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  1. 1.   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. 2.   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. 3.   Spatiotemporal modulation of growth factors directs the generation of multilineage mouse embryonic stem cell-derived mammary organoids
  2. Sahu,Sounak; Sahoo, Sarthak; Sullivan,Teresa; O'Sullivan,Theresa; Turan,Sevilay; Albaugh,Mary; Burkett,Sandra; Tran,Bao; Salomon,David; Kozlov,Serguei; Koehler, Karl R; Jolly, Mohit Kumar; Sharan,Shyam
  3. Developmental Cell. 2024, Jan 22; 59
  1. 4.   Phenotypic plasticity and reduced tissue retention of exhausted tumor-infiltrating T cells following neoadjuvant immunotherapy in head and neck cancer
  2. Sievers, Cem; Craveiro, Marco; Friedman, Jay; Robbins, Yvette; Yang, Xinping; Bai, Ke; Nguyen, Andy; Redman, Jason M; Chari,Raj; Soon-Shiong, Patrick; Schlom, Jeffrey; Gulley, James; Allen, Clint T
  3. Cancer Cell. 2023, Apr 12; 41(5): 887-902.e5.
  1. 5.   Single-cell sequencing reveals activation of core transcription factors in PRC2-deficient malignant peripheral nerve sheath tumor
  2. Zhang, Xiyuan; Lou, Hannah E; Gopalan, Vishaka; Liu, Zhihui; Jafarah, Hilda M; Lei, Haiyan; Jones, Paige; Sayers, Carly M; Yohe, Marielle E; Chittiboina, Prashant; Widemann, Brigitte C; Thiele, Carol J; Kelly,Michael; Hannenhalli, Sridhar; Shern, Jack F
  3. Cell Reports. 2022, Sep 20; 40(12): 111363.
  1. 6.   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. 7.   A phenotypic signature that identifies neoantigen-reactive T cells in fresh human lung cancers
  2. Hanada, Ken-Ichi; Zhao, Chihao; Gil-Hoyos, Raul; Gartner, Jared J; Chow-Parmer, Christopher; Lowery, Frank J; Krishna, Sri; Prickett, Todd D; Kivitz, Scott; Parkhurst, Maria R; Wong,Nathan; Rae, Zachary; Kelly, Michael C; Goff, Stephanie L; Robbins, Paul F; Rosenberg, Steven A; Yang, James C
  3. Cancer Cell. 2022, Apr 13;
  1. 8.   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. 9.   An Integrated Epigenomic and Transcriptomic Map of Mouse and Human aß T Cell Development
  2. Chopp, Laura B; Gopalan, Vishaka; Ciucci, Thomas; Ruchinskas,Allison; Rae, Zachary; Lagarde, Manon; Gao, Yayi; Li, Caiyi; Bosticardo, Marita; Pala, Francesca; Livak, Ferenc; Kelly,Michael; Hannenhalli, Sridhar; Bosselut, Rémy
  3. Immunity. 2020, Dec 15; 53(6): 1182-1201.e8.
  1. 10.   Oncogenic mutant RAS signaling activity is rescaled by the ERK/MAPK pathway
  2. Gillies, Taryn E; Pargett, Michael; Silva, Jillian M; Teragawa, Carolyn K; McCormick, Frank; Albeck, John G
  3. Molecular systems biology. 2020, Oct; 16(10): e9518.
  1. 11.   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. 12.   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.
  1. 13.   Tumor Cell Biodiversity Drives Microenvironmental Reprogramming in Liver Cancer
  2. Ma, Lichun; Hernandez,Maria; Zhao,Yongmei; Mehta,Monika; Tran,Bao; Kelly,Michael; Rae,Zachary; Hernandez, Jonathan M; Davis, Jeremy L; Martin, Sean P; Kleiner, David E; Hewitt, Stephen M; Ylaya, Kris; Wood, Bradford J; Greten, Tim F; Wang, Xin Wei
  3. Cancer cell. 2019, Oct 14; 36(4): 418-430.
  1. 14.   The Emergence and Functional Fitness of Memory CD4+ T Cells Require the Transcription Factor Thpok
  2. Ciucci, Thomas; Vacchio, Melanie S; Gao, Yayi; Tomassoni Ardori, Francesco; Candia, Julian; Mehta, Monika; Zhao, Yongmei; Tran, Bao; Pepper, Marion; Tessarollo, Lino; McGavern, Dorian B; Bosselut, Rémy
  3. Immunity. 2019, Jan 15; 50(1): 91-105.e4.
  1. 15.   Glycan Masking Focuses Immune Responses to the HIV-1 CD4-Binding Site and Enhances Elicitation of VRC01-Class Precursor Antibodies
  2. Duan, Hongying; Chen, Xuejun; Boyington, Jeffrey C; Cheng, Cheng; Zhang, Yi; Jafari, Alexander J; Stephens, Tyler; Tsybovsky, Yaroslav; Kalyuzhniy, Oleksandr; Zhao, Peng; Menis, Sergey; Nason, Martha C; Normandin, Erica; Mukhamedova, Maryam; DeKosky, Brandon J; Wells, Lance; Schief, William R; Tian, Ming; Alt, Frederick W; Kwong, Peter D; Mascola, John R
  3. Immunity. 2018, Aug 21; 49(2): 301-311.e5.
  1. 16.   Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART
  2. Wiegand, Ann; Spindler, Jon; Hong, Feiyu F; Shao, Wei; Cyktor, Joshua C; Cillo, Anthony R; Halvas, Elias K; Coffin, John; Mellors, John W; Kearney, Mary
  3. Proceedings of the National Academy of Sciences of the United States of America. 2017, Apr 17; 114(18): E3659-E3668.
  1. 17.   High-throughput single-molecule screen for small-molecule perturbation of splicing and transcription kinetics
  2. Day, C. R.; Chen, H.; Coulon, A.; Meier, J. L.; Larson, D. R.
  3. Methods (San Diego, Calif.). 2016, 1-Mar; 96: 59-68.
  1. 18.   Characterization of rhesus macaque natural killer activity against a rhesus-derived target cell line at the single-cell level
  2. Andersen, H.; Rossio, J. L.; Coalter, V.; Poore, B.; Martin, M. P.; Carrington, M.; Lifson, J. D.
  3. Cellular Immunology. 2004, SEP-OCT; 231(1-2): 85-95.
  1. 19.   Efficiency of interphase fluorescence in situ hybridization for BCR/ABL on peripheral blood smears for monitoring of CML patients: a comparison with bone marrow findings
  2. Akel, S.; Kolialexi, A.; Mavrou, A.; Metaxotou, C.; Loukopoulos, D.; Yataganas, X.
  3. Clinical and Laboratory Haematology. 2002 24(6): 361-367.
  1. 20.   Degradable Dump Outer Primers in Merged Tandem (M/T)-Nested Pcr - Low- and Single-Copy Dna Target Amplification
  2. Grace, M. B.; Buzard, G. S.; Hughes, M. R.; Gorelangton, R. E.
  3. Analytical Biochemistry. 1998 263(1): 85-92.
  1. 21.   Single-cell RNA sequencing reveals cancer stem-like cells and dynamics in tumor microenvironment during cholangiocarcinoma progression
  2. Golino, Jihye L; Bian, Jing; Wang, Xin; Fu, Jianyang; Zhu, Xiao Bin; Yeo, Julie; Kelly,Michael; Escorcia, Freddy E; Cam, Maggie; Xie, Changqing
  3. Frontiers in Cell and Developmental Biology. 2023 11: 1250215.
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