liu, Honglian, Zhang, Anna Junxia, Lee, Andrew Chak-Yiu, Liu, Wen-Chun, Jangra, Sonia, Escalera, Alba, Aydillo, Teresa, Melo, Betsaida Salom, Guccione, Ernesto, Sebra, Robert, Shum, Elaine, Bakker, Jan, Kaufman, David A., Moreira, Andre L., Carossino, Mariano, Balasuriya, Udeni B.R., Byun, Minji, Albrecht, Randy A., Schotsaert, Michael, Garcia-Sastre, Adolfo, Chanda, Sumit K., Miraldi, Emily R., Jeyasekharan, Anand D., TenOever, Benjamin R., Spivakov, Mikhail, Weirauch, Matthew T., Heinz, Sven, Chen, Honglin, Benner, Christopher, Richt, Juergen A., Marazzi, Ivan
Publicado 2021