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148 results on '"Song, Yizhe"'

1. SenNet recommendations for detecting senescent cells in different tissues

Author

Suryadevara, Vidyani, Hudgins, Adam D., Rajesh, Adarsh, Pappalardo, Alberto, Karpova, Alla, Dey, Amit K., Hertzel, Ann, Agudelo, Anthony, Rocha, Azucena, Soygur, Bikem, Schilling, Birgit, Carver, Chase M., Aguayo-Mazzucato, Cristina, Baker, Darren J., Bernlohr, David A., Jurk, Diana, Mangarova, Dilyana B., Quardokus, Ellen M., Enninga, Elizabeth Ann L., Schmidt, Elizabeth L., Chen, Feng, Duncan, Francesca E., Cambuli, Francesco, Kaur, Gagandeep, Kuchel, George A., Lee, Gung, Daldrup-Link, Heike E., Martini, Helene, Phatnani, Hemali, Al-Naggar, Iman M., Rahman, Irfan, Nie, Jia, Passos, João F., Silverstein, Jonathan C., Campisi, Judith, Wang, Julia, Iwasaki, Kanako, Barbosa, Karina, Metis, Kay, Nernekli, Kerem, Niedernhofer, Laura J., Ding, Li, Wang, Lichao, Adams, Lisa C., Ruiyang, Liu, Doolittle, Madison L., Teneche, Marcos G., Schafer, Marissa J., Xu, Ming, Hajipour, Mohammadjavad, Boroumand, Mozhgan, Basisty, Nathan, Sloan, Nicholas, Slavov, Nikolai, Kuksenko, Olena, Robson, Paul, Gomez, Paul T., Vasilikos, Periklis, Adams, Peter D., Carapeto, Priscila, Zhu, Quan, Ramasamy, Ramalakshmi, Perez-Lorenzo, Rolando, Fan, Rong, Dong, Runze, Montgomery, Ruth R., Shaikh, Sadiya, Vickovic, Sanja, Yin, Shanshan, Kang, Shoukai, Suvakov, Sonja, Khosla, Sundeep, Garovic, Vesna D., Menon, Vilas, Xu, Yanxin, Song, Yizhe, Suh, Yousin, Dou, Zhixun, and Neretti, Nicola

Published
2024
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2. Epigenetic regulation during cancer transitions across 11 tumour types

Author

Terekhanova, Nadezhda V., Karpova, Alla, Liang, Wen-Wei, Strzalkowski, Alexander, Chen, Siqi, Li, Yize, Southard-Smith, Austin N., Iglesia, Michael D., Wendl, Michael C., Jayasinghe, Reyka G., Liu, Jingxian, Song, Yizhe, Cao, Song, Houston, Andrew, Liu, Xiuting, Wyczalkowski, Matthew A., Lu, Rita Jui-Hsien, Caravan, Wagma, Shinkle, Andrew, Naser Al Deen, Nataly, Herndon, John M., Mudd, Jacqueline, Ma, Cong, Sarkar, Hirak, Sato, Kazuhito, Ibrahim, Omar M., Mo, Chia-Kuei, Chasnoff, Sara E., Porta-Pardo, Eduard, Held, Jason M., Pachynski, Russell, Schwarz, Julie K., Gillanders, William E., Kim, Albert H., Vij, Ravi, DiPersio, John F., Puram, Sidharth V., Chheda, Milan G., Fuh, Katherine C., DeNardo, David G., Fields, Ryan C., Chen, Feng, Raphael, Benjamin J., and Ding, Li

Published
2023
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3. Pan-cancer proteogenomics characterization of tumor immunity

Author

Abelin, Jennifer, Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Özgün, Bavarva, Jasmin, Birger, Chet, Birrer, Michael J., Cao, Song, Carr, Steven A., Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Saravana M., Ding, Li, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Foltz, Steven M., Francis, Alicia, Geffen, Yifat, Getz, Gad, Heiman, David I., Hong, Runyu, Hu, Yingwei, Huang, Chen, Jaehnig, Eric J., Jewell, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, McDermott, Jason, McKerrow, Wilson, Mesri, Mehdi, Mumphrey, Michael Brodie, Newton, Chelsea J., Oldroyd, Robert, Payne, Samuel H., Pugliese, Pietro, Rodland, Karin D., Rodrigues, Fernanda Martins, Ruggles, Kelly V., Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Schürer, Stephan, Shi, Zhiao, Smith, Richard D., Song, Feng, Song, Yizhe, Stathias, Vasileios, Storrs, Erik P., Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Li, Qing Kay, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Petralia, Francesca, Ma, Weiping, Yaron, Tomer M., Caruso, Francesca Pia, Tignor, Nicole, Wang, Joshua M., Charytonowicz, Daniel, Johnson, Jared L., Huntsman, Emily M., Marino, Giacomo B., Calinawan, Anna, Evangelista, John Erol, Selvan, Myvizhi Esai, Chowdhury, Shrabanti, Rykunov, Dmitry, Krek, Azra, Song, Xiaoyu, Turhan, Berk, Christianson, Karen E., Lewis, David A., Deng, Eden Z., Clarke, Daniel J.B., Whiteaker, Jeffrey R., Kennedy, Jacob J., Zhao, Lei, Segura, Rossana Lazcano, Batra, Harsh, Raso, Maria Gabriela, Parra, Edwin Roger, Soundararajan, Rama, Tang, Ximing, Li, Yize, Yi, Xinpei, Satpathy, Shankha, Wang, Ying, Wiznerowicz, Maciej, González-Robles, Tania J., Iavarone, Antonio, Gosline, Sara J.C., Reva, Boris, Robles, Ana I., Nesvizhskii, Alexey I., Mani, D.R., Gillette, Michael A., Klein, Robert J., Cieslik, Marcin, Zhang, Bing, Paulovich, Amanda G., Sebra, Robert, Gümüş, Zeynep H., Hostetter, Galen, Fenyö, David, Omenn, Gilbert S., Cantley, Lewis C., Ma'ayan, Avi, Lazar, Alexander J., Ceccarelli, Michele, and Wang, Pei

Published
2024
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4. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Author

Aguet, François, Akiyama, Yo, An, Eunkyung, Anand, Shankara, Anurag, Meenakshi, Babur, Ozgun, Bavarva, Jasmin, Birger, Chet, Birrer, Michael, Calinawan, Anna, Cantley, Lewis C., Cao, Song, Carr, Steve, Ceccarelli, Michele, Chan, Daniel, Chinnaiyan, Arul, Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin, Clauser, Karl, Colaprico, Antonio, Zhou, Daniel Cui, da Veiga Leprevost, Felipe, Day, Corbin, Dhanasekaran, Mohan, Domagalski, Marcin, Dou, Yongchao, Druker, Brian, Edwards, Nathan, Ellis, Matthew, Selvan, Myvizhi Esai, Francis, Alicia, Getz, Gad, Gillette, Michael A., Robles, Tania Gonzalez, Gosline, Sara, Gümüş, Zeynep, Heiman, David, Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Iavarone, Antonio, Jaehnig, Eric, Jewel, Scott, Ji, Jiayi, Jiang, Wen, Lee Johnson, Jared, Katsnelson, Lizabeth, Ketchum, Karen, Krug, Karsten, Kumar-Sinha, Chandan, Lei, Jonathan, Liao, Yuxing, Lindgren, Caleb, Liu, Tao, Liu, Wenke, Ma, Weiping, Rodrigues, Fernanda Martins, McKerrow, Wilson, Mesri, Mehdi, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert, Paulovich, Amanda, Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Ruggles, Kelly, Rykunov, Dmitry, Satpathy, Shankha, Savage, Sara, Schadt, Eric, Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Dick, Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik, Tan, Jimin, Terekhanova, Nadezhda, Thangudu, Ratna, Thiagarajan, Mathangi, Tignor, Nicole, Wang, Joshua, Wang, Liang-Bo, Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wu, Yige, Yao, Lijun, Yaron, Tomer M., Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Qing, Zhang, Xu, Zhang, Zhen, Chan, Daniel W., Dhanasekaran, Saravana M., Schürer, Stephan, Smith, Richard D., Wyczalkowski, Matthew A., Liang, Wen-Wei, Lu, Rita Jui-Hsien, Jayasinghe, Reyka G., Foltz, Steven M., Porta-Pardo, Eduard, Geffen, Yifat, Wendl, Michael C., Lazcano, Rossana, Kolodziejczak, Iga, Song, Yizhe, Govindan, Akshay, Demicco, Elizabeth G., Li, Xiang, Li, Yize, Sethuraman, Sunantha, Payne, Samuel H., Fenyö, David, Rodriguez, Henry, Wiznerowicz, Maciej, Shen, Hui, Mani, D.R., Rodland, Karin D., Lazar, Alexander J., Robles, Ana I., and Ding, Li

Published
2023
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6. Pan-cancer proteogenomics connects oncogenic drivers to functional states

Author

An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Calinawan, Anna, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Selvan, Myvizhi Esai, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Huntsman, Emily, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Lei, Jonathan T., Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Ma, Weiping, McKerrow, Wilson, Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Tan, Jimin, Thangudu, Ratna R., Tignor, Nicole, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Li, Yize, Porta-Pardo, Eduard, Tokheim, Collin, Bailey, Matthew H., Yaron, Tomer M., Stathias, Vasileios, Geffen, Yifat, Imbach, Kathleen J., Cao, Song, Anand, Shankara, Akiyama, Yo, Liu, Wenke, Wyczalkowski, Matthew A., Song, Yizhe, Storrs, Erik P., Wendl, Michael C., Zhang, Wubing, Sibai, Mustafa, Ruiz-Serra, Victoria, Liang, Wen-Wei, Terekhanova, Nadezhda V., Rodrigues, Fernanda Martins, Clauser, Karl R., Heiman, David I., Zhang, Qing, Aguet, Francois, Calinawan, Anna P., Dhanasekaran, Saravana M., Birger, Chet, Satpathy, Shankha, Zhou, Daniel Cui, Wang, Liang-Bo, Baral, Jessika, Johnson, Jared L., Huntsman, Emily M., Pugliese, Pietro, Colaprico, Antonio, Iavarone, Antonio, Chheda, Milan G., Ricketts, Christopher J., Fenyö, David, Payne, Samuel H., Rodriguez, Henry, Robles, Ana I., Gillette, Michael A., Kumar-Sinha, Chandan, Lazar, Alexander J., Cantley, Lewis C., Getz, Gad, and Ding, Li

Published
2023
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7. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author

An, Eunkyung, Anurag, Meenakshi, Bavarva, Jasmin, Birrer, Michael J., Babur, Özgün, Cao, Song, Ceccarelli, Michele, Chan, Daniel W., Chinnaiyan, Arul M., Cho, Hanbyul, Chowdhury, Shrabanti, Cieslik, Marcin P., Colaprico, Antonio, Carr, Steven A., da Veiga Leprevost, Felipe, Day, Corbin, Domagalski, Marcin J., Dou, Yongchao, Druker, Brian J., Edwards, Nathan, Ellis, Matthew J., Fenyo, David, Foltz, Steven M., Francis, Alicia, Gonzalez Robles, Tania J., Gosline, Sara J.C., Gümüş, Zeynep H., Hiltke, Tara, Hong, Runyu, Hostetter, Galen, Hu, Yingwei, Huang, Chen, Iavarone, Antonio, Jaehnig, Eric J., Jewel, Scott D., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Kolodziejczak, Iga, Kumar-Sinha, Chandan, Krug, Karsten, Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Liu, Tao, Liu, Wenke, Ma, Weiping, McKerrow, Wilson, Mesri, Mehdi, Mani, D.R., Nesvizhskii, Alexey I., Newton, Chelsea, Oldroyd, Robert, Omenn, Gilbert S., Paulovich, Amanda G., Petralia, Francesca, Pugliese, Pietro, Reva, Boris, Rodland, Karin D., Ruggles, Kelly V., Rykunov, Dmitry, Rodrigues, Fernanda Martins, Savage, Sara R., Schadt, Eric E., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Smith, Richard D., Song, Xiaoyu, Stathias, Vasileios, Storrs, Erik P., Schürer, Stephan, Selvan, Myvizhi Esai, Tan, Jimin, Terekhanova, Nadezhda V., Thangudu, Ratna R., Tignor, Nicole, Thiagarajan, Mathangi, Wang, Joshua M., Wang, Pei, Wang, Ying (Cindy), Wen, Bo, Wiznerowicz, Maciej, Wu, Yige, Wyczalkowski, Matthew A., Yao, Lijun, Yi, Xinpei, Zhang, Bing, Zhang, Hui, Zhang, Xu, Zhang, Zhen, Zhou, Daniel Cui, Geffen, Yifat, Anand, Shankara, Akiyama, Yo, Yaron, Tomer M., Song, Yizhe, Johnson, Jared L., Govindan, Akshay, Li, Yize, Huntsman, Emily, Wang, Liang-Bo, Birger, Chet, Heiman, David I., Zhang, Qing, Miller, Mendy, Maruvka, Yosef E., Haradhvala, Nicholas J., Calinawan, Anna, Belkin, Saveliy, Kerelsky, Alexander, Clauser, Karl R., Satpathy, Shankha, Payne, Samuel H., Gillette, Michael A., Dhanasekaran, Saravana M., Rodriguez, Henry, Robles, Ana I., Lazar, Alexander J., Aguet, François, Cantley, Lewis C., Ding, Li, and Getz, Gad

Published
2023
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8. Proteogenomic data and resources for pan-cancer analysis

Author

Lazar, Alexander J., Paulovich, Amanda G., Colaprico, Antonio, Iavarone, Antonio, Chinnaiyan, Arul M., Druker, Brian J., Kumar-Sinha, Chandan, Newton, Chelsea J., Huang, Chen, Mani, D.R., Smith, Richard D., Huntsman, Emily, Schadt, Eric E., An, Eunkyung, Petralia, Francesca, Hostetter, Galen, Omenn, Gilbert S., Cho, Hanbyul, Rodriguez, Henry, Zhang, Hui, Kolodziejczak, Iga, Johnson, Jared L., Bavarva, Jasmin, Tan, Jimin, Rodland, Karin D., Clauser, Karl R., Krug, Karsten, Cantley, Lewis C., Wiznerowicz, Maciej, Ellis, Matthew J., Anurag, Meenakshi, Mesri, Mehdi, Gillette, Michael A., Birrer, Michael J., Ceccarelli, Michele, Dhanasekaran, Saravana M., Edwards, Nathan, Tignor, Nicole, Babur, Özgün, Pugliese, Pietro, Gosline, Sara J.C., Jewell, Scott D., Satpathy, Shankha, Chowdhury, Shrabanti, Schürer, Stephan, Carr, Steven A., Liu, Tao, Hiltke, Tara, Yaron, Tomer M., Stathias, Vasileios, Liu, Wenke, Zhang, Xu, Song, Yizhe, Zhang, Zhen, Chan, Daniel W., Li, Yize, Dou, Yongchao, Da Veiga Leprevost, Felipe, Geffen, Yifat, Calinawan, Anna P., Aguet, François, Akiyama, Yo, Anand, Shankara, Birger, Chet, Cao, Song, Chaudhary, Rekha, Chilappagari, Padmini, Cieslik, Marcin, Zhou, Daniel Cui, Day, Corbin, Domagalski, Marcin J., Esai Selvan, Myvizhi, Fenyö, David, Foltz, Steven M., Francis, Alicia, Gonzalez-Robles, Tania, Gümüş, Zeynep H., Heiman, David, Holck, Michael, Hong, Runyu, Hu, Yingwei, Jaehnig, Eric J., Ji, Jiayi, Jiang, Wen, Katsnelson, Lizabeth, Ketchum, Karen A., Klein, Robert J., Lei, Jonathan T., Liang, Wen-Wei, Liao, Yuxing, Lindgren, Caleb M., Ma, Weiping, Ma, Lei, MacCoss, Michael J., Martins Rodrigues, Fernanda, McKerrow, Wilson, Nguyen, Ngoc, Oldroyd, Robert, Pilozzi, Alexander, Reva, Boris, Rudnick, Paul, Ruggles, Kelly V., Rykunov, Dmitry, Savage, Sara R., Schnaubelt, Michael, Schraink, Tobias, Shi, Zhiao, Singhal, Deepak, Song, Xiaoyu, Storrs, Erik, Terekhanova, Nadezhda V., Thangudu, Ratna R., Thiagarajan, Mathangi, Wang, Liang-Bo, Wang, Joshua M., Wang, Ying, Wen, Bo, Wu, Yige, Wyczalkowski, Matthew A., Xin, Yi, Yao, Lijun, Yi, Xinpei, Zhang, Qing, Zuhl, Maya, Getz, Gad, Ding, Li, Nesvizhskii, Alexey I., Wang, Pei, Robles, Ana I., Zhang, Bing, and Payne, Samuel H.

Published
2023
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10. Health Care Provider Clustering Using Fusion Penalty in Quasi‐Likelihood.

Author

Liu, Lili, He, Kevin, Wang, Di, Ma, Shujie, Qu, Annie, Luan, Yihui, Miller, J. Philip, Song, Yizhe, and Liu, Lei

Abstract

There has been growing research interest in developing methodology to evaluate the health care providers' performance with respect to a patient outcome. Random and fixed effects models are traditionally used for such a purpose. We propose a new method, using a fusion penalty to cluster health care providers based on quasi‐likelihood. Without any priori knowledge of grouping information, our method provides a desirable data‐driven approach for automatically clustering health care providers into different groups based on their performance. Further, the quasi‐likelihood is more flexible and robust than the regular likelihood in that no distributional assumption is needed. An efficient alternating direction method of multipliers algorithm is developed to implement the proposed method. We show that the proposed method enjoys the oracle properties; namely, it performs as well as if the true group structure were known in advance. The consistency and asymptotic normality of the estimators are established. Simulation studies and analysis of the national kidney transplant registry data demonstrate the utility and validity of our method. [ABSTRACT FROM AUTHOR]

Published
2024
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11. Pan-cancer proteogenomics characterization of tumor immunity

Author

Petralia, Francesca, primary, Ma, Weiping, additional, Yaron, Tomer M., additional, Caruso, Francesca Pia, additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Charytonowicz, Daniel, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Marino, Giacomo B., additional, Calinawan, Anna, additional, Evangelista, John Erol, additional, Selvan, Myvizhi Esai, additional, Chowdhury, Shrabanti, additional, Rykunov, Dmitry, additional, Krek, Azra, additional, Song, Xiaoyu, additional, Turhan, Berk, additional, Christianson, Karen E., additional, Lewis, David A., additional, Deng, Eden Z., additional, Clarke, Daniel J.B., additional, Whiteaker, Jeffrey R., additional, Kennedy, Jacob J., additional, Zhao, Lei, additional, Segura, Rossana Lazcano, additional, Batra, Harsh, additional, Raso, Maria Gabriela, additional, Parra, Edwin Roger, additional, Soundararajan, Rama, additional, Tang, Ximing, additional, Li, Yize, additional, Yi, Xinpei, additional, Satpathy, Shankha, additional, Wang, Ying, additional, Wiznerowicz, Maciej, additional, González-Robles, Tania J., additional, Iavarone, Antonio, additional, Gosline, Sara J.C., additional, Reva, Boris, additional, Robles, Ana I., additional, Nesvizhskii, Alexey I., additional, Mani, D.R., additional, Gillette, Michael A., additional, Klein, Robert J., additional, Cieslik, Marcin, additional, Zhang, Bing, additional, Paulovich, Amanda G., additional, Sebra, Robert, additional, Gümüş, Zeynep H., additional, Hostetter, Galen, additional, Fenyö, David, additional, Omenn, Gilbert S., additional, Cantley, Lewis C., additional, Ma'ayan, Avi, additional, Lazar, Alexander J., additional, Ceccarelli, Michele, additional, Wang, Pei, additional, Abelin, Jennifer, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cao, Song, additional, Carr, Steven A., additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Ding, Li, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Heiman, David I., additional, Hong, Runyu, additional, Hu, Yingwei, additional, Huang, Chen, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, McDermott, Jason, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Mumphrey, Michael Brodie, additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Payne, Samuel H., additional, Pugliese, Pietro, additional, Rodland, Karin D., additional, Rodrigues, Fernanda Martins, additional, Ruggles, Kelly V., additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Feng, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Li, Qing Kay, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2024
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13. Deep learning integrates histopathology and proteogenomics at a pan-cancer level

Author

Wang, Joshua M., primary, Hong, Runyu, additional, Demicco, Elizabeth G., additional, Tan, Jimin, additional, Lazcano, Rossana, additional, Moreira, Andre L., additional, Li, Yize, additional, Calinawan, Anna, additional, Razavian, Narges, additional, Schraink, Tobias, additional, Gillette, Michael A., additional, Omenn, Gilbert S., additional, An, Eunkyung, additional, Rodriguez, Henry, additional, Tsirigos, Aristotelis, additional, Ruggles, Kelly V., additional, Ding, Li, additional, Robles, Ana I., additional, Mani, D.R., additional, Rodland, Karin D., additional, Lazar, Alexander J., additional, Liu, Wenke, additional, Fenyö, David, additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Özgün, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael J., additional, Cantley, Lewis C., additional, Cao, Song, additional, Carr, Steven A., additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Clauser, Karl R., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Saravana M., additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Geffen, Yifat, additional, Getz, Gad, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Heiman, David I., additional, Hiltke, Tara, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewell, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Johnson, Jared L., additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea J., additional, Oldroyd, Robert, additional, Paulovich, Amanda G., additional, Payne, Samuel H., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rykunov, Dmitry, additional, Satpathy, Shankha, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schürer, Stephan, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Song, Yizhe, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Tignor, Nicole, additional, Wang, Liang-Bo, additional, Wang, Pei, additional, Wang, Ying, additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yaron, Tomer M., additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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15. Pan-cancer proteogenomics connects oncogenic drivers to functional states

Author

Li, Yize, primary, Porta-Pardo, Eduard, additional, Tokheim, Collin, additional, Bailey, Matthew H., additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Geffen, Yifat, additional, Imbach, Kathleen J., additional, Cao, Song, additional, Anand, Shankara, additional, Akiyama, Yo, additional, Liu, Wenke, additional, Wyczalkowski, Matthew A., additional, Song, Yizhe, additional, Storrs, Erik P., additional, Wendl, Michael C., additional, Zhang, Wubing, additional, Sibai, Mustafa, additional, Ruiz-Serra, Victoria, additional, Liang, Wen-Wei, additional, Terekhanova, Nadezhda V., additional, Rodrigues, Fernanda Martins, additional, Clauser, Karl R., additional, Heiman, David I., additional, Zhang, Qing, additional, Aguet, Francois, additional, Calinawan, Anna P., additional, Dhanasekaran, Saravana M., additional, Birger, Chet, additional, Satpathy, Shankha, additional, Zhou, Daniel Cui, additional, Wang, Liang-Bo, additional, Baral, Jessika, additional, Johnson, Jared L., additional, Huntsman, Emily M., additional, Pugliese, Pietro, additional, Colaprico, Antonio, additional, Iavarone, Antonio, additional, Chheda, Milan G., additional, Ricketts, Christopher J., additional, Fenyö, David, additional, Payne, Samuel H., additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Gillette, Michael A., additional, Kumar-Sinha, Chandan, additional, Lazar, Alexander J., additional, Cantley, Lewis C., additional, Getz, Gad, additional, Ding, Li, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Calinawan, Anna, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Lei, Jonathan T., additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Ma, Weiping, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Tan, Jimin, additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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16. Integrative multi-omic cancer profiling reveals DNA methylation patterns associated with therapeutic vulnerability and cell-of-origin

Author

Liang, Wen-Wei, primary, Lu, Rita Jui-Hsien, additional, Jayasinghe, Reyka G., additional, Foltz, Steven M., additional, Porta-Pardo, Eduard, additional, Geffen, Yifat, additional, Wendl, Michael C., additional, Lazcano, Rossana, additional, Kolodziejczak, Iga, additional, Song, Yizhe, additional, Govindan, Akshay, additional, Demicco, Elizabeth G., additional, Li, Xiang, additional, Li, Yize, additional, Sethuraman, Sunantha, additional, Payne, Samuel H., additional, Fenyö, David, additional, Rodriguez, Henry, additional, Wiznerowicz, Maciej, additional, Shen, Hui, additional, Mani, D.R., additional, Rodland, Karin D., additional, Lazar, Alexander J., additional, Robles, Ana I., additional, Ding, Li, additional, Aguet, François, additional, Akiyama, Yo, additional, An, Eunkyung, additional, Anand, Shankara, additional, Anurag, Meenakshi, additional, Babur, Ozgun, additional, Bavarva, Jasmin, additional, Birger, Chet, additional, Birrer, Michael, additional, Calinawan, Anna, additional, Cantley, Lewis C., additional, Cao, Song, additional, Carr, Steve, additional, Ceccarelli, Michele, additional, Chan, Daniel, additional, Chinnaiyan, Arul, additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin, additional, Clauser, Karl, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Dhanasekaran, Mohan, additional, Domagalski, Marcin, additional, Dou, Yongchao, additional, Druker, Brian, additional, Edwards, Nathan, additional, Ellis, Matthew, additional, Selvan, Myvizhi Esai, additional, Francis, Alicia, additional, Getz, Gad, additional, Gillette, Michael A., additional, Robles, Tania Gonzalez, additional, Gosline, Sara, additional, Gümüş, Zeynep, additional, Heiman, David, additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Huntsman, Emily, additional, Iavarone, Antonio, additional, Jaehnig, Eric, additional, Jewel, Scott, additional, Ji, Jiayi, additional, Jiang, Wen, additional, Lee Johnson, Jared, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen, additional, Krug, Karsten, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan, additional, Liao, Yuxing, additional, Lindgren, Caleb, additional, Liu, Tao, additional, Liu, Wenke, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Mesri, Mehdi, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert, additional, Paulovich, Amanda, additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Ruggles, Kelly, additional, Rykunov, Dmitry, additional, Satpathy, Shankha, additional, Savage, Sara, additional, Schadt, Eric, additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Dick, additional, Song, Xiaoyu, additional, Stathias, Vasileios, additional, Storrs, Erik, additional, Tan, Jimin, additional, Terekhanova, Nadezhda, additional, Thangudu, Ratna, additional, Thiagarajan, Mathangi, additional, Tignor, Nicole, additional, Wang, Joshua, additional, Wang, Liang-Bo, additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wu, Yige, additional, Yao, Lijun, additional, Yaron, Tomer M., additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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17. Pan-cancer analysis of post-translational modifications reveals shared patterns of protein regulation

Author

Geffen, Yifat, primary, Anand, Shankara, additional, Akiyama, Yo, additional, Yaron, Tomer M., additional, Song, Yizhe, additional, Johnson, Jared L., additional, Govindan, Akshay, additional, Babur, Özgün, additional, Li, Yize, additional, Huntsman, Emily, additional, Wang, Liang-Bo, additional, Birger, Chet, additional, Heiman, David I., additional, Zhang, Qing, additional, Miller, Mendy, additional, Maruvka, Yosef E., additional, Haradhvala, Nicholas J., additional, Calinawan, Anna, additional, Belkin, Saveliy, additional, Kerelsky, Alexander, additional, Clauser, Karl R., additional, Krug, Karsten, additional, Satpathy, Shankha, additional, Payne, Samuel H., additional, Mani, D.R., additional, Gillette, Michael A., additional, Dhanasekaran, Saravana M., additional, Thiagarajan, Mathangi, additional, Mesri, Mehdi, additional, Rodriguez, Henry, additional, Robles, Ana I., additional, Carr, Steven A., additional, Lazar, Alexander J., additional, Aguet, François, additional, Cantley, Lewis C., additional, Ding, Li, additional, Getz, Gad, additional, An, Eunkyung, additional, Anurag, Meenakshi, additional, Bavarva, Jasmin, additional, Birrer, Michael J., additional, Cao, Song, additional, Ceccarelli, Michele, additional, Chan, Daniel W., additional, Chinnaiyan, Arul M., additional, Cho, Hanbyul, additional, Chowdhury, Shrabanti, additional, Cieslik, Marcin P., additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, da Veiga Leprevost, Felipe, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Dou, Yongchao, additional, Druker, Brian J., additional, Edwards, Nathan, additional, Ellis, Matthew J., additional, Selvan, Myvizhi Esai, additional, Fenyo, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez Robles, Tania J., additional, Gosline, Sara J.C., additional, Gümüş, Zeynep H., additional, Hiltke, Tara, additional, Hong, Runyu, additional, Hostetter, Galen, additional, Hu, Yingwei, additional, Huang, Chen, additional, Iavarone, Antonio, additional, Jaehnig, Eric J., additional, Jewel, Scott D., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Kolodziejczak, Iga, additional, Kumar-Sinha, Chandan, additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Liu, Tao, additional, Liu, Wenke, additional, Ma, Weiping, additional, Rodrigues, Fernanda Martins, additional, McKerrow, Wilson, additional, Nesvizhskii, Alexey I., additional, Newton, Chelsea, additional, Oldroyd, Robert, additional, Omenn, Gilbert S., additional, Paulovich, Amanda G., additional, Petralia, Francesca, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rodland, Karin D., additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schadt, Eric E., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Smith, Richard D., additional, Song, Xiaoyu, additional, Stathias, Vasileios, additional, Storrs, Erik P., additional, Tan, Jimin, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Tignor, Nicole, additional, Wang, Joshua M., additional, Wang, Pei, additional, Wang, Ying (Cindy), additional, Wen, Bo, additional, Wiznerowicz, Maciej, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Bing, additional, Zhang, Hui, additional, Zhang, Xu, additional, and Zhang, Zhen, additional

Published
2023
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18. Proteogenomic data and resources for pan-cancer analysis

Author

Li, Yize, primary, Dou, Yongchao, additional, Da Veiga Leprevost, Felipe, additional, Geffen, Yifat, additional, Calinawan, Anna P., additional, Aguet, François, additional, Akiyama, Yo, additional, Anand, Shankara, additional, Birger, Chet, additional, Cao, Song, additional, Chaudhary, Rekha, additional, Chilappagari, Padmini, additional, Cieslik, Marcin, additional, Colaprico, Antonio, additional, Zhou, Daniel Cui, additional, Day, Corbin, additional, Domagalski, Marcin J., additional, Esai Selvan, Myvizhi, additional, Fenyö, David, additional, Foltz, Steven M., additional, Francis, Alicia, additional, Gonzalez-Robles, Tania, additional, Gümüş, Zeynep H., additional, Heiman, David, additional, Holck, Michael, additional, Hong, Runyu, additional, Hu, Yingwei, additional, Jaehnig, Eric J., additional, Ji, Jiayi, additional, Jiang, Wen, additional, Katsnelson, Lizabeth, additional, Ketchum, Karen A., additional, Klein, Robert J., additional, Lei, Jonathan T., additional, Liang, Wen-Wei, additional, Liao, Yuxing, additional, Lindgren, Caleb M., additional, Ma, Weiping, additional, Ma, Lei, additional, MacCoss, Michael J., additional, Martins Rodrigues, Fernanda, additional, McKerrow, Wilson, additional, Nguyen, Ngoc, additional, Oldroyd, Robert, additional, Pilozzi, Alexander, additional, Pugliese, Pietro, additional, Reva, Boris, additional, Rudnick, Paul, additional, Ruggles, Kelly V., additional, Rykunov, Dmitry, additional, Savage, Sara R., additional, Schnaubelt, Michael, additional, Schraink, Tobias, additional, Shi, Zhiao, additional, Singhal, Deepak, additional, Song, Xiaoyu, additional, Storrs, Erik, additional, Terekhanova, Nadezhda V., additional, Thangudu, Ratna R., additional, Thiagarajan, Mathangi, additional, Wang, Liang-Bo, additional, Wang, Joshua M., additional, Wang, Ying, additional, Wen, Bo, additional, Wu, Yige, additional, Wyczalkowski, Matthew A., additional, Xin, Yi, additional, Yao, Lijun, additional, Yi, Xinpei, additional, Zhang, Hui, additional, Zhang, Qing, additional, Zuhl, Maya, additional, Getz, Gad, additional, Ding, Li, additional, Nesvizhskii, Alexey I., additional, Wang, Pei, additional, Robles, Ana I., additional, Zhang, Bing, additional, Payne, Samuel H., additional, Lazar, Alexander J., additional, Paulovich, Amanda G., additional, Iavarone, Antonio, additional, Chinnaiyan, Arul M., additional, Druker, Brian J., additional, Kumar-Sinha, Chandan, additional, Newton, Chelsea J., additional, Huang, Chen, additional, Mani, D.R., additional, Smith, Richard D., additional, Huntsman, Emily, additional, Schadt, Eric E., additional, An, Eunkyung, additional, Petralia, Francesca, additional, Hostetter, Galen, additional, Omenn, Gilbert S., additional, Cho, Hanbyul, additional, Rodriguez, Henry, additional, Kolodziejczak, Iga, additional, Johnson, Jared L., additional, Bavarva, Jasmin, additional, Tan, Jimin, additional, Rodland, Karin D., additional, Clauser, Karl R., additional, Krug, Karsten, additional, Cantley, Lewis C., additional, Wiznerowicz, Maciej, additional, Ellis, Matthew J., additional, Anurag, Meenakshi, additional, Mesri, Mehdi, additional, Gillette, Michael A., additional, Birrer, Michael J., additional, Ceccarelli, Michele, additional, Dhanasekaran, Saravana M., additional, Edwards, Nathan, additional, Tignor, Nicole, additional, Babur, Özgün, additional, Gosline, Sara J.C., additional, Jewell, Scott D., additional, Satpathy, Shankha, additional, Chowdhury, Shrabanti, additional, Schürer, Stephan, additional, Carr, Steven A., additional, Liu, Tao, additional, Hiltke, Tara, additional, Yaron, Tomer M., additional, Stathias, Vasileios, additional, Liu, Wenke, additional, Zhang, Xu, additional, Song, Yizhe, additional, and Zhang, Zhen, additional

Published
2023
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24. Data from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Author

Yao, Lijun, primary, Wang, Julia T., primary, Jayasinghe, Reyka G., primary, O'Neal, Julie, primary, Tsai, Chia-Feng, primary, Rettig, Michael P., primary, Song, Yizhe, primary, Liu, Ruiyang, primary, Zhao, Yanyan, primary, Ibrahim, Omar M., primary, Fiala, Mark A., primary, Fortier, Julie M., primary, Chen, Siqi, primary, Gehrs, Leah, primary, Rodrigues, Fernanda Martins, primary, Wendl, Michael C., primary, Kohnen, Daniel, primary, Shinkle, Andrew, primary, Cao, Song, primary, Foltz, Steven M., primary, Zhou, Daniel Cui, primary, Storrs, Erik, primary, Wyczalkowski, Matthew A., primary, Mani, Smrithi, primary, Goldsmith, Scott R., primary, Zhu, Ying, primary, Hamilton, Mark, primary, Liu, Tao, primary, Chen, Feng, primary, Vij, Ravi, primary, Ding, Li, primary, and DiPersio, John F., primary

Published
2023
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25. Table S5 from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Author

Yao, Lijun, primary, Wang, Julia T., primary, Jayasinghe, Reyka G., primary, O'Neal, Julie, primary, Tsai, Chia-Feng, primary, Rettig, Michael P., primary, Song, Yizhe, primary, Liu, Ruiyang, primary, Zhao, Yanyan, primary, Ibrahim, Omar M., primary, Fiala, Mark A., primary, Fortier, Julie M., primary, Chen, Siqi, primary, Gehrs, Leah, primary, Rodrigues, Fernanda Martins, primary, Wendl, Michael C., primary, Kohnen, Daniel, primary, Shinkle, Andrew, primary, Cao, Song, primary, Foltz, Steven M., primary, Zhou, Daniel Cui, primary, Storrs, Erik, primary, Wyczalkowski, Matthew A., primary, Mani, Smrithi, primary, Goldsmith, Scott R., primary, Zhu, Ying, primary, Hamilton, Mark, primary, Liu, Tao, primary, Chen, Feng, primary, Vij, Ravi, primary, Ding, Li, primary, and DiPersio, John F., primary

Published
2023
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26. Supplementary Figures from Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Author

Yao, Lijun, primary, Wang, Julia T., primary, Jayasinghe, Reyka G., primary, O'Neal, Julie, primary, Tsai, Chia-Feng, primary, Rettig, Michael P., primary, Song, Yizhe, primary, Liu, Ruiyang, primary, Zhao, Yanyan, primary, Ibrahim, Omar M., primary, Fiala, Mark A., primary, Fortier, Julie M., primary, Chen, Siqi, primary, Gehrs, Leah, primary, Rodrigues, Fernanda Martins, primary, Wendl, Michael C., primary, Kohnen, Daniel, primary, Shinkle, Andrew, primary, Cao, Song, primary, Foltz, Steven M., primary, Zhou, Daniel Cui, primary, Storrs, Erik, primary, Wyczalkowski, Matthew A., primary, Mani, Smrithi, primary, Goldsmith, Scott R., primary, Zhu, Ying, primary, Hamilton, Mark, primary, Liu, Tao, primary, Chen, Feng, primary, Vij, Ravi, primary, Ding, Li, primary, and DiPersio, John F., primary

Published
2023
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27. Single-Cell Discovery and Multiomic Characterization of Therapeutic Targets in Multiple Myeloma

Author

Yao, Lijun, primary, Wang, Julia T., additional, Jayasinghe, Reyka G., additional, O'Neal, Julie, additional, Tsai, Chia-Feng, additional, Rettig, Michael P., additional, Song, Yizhe, additional, Liu, Ruiyang, additional, Zhao, Yanyan, additional, Ibrahim, Omar M., additional, Fiala, Mark A., additional, Fortier, Julie M., additional, Chen, Siqi, additional, Gehrs, Leah, additional, Rodrigues, Fernanda Martins, additional, Wendl, Michael C., additional, Kohnen, Daniel, additional, Shinkle, Andrew, additional, Cao, Song, additional, Foltz, Steven M., additional, Zhou, Daniel Cui, additional, Storrs, Erik, additional, Wyczalkowski, Matthew A., additional, Mani, Smrithi, additional, Goldsmith, Scott R., additional, Zhu, Ying, additional, Hamilton, Mark, additional, Liu, Tao, additional, Chen, Feng, additional, Vij, Ravi, additional, Ding, Li, additional, and DiPersio, John F., additional

Published
2023
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29. Protective Effects of Lovastatin in a Population‐Based ALS Study and Mouse Model.

Author

Kreple, Collin J., Searles Nielsen, Susan, Schoch, Kathleen M., Shen, Tao, Shabsovich, Mark, Song, Yizhe, Racette, Brad A., and Miller, Timothy M.

Subjects
LABORATORY mice, LOVASTATIN, MOTOR neuron diseases, ANIMAL disease models, AMYOTROPHIC lateral sclerosis
Abstract

Objective: The objective of this study was to use a novel combined pharmacoepidemiologic and amyotrophic lateral sclerosis (ALS) mouse model approach to identify potential motor neuron protective medications. Methods: We constructed a large, population‐based case‐control study to investigate motor neuron disease (MND) among US Medicare beneficiaries aged 66 to 90 in 2009. We included 1,128 incident MND cases and 56,400 age, sex, race, and ethnicity matched controls. We calculated MND relative risk for >1,000 active ingredients represented in Part D (pharmacy) claims in 2006 to 2007 (>1 year before diagnosis/reference). We then applied a comprehensive screening approach to select medications for testing in SOD1G93A mice: sulfasalazine, telmisartan, and lovastatin. We treated mice with the human dose equivalent of the medication or vehicle via subcutaneous osmotic pump before onset of weakness. We then assessed weight, gait, and survival. In additional mice, we conducted histological studies. Results: We observed previously established medical associations for MND and an inverse dose–response association between lovastatin and MND, with 28% reduced risk at 40 mg/day. In SOD1G93A mouse studies, sulfasalazine and telmisartan conferred no benefit, whereas lovastatin treatment delayed onset and prolonged survival. Lovastatin treated mice also had less microgliosis, misfolded SOD1, and spinal motor neuron loss in the ventral horn. Interpretation: Lovastatin reduced the risk of ALS in humans, which was confirmed in an ALS mouse model by delayed symptom onset, prolonged survival, and preservation of motor neurons. Although further studies to understand the mechanism are required, lovastatin may represent a potential neuroprotective therapy for patients with ALS. These data demonstrate the utility of a combined pharmacoepidemiologic and mouse model approach. ANN NEUROL 2023;93:881–892 [ABSTRACT FROM AUTHOR]

Published
2023
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33. Development of a 48-Well Dynamic Suspension Culture System for Pancreatic Differentiation from Human Embryonic Stem Cells

Author

Peiwen Xing, Zhensheng Ou, Qunrui Ye, Wenjia Li, Yinghua Chen, Xiuli Wang, Song Yizhe, Leilei Guo, Decan Liang, Jing Liu, Jingqiu Li, Shidu Zhang, Tingting Tang, and Xiaoqian Chen

Subjects
Pluripotent Stem Cells, Cell growth, Cell, Human Embryonic Stem Cells, Cell Culture Techniques, Cell Differentiation, Biology, Cell morphology, Embryonic stem cell, Cell biology, Cell therapy, medicine.anatomical_structure, medicine, Humans, Viability assay, Stem cell, Induced pluripotent stem cell, Cells, Cultured
Abstract

BACKGROUND Human pluripotent stem cells (hPSCs) have started to emerge as a potential tool with application in fields of drug discovery, disease modelling and cell therapy. A variety of protocols for culturing and differentiating pluripotent stem cells into pancreatic β like cells have been published. However, small-scale dynamic suspension culture systems, which could be applied toward systematically optimizing production strategies for cell replacement therapies to accelerate the pace of their discovery and development toward the clinic, are overlooked. METHODS Human embryonic stem cell (hESC) line H9 was used to establish the novel 48-well dynamic suspension culture system. The effects of various rotational speeds and culture medium volumes on cell morphology, cell proliferation, cell viability and cell phenotype were evaluated. Effect of cell density on the pancreatic differentiation efficiency from H9 cells in 48-well plates was further investigated. In vitro the function of pancreatic β like cells was assessed by measuring glucose-stimulated insulin secretion. MAIN RESULTS A 48-well dynamic suspension culture system for hESC expansion as cell aggregates was developed. With optimized rotational speed and culture medium volume, hESCs maintained normal karyotype, viability and pluripotency. Furthermore, the system can also support the hESC aggregates subsequent differentiation into functional pancreatic β like cells after optimizing initial cell seeding density. CONCLUSION A controllable 48-well suspension culture system in microplates for hESCs maintenance, expansion and pancreatic differentiation was developed, which may provide an efficient platform for high-throughput drug screening.

Published
2021

35. Development of a 48-Well Dynamic Suspension Culture System for Pancreatic Differentiation from Human Embryonic Stem Cells

Author

Song, Yizhe, primary, Chen, Xiaoqian, additional, Liang, Decan, additional, Liu, Jing, additional, Li, Jingqiu, additional, Ou, Zhensheng, additional, Tang, Tingting, additional, Xing, Peiwen, additional, Guo, Leilei, additional, Zhang, Shidu, additional, Ye, Qunrui, additional, Li, Wenjia, additional, Chen, Yinghua, additional, and Wang, Xiuli, additional

Published
2021
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37. Generation and characterization of a human iPSC line HECi001-A from a healthy adult donor pancreata

Author

Song, Yizhe, primary, Liu, Jing, additional, Li, Jingqiu, additional, Ou, Zhensheng, additional, Liang, Decan, additional, Chen, Xiaoqian, additional, Tang, Tingting, additional, Xing, Peiwen, additional, Guo, Leilei, additional, Ye, Qunrui, additional, Chen, Xiaofeng, additional, Li, Wenjia, additional, Chen, Yinghua, additional, and Wang, Xiuli, additional

Published
2021
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38. In-Depth Characterization of the High Risk-Associated Tumor Immune Landscape in Multiple Myeloma

Author

Pita-Juarez, Yered, Karagkouni, Dimitra, Gonzalez-Kozlova, Edgar, Ma, Yuling, Yao, Lijun, Pilcher, William, Thomas, Beena, Lagana, Alessandro, Satpathy, Sarthak, Bhasin, Swati, Song, Yizhe, Vij, Ravi, D'Souza, Darwin, Dawson, Travis, Kelly, Geoffrey, Schulman, Jessica Wendy, Kumar, Shaji Kunnathu, Avigan, David, Kim-Schulze, Seunghee, Ding, Li, Cho, Hearn Jay, Kourelis, Taxiarchis, Lepisto, Eva, Bhasin, Manoj, Cook, April, Hamilton, Mark, Mulligan, George, Network, Immune, Vlachos, Ioannis, and Gnjatic, Sacha

Published
2023
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41. P-404 Single-cell profiling reveals inflammaging-associated dysregulations in rapidly progressing multiple myeloma patients

Author

Pilcher, William, Yao, Lijun, Kozlova, Edgar Gonzalez, Pita-Juarez, Yered, Karagkouni, Dimitra, Ma, Yuling, Thomas, Beena, Satpathy, Sarthak, Bhasin, Swati, Song, Yizhe, Wang, Julia, Dawson, Travis, D'souza, Darwin, Network, Immune, Schulman, Jessica, Pabustan, Nick, Cook, April, Cho, Hearn Jay, Mulligan, George, Hamilton, Mark, Kourelis, Taxiarchis, Vlachos, Ioannis, Gnjatic, Sacha, Ding, Li, and Bhasin, Manoj

Published
2023
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44. Affinity-based human mobility pattern for improved region function discovering

Author

Luo Angen, Xu Yajing, Song Yizhe, Xue Chao, and Li Gongfu

Subjects
050210 logistics & transportation, Kullback–Leibler divergence, Computer Networks and Communications, Computer science, business.industry, Node (networking), 05 social sciences, Kernel density estimation, Process (computing), 02 engineering and technology, Function (mathematics), Complex network, computer.software_genre, 020204 information systems, Urbanization, 0502 economics and business, Signal Processing, Metric (mathematics), 0202 electrical engineering, electronic engineering, information engineering, Data mining, Artificial intelligence, business, computer, Information Systems
Abstract

The process of urbanization is formed by regular movements of human beings. It yields different functional zones in a city, such as residential zone and commercial zone. Consequently, there exists a close connection between the human mobility pattern and the city's zones. However, it is not easy to collect large-scale society-wide data that can precisely capture the underlying relations between the individual's movement and the regional functions. Hence, our knowledge for understanding the basic patterns of human mobility is still limited. In order to discover the functions of different regions in a city, we propose an affinity based method in this paper. The affinity is a recently introduced metric for measuring the correlation of two connecting node in a complex network. The proposed model groups different functional zones by measuring user's arrival/departure distribution via relative entropy. In addition to this, we also identify the intensity of each functional zone by taking kernel density estimation (KDE) method. In the end, some experiments are conducted to evaluate our method with a large-scale real-life dataset, which consists of 3 million cellphone users' records from a period of one month. Our findings on the interaction between the mobility pattern and the regional functions can capture the city dynamics efficiently and provide a valuable reference for urban planners.

Published
2016
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50. A Patch-based Sparse Representation for Sketch Recognition

Author

Zhang Honggang, Qi Yonggang, Song Yizhe, and Tan Zhenghua

Subjects
Computer science, Sketch recognition, business.industry, Feature extraction, ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION, Pattern recognition, Sparse approximation, Sketch, Histogram of oriented gradients, Histogram, Computer vision, Shape context, Artificial intelligence, business, Image retrieval, ComputingMethodologies_COMPUTERGRAPHICS
Abstract

Categorizing free-hand human sketches has profoundimplications in applications such as human computerinteraction and image retrieval. The task is non-trivial due tothe iconic nature of sketches, signified by large variances in bothappearance and structure when compared with photographs. Oneof the most fundamental problem is how to effectively describea sketch image. Many existing descriptors, such as Histogramof Oriented Gradients (HOG) and Shape Context (SC), haveachieved great success. Moreover, some works have attemptedto design features specifically engineered for sketches, such asSymmetric-aware Flip Invariant Sketch Histogram (SYM-FISH).We present a novel patch-based sparse representation (PSR)for describing sketch image and it is evaluated under a sketchrecognition framework. Extensive experiments on a large scalehuman drawn sketch dataset demonstrate the effectiveness of theproposed method.

Published
2014
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