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作者：Fu, Xi; Mo, Shentong; Buendia, Alejandro; Laurent, Anouchka P.; Shao, Anqi; Alvarez-Torres, Maria del Mar; Yu, Tianji; Tan, Jimin; Su, Jiayu; Sagatelian, Romella; Ferrando, Adolfo A.; Ciccia, Alberto; Lan, Yanyan; Owens, David M.; Palomero, Teresa; Xing, Eric P.; Rabadan, Raul
作者单位：Columbia University; Columbia University; Mohamed bin Zayed University of Artificial Intelligence MBZUAI; Carnegie Mellon University; Columbia University; Columbia University; New York University; Regeneron; Columbia University; Tsinghua University; Tsinghua University; Columbia University
摘要：Transcriptional regulation, which involves a complex interplay between regulatory sequences and proteins, directs all biological processes. Computational models of transcription lack generalizability to accurately extrapolate to unseen cell types and conditions. Here we introduce GET (general expression transformer), an interpretable foundation model designed to uncover regulatory grammars across 213 human fetal and adult cell types1,2. Relying exclusively on chromatin accessibility data and s...
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作者：Moorman, A. R.; Benitez, E. K.; Cambuli, F.; Jiang, Q.; Mahmoud, A.; Lumish, M.; Hartner, S.; Balkaran, S.; Bermeo, J.; Asawa, S.; Firat, C.; Saxena, A.; Wu, F.; Luthra, A.; Burdziak, C.; Xie, Y.; Sgambati, V.; Luckett, K.; Li, Y.; Yi, Z.; Masilionis, I.; Soares, K.; Pappou, E.; Yaeger, R.; Kingham, P.; Jarnagin, W.; Paty, P.; Weiser, M. R.; Mazutis, L.; D'Angelica, M.; Shia, J.; Garcia-Aguilar, J.; Nawy, T.; Hollmann, T. J.; Chaligne, R.; Sanchez-Vega, F.; Sharma, R.; Pe'er, D.; Ganesh, K.
作者单位：Memorial Sloan Kettering Cancer Center; Memorial Sloan Kettering Cancer Center; Cornell University; Weill Cornell Medicine; Memorial Sloan Kettering Cancer Center; Memorial Sloan Kettering Cancer Center; Memorial Sloan Kettering Cancer Center; Howard Hughes Medical Institute; University System of Ohio; Case Western Reserve University; Bristol-Myers Squibb
摘要：As cancers progress, they become increasingly aggressive-metastatic tumours are less responsive to first-line therapies than primary tumours, they acquire resistance to successive therapies and eventually cause death1,2. Mutations are largely conserved between primary and metastatic tumours from the same patients, suggesting that non-genetic phenotypic plasticity has a major role in cancer progression and therapy resistance3-5. However, we lack an understanding of metastatic cell states and th...
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作者：[Anonymous]
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作者：Brozek, Alicja; Theodoris, Christina V.
作者单位：University of California System; University of California San Francisco; The J David Gladstone Institutes; University of California System; University of California San Francisco; University of California System; University of California San Francisco
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作者：Min, Yongyi
摘要：A statistician offers a masterful guide to embracing the unknown.
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作者：Mitchell, Dann
作者单位：University of Bristol
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作者：Kessler, Michael D.; Damask, Amy; O'Keeffe, Sean; Banerjee, Nilanjana; Li, Dadong; Watanabe, Kyoko; Marketta, Anthony; Van Meter, Michael; Semrau, Stefan; Horowitz, Julie; Tang, Jing; Kosmicki, Jack A.; Rajagopal, Veera M.; Zou, Yuxin; Houvras, Yariv; Ghosh, Arkopravo; Gillies, Christopher; Mbatchou, Joelle; White, Ryan R.; Verweij, Niek; Bovijn, Jonas; Parikshak, Neelroop N.; Leblanc, Michelle G.; Jones, Marcus; Glass, David J.; Lotta, Luca A.; Cantor, Michael N.; Atwal, Gurinder S.; Locke, Adam E.; Ferreira, Manuel A. R.; Deering, Raquel; Paulding, Charles; Shuldiner, Alan R.; Thurston, Gavin; Ferrando, Adolfo A.; Salerno, Will; Reid, Jeffrey G.; Overton, John D.; Marchini, Jonathan; Kang, Hyun M.; Baras, Aris; Abecasis, Goncalo R.; Jorgenson, Eric
作者单位：Regeneron; Regeneron
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作者：Rosenzweig, Amy C.
作者单位：Northwestern University; Northwestern University
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作者：Arce, Maya M.; Umhoefer, Jennifer M.; Arang, Nadia; Kasinathan, Sivakanthan; Freimer, Jacob W.; Steinhart, Zachary; Shen, Haolin; Pham, Minh T. N.; Ota, Mineto; Wadhera, Anika; Dajani, Rama; Dorovskyi, Dmytro; Chen, Yan Yi; Liu, Qi; Zhou, Yuan; Swaney, Danielle L.; Obernier, Kirsten; Shy, Brian R.; Carnevale, Julia; Satpathy, Ansuman T.; Krogan, Nevan J.; Pritchard, Jonathan K.; Marson, Alexander
作者单位：University of California System; University of California San Francisco; University of California System; University of California San Francisco; University of California System; University of California San Francisco; Stanford University; Stanford University; Stanford University; University of California System; University of California San Francisco; The J David Gladstone Institutes; University of California System; University of California San Francisco; University of California System; University of California San Francisco; University of California System; University of California San Francisco; UCSF Medical Center; UCSF Helen Diller Family Comprehensive Cancer Center; University of California System; University of California San Francisco; Stanford University; University of California System; University of California Berkeley; University of California System; University of California San Francisco; University of California System; University of California San Francisco
摘要：The ability of cells to maintain distinct identities and respond to transient environmental signals requires tightly controlled regulation of gene networks1, 2-3. These dynamic regulatory circuits that respond to extracellular cues in primary human cells remain poorly defined. The need for context-dependent regulation is prominent in T cells, where distinct lineages must respond to diverse signals to mount effective immune responses and maintain homeostasis4, 5, 6, 7-8. Here we performed CRISP...
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作者：Wang, Tongtong; Teng, Bochuan; Yao, Dickson R.; Gao, Wei; Oka, Yuki
作者单位：California Institute of Technology; California Institute of Technology
摘要：The autonomic nervous system orchestrates the functions of the brain and body through the sympathetic and parasympathetic pathways1. However, our understanding of the autonomic system, especially the sympathetic system, at the cellular and molecular levels is severely limited. Here we show topological representations of individual visceral organs in the major abdominal sympathetic ganglion complex. Using multi-modal transcriptomic analyses, we identified molecularly distinct sympathetic popula...
