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  1. 1.   Noncanonical circRNA biogenesis driven by alpha and gamma herpesviruses
  2. Dremel, Sarah E; Koparde,Vishal; Arbuckle, Jesse H; Hogan, Chad H; Kristie, Thomas M; Krug, Laurie T; Conrad, Nicholas K; Ziegelbauer, Joseph M
  3. The EMBO Journal. 2025, Mar 03;
  1. 2.   Proteomic and serologic assessments of responses to mRNA-1273 and BNT162b2 vaccines in human recipient sera
  2. Hickey,Thomas; Mudunuri,Uma; Hempel,Heidi; Kemp,Troy; Roche,Nancy; Talsania, Keyur; Sellers, Brian A; Cherry, James M; Pinto,Ligia
  3. Frontiers in Immunology. 2025, Jan 27; 15: 1502458.
  1. 3.   A KSHV RNA-binding protein promotes FOS to inhibit nuclease AEN and transactivate RGS2 for AKT phosphorylation
  2. Majerciak,Vladimir; Alvarado-Hernandez, Beatriz; Ma, Yanping; Duduskar, Shivalee; Lobanov, Alexei; Cam, Maggie; Zheng,Zhi-Ming
  3. mBio. 2024, Dec 10; e0317224.
  1. 4.   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. 5.   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. 6.   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. 7.   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. 8.   Kinetically Controlled Polyelectrolyte Complex Assembly of microRNA-Peptide Nanoparticles toward Treating Mesothelioma
  2. Anderson,Caleb; Singh, Anand; Stephens,Tyler; Hoang, Chuong D; Schneider,Joel
  3. Advanced Materials (Deerfield Beach, Fla.). 2024, Mar 26; e2314367.
  1. 9.   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. 10.   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. 11.   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. 12.   Matrin3 regulates mitotic spindle dynamics by controlling alternative splicing of CDC14B
  2. Muys, Bruna R; Shrestha, Roshan L; Anastasakis, Dimitrios G; Pongor, Lorinc; Li, Xiao Ling; Grammatikakis, Ioannis; Polash, Ahsan; Chari,Raj; Gorospe, Myriam; Harris, Curtis C; Aladjem, Mirit I; Basrai, Munira A; Hafner, Markus; Lal, Ashish
  3. Cell Reports. 2023, Mar 15; 42(3): 112260.
  1. 13.   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. 14.   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. 15.   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. 16.   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. 17.   Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis
  2. Han, Hong; Best, Andrew J; Braunschweig, Ulrich; Mikolajewicz, Nicholas; Li, Jack Daiyang; Roth, Jonathan; Chowdhury, Fuad; Mantica, Federica; Nabeel-Shah, Syed; Parada, Guillermo; Brown, Kevin R; O'Hanlon, Dave; Wei, Jiarun; Yao, Yuxi; Zid, Abdelrahman Abou; Comsa, Lim Caden; Jen, Mark; Wang, Jenny; Datti, Alessandro; Gonatopoulos Pournatzis,Thomas; Weatheritt, Robert J; Greenblatt, Jack F; Wrana, Jeffrey L; Irimia, Manuel; Gingras, Anne-Claude; Moffat, Jason; Blencowe, Benjamin J
  3. Molecular Cell. 2022, Jul 31; 82(16): 2982-2999.
  1. 18.   Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo
  2. Ke, Weina; Chandler, Morgan; Cedrone,Edward; Saito, Renata F; Rangel, Maria Cristina; de Souza Junqueira, Mara; Wang, Jian; Shi, Da; Truong, Nguyen; Richardson, Melina; Rolband, Lewis A; Dréau, Didier; Bedocs, Peter; Chammas, Roger; Dokholyan, Nikolay V; Dobrovolskaia,Marina; Afonin, Kirill A
  3. Nano Letters. 2022, Jul 05;
  1. 19.   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. 20.   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. 21.   MYC assembles and stimulates topoisomerases 1 and 2 in a "topoisome"
  2. Das, Subhendu K.; Kuzin, Vladislav; Cameron, Donald P.; Sanford, Suzanne; Jha, Rajiv Kumar; Nie, Zuqin; Rosello, Marta Trullols; Holewinski,Ronald; Andresson,Thorkell; Wisniewski, Jan; Natsume, Toyoaki; Price, David H.; Lewis, Brian A.; Kouzine, Fedor; Levens, David; Baranello, Laura
  3. Molecular Cell. 2022, Jan 6; 82(1): 140-158. e12.
  1. 22.   Flexible pri-miRNA structures enable tunable production of 5' isomiRs
  2. Bofill De Ros,Xavier; Hong,Zhenyi; Birkenfeld, Ben; Alamo-Ortiz,Sarangelica; Yang,Acong; Dai,Lisheng; Gu,Shuo
  3. RNA Biology. 2022, Jan; 19(1): 279-289.
  1. 23.   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. 24.   Iterative epigenomic analyses in the same single cell
  2. Ohnuki, Hidetaka; Venzon, David J.; Lobanov,Alexei; Tosato, Giovanna
  3. Genome Research. 2021, Oct; 31(11): 1819-1830.
  1. 25.   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;
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