Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

por Qu, Kun, Garamszegi, Sara, Wu, Felix, Thorvaldsdottir, Helga, Liefeld, Ted, Ocana, Marco, Borges-Rivera, Diego, Pochet, Nathalie, Robinson, James T., Demchak, Barry, Hull, Tim, Ben-Artzi, Gil, Blankenberg, Daniel, Barber, Galt P., Lee, Brian T., Kuhn, Robert M., Nekrutenko, Anton, Segal, Eran, Ideker, Trey, Reich, Michael, Regev, Aviv, Chang, Howard Y., Mesirov, Jill P.
Publicado 2016

Genome-wide CRISPR screen identifies PRC2 and KMT2D-COMPASS as regulators of distinct EMT trajectories that contribute differentially to metastasis

por Zhang, Yun, Donaher, Joana Liu, Das, Sunny, Li, Xin, Reinhardt, Ferenc, Krall, Jordan A., Lambert, Arthur W., Thiru, Prathapan, Keys, Heather R., Khan, Mehreen, Hofree, Matan, Wilson, Molly M., Yedier-Bayram, Ozlem, Lack, Nathan A., Onder, Tamer T., Bagci-Onder, Tugba, Tyler, Michael, Tirosh, Itay, Regev, Aviv, Lees, Jacqueline A., Weinberg, Robert A.
Publicado 2022

A molecular network of the aging human brain provides insights into the pathology and cognitive decline of Alzheimer’s disease

por Mostafavi, Sara, Gaiteri, Chris, Sullivan, Sarah E., White, Charles C., Tasaki, Shinya, Xu, Jishu, Taga, Mariko, Klein, Hans-Ulrich, Patrick, Ellis, Komashko, Vitalina, McCabe, Cristin, Smith, Robert, Bradshaw, Elizabeth M., Root, David E., Regev, Aviv, Yu, Lei, Chibnik, Lori B., Schneider, Julie A., Young-Pearse, Tracy L., Bennett, David A., De Jager, Philip L.
Publicado 2018

Multiplexed single-cell transcriptional response profiling to define cancer vulnerabilities and therapeutic mechanism of action

por McFarland, James M., Paolella, Brenton R., Warren, Allison, Geiger-Schuller, Kathryn, Shibue, Tsukasa, Rothberg, Michael, Kuksenko, Olena, Colgan, William N., Jones, Andrew, Chambers, Emily, Dionne, Danielle, Bender, Samantha, Wolpin, Brian M., Ghandi, Mahmoud, Tirosh, Itay, Rozenblatt-Rosen, Orit, Roth, Jennifer A., Golub, Todd R., Regev, Aviv, Aguirre, Andrew J., Vazquez, Francisca, Tsherniak, Aviad
Publicado 2020

An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets

por Zhang, Huiyuan, Madi, Asaf, Yosef, Nir, Chihara, Norio, Awasthi, Amit, Pot, Caroline, Lambden, Conner, Srivastava, Amitabh, Burkett, Patrick R., Nyman, Jackson, Christian, Elena, Etminan, Yasaman, Lee, Annika, Stroh, Helene, Xia, Junrong, Karwacz, Katarzyna, Thakore, Pratiksha I., Acharya, Nandini, Schnell, Alexandra, Wang, Chao, Apetoh, Lionel, Rozenblatt-Rosen, Orit, Anderson, Ana C., Regev, Aviv, Kuchroo, Vijay K.
Publicado 2020

Functional analyses and single cell immunoprofiling uncover sex-specific differences in SARS-CoV2 immune memory development

por Eraslan, Basak, Brown, Eric, Benson, Maura, Amir-Zilberstein, Liat, Park, Sung-Moo, Tusi, Betsabeh, Pokatayev, Vladislav, Hecht, Cody, Pishesha, Novalia, Phillips, Devan, Kim, Andy, Zhang, Shuting, Gaca, Anthony, Ghantous, Fadi, Delorey, Toni, Livny, Jonathan, Baden, Lindsey, Rozenblatt-Rosen, Orit, Graham, Daniel, Regev, Aviv, Seaman, Michael, Woolley, Ann, Cosimi, Lisa, Hung, Deborah, Deguine, Jacques, Xavier, Ramnik
Publicado 2022

A deep learning algorithm to predict risk of pancreatic cancer from disease trajectories

por Placido, Davide, Yuan, Bo, Hjaltelin, Jessica X., Zheng, Chunlei, Haue, Amalie D., Chmura, Piotr J., Yuan, Chen, Kim, Jihye, Umeton, Renato, Antell, Gregory, Chowdhury, Alexander, Franz, Alexandra, Brais, Lauren, Andrews, Elizabeth, Marks, Debora S., Regev, Aviv, Ayandeh, Siamack, Brophy, Mary T., Do, Nhan V., Kraft, Peter, Wolpin, Brian M., Rosenthal, Michael H., Fillmore, Nathanael R., Brunak, Søren, Sander, Chris
Publicado 2023

Genetic determinants of co-accessible chromatin regions in activated T cells across humans

por Gate, Rachel E., Cheng, Christine S., Aiden, Aviva P., Siba, Atsede, Tabaka, Marcin, Lituiev, Dmytro, Machol, Ido, Gordon, M. Grace, Subramaniam, Meena, Shamim, Muhammad, Hougen, Kendrick L., Wortman, Ivo, Huang, Su-Chen, Durand, Neva C., Feng, Ting, De Jager, Philip L., Chang, Howard Y., Aiden, Erez Lieberman, Benoist, Christophe, Beer, Michael A., Ye, Chun J., Regev, Aviv
Publicado 2018

Genetic analysis of isoform usage in the human anti-viral response reveals influenza-specific regulation of ERAP2 transcripts under balancing selection

por Ye, Chun Jimmie, Chen, Jenny, Villani, Alexandra-Chloé, Gate, Rachel E., Subramaniam, Meena, Bhangale, Tushar, Lee, Mark N., Raj, Towfique, Raychowdhury, Raktima, Li, Weibo, Rogel, Noga, Simmons, Sean, Imboywa, Selina H., Chipendo, Portia I., McCabe, Cristin, Lee, Michelle H., Frohlich, Irene Y., Stranger, Barbara E., De Jager, Philip L., Regev, Aviv, Behrens, Tim, Hacohen, Nir
Publicado 2018

The microbiota regulate neuronal function and fear extinction learning

por Chu, Coco, Murdock, Mitchell H., Jing, Deqiang, Won, Tae Hyung, Chung, Hattie, Kressel, Adam M., Tsaava, Tea, Addorisio, Meghan E., Putzel, Gregory G., Zhou, Lei, Bessman, Nicholas J., Yang, Ruirong, Moriyama, Saya, Parkhurst, Christopher N., Li, Anfei, Meyer, Heidi C., Teng, Fei, Chavan, Sangeeta S., Tracey, Kevin J., Regev, Aviv, Schroeder, Frank C., Lee, Francis S., Liston, Conor, Artis, David
Publicado 2019

GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome

por Bonfiglio, Ferdinando, Liu, Xingrong, Smillie, Christopher, Pandit, Anita, Kurilshikov, Alexander, Bacigalupe, Rodrigo, Zheng, Tenghao, Nim, Hieu, Garcia-Etxebarria, Koldo, Bujanda, Luis, Andreasson, Anna, Agreus, Lars, Walter, Susanna, Abecasis, Gonçalo, Eijsbouts, Chris, Jostins, Luke, Parkes, Miles, Hughes, David A., Timpson, Nicholas, Raes, Jeroen, Franke, Andre, Kennedy, Nicholas A., Regev, Aviv, Zhernakova, Alexandra, Simren, Magnus, Camilleri, Michael, D’Amato, Mauro
Publicado 2021

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

por Montoro, Daniel T., Haber, Adam L., Biton, Moshe, Vinarsky, Vladimir, Lin, Brian, Birket, Susan, Yuan, Feng, Chen, Sijia, Leung, Hui Min, Villoria, Jorge, Rogel, Noga, Burgin, Grace, Tsankov, Alexander, Waghray, Avinash, Slyper, Michal, Waldmann, Julia, Nguyen, Lan, Dionne, Danielle, Rozenblatt-Rosen, Orit, Tata, Purushothama Rao, Mou, Hongmei, Shivaraju, Manjunatha, Bihler, Hermann, Mense, Martin, Tearney, Guillermo J., Rowe, Steven M., Engelhardt, John F., Regev, Aviv, Rajagopal, Jayaraj
Publicado 2018

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

por Schapiro, Denis, Sokolov, Artem, Yapp, Clarence, Chen, Yu-An, Muhlich, Jeremy L., Hess, Joshua, Creason, Allison L., Nirmal, Ajit J., Baker, Gregory J., Nariya, Maulik K., Lin, Jia-Ren, Maliga, Zoltan, Jacobson, Connor A., Hodgman, Matthew W., Ruokonen, Juha, Farhi, Samouil L., Abbondanza, Domenic, McKinley, Eliot T., Persson, Daniel, Betts, Courtney, Sivagnanam, Shamilene, Regev, Aviv, Goecks, Jeremy, Coffey, Robert J., Coussens, Lisa M., Santagata, Sandro, Sorger, Peter K.
Publicado 2021

Mouse fetal growth restriction through parental and fetal immune gene variation and intercellular communications cascade

por Kaur, Gurman, Porter, Caroline B. M., Ashenberg, Orr, Lee, Jack, Riesenfeld, Samantha J., Hofree, Matan, Aggelakopoulou, Maria, Subramanian, Ayshwarya, Kuttikkatte, Subita Balaram, Attfield, Kathrine E., Desel, Christiane A. E., Davies, Jessica L., Evans, Hayley G., Avraham-Davidi, Inbal, Nguyen, Lan T., Dionne, Danielle A., Neumann, Anna E., Jensen, Lise Torp, Barber, Thomas R., Soilleux, Elizabeth, Carrington, Mary, McVean, Gil, Rozenblatt-Rosen, Orit, Regev, Aviv, Fugger, Lars
Publicado 2022

Single cell RNA sequencing of human microglia uncovers a subset associated with Alzheimer’s disease

por Olah, Marta, Menon, Vilas, Habib, Naomi, Taga, Mariko F., Ma, Yiyi, Yung, Christina J., Cimpean, Maria, Khairallah, Anthony, Coronas-Samano, Guillermo, Sankowski, Roman, Grün, Dominic, Kroshilina, Alexandra A., Dionne, Danielle, Sarkis, Rani A., Cosgrove, Garth R., Helgager, Jeffrey, Golden, Jeffrey A., Pennell, Page B., Prinz, Marco, Vonsattel, Jean Paul G., Teich, Andrew F., Schneider, Julie A., Bennett, David A., Regev, Aviv, Elyaman, Wassim, Bradshaw, Elizabeth M., De Jager, Philip L.
Publicado 2020

Tumor and immune reprogramming during immunotherapy in advanced renal cell carcinoma

por Bi, Kevin, He, Meng Xiao, Bakouny, Ziad, Kanodia, Abhay, Napolitano, Sara, Wu, Jingyi, Grimaldi, Grace, Braun, David A., Cuoco, Michael S., Mayorga, Angie, DelloStritto, Laura, Bouchard, Gabrielle, Steinharter, John, Tewari, Alok K., Vokes, Natalie I., Shannon, Erin, Sun, Maxine, Park, Jihye, Chang, Steven L., McGregor, Bradley A., Haq, Rizwan, Denize, Thomas, Signoretti, Sabina, Guerriero, Jennifer L., Vigneau, Sébastien, Rozenblatt-Rosen, Orit, Rotem, Asaf, Regev, Aviv, Choueiri, Toni K., Van Allen, Eliezer M.
Publicado 2021

Mitogenic and progenitor gene programmes in single pilocytic astrocytoma cells

por Reitman, Zachary J., Paolella, Brenton R., Bergthold, Guillaume, Pelton, Kristine, Becker, Sarah, Jones, Robert, Sinai, Claire E., Malkin, Hayley, Huang, Ying, Grimmet, Leslie, Herbert, Zachary T., Sun, Yu, Weatherbee, Jessica L., Alberta, John A., Daley, John F., Rozenblatt-Rosen, Orit, Condurat, Alexandra L., Qian, Kenin, Khadka, Prasidda, Segal, Rosalind A., Haas-Kogan, Daphne, Filbin, Mariella G., Suva, Mario L., Regev, Aviv, Stiles, Charles D., Kieran, Mark W., Goumnerova, Liliana, Ligon, Keith L., Shalek, Alex K., Bandopadhayay, Pratiti, Beroukhim, Rameen
Publicado 2019

Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

por Liu, David, Schilling, Bastian, Liu, Derek, Sucker, Antje, Livingstone, Elisabeth, Jerby-Arnon, Livnat, Zimmer, Lisa, Gutzmer, Ralf, Satzger, Imke, Loquai, Carmen, Grabbe, Stephan, Vokes, Natalie, Margolis, Claire A., Conway, Jake, He, Meng Xiao, Elmarakeby, Haitham, Dietlein, Felix, Miao, Diana, Tracy, Adam, Gogas, Helen, Goldinger, Simone M., Utikal, Jochen, Blank, Christian U., Rauschenberg, Ricarda, von Bubnoff, Dagmar, Krackhardt, Angela, Weide, Benjamin, Haferkamp, Sebastian, Kiecker, Felix, Izar, Ben, Garraway, Levi, Regev, Aviv, Flaherty, Keith, Paschen, Annette, Van Allen, Eliezer M., Schadendorf, Dirk
Publicado 2019

Author Correction: Integrative molecular and clinical modeling of clinical outcomes to PD1 blockade in patients with metastatic melanoma

por Liu, David, Schilling, Bastian, Liu, Derek, Sucker, Antje, Livingstone, Elisabeth, Jerby-Arnon, Livnat, Zimmer, Lisa, Gutzmer, Ralf, Satzger, Imke, Loquai, Carmen, Grabbe, Stephan, Vokes, Natalie, Margolis, Claire A., Conway, Jake, He, Meng Xiao, Elmarakeby, Haitham, Dietlein, Felix, Miao, Diana, Tracy, Adam, Gogas, Helen, Goldinger, Simone M., Utikal, Jochen, Blank, Christian U., Rauschenberg, Ricarda, von Bubnoff, Dagmar, Krackhardt, Angela, Weide, Benjamin, Haferkamp, Sebastian, Kiecker, Felix, Izar, Ben, Garraway, Levi, Regev, Aviv, Flaherty, Keith, Paschen, Annette, Van Allen, Eliezer M., Schadendorf, Dirk
Publicado 2020

Skin-resident innate lymphoid cells converge on a pathogenic effector state

por Bielecki, Piotr, Riesenfeld, Samantha J., Hütter, Jan-Christian, Triglia, Elena Torlai, Kowalczyk, Monika S., Ricardo-Gonzalez, Roberto R., Lian, Mi, Vesely, Maria C. Amezcua, Kroehling, Lina, Xu, Hao, Slyper, Michal, Muus, Christoph, Ludwig, Leif S., Christian, Elena, Tao, Liming, Kedaigle, Amanda J., Steach, Holly R., York, Autumn G., Skadow, Mathias H., Yaghoubi, Parastou, Dionne, Danielle, Jarret, Abigail, McGee, Heather M., Porter, Caroline B. M., Licona-Limón, Paula, Bailis, Will, Jackson, Ruaidhrí, Gagliani, Nicola, Gasteiger, Georg, Locksley, Richard M., Regev, Aviv, Flavell, Richard A.
Publicado 2021