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  1. 1.   PKR activation-induced mitochondrial dysfunction in HIV-transgenic mice with nephropathy
  2. Yoshida, Teruhiko; Latt, Khun Zaw; Rosenberg, Avi Z; Santo, Briana A; Myakala, Komuraiah; Ishimoto,Yu; Zhao, Yongmei; Shrivastav, Shashi; Jones, Bryce A; Yang, Xiaoping; Wang, Xiaoxin X; Tutino, Vincent M; Sarder, Pinaki; Levi, Moshe; Okamoto, Koji; Winkler, Cheryl A; Kopp, Jeffrey B
  3. eLife. 2024, Aug 29; 12
  1. 2.   Multi-scale signaling and tumor evolution in high-grade gliomas
  2. Liu, Jingxian; Cao, Song; Imbach, Kathleen J; Gritsenko, Marina A; Lih, Tung-Shing M; Kyle, Jennifer E; Yaron-Barir, Tomer M; Binder, Zev A; Li, Yize; Strunilin, Ilya; Wang, Yi-Ting; Tsai, Chia-Feng; Ma, Weiping; Chen, Lijun; Clark, Natalie M; Shinkle, Andrew; Naser Al Deen, Nataly; Caravan, Wagma; Houston, Andrew; Simin, Faria Anjum; Wyczalkowski, Matthew A; Wang, Liang-Bo; Storrs, Erik; Chen, Siqi; Illindala, Ritvik; Li, Yuping D; Jayasinghe, Reyka G; Rykunov, Dmitry; Cottingham, Sandra L; Chu, Rosalie K; Weitz, Karl K; Moore, Ronald J; Sagendorf, Tyler; Petyuk, Vladislav A; Nestor, Michael; Bramer, Lisa M; Stratton, Kelly G; Schepmoes, Athena A; Couvillion, Sneha P; Eder, Josie; Kim, Young-Mo; Gao, Yuqian; Fillmore, Thomas L; Zhao, Rui; Monroe, Matthew E; Southard-Smith, Austin N; Li, Yang E; Jui-Hsien Lu, Rita; Johnson, Jared L; Wiznerowicz, Maciej; Hostetter, Galen; Newton, Chelsea J; Ketchum, Karen A; Thangudu, Ratna R; Barnholtz-Sloan, Jill S; Wang, Pei; Fenyö, David; An, Eunkyung; Thiagarajan,Mathangi; Robles, Ana I; Mani, D R; Smith, Richard D; Porta-Pardo, Eduard; Cantley, Lewis C; Iavarone, Antonio; Chen, Feng; Mesri, Mehdi; Nasrallah, MacLean P; Zhang, Hui; Resnick, Adam C; Chheda, Milan G; Rodland, Karin D; Liu, Tao; Ding, Li
  3. Cancer Cell. 2024, Jul 08; 42(7): 1217-1238.e19.
  1. 3.   NAD deficiency contributes to progressive kidney disease in HIV nephropathy mice
  2. Yoshida, Teruhiko; Myakala, Komuraiah; Jones, Bryce A; Wang, Xiaoxin X; Shrivastav, Shashi; Santo, Briana A; Patel, Tatsat R; Zhao,Yongmei; Tutino, Vincent M; Sarder, Pinaki; Rosenberg, Avi Z; Winkler,Cheryl; Levi, Moshe; Kopp, Jeffrey B
  3. American Journal of Physiology. Renal physiology. 2024, Jul 04;
  1. 4.   Aberrant spliceosome activity via elevated intron retention and upregulation and phosphorylation of SF3B1 in chronic lymphocytic leukemia
  2. Kashyap, Manoj Kumar; Karathia,Hiren; Kumar, Deepak; Vera Alvarez, Roberto; Forero-Forero, Jose Vicente; Moreno, Eider; Lujan, Juliana Velez; Amaya-Chanaga, Carlos Ivan; Vidal, Newton Medeiros; Yu, Zhe; Ghia, Emanuela M; Lengerke-Diaz, Paula A; Achinko, Daniel; Choi, Michael Y; Rassenti, Laura Z; Mariño-Ramírez, Leonardo; Mount, Stephen M; Hannenhalli, Sridhar; Kipps, Thomas J; Castro, Januario E
  3. Molecular Therapy. Nucleic acids. 2024, Jun 11; 35(2): 102202.
  1. 5.   Multi-omic profiling of follicular lymphoma reveals changes in tissue architecture and enhanced stromal remodeling in high-risk patients
  2. Radtke, Andrea J; Postovalova, Ekaterina; Varlamova, Arina; Bagaev, Alexander; Sorokina, Maria; Kudryashova, Olga; Meerson, Mark; Polyakova, Margarita; Galkin, Ilia; Svekolkin, Viktor; Isaev, Sergey; Wiebe, Daniil; Sharun, Anna; Sarachakov, Alexander; Perelman, Grigory; Lozinsky, Yaroslav; Yaniv, Ziv; Lowekamp, Bradley C; Speranza, Emily; Yao, Li; Pittaluga, Stefania; Shaffer, Arthur L; Jonigk, Danny; Phelan, James D; Davies-Hill, Theresa; Huang, Da Wei; Ovcharov, Pavel; Nomie, Krystle; Nuzhdina, Ekaterina; Kotlov, Nikita; Ataullakhanov, Ravshan; Fowler, Nathan; Kelly,Michael; Muppidi, Jagan; Davis, Jeremy L; Hernandez, Jonathan M; Wilson, Wyndham H; Jaffe, Elaine S; Staudt, Louis M; Roschewski, Mark; Germain, Ronald N
  3. Cancer Cell. 2024, Feb 21; 42
  1. 6.   Purification of Circular RNAs Using Poly(A) Tailing Followed by RNase R Digestion
  2. Xiao, Mei-Sheng; Wilusz, Jeremy E
  3. Methods in Molecular Biology (Clifton, N.J.). 2024 2765: 3-19.
  1. 7.   Attenuation of aggressive tumor progression of anaplastic thyroid cancer by p53
  2. Hwang, Eunmi; Kruhlak, Michael; Wong,Nathan; Chari,Raj; Kimura, Takahito; Cheng, Sheue-Yann
  3. American Journal of Cancer Research. 2024 14(9): 4429-4444.
  1. 8.   Comparison between qPCR and RNA-seq reveals challenges of quantifying HLA expression
  2. Aguiar, Vitor R C; Castelli, Erick C; Single, Richard M; Bashirova,Arman; Ramsuran,Veron; Kulkarni, Smita; Augusto, Danillo G; Martin,Pat; Gutierrez-Arcelus, Maria; Carrington, Mary; Meyer, Diogo
  3. Immunogenetics. 2023, Jan 28;
  1. 9.   Graph embedding and Gaussian mixture variational autoencoder network for end-to-end analysis of single-cell RNA sequencing data
  2. Xu, Junlin; Xu, Jielin; Meng, Yajie; Lu, Changcheng; Cai, Lijun; Zeng, Xiangxiang; Nussinov,Ruth; Cheng, Feixiong
  3. Cell Reports Methods. 2023, Jan 23; 3(1): 100382.
  1. 10.   Histopathologic and proteogenomic heterogeneity reveals features of clear cell renal cell carcinoma aggressiveness
  2. Li, Yize; Lih, Tung-Shing M; Dhanasekaran, Saravana M; Mannan, Rahul; Chen, Lijun; Cieslik, Marcin; Wu, Yige; Lu, Rita Jiu-Hsien; Clark, David J; Kolodziejczak, Iga; Hong, Runyu; Chen, Siqi; Zhao, Yanyan; Chugh, Seema; Caravan, Wagma; Naser Al Deen, Nataly; Hosseini, Noshad; Newton, Chelsea J; Krug, Karsten; Xu, Yuanwei; Cho, Kyung-Cho; Hu, Yingwei; Zhang, Yuping; Kumar-Sinha, Chandan; Ma, Weiping; Calinawan, Anna; Wyczalkowski, Matthew A; Wendl, Michael C; Wang, Yuefan; Guo, Shenghao; Zhang, Cissy; Le, Anne; Dagar, Aniket; Hopkins, Alex; Cho, Hanbyul; Leprevost, Felipe da Veiga; Jing, Xiaojun; Teo, Guo Ci; Liu, Wenke; Reimers, Melissa A; Pachynski, Russell; Lazar, Alexander J; Chinnaiyan, Arul M; Van Tine, Brian A; Zhang, Bing; Rodland, Karin D; Getz, Gad; Mani, D R; Wang, Pei; Chen, Feng; Hostetter, Galen; Thiagarajan,Mathangi; Linehan, W Marston; Fenyö, David; Jewell, Scott D; Omenn, Gilbert S; Mehra, Rohit; Wiznerowicz, Maciej; Robles, Ana I; Mesri, Mehdi; Hiltke, Tara; An, Eunkyung; Rodriguez, Henry; Chan, Daniel W; Ricketts, Christopher J; Nesvizhskii, Alexey I; Zhang, Hui; Ding, Li
  3. Cancer Cell. 2023, Jan 9; 41(1): 139-163.
  1. 11.   Transcriptomic Analysis of Human Podocytes In Vitro: Effects of Differentiation and APOL1 Genotype
  2. Yoshida, Teruhiko; Latt, Khun Zaw; Rosenberg, Avi Z; Shrivastav, Shashi; Heymann, Jurgen; Halushka, Marc K; Winkler,Cheryl; Kopp, Jeffrey B
  3. Kidney International Reports. 2023, Jan; 8(1): 164-178.
  1. 12.   A Phase II Study of Pembrolizumab in Combination with Capecitabine and Oxaliplatin with Molecular Profiling in Patients with Advanced Biliary Tract Carcinoma
  2. Monge, Cecilia; Pehrsson,Erica; Xie, Changqing; Duffy, Austin G; Mabry, Donna; Wood, Bradford J; Kleiner, David E; Steinberg, Seth M; Figg, William D; Redd, Bernadette; Budhu, Anuradha; Wang, Sophie; Tandon,Mayank; Ma, Lichun; Wei Wang, Xin; Greten, Tim F
  3. The Oncologist. 2022, Mar 11; 27(3): e273-e285.
  1. 13.   Urine Single-Cell RNA Sequencing in Focal Segmental Glomerulosclerosis Reveals Inflammatory Signatures
  2. Latt, Khun Zaw; Heymann, Jurgen; Jessee, Joseph H; Rosenberg, Avi Z; Berthier, Celine C; Arazi, Arnon; Eddy, Sean; Yoshida, Teruhiko; Zhao,Yongmei; Chen,Vicky; Nelson,George; Cam,Maggie; Kumar,Parimal; Mehta,Monika; Kelly,Michael; Kretzler, Matthias; Ray, Patricio E; Moxey-Mims, Marva; Gorman, Gregory H; Lechner, Brent L; Regunathan-Shenk, Renu; Raj, Dominic S; Susztak, Katalin; Winkler,Cheryl; Kopp, Jeffrey B
  3. Kidney International Reports. 2022, Feb; 7(2): 289-304.
  1. 14.   Molecular Signature and Immune Landscape of HCV-Associated Hepatocellular Carcinoma (HCC): Differences and Similarities with HBV-HCC
  2. De Battista, Davide; Zamboni, Fausto; Gerstein, Hannah; Sato, Shinya; Markowitz,Tovah; Lack,Justin; Engle, Ronald E; Farci, Patrizia
  3. Journal of hepatocellular carcinoma. 2021, Nov 21; 8: 1399-1413.
  1. 15.   Clinical Implications of Inter- and Intra-Tumor Heterogeneity of Immune Cell Markers in Lung Cancer
  2. Zhao, Wei; Zhu, Bin; Hutchinson,Amy; Pesatori, Angela Cecilia; Consonni, Dario; Caporaso, Neil E; Zhang, Tongwu; Wang,Difei; Shi, Jianxin; Landi, Maria Teresa
  3. Journal of the National Cancer Institute. 2021, Aug 17;
  1. 16.   Experimental Babesia rossi infection induces hemolytic, metabolic, and viral response pathways in the canine host
  2. Smith, Rachel L; Goddard, Amelia; Boddapati, Arun; Brooks, Steven; Schoeman, Johan P; Lack,Justin; Leisewitz, Andrew; Ackerman, Hans
  3. BMC genomics. 2021, Aug 16; 22(1): 619.
  1. 17.   CAR T cells targeting tumor-associated exons of glypican 2 regress neuroblastoma in mice
  2. Li, Nan; Torres, Madeline B.; Spetz, Madeline R.; Wang, Ruixue; Peng, Luyi; Tian, Meijie; Dower, Christopher M.; Nguyen, Rosa; Sun, Ming; Tai, Chin-Hsien; de Val, Natalia; Cachau,Raul; Wu, Xiaolin; Hewitt, Stephen M.; Kaplan, Rosandra N.; Khan, Javed; St Croix,Brad; Thiele, Carol J.; Ho, Mitchell
  3. Cell reports. Medicine. 2021, Jun 15; 2(6):
  1. 18.   Proteogenomic insights into the biology and treatment of HPV-negative head and neck squamous cell carcinoma
  2. Huang, Chen; Chen, Lijun; Savage, Sara R.; Eguez, Rodrigo Vargas; Dou, Yongchao; Li, Yize; Leprevost, Felipe da Veiga; Jaehnig, Eric J.; Lei, Jonathan T.; Wen, Bo; Schnaubelt, Michael; Krug, Karsten; Song, Xiaoyu; Cieslik, Marcin; Chang, Hui-Yin; Wyczalkowski, Matthew A.; Li, Kai; Colaprico, Antonio; Li, Qing Kay; Clark, David J.; Hu, Yingwei; Cao, Liwei; Pan, Jianbo; Wang, Yuefan; Cho, Kyung-Cho; Shi, Zhiao; Liao, Yuxing; Jiang, Wen; Anurag, Meenakshi; Ji, Jiayi; Yoo, Seungyeul; Zhou, Daniel Cui; Liang, Wen-Wei; Wendl, Michael; Vats, Pankaj; Carr, Steven A.; Mani, D. R.; Zhang, Zhen; Qian, Jiang; Chen, Xi S.; Pico, Alexander R.; Wang, Pei; Chinnaiyan, Arul M.; Ketchum, Karen A.; Kinsinger, Christopher R.; Robles, Ana; An, Eunkyung; Hiltke, Tara; Mesri, Mehdi; Thiagarajan,Mathangi; Weaver, Alissa M.; Sikora, Andrew G.; Lubinski, Jan; Wierzbicka, Malgorzata; Wiznerowicz, Maciej; Satpathy, Shankha; Gillette, Michael A.; Miles, George; Ellis, Matthew J.; Omenn, Gilbert S.; Rodriguez, Henry; Boja, Emily S.; Dhanasekaran, Saravana M.; Ding, Li; Nesvizhskii, Alexey; El-Naggar, Adel K.; Chan, Daniel W.; Zhang, Hui; Zhang, Bing
  3. Cancer Cell. 2021, Mar 8; 39(3): 361-379.
  1. 19.   IFN gamma Is a Key Link between Obesity and Th1-Mediated AutoImmune Diseases
  2. Bae,Heekyong; Choi, Myung-Sook; Kim, Suntae; Young,Howard; Gershwin, M. Eric; Jeon, Seon-Min; Kwon, Eun-Young
  3. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. 2021, Jan; 22(1):
  1. 20.   The GTEx Consortium atlas of genetic regulatory effects across human tissues
  2. Aguet, Francois; Barbeira, Alvaro N.; Bonazzola, Rodrigo; Brown, Andrew; Castel, Stephane E.; Jo, Brian; Kasela, Silva; Kim-Hellmuth, Sarah; Liang, Yanyu; Parsana, Princy; Flynn, Elise; Fresard, Laure; Gamazon, Eric R.; Hamel, Andrew R.; He, Yuan; Hormozdiari, Farhad; Mohammadi, Pejman; Munoz-Aguirre, Manuel; Ardlie, Kristin G.; Battle, Alexis; Bonazzola, Rodrigo; Brown, Christopher D.; Cox, Nancy; Dermitzakis, Emmanouil T.; Engelhardt, Barbara E.; Garrido-Martin, Diego; Gay, Nicole R.; Getz, Gad; Guigo, Roderic; Hamel, Andrew R.; Handsaker, Robert E.; He, Yuan; Hoffman, Paul J.; Hormozdiari, Farhad; Im, Hae Kyung; Jo, Brian; Kasela, Silva; Kashin, Seva; Kim-Hellmuth, Sarah; Kwong, Alan; Lappalainen, Tuuli; Li, Xiao; Liang, Yanyu; MacArthur, Daniel G.; Mohammadi, Pejman; Montgomery, Stephen B.; Munoz-Aguirre, Manuel; Rouhana, John M.; Hormozdiari, Farhad; Im, Hae Kyung; Kim-Hellmuth, Sarah; Ardlie, Kristin G.; Getz, Gad; Guigo, Roderic; Im, Hae Kyung; Lappalainen, Tuuli; Montgomery, Stephen B.; Im, Hae Kyung; Lappalainen, Tuuli; Lappalainen, Tuuli; Anand, Shankara; Gabriel, Stacey; Getz, Gad; Graubert, Aaron; Hadley, Kane; Handsaker, Robert E.; Huang, Katherine H.; Kashin, Seva; Li, Xiao; MacArthur, Daniel G.; Meier, Samuel R.; Nedzel, Jared L.; Balliu, Brunilda; Conrad, Don; Cotter, Daniel J.; Das, Sayantan; de Goede, Olivia M.; Eskin, Eleazar; Eulalio, Tiffany Y.; Ferraro, Nicole M.; Garrido-Martin, Diego; Gay, Nicole R.; Getz, Gad; Graubert, Aaron; Guigo, Roderic; Hadley, Kane; Hamel, Andrew R.; Handsaker, Robert E.; He, Yuan; Hoffman, Paul J.; Hormozdiari, Farhad; Hou, Lei; Huang, Katherine H.; Im, Hae Kyung; Jo, Brian; Kasela, Silva; Kashin, Seva; Kellis, Manolis; Kim-Hellmuth, Sarah; Kwong, Alan; Lappalainen, Tuuli; Li, Xiao; Li, Xin; Liang, Yanyu; MacArthur, Daniel G.; Mangul, Serghei; Meier, Samuel R.; Mohammadi, Pejman; Montgomery, Stephen B.; Munoz-Aguirre, Manuel; Nachun, Daniel C.; Nedzel, Jared L.; Nguyen, Duyen Y.; Nobel, Andrew B.; Park, YoSon; Reverter, Ferran; Sabatti, Chiara; Saha, Ashis; Segre, Ayellet; Stephens, Matthew; Strober, Benjamin J.; Teran, Nicole A.; Todres, Ellen; Vinuela, Ana; Wang, Gao; Wen, Xiaoquan; Wright, Fred; Wucher, Valentin; Zou, Yuxin; Ferreira, Pedro G.; Li, Gen; Mele, Marta; Yeger-Lotem, Esti; Barcus, Mary E.; Bradbury, Debra; Krubit,Tanya; McLean,Jeff; Qi,Liqun; Robinson, Karna; Roche,Nancy; Smith, Anna M.; Tabor,David; Undale, Anita; Bridge, Jason; Brigham, Lori E.; Foster, Barbara A.; Gillard, Bryan M.; Hasz, Richard; Hunter, Marcus; Johns, Christopher; Johnson, Mark; Karasik, Ellen; Kopen, Gene; Leinweber, William F.; McDonald, Alisa; Moser, Michael T.; Myer, Kevin; Ramsey, Kimberley D.; Roe, Brian; Shad, Saboor; Thomas, Jeffrey A.; Walters, Gary; Washington, Michael; Wheeler, Joseph; Jewell, Scott D.; Rohrer, Daniel C.; Valley, Dana R.; Davis, David A.; Mash, Deborah C.; Branton, Philip A.; Sobin, Leslie; Barker, Laura K.; Gardiner, Heather M.; Mosavel, Maghboeba; Siminoff, Laura A.; Flicek, Paul; Haeussler, Maximilian; Juettemann, Thomas; Kent, W. James; Lee, Christopher M.; Powell, Conner C.; Rosenbloom, Kate R.; Ruffier, Magali; Sheppard, Dan; Taylor, Kieron; Trevanion, Stephen J.; Zerbino, Daniel R.; Abell, Nathan S.; Akey, Joshua; Chen, Lin; Demanelis, Kathryn; Doherty, Jennifer A.; Feinberg, Andrew P.; Hansen, Kasper D.; Hickey, Peter F.; Hou, Lei; Jasmine, Farzana; Jiang, Lihua; Kaul, Rajinder; Kellis, Manolis; Kibriya, Muhammad G.; Li, Jin Billy; Li, Qin; Lin, Shin; Linder, Sandra E.; Montgomery, Stephen B.; Oliva, Meritxell; Park, Yongjin; Pierce, Brandon L.; Rizzardi, Lindsay F.; Skol, Andrew D.; Smith, Kevin S.; Snyder, Michael; Stamatoyannopoulos, John; Tang, Hua; Wang, Meng; Carithers, Latarsha J.; Guan, Ping; Koester, Susan E.; Little, A. Roger; Moore, Helen M.; Nierras, Concepcion R.; Rao, Abhi K.; Vaught, Jimmie B.; Volpi, Simona
  3. SCIENCE. 2020, SEP 11; 369(6509): 1318-+.
  1. 21.   Conventional Co-Housing Modulates Murine Gut Microbiota and Hematopoietic Gene Expression
  2. Chen, Jichun; Zhang, Shuling; Feng, Xingmin; Wu, Zhijie; Dubois, Wendy; Thovarai,Vishal; Ahluwalia, Sonia; Gao, Shouguo; Chen, Jinguo; Peat, Tyler; Sen,Shurjo; Trinchieri, Giorgio; Young, Neal S; Mock, Beverly A
  3. International journal of molecular sciences. 2020, SEP; 21(17):
  1. 22.   Differential Expression of the Transcription Factor GATA3 Specifies Lineage and Functions of Innate Lymphoid Cells
  2. Zhong, Chao; Zheng, Mingzhu; Cui, Kairong; Martins, Andrew J; Hu, Gangqing; Li, Dan; Tessarollo,Lino; Kozlov,Serguei; Keller,Jonathan; Tsang, John S; Zhao, Keji; Zhu, Jinfang
  3. Immunity. 2020, JAN 14; 52(1): 83-+.
  1. 23.   Head and neck squamous cancer progression is marked by CLIC4 attenuation in tumor epithelium and reciprocal stromal upregulation of miR-142-3p, a novel post-transcriptional regulator of CLIC4
  2. Carofino, Brandi L; Dinshaw, Kayla M; Ho, Pui Yan; Cataisson, Christophe; Michalowski, Aleksandra M; Ryscavage, Andrew; Alkhas, Addie; Wong,Nathan; Koparde,Vishal; Yuspa, Stuart H
  3. Oncotarget. 2019, Dec 31; 10(68): 7251-7275.
  1. 24.   Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27
  2. Hu, Xiaojun; Goswami,Suranjana; Qiu,Ju; Chen,Qian; Laverdure,Sylvain; Sherman,Brad; Imamichi,Tomozumi
  3. International journal of molecular sciences. 2019, Dec 09; 20(24):
  1. 25.   Single-Cell Profiling Defines Transcriptomic Signatures Specific to Tumor-Reactive versus Virus-Responsive CD4+ T Cells
  2. Magen, Assaf; Nie, Jia; Ciucci, Thomas; Tamoutounour, Samira; Zhao,Yongmei; Mehta,Monika; Tran,Bao; McGavern, Dorian B; Hannenhalli, Sridhar; Bosselut, Rémy
  3. Cell reports. 2019, Dec 03; 29(10): 3019-3032.e6.
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