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2024

2024 Publications

Yocelyn Recinos, Suying Bao, Xiaojian Wang, Brittany Phillips, Yow-Tyng Yeh, Sebastien Weyn-Vanhentenryck, Maurice Swanson, Chaolin Zhang .  2024.   Lineage-specific splicing regulation of MAPT gene in the primate brain.. Cell genomics. 4 (6) :100563 ▶ Go to Pubmed
Yocelyn Recinos, Dmytro Ustianenko, Yow-Tyng Yeh, Xiaojian Wang, Martin Jacko, Lekha Yesantharao V, Qiyang Wu, Chaolin Zhang .  2024.   CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements.. Nature communications. 15 (1) :3839 ▶ Go to Pubmed
Huijuan Feng, Xiang-Jun Lu, Suvrajit Maji, Linxi Liu, Dmytro Ustianenko, Noam Rudnick, Chaolin Zhang .  2024.   Structure-based prediction and characterization of photo-crosslinking in native protein-RNA complexes.. Nature communications. 15 (1) :2279 ▶ Go to Pubmed
Giuseppe Leuzzi, Alessandro Vasciaveo, Angelo Taglialatela, Xiao Chen, Tessa Firestone, Allison Hickman, Wendy Mao, Tanay Thakar, Alina Vaitsiankova, Jen-Wei Huang, Raquel Cuella-Martin, Samuel Hayward, Jordan Kesner, Ali Ghasemzadeh, Tarun Nambiar, Patricia Ho, Alexander Rialdi, Maxime Hebrard, Yinglu Li, Jinmei Gao, Saarang Gopinath, Oluwatobi Adeleke, Bryan Venters, Charles Drake, Richard Baer, Benjamin Izar, Ernesto Guccione, Michael-Christopher Keogh, Raphael Guerois, Lu Sun, Chao Lu, Andrea Califano, Alberto Ciccia .  2024.   SMARCAL1 is a dual regulator of innate immune signaling and PD-L1 expression that promotes tumor immune evasion.. Cell. ▶ Go to Pubmed
Giangela Stokes, Zhuowei Li, Nicole Talaba, William Genthe, Maria Brix, Betty Pham, Mark Wienhold, Gracia Sandok, Rebecca Hernan, Julia Wynn, Haiyang Tang, Diana Tabima, Allison Rodgers, Timothy Hacker, Naomi Chesler, Pan Zhang, Rabi Murad, Jason Yuan, Yufeng Shen, Wendy Chung, David McCulley .  2024.   Rescuing lung development through embryonic inhibition of histone acetylation.. Science translational medicine. 16 (732) :eadc8930 ▶ Go to Pubmed
Alexander Goldberg, Athanassios Dovas, Daniela Torres, Sohani Sharma, Angeliki Mela, Edward Merricks, Markel Olabarria, Leila Shokooh, Hanzhi Zhao, Corina Kotidis, Peter Calvaresi, Ashwin Viswanathan, Matei Banu, Aida Razavilar, Tejaswi Sudhakar, Ankita Saxena, Cole Chokran, Nelson Humala, Aayushi Mahajan, Weihao Xu, Jordan Metz, Cady Chen, Eric Bushong, Daniela Boassa, Mark Ellisman, Elizabeth Hillman, Guy McKhann, Brian Gill, Steven Rosenfeld, Catherine Schevon, Jeffrey Bruce, Peter Sims, Darcy Peterka, Peter Canoll .  2024.   Glioma-Induced Alterations in Excitatory Neurons are Reversed by mTOR Inhibition.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Steven Wells, Daniel Rainbow, Michal Mark, Peter Szabo, Can Ergen, Ana Maceiras, Daniel Caron, Elior Rahmani, Eli Benuck, Valeh Amiri, David Chen, Allon Wagner, Sarah Howlett, Lorna Jarvis, Karen Ellis, Masaru Kubota, Rei Matsumoto, Krishnaa Mahbubani, Kouresh Saeb-Parsy, Cecilia Dominguez-Conde, Laura Richardson, Chuan Xu, Shuang Li, Lira Mamanova, Liam Bolt, Alicja Wilk, Sarah Teichmann, Donna Farber, Peter Sims, Joanne Jones, Nir Yosef .  2024.   Multimodal profiling reveals tissue-directed signatures of human immune cells altered with age.. bioRxiv : the preprint server for biology. ▶ Go to Pubmed
Marta Galanti, Juan Patiño-Galindo, Ioan Filip, Haruka Morita, Angelica Galianese, Mariam Youssef, Devon Comito, Chanel Ligon, Benjamin Lane, Nelsa Matienzo, Sadiat Ibrahim, Eudosie Tagne, Atinuke Shittu, Oliver Elliott, Tomin Perea-Chamblee, Sanjay Natesan, Daniel Rosenbloom, Jeffrey Shaman, Raul Rabadan .  2024.   Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people.. PLoS biology. 22 (1) :e3002089 ▶ Go to Pubmed
Deirdre Ricaurte, Yiming Huang, Ravi Sheth, Diego Gelsinger, Andrew Kaufman, Harris Wang .  2024.   High-throughput transcriptomics of 409 bacteria-drug pairs reveals drivers of gut microbiota perturbation.. Nature microbiology. ▶ Go to Pubmed
Diego Gelsinger, Phuc Vo, Sanne Klompe, Carlotta Ronda, Harris Wang, Samuel Sternberg .  2024.   Bacterial genome engineering using CRISPR-associated transposases.. Nature protocols. ▶ Go to Pubmed
Diego Gelsinger, Phuc Vo, Sanne Klompe, Carlotta Ronda, Harris Wang, Samuel Sternberg .  2024.   Bacterial genome engineering using CRISPR-associated transposases.. Nature protocols. ▶ Go to Pubmed
Hubert Pakula, Mohamed Omar, Ryan Carelli, Filippo Pederzoli, Giuseppe Fanelli, Tania Pannellini, Fabio Socciarelli, Lucie Van Emmenis, Silvia Rodrigues, Caroline Fidalgo-Ribeiro, Pier Nuzzo, Nicholas Brady, Wikum Dinalankara, Madhavi Jere, Itzel Valencia, Christopher Saladino, Jason Stone, Caitlin Unkenholz, Richard Garner, Mohammad Alexanderani, Francesca Khani, Francisca de Almeida, Cory Abate-Shen, Matthew Greenblatt, David Rickman, Christopher Barbieri, Brian Robinson, Luigi Marchionni, Massimo Loda .  2024.   Distinct mesenchymal cell states mediate prostate cancer progression.. Nature communications. 15 (1) :363 ▶ Go to Pubmed
Haiqing Zhao, Hao Wu, Alex Guseman, Dulith Abeykoon, Christina Camara, Yamini Dalal, David Fushman, Garegin Papoian .  2024.   The role of cryptic ancestral symmetry in histone folding mechanisms across Eukarya and Archaea.. PLoS computational biology. 20 (1) :e1011721 ▶ Go to Pubmed
Jianing Fu, Zicheng Wang, Mercedes Martinez, Aleksandar Obradovic, Wenyu Jiao, Kristjana Frangaj, Rebecca Jones, Xinzheng Guo V, Ya Zhang, Wan-I Kuo, Huaibin Ko, Alina Iuga, Constanza Muntnich, Adriana Rey, Kortney Rogers, Julien Zuber, Wenji Ma, Michelle Miron, Donna Farber, Joshua Weiner, Tomoaki Kato, Yufeng Shen, Megan Sykes .  2024.   Plasticity of intragraft alloreactive T cell clones in human gut correlates with transplant outcomes.. The Journal of experimental medicine. 221 (1) ▶ Go to Pubmed