hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data von Lareau, Caleb A, Aryee, Martin J

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Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors von Grünewald, Julian, Zhou, Ronghao, Garcia, Sara P., Iyer, Sowmya, Lareau, Caleb A., Aryee, Martin J., Joung, J. Keith

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Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation von Buenrostro, Jason D., Corces, M. Ryan, Lareau, Caleb A., Wu, Beijing, Schep, Alicia N., Aryee, Martin J., Majeti, Ravindra, Chang, Howard Y., Greenleaf, William J.

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Clonal expansion and epigenetic inheritance of long-lasting NK cell memory von Rückert, Timo, Lareau, Caleb A., Mashreghi, Mir-Farzin, Ludwig, Leif S., Romagnani, Chiara

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Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations von Fulco, Charles P., Nasser, Joseph, Jones, Thouis R., Munson, Glen, Bergman, Drew T., Subramanian, Vidya, Grossman, Sharon R., Anyoha, Rockwell, Doughty, Benjamin R., Patwardhan, Tejal A., Nguyen, Tung H., Kane, Michael, Perez, Elizabeth M., Durand, Neva C., Lareau, Caleb A., Stamenova, Elena K., Aiden, Erez Lieberman, Lander, Eric S., Engreitz, Jesse M.

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Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility von Lareau, Caleb A., Duarte, Fabiana M., Chew, Jennifer G., Kartha, Vinay K., Burkett, Zach D., Kohlway, Andrew S., Pokholok, Dmitry, Aryee, Martin J., Steemers, Frank J., Lebofsky, Ronald, Buenrostro, Jason D.

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Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics von Ludwig, Leif S., Lareau, Caleb A., Ulirsch, Jacob C., Christian, Elena, Muus, Christoph, Li, Lauren H., Pelka, Karin, Ge, Will, Oren, Yaara, Brack, Alison, Law, Travis, Rodman, Christopher, Chen, Jonathan H., Boland, Genevieve M., Hacohen, Nir, Rozenblatt-Rosen, Orit, Aryee, Martin J., Buenrostro, Jason D., Regev, Aviv, Sankaran, Vijay G.

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The cis-Regulatory Atlas of the Mouse Immune System von Yoshida, Hideyuki, Lareau, Caleb A., Ramirez, Ricardo N., Rose, Samuel A., Maier, Barbara, Wroblewska, Aleksandra, Desland, Fiona, Chudnovskiy, Aleksey, Mortha, Arthur, Dominguez, Claudia, Tellier, Julie, Kim, Edy, Dwyer, Dan, Shinton, Susan, Nabekura, Tsukasa, Qi, YiLin, Yu, Bingfei, Robinette, Michelle, Kim, Ki-Wook, Wagers, Amy, Rhoads, Andrew, Nutt, Stephen L., Brown, Brian D., Mostafavi, Sara, Buenrostro, Jason D., Benoist, Christophe

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A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation von Michel, Brittany C., D’Avino, Andrew R., Cassel, Seth H., Mashtalir, Nazar, McKenzie, Zachary M., McBride, Matthew J., Valencia, Alfredo M., Zhou, Qianhe, Bocker, Michael, Soares, Luis M. M., Pan, Joshua, Remillard, David I., Lareau, Caleb A., Zullow, Hayley J., Fortoul, Nora, Gray, Nathanael S., Bradner, James E., Chan, Ho Man, Kadoch, Cigall

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Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM von Chen, Huidong, Albergante, Luca, Hsu, Jonathan Y., Lareau, Caleb A., Lo Bosco, Giosuè, Guan, Jihong, Zhou, Shuigeng, Gorban, Alexander N., Bauer, Daniel E., Aryee, Martin J., Langenau, David M., Zinovyev, Andrei, Buenrostro, Jason D., Yuan, Guo-Cheng, Pinello, Luca

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Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC von Fiskin, Evgenij, Lareau, Caleb A., Ludwig, Leif S., Eraslan, Gökcen, Liu, Feimei, Ring, Aaron M., Xavier, Ramnik J., Regev, Aviv

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The SARS-CoV-2 RNA–protein interactome in infected human cells von Schmidt, Nora, Lareau, Caleb A., Keshishian, Hasmik, Ganskih, Sabina, Schneider, Cornelius, Hennig, Thomas, Melanson, Randy, Werner, Simone, Wei, Yuanjie, Zimmer, Matthias, Ade, Jens, Kirschner, Luisa, Zielinski, Sebastian, Dölken, Lars, Lander, Eric S., Caliskan, Neva, Fischer, Utz, Vogel, Jörg, Carr, Steven A., Bodem, Jochen, Munschauer, Mathias

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Inference and effects of barcode multiplets in droplet-based single-cell assays von Lareau, Caleb A., Ma, Sai, Duarte, Fabiana M., Buenrostro, Jason D.

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Interrogation of human hematopoiesis at single-cell and single-variant resolution von Ulirsch, Jacob C., Lareau, Caleb A., Bao, Erik L., Ludwig, Leif S., Guo, Michael H., Benner, Christian, Satpathy, Ansuman T., Kartha, Vinay K., Salem, Rany M., Hirschhorn, Joel N., Finucane, Hilary K., Aryee, Martin J., Buenrostro, Jason D., Sankaran, Vijay G.

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Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis von Ludwig, Leif S, Lareau, Caleb A, Bao, Erik L, Nandakumar, Satish K, Muus, Christoph, Ulirsch, Jacob C, Chowdhary, Kaitavjeet, Buenrostro, Jason D, Mohandas, Narla, An, Xiuli, Aryee, Martin J, Regev, Aviv, Sankaran, Vijay G

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Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation von Basak, Anindita, Munschauer, Mathias, Lareau, Caleb A., Montbleau, Kara E., Ulirsch, Jacob C., Hartigan, Christina R., Schenone, Monica, Lian, John, Wang, Yaomei, Huang, Yumin, Wu, Xianfang, Gehrke, Lee, Rice, Charles M., An, Xiuli, Christou, Helen A., Mohandas, Narla, Carr, Steven A., Chen, Jane-Jane, Orkin, Stuart H., Lander, Eric S., Sankaran, Vijay G.

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Identifying optimal tumor-associated antigen combinations with single-cell genomics to enable multi-targeting therapies von Nix, Matthew A., Lareau, Caleb A., Verboon, Jeffrey, Kugler, David G.

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Single-cell chromatin state analysis with Signac von Stuart, Tim, Srivastava, Avi, Madad, Shaista, Lareau, Caleb A., Satija, Rahul

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Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics von Lareau, Caleb A., Romagnani, Chiara, Ludwig, Leif S.

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Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks von Pelikan, Richard C., Kelly, Jennifer A., Fu, Yao, Lareau, Caleb A., Tessneer, Kandice L., Wiley, Graham B., Wiley, Mandi M., Glenn, Stuart B., Harley, John B., Guthridge, Joel M., James, Judith A., Aryee, Martin J., Montgomery, Courtney, Gaffney, Patrick M.

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