STAR Chimeric Post for rapid detection of circular RNA and fusion transcripts

por Akers, Nicholas K, Schadt, Eric E, Losic, Bojan
Publicado 2018

Tumor fitness, immune exhaustion and clinical outcomes: impact of immune checkpoint inhibitors

por Bubie, Adrian, Gonzalez-Kozlova, Edgar, Akers, Nicholas, Villanueva, Augusto, Losic, Bojan
Publicado 2020

Landscape of oncoviral genotype and co-infection via human papilloma and hepatitis B viral tumor in situ profiling

por Bubie, Adrian, Zoulim, Fabien, Testoni, Barbara, Miles, Brett, Posner, Marshall, Villanueva, Augusto, Losic, Bojan
Publicado 2021

Tumoral and immune heterogeneity in an anti-PD-1-responsive glioblastoma: a case study

por Restrepo, Paula, Yong, Raymund, Laface, Ilaria, Tsankova, Nadejda, Nael, Kambiz, Akturk, Guray, Sebra, Robert, Gnjatic, Sacha, Hormigo, Adilia, Losic, Bojan
Publicado 2020

The transcriptomic response of cells to a drug combination is more than the sum of the responses to the monotherapies

por Diaz, Jennifer EL, Ahsen, Mehmet Eren, Schaffter, Thomas, Chen, Xintong, Realubit, Ronald B, Karan, Charles, Califano, Andrea, Losic, Bojan, Stolovitzky, Gustavo
Publicado 2020

Systems Genetic Analyses Highlight a TGFβ-FOXO3 Dependent Striatal Astrocyte Network Conserved across Species and Associated with Stress, Sleep, and Huntington’s Disease

por Scarpa, Joseph R., Jiang, Peng, Losic, Bojan, Readhead, Ben, Gao, Vance D., Dudley, Joel T., Vitaterna, Martha H., Turek, Fred W., Kasarskis, Andrew
Publicado 2016

WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing

por Holt, Carson, Losic, Bojan, Pai, Deepa, Zhao, Zhen, Trinh, Quang, Syam, Sujata, Arshadi, Niloofar, Jang, Gun Ho, Ali, Johar, Beck, Tim, McPherson, John, Muthuswamy, Lakshmi B.
Publicado 2014

A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients

por Peters, Lauren A., Friedman, Joshua R., Stojmirovic, Aleksandar, Hagen, Jacob, Houten, Sander, Dodatko, Tetyana, Amaro, Mariana P., Restrepo, Paula, Chai, Zhi, Rodrigo Mora, J., Raymond, Holly A., Curran, Mark, Dobrin, Radu, Das, Anuk, Xiong, Huabao, Schadt, Eric E., Argmann, Carmen, Losic, Bojan
Publicado 2023

Epigenetic regulation of brain region-specific microglia clearance activity

por Ayata, Pinar, Badimon, Ana, Strasburger, Hayley J., Duff, Mary Kaye, Montgomery, Sarah E., Loh, Yong-Hwee E., Ebert, Anja, Pimenova, Anna A., Ramirez, Brianna R., Chan, Andrew T., Sullivan, Josefa M., Purushothaman, Immanuel, Scarpa, Joseph R., Goate, Alison M., Busslinger, Meinrad, Shen, Li, Losic, Bojan, Schaefer, Anne
Publicado 2018

Open Problems in Extracellular RNA Data Analysis: Insights From an ERCC Online Workshop

por Alexander, Roger P., Kitchen, Robert R, Tosar, Juan Pablo, Roth, Matthew, Mestdagh, Pieter, Max, Klaas E. A., Rozowsky, Joel, Kaczor-Urbanowicz, Karolina Elżbieta, Chang, Justin, Balaj, Leonora, Losic, Bojan, Van Nostrand, Eric L., LaPlante, Emily, Mateescu, Bogdan, White, Brian S., Yu, Rongshan, Milosavljevic, Aleksander, Stolovitzky, Gustavo, Spengler, Ryan M.
Publicado 2022

Transcriptomic characterization of cancer-testis antigens identifies MAGEA3 as a driver of tumor progression in hepatocellular carcinoma

por Craig, Amanda J., Garcia-Lezana, Teresa, Ruiz de Galarreta, Marina, Villacorta-Martin, Carlos, Kozlova, Edgar G., Martins-Filho, Sebastiao N., von Felden, Johann, Ahsen, Mehmet Eren, Bresnahan, Erin, Hernandez-Meza, Gabriela, Labgaa, Ismail, D’Avola, Delia, Schwartz, Myron, Llovet, Josep M., Sia, Daniela, Thung, Swan, Losic, Bojan, Lujambio, Amaia, Villanueva, Augusto
Publicado 2021

A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses

por Comella, Phillip H., Gonzalez-Kozlova, Edgar, Kosoy, Roman, Charney, Alexander W., Peradejordi, Irene Font, Chandrasekar, Shreya, Tyler, Scott R., Wang, Wenhui, Losic, Bojan, Zhu, Jun, Hoffman, Gabriel E., Kim-Schulze, Seunghee, Qi, Jingjing, Patel, Manishkumar, Kasarskis, Andrew, Suarez-Farinas, Mayte, Gümüş, Zeynep H., Argmann, Carmen, Merad, Miriam, Becker, Christian, Beckmann, Noam D., Schadt, Eric E.
Publicado 2021

Insights into beta cell regeneration for diabetes via integration of molecular landscapes in human insulinomas

por Wang, Huan, Bender, Aaron, Wang, Peng, Karakose, Esra, Inabnet, William B., Libutti, Steven K., Arnold, Andrew, Lambertini, Luca, Stang, Micheal, Chen, Herbert, Kasai, Yumi, Mahajan, Milind, Kinoshita, Yayoi, Fernandez-Ranvier, Gustavo, Becker, Thomas C., Takane, Karen K., Walker, Laura A., Saul, Shira, Chen, Rong, Scott, Donald K., Ferrer, Jorge, Antipin, Yevgeniy, Donovan, Michael, Uzilov, Andrew V., Reva, Boris, Schadt, Eric E., Losic, Bojan, Argmann, Carmen, Stewart, Andrew F.
Publicado 2017

Intratumoral heterogeneity and clonal evolution in liver cancer

por Losic, Bojan, Craig, Amanda J., Villacorta-Martin, Carlos, Martins-Filho, Sebastiao N., Akers, Nicholas, Chen, Xintong, Ahsen, Mehmet E., von Felden, Johann, Labgaa, Ismail, DʹAvola, Delia, Allette, Kimaada, Lira, Sergio A., Furtado, Glaucia C., Garcia-Lezana, Teresa, Restrepo, Paula, Stueck, Ashley, Ward, Stephen C., Fiel, Maria I., Hiotis, Spiros P., Gunasekaran, Ganesh, Sia, Daniela, Schadt, Eric E., Sebra, Robert, Schwartz, Myron, Llovet, Josep M., Thung, Swan, Stolovitzky, Gustavo, Villanueva, Augusto
Publicado 2020

A functional genomics predictive network model identifies regulators of inflammatory bowel disease

por Peters, Lauren A, Perrigoue, Jacqueline, Mortha, Arthur, Iuga, Alina, Song, Won-min, Neiman, Eric M, Llewellyn, Sean R, Di Narzo, Antonio, Kidd, Brian A, Telesco, Shannon E, Zhao, Yongzhong, Stojmirovic, Aleksandar, Sendecki, Jocelyn, Shameer, Khader, Miotto, Riccardo, Losic, Bojan, Shah, Hardik, Lee, Eunjee, Wang, Minghui, Faith, Jeremiah J, Kasarskis, Andrew, Brodmerkel, Carrie, Curran, Mark, Das, Anuk, Friedman, Joshua R, Fukui, Yoshinori, Humphrey, Mary Beth, Iritani, Brian M, Sibinga, Nicholas, Tarrant, Teresa K, Argmann, Carmen, Hao, Ke, Roussos, Panos, Zhu, Jun, Zhang, Bin, Dobrin, Radu, Mayer, Lloyd F, Schadt, Eric E
Publicado 2017

Intestinal Inflammation Modulates the Expression of ACE2 and TMPRSS2 and Potentially Overlaps With the Pathogenesis of SARS-CoV-2–related Disease

por Suárez-Fariñas, Mayte, Tokuyama, Minami, Wei, Gabrielle, Huang, Ruiqi, Livanos, Alexandra, Jha, Divya, Levescot, Anais, Irizar, Haritz, Kosoy, Roman, Cording, Sascha, Wang, Wenhui, Losic, Bojan, Ungaro, Ryan C., Di’Narzo, Antonio, Martinez-Delgado, Gustavo, Suprun, Maria, Corley, Michael J., Stojmirovic, Aleksandar, Houten, Sander M., Peters, Lauren, Curran, Mark, Brodmerkel, Carrie, Perrigoue, Jacqueline, Friedman, Joshua R., Hao, Ke, Schadt, Eric E., Zhu, Jun, Ko, Huaibin M., Cho, Judy, Dubinsky, Marla C., Sands, Bruce E., Ndhlovu, Lishomwa, Cerf-Bensusan, Nadine, Kasarskis, Andrew, Colombel, Jean-Frederic, Harpaz, Noam, Argmann, Carmen, Mehandru, Saurabh
Publicado 2021

Gut microbiota density influences host physiology and is shaped by host and microbial factors

por Contijoch, Eduardo J, Britton, Graham J, Yang, Chao, Mogno, Ilaria, Li, Zhihua, Ng, Ruby, Llewellyn, Sean R, Hira, Sheela, Johnson, Crystal, Rabinowitz, Keren M, Barkan, Revital, Dotan, Iris, Hirten, Robert P, Fu, Shih-Chen, Luo, Yuying, Yang, Nancy, Luong, Tramy, Labrias, Philippe R, Lira, Sergio, Peter, Inga, Grinspan, Ari, Clemente, Jose C, Kosoy, Roman, Kim-Schulze, Seunghee, Qin, Xiaochen, Castillo, Anabella, Hurley, Amanda, Atreja, Ashish, Rogers, Jason, Fasihuddin, Farah, Saliaj, Merjona, Nolan, Amy, Reyes-Mercedes, Pamela, Rodriguez, Carina, Aly, Sarah, Santa-Cruz, Kenneth, Peters, Lauren, Suárez-Fariñas, Mayte, Huang, Ruiqi, Hao, Ke, Zhu, Jun, Zhang, Bin, Losic, Bojan, Irizar, Haritz, Song, Won-Min, Di Narzo, Antonio, Wang, Wenhui, Cohen, Benjamin L, DiMaio, Christopher, Greenwald, David, Itzkowitz, Steven, Lucas, Aimee, Marion, James, Maser, Elana, Ungaro, Ryan, Naymagon, Steven, Novak, Joshua, Shah, Brijen, Ullman, Thomas, Rubin, Peter, George, James, Legnani, Peter, Telesco, Shannon E, Friedman, Joshua R, Brodmerkel, Carrie, Plevy, Scott, Cho, Judy H, Colombel, Jean-Frederic, Schadt, Eric E, Argmann, Carmen, Dubinsky, Marla, Kasarskis, Andrew, Sands, Bruce, Faith, Jeremiah J
Publicado 2019

Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children

por Beckmann, Noam D., Comella, Phillip H., Cheng, Esther, Lepow, Lauren, Beckmann, Aviva G., Mouskas, Konstantinos, Simons, Nicole W., Hoffman, Gabriel E., Francoeur, Nancy J., Del Valle, Diane Marie, Kang, Gurpawan, Moya, Emily, Wilkins, Lillian, Le Berichel, Jessica, Chang, Christie, Marvin, Robert, Calorossi, Sharlene, Lansky, Alona, Walker, Laura, Yi, Nancy, Yu, Alex, Hartnett, Matthew, Eaton, Melody, Hatem, Sandra, Jamal, Hajra, Akyatan, Alara, Tabachnikova, Alexandra, Liharska, Lora E., Cotter, Liam, Fennessey, Brian, Vaid, Akhil, Barturen, Guillermo, Tyler, Scott R., 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, Argueta, Kimberly, Harris, Jocelyn, Karekar, Neha, Batchelor, Craig, Lacunza, Jose, Yishak, Mahlet, Tuballes, Kevin, Scott, Leisha, Kumar, Arvind, Jaladanki, Suraj, Thompson, Ryan, Clark, Evan, Losic, Bojan, 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, 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.
Publicado 2020

Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children

por 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.
Publicado 2021