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  1. 1.   The human oral microbiome and risk of colorectal cancer within three prospective cohort studies in the United States
  2. Vogtmann, Emily; Yano, Yukiko; Zouiouich, Semi; Hua,Xing; Wan, Yunhu; Purandare, Vaishnavi; Li, Shilan; Dagnall,Casey; Jones, Kristine; Hicks,Belynda; Hutchinson,Amy; Caporaso, J Gregory; Wheeler, William; Huang, Wen-Yi; Freedman, Neal D; Sandler, Dale P; Beane Freeman, Laura E; Liao, Linda M; Gail, Mitchell H; Shi, Jianxin; Abnet, Christian C; Sinha, Rashmi
  3. Cancer. 2025, Mar 15; 131(6): e35802.
  1. 2.   Viral Burden and Illness Severity During Acute SARS-CoV-2 Infection Predict Persistent Long COVID Symptoms
  2. Brandstetter Figueroa, Elisabeth; Frosch, Anne E P; Burrack, Kristina S; Dileepan, Gayathri; Goldsmith, Rachael; Harris, Morgan; Ikeogu, Nwando; Jibrell, Hodan; Thayalan, Sangeitha; Dewar,Robin; Shenoy, Chetan; Sereti, Irini; Baker, Jason V
  3. Open Forum Infectious Diseases. 2025, Feb; 12(2): ofaf048.
  1. 3.   Single-cell transcriptional analysis of murine norovirus infection in a human intestinal cell line
  2. Matsushima, Yuki; Levenson, Eric A; Chaimongkol, Natthawan; Harris, Loyall; Zhao,Yongmei; Turan,Sevilay; Otaizo-Carrasquero, Francisco; Ganesan, Sundar; Hornick, Katherine M; Martens, Craig; Sosnovtsev, Stanislav V; Green, Kim Y
  3. Journal of Virology. 2024, Oct 30; e0161724.
  1. 4.   Genomes and epigenomes of matched normal and tumor breast tissue reveal diverse evolutionary trajectories and tumor-host interactions
  2. Zhu, Bin; Tapinos, Avraam; Koka, Hela; Yi Lee, Priscilla Ming; Zhang, Tongwu; Zhu, Wei; Wang, Xiaoyu; Klein, Alyssa; Lee, DongHyuk; Tse, Gary M; Tsang, Koon-Ho; Wu, Cherry; Hua, Min; Highfill,Chad; Lenz,Petra; Zhou,Weiyin; Wang,Difei; Luo,Wen; Jones,Kristine; Hutchinson,Amy; Hicks,Belynda; Garcia-Closas, Montserrat; Chanock, Stephen; Tse, Lap Ah; Wedge, David C; Yang, Xiaohong R
  3. American Journal of Human Genetics. 2024, Oct 29;
  1. 5.   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. 6.   Hemophagocytic Lymphohistiocytosis Gene Variants in Severe Aplastic Anemia and Their Impact on Hematopoietic Cell Transplantation Outcomes
  2. Rafati, Maryam; McReynolds, Lisa J; Wang, Youjin; Hicks,Belynda; Jones,Kristine; Spellman, Stephen R; He, Meilun; Bolon, Yung-Tsi; Arrieta-Bolaños, Esteban; Saultz, Jennifer N; Lee, Stephanie J; Savage, Sharon A; Gadalla, Shahinaz M
  3. Transplantation and Cellular Therapy. 2024, Aug ; 30(8): 770e1-770e10.
  1. 7.   Single-nucleus RNA sequencing reveals loss of DCT1 renal tubules in HIV Vpr transgenic mice
  2. Latt, Khun Zaw; Yoshida, Teruhiko; Shrivastav, Shashi; Abedini, Amin; Reece, Jeff M; Sun, Zeguo; Lee, Hewang; Okamoto, Koji; Dagur, Pradeep; Ishimoto, Yu; Heymann, Jurgen; Zhao,Yongmei; Chung, Joon-Yong; Hewitt, Stephen; Jose, Pedro A; Lee, Kyung; He, John Cijiang; Winkler,Cheryl; Knepper, Mark A; Kino, Tomoshige; Rosenberg, Avi Z; Susztak, Katalin; Kopp, Jeffrey B
  3. The American Journal of Pathology. 2024, Jul 18;
  1. 8.   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. 9.   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. 10.   Evaluation of somatic copy number variation detection by NGS technologies and bioinformatics tools on a hyper-diploid cancer genome
  2. Masood, Daniall; Ren, Luyao; Nguyen, Cu; Brundu, Francesco G; Zheng, Lily; Zhao,Yongmei; Jaeger, Erich; Li, Yong; Cha, Seong Won; Halpern, Aaron; Truong, Sean; Virata, Michael; Yan, Chunhua; Chen, Qingrong; Pang, Andy; Alberto, Reyes; Xiao, Chunlin; Yang, Zhaowei; Chen, Wanqiu; Wang, Charles; Cross, Frank; Catreux, Severine; Shi, Leming; Beaver, Julia A; Xiao, Wenming; Meerzaman, Daoud M
  3. Genome Biology. 2024, Jun 20; 25(1): 163.
  1. 11.   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. 12.   The Janus kinase 1 is critical for pancreatic cancer initiation and progression
  2. Shrestha, Hridaya; Rädler, Patrick D; Dennaoui, Rayane; Wicker, Madison N; Rajbhandari, Nirakar; Sun, Yunguang; Peck, Amy R; Vistisen, Kerry; Triplett, Aleata A; Beydoun, Rafic; Sterneck,Esta; Saur, Dieter; Rui, Hallgeir; Wagner, Kay-Uwe
  3. Cell Reports. 2024, May 10; 43(5): 114202.
  1. 13.   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. 14.   Insights into the mechanisms and structure of breakage-fusion-bridge cycles in cervical cancer using long-read sequencing
  2. Rodriguez, Isabel; Rossi, Nicole M; Keskus, Ayse G; Xie, Yi; Ahmad, Tanveer; Bryant, Asher; Lou,Hong; Paredes, Jesica Godinez; Milano, Rose; Rao, Nina; Tulsyan, Sonam; Boland, Joseph F; Luo,Wen; Liu,Jia; O'Hanlon, Tim; Bess, Jazmyn; Mukhina, Vera; Gaykalova, Daria; Yuki, Yuko; Malik, Laksh; Billingsley, Kimberley J; Blauwendraat, Cornelis; Carrington, Mary; Yeager,Meredith; Mirabello, Lisa; Kolmogorov, Mikhail; Dean, Michael
  3. American Journal of Human Genetics. 2024, Jan 25;
  1. 15.   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. 16.   Viral escape mutations do not account for non-protection from SIVmac239 challenge in RhCMV/SIV vaccinated rhesus macaques
  2. Bimber, Benjamin N; Sunshine, Justine; McElfresh, G W; Reed, Jason S; Pathak, Reese; Bateman, Katherine B; Hughes, Colette M; Gilbride, Roxanne M; Ford, Julia C; Morrow, David; Lifson,Jeffrey; Sacha, Jonah B; Hansen, Scott G; Picker, Louis J
  3. Frontiers in Immunology. 2024 15: 1444621.
  1. 17.   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. 18.   Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing
  2. Craig, Amanda J; Silveira, Maruhen A Datsch; Ma, Lichun; Revsine, Mahler; Wang, Limin; Heinrich, Sophia; Rae, Zachary; Ruchinskas, Allison; Dadkhah,Kimia; Do, Whitney; Behrens, Shay; Mehrabadi, Farid R; Dominguez, Dana A; Forgues, Marshonna; Budhu, Anuradha; Chaisaingmongkol, Jittiporn; Hernandez, Jonathan M; Davis, Jeremy L; Tran,Bao; Marquardt, Jens U; Ruchirawat, Mathuros; Kelly, Michael; Greten, Tim F; Wang, Xin W
  3. Cell Reports. 2023, Nov 17; 42(11): 113446.
  1. 19.   Development of a bicistronic anti-CD19/CD20 CAR construct including abrogation of unexpected nucleic acid sequence deletions
  2. Lam, Norris; Finney, Richard; Yang, Shicheng; Choi, Stephanie; Wu,Xiaolin; Cutmore, Lauren; Andrade, Jorge; Huang, Lei; Amatya, Christina; Cam, Margaret; Kochenderfer, James N
  3. Molecular Therapy Oncolytics. 2023, Sep 21; 30: 132-149.
  1. 20.   Robust regulation of transcription pausing in Escherichia coli by the ubiquitous elongation factor NusG
  2. Yakhnin,Alex; Bubunenko,Mikhail; Mandell, Zachary F; Lubkowska,Lucyna; Husher, Sara; Babitzke, Paul; Kashlev,Mikhail
  3. Proceedings of the National Academy of Sciences of the United States of America. 2023, Jun 13; 120(24): e2221114120.
  1. 21.   Whole organism profiling of the Timp gene family
  2. Peeney, David; Fan, Yu; Gurung, Sadeechya; Lazaroff, Carolyn; Ratnayake, Shashikala; Warner,Andrew; Karim,Baktiar; Meerzaman, Daoud; Stetler-Stevenson, William G
  3. Matrix Biology Plus. 2023, Jun; 18: 100132.
  1. 22.   Heat shock factor 1 (HSF1) specifically potentiates c-MYC-mediated transcription independently of the canonical heat shock response
  2. Xu, Meng; Lin,Ling; Ram,Babul; Shriwas,Omprakash; Chuang, Kun-Han; Dai, Siyuan; Su, Kuo-Hui; Tang, Zijian; Dai,Chengkai
  3. Cell Reports. 2023, May 23; 42(6): 112557.
  1. 23.   Protocol for using single-cell sequencing to study the heterogeneity of NF1 nerve sheath tumors from clinical biospecimens
  2. Zhang, Xiyuan; Gopalan, Vishaka; Syed,Neeraja; Hannenhalli, Sridhar; Shern, Jack F
  3. STAR Protocols. 2023, May 10; 4(2): 102297.
  1. 24.   Transfer learning in a biomaterial fibrosis model identifies in vivo senescence heterogeneity and contributions to vascularization and matrix production across species and diverse pathologies
  2. Cherry, Christopher; Andorko, James I; Krishnan, Kavita; Mejías, Joscelyn C; Nguyen, Helen Hieu; Stivers, Katlin B; Gray-Gaillard, Elise F; Ruta, Anna; Han, Jin; Hamada, Naomi; Hamada, Masakazu; Sturmlechner, Ines; Trewartha, Shawn; Michel, John H; Davenport Huyer, Locke; Wolf,Matthew; Tam, Ada J; Peña, Alexis N; Keerthivasan, Shilpa; Le Saux, Claude Jordan; Fertig, Elana J; Baker, Darren J; Housseau, Franck; van Deursen, Jan M; Pardoll, Drew M; Elisseeff, Jennifer H
  3. GeroScience. 2023, Apr 20;
  1. 25.   Targeted long-read sequencing of the Ewing sarcoma 6p25.1 susceptibility locus identifies germline-somatic interactions with EWSR1-FLI1 binding
  2. Lee, Olivia W; Rodrigues, Calvin; Lin, Shu-Hong; Luo,Wen; Jones,Kristine; Brown, Derek W; Zhou,Weiyin; Karlins, Eric; Khan, Sairah M; Baulande, Sylvain; Raynal, Virginie; Surdez, Didier; Reynaud, Stephanie; Rubio, Rebeca Alba; Zaidi, Sakina; Grossetête, Sandrine; Ballet, Stelly; Lapouble, Eve; Laurence, Valérie; Pierron, Gaelle; Gaspar, Nathalie; Corradini, Nadège; Marec-Bérard, Perrine; Rothman, Nathaniel; Dagnall, Casey L; Burdett, Laurie; Manning, Michelle; Wyatt, Kathleen; Yeager, Meredith; Chari,Raj; Leisenring, Wendy M; Kulozik, Andreas E; Kriebel, Jennifer; Meitinger, Thomas; Strauch, Konstantin; Kirchner, Thomas; Dirksen, Uta; Mirabello, Lisa; Tucker, Margaret A; Tirode, Franck; Armstrong, Gregory T; Bhatia, Smita; Robison, Leslie L; Yasui, Yutaka; Romero-Pérez, Laura; Hartmann, Wolfgang; Metzler, Markus; Diver, W Ryan; Lori, Adriana; Freedman, Neal D; Hoover, Robert N; Morton, Lindsay M; Chanock, Stephen J; Grünewald, Thomas G P; Delattre, Olivier; Machiela, Mitchell J
  3. American Journal of Human Genetics. 2023, Mar 2; 110(3): 427-441.
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