Optical control of mammalian endogenous transcription and epigenetic states von Konermann, Silvana, Brigham, Mark D., Trevino, Alexandro E., Hsu, Patrick D., Heidenreich, Matthias, Le Cong, Platt, Randall J., Scott, David A., Church, George M., Zhang, Feng

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Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution von Trevino, Alexandro E., Müller, Fabian, Andersen, Jimena, Sundaram, Laksshman, Kathiria, Arwa, Shcherbina, Anna, Farh, Kyle, Chang, Howard Y., Pașca, Anca M., Kundaje, Anshul, Pașca, Sergiu P., Greenleaf, William J.

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Diverse lncRNA mechanisms in brain development and disease von Ang, Cheen Euong, Trevino, Alexandro E, Chang, Howard Y

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Chromatin accessibility dynamics in a model of human forebrain development von Trevino, Alexandro E, Sinnott-Armstrong, Nasa, Andersen, Jimena, Yoon, Se-Jin, Huber, Nina, Pritchard, Jonathan K, Chang, Howard Y, Greenleaf, William J, Pașca, Sergiu P

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Genome editing using Cas9 nickases von Trevino, Alexandro E, Zhang, Feng

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Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex von Konermann, Silvana, Brigham, Mark D., Trevino, Alexandro E., Joung, Julia, Abudayyeh, Omar O., Barcena, Clea, Hsu, Patrick D., Habib, Naomi, Gootenberg, Jonathan S., Nishimasu, Hiroshi, Nureki, Osamu, Zhang, Feng

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Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells von Wu, Xuebing, Scott, David A, Kriz, Andrea J, Chiu, Anthony C, Hsu, Patrick D, Dadon, Daniel B, Cheng, Albert W, Trevino, Alexandro E, Konermann, Silvana, Chen, Sidi, Jaenisch, Rudolf, Zhang, Feng, Sharp, Phillip A

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Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum von Marinov, Georgi K., Trevino, Alexandro E., Xiang, Tingting, Kundaje, Anshul, Grossman, Arthur R., Greenleaf, William J.

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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues von Corces, M Ryan, Trevino, Alexandro E, Hamilton, Emily G, Greenside, Peyton G, Sinnott-Armstrong, Nicholas A, Vesuna, Sam, Satpathy, Ansuman T, Rubin, Adam J, Montine, Kathleen S, Wu, Beijing, Kathiria, Arwa, Cho, Seung Woo, Mumbach, Maxwell R, Carter, Ava C, Kasowski, Maya, Orloff, Lisa A, Risca, Viviana I, Kundaje, Anshul, Khavari, Paul A, Montine, Thomas J, Greenleaf, William J, Chang, Howard Y

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Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements von Tycko, Josh, Wainberg, Michael, Marinov, Georgi K., Ursu, Oana, Hess, Gaelen T., Ego, Braeden K., Aradhana, Li, Amy, Truong, Alisa, Trevino, Alexandro E., Spees, Kaitlyn, Yao, David, Kaplow, Irene M., Greenside, Peyton G., Morgens, David W., Phanstiel, Douglas H., Snyder, Michael P., Bintu, Lacramioara, Greenleaf, William J., Kundaje, Anshul, Bassik, Michael C.

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Nociceptor neurons affect cancer immunosurveillance von Balood, Mohammad, Ahmadi, Maryam, Eichwald, Tuany, Ahmadi, Ali, Majdoubi, Abdelilah, Roversi, Karine, Roversi, Katiane, Lucido, Christopher T., Restaino, Anthony C., Huang, Siyi, Ji, Lexiang, Huang, Kai-Chih, Semerena, Elise, Thomas, Sini C., Trevino, Alexandro E., Merrison, Hannah, Parrin, Alexandre, Doyle, Benjamin, Vermeer, Daniel W., Spanos, William C., Williamson, Caitlin S., Seehus, Corey R., Foster, Simmie L., Dai, Hongyue, Shu, Chengyi J., Rangachari, Manu, Thibodeau, Jacques, V. Del Rincon, Sonia, Drapkin, Ronny, Rafei, Moutih, Ghasemlou, Nader, Vermeer, Paola D., Woolf, Clifford J., Talbot, Sebastien

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CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping von Marinov, Georgi K, Kim, Samuel H, Bagdatli, S Tansu, Higashino, Soon Il, Trevino, Alexandro E, Tycko, Josh, Wu, Tong, Bintu, Lacramioara, Bassik, Michael C, He, Chuan, Kundaje, Anshul, Greenleaf, William J

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Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity von Ran, F. Ann, Hsu, Patrick D., Lin, Chie-Yu, Gootenberg, Jonathan S., Konermann, Silvana, Trevino, Alexandro E., Scott, David A., Inoue, Azusa, Matoba, Shogo, Zhang, Yi, Zhang, Feng

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Single‐Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis von Zamani, Maedeh, Cheng, Yu‐Hao, Charbonier, Frank, Gupta, Vivek Kumar, Mayer, Aaron T., Trevino, Alexandro E., Quertermous, Thomas, Chaudhuri, Ovijit, Cahan, Patrick, Huang, Ngan F.

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Spatial proteomics of human diabetic kidney disease, from health to class III von Kondo, Ayano, McGrady, Monee, Nallapothula, Dhiraj, Ali, Hira, Trevino, Alexandro E., Lam, Amy, Preska, Ryan, D’Angio, H. Blaize, Wu, Zhenqin, Lopez, Lauren N., Badhesha, Harshanna K., Vargas, Chenoa R., Ramesh, Achyuta, Wiegley, Nasim, Han, Seung Seok, Dall’Era, Marc, Jen, Kuang-Yu, Mayer, Aaron T., Afkarian, Maryam

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Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens von Wu, Zhenqin, Trevino, Alexandro E., Wu, Eric, Swanson, Kyle, Kim, Honesty J., D’Angio, H. Blaize, Preska, Ryan, Charville, Gregory W., Dalerba, Piero D., Egloff, Ann Marie, Uppaluri, Ravindra, Duvvuri, Umamaheswar, Mayer, Aaron T., Zou, James

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PVDF-Fe3O4 nanocomposites: spectroscopic investigations von Chipara, Dorina M., Trevino, Alexandro, Lozano, Karen, Hoke, Bryan, Martirosyan, Karen S., Chipara, Mircea

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7-UP: Generating in silico CODEX from a small set of immunofluorescence markers von Wu, Eric, Trevino, Alexandro E, Wu, Zhenqin, Swanson, Kyle, Kim, Honesty J, D'Angio, H Blaize, Preska, Ryan, Chiou, Aaron E, Charville, Gregory W, Dalerba, Piero, Duvvuri, Umamaheswar, Colevas, Alexander D, Levi, Jelena, Bedi, Nikita, Chang, Serena, Sunwoo, John, Egloff, Ann Marie, Uppaluri, Ravindra, Mayer, Aaron T, Zou, James

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899 emObject: domain specific data abstraction for spatial omics von Baker, Ethan, Mayer, Aaron, Trevino, Alexandro E

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1290 Quantitative cell morphology featurization in multiplexed immunofluorescence images reveals tumor subtypes in cancer microenvironments von Huang, Rita, Mayer, Aaron, Trevino, Alexandro E

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