Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution
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.
Published in Cell (16.09.2021)
Published in Cell (16.09.2021)
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Chromatin accessibility dynamics in a model of human forebrain development
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
Published in Science (American Association for the Advancement of Science) (24.01.2020)
Published in Science (American Association for the Advancement of Science) (24.01.2020)
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Optical control of mammalian endogenous transcription and epigenetic states
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
Published in Nature (London) (22.08.2013)
Published in Nature (London) (22.08.2013)
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Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum
Marinov, Georgi K., Trevino, Alexandro E., Xiang, Tingting, Kundaje, Anshul, Grossman, Arthur R., Greenleaf, William J.
Published in Nature genetics (01.05.2021)
Published in Nature genetics (01.05.2021)
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Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements
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.
Published in Nature communications (06.09.2019)
Published in Nature communications (06.09.2019)
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CasKAS: direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping
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
Published in Genome Biology (21.04.2023)
Published in Genome Biology (21.04.2023)
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Diverse lncRNA mechanisms in brain development and disease
Ang, Cheen Euong, Trevino, Alexandro E, Chang, Howard Y
Published in Current opinion in genetics & development (01.12.2020)
Published in Current opinion in genetics & development (01.12.2020)
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Journal Article
Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
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
Published in Nature (London) (29.01.2015)
Published in Nature (London) (29.01.2015)
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Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
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
Published in Nature biotechnology (01.07.2014)
Published in Nature biotechnology (01.07.2014)
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An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues
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
Published in Nature methods (01.10.2017)
Published in Nature methods (01.10.2017)
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Nociceptor neurons affect cancer immunosurveillance
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
Published in Nature (London) (10.11.2022)
Published in Nature (London) (10.11.2022)
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Journal Article
Single‐Cell Transcriptomic Census of Endothelial Changes Induced by Matrix Stiffness and the Association with Atherosclerosis
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.
Published in Advanced functional materials (17.11.2022)
Published in Advanced functional materials (17.11.2022)
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Spatial proteomics of human diabetic kidney disease, from health to class III
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
Published in Diabetologia (01.09.2024)
Published in Diabetologia (01.09.2024)
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899 emObject: domain specific data abstraction for spatial omics
Baker, Ethan, Mayer, Aaron, Trevino, Alexandro E
Published in Journal for immunotherapy of cancer (01.11.2023)
Published in Journal for immunotherapy of cancer (01.11.2023)
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Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens
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
Published in Nature biomedical engineering (01.12.2022)
Published in Nature biomedical engineering (01.12.2022)
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