Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model von Townes, F William, Hicks, Stephanie C, Aryee, Martin J, Irizarry, Rafael A

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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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Global causes of diarrheal disease mortality in children <5 years of age: a systematic review von Lanata, Claudio F, Fischer-Walker, Christa L, Olascoaga, Ana C, Torres, Carla X, Aryee, Martin J, Black, Robert E

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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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Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing von Tsai, Shengdar Q, Wyvekens, Nicolas, Khayter, Cyd, Foden, Jennifer A, Thapar, Vishal, Reyon, Deepak, Goodwin, Mathew J, Aryee, Martin J, Joung, J Keith

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Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays von Aryee, Martin J., Jaffe, Andrew E., Corrada-Bravo, Hector, Ladd-Acosta, Christine, Feinberg, Andrew P., Hansen, Kasper D., Irizarry, Rafael A.

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Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells von Kleinstiver, Benjamin P, Tsai, Shengdar Q, Prew, Michelle S, Nguyen, Nhu T, Welch, Moira M, Lopez, Jose M, McCaw, Zachary R, Aryee, Martin J, Joung, J Keith

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Diarrhea incidence in low- and middle-income countries in 1990 and 2010: a systematic review von Fischer Walker, Christa L, Perin, Jamie, Aryee, Martin J, Boschi-Pinto, Cynthia, Black, Robert E

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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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Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis von Liu, Yun, Aryee, Martin J, Padyukov, Leonid, Fallin, M Daniele, Hesselberg, Espen, Runarsson, Arni, Reinius, Lovisa, Acevedo, Nathalie, Taub, Margaret, Ronninger, Marcus, Shchetynsky, Klementy, Scheynius, Annika, Kere, Juha, Alfredsson, Lars, Klareskog, Lars, Ekström, Tomas J, Feinberg, Andrew P

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Activities and specificities of CRISPR/Cas9 and Cas12a nucleases for targeted mutagenesis in maize von Lee, Keunsub, Zhang, Yingxiao, Kleinstiver, Benjamin P., Guo, Jimmy A., Aryee, Martin J., Miller, Jonah, Malzahn, Aimee, Zarecor, Scott, Lawrence‐Dill, Carolyn J., Joung, J. Keith, Qi, Yiping, Wang, Kan

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High levels of AAV vector integration into CRISPR-induced DNA breaks von Hanlon, Killian S., Kleinstiver, Benjamin P., Garcia, Sara P., Zaborowski, Mikołaj P., Volak, Adrienn, Spirig, Stefan E., Muller, Alissa, Sousa, Alexander A., Tsai, Shengdar Q., Bengtsson, Niclas E., Lööv, Camilla, Ingelsson, Martin, Chamberlain, Jeffrey S., Corey, David P., Aryee, Martin J., Joung, J. Keith, Breakefield, Xandra O., Maguire, Casey A., György, Bence

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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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A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression von Guintivano, Jerry, Aryee, Martin J., Kaminsky, Zachary A.

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Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts von Daley, George Q, Feinberg, Andrew P, Doi, Akiko, Park, In-Hyun, Wen, Bo, Murakami, Peter, Aryee, Martin J, Irizarry, Rafael, Herb, Brian, Ladd-Acosta, Christine, Rho, Junsung, Loewer, Sabine, Miller, Justine, Schlaeger, Thorsten

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Estimating diarrhea mortality among young children in low and middle income countries von Walker, Christa L Fischer, Aryee, Martin J, Boschi-Pinto, Cynthia, Black, Robert E

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Donor cell type can influence the epigenome and differentiation potential of human induced pluripotent stem cells von Kim, Kitai, Zhao, Rui, Doi, Akiko, Ng, Kitwa, Unternaehrer, Juli, Cahan, Patrick, Hongguang, Huo, Loh, Yuin-Han, Aryee, Martin J, Lensch, M William, Li, Hu, Collins, James J, Feinberg, Andrew P, Daley, George Q

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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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EWS-FLI1 Utilizes Divergent Chromatin Remodeling Mechanisms to Directly Activate or Repress Enhancer Elements in Ewing Sarcoma von Riggi, Nicolò, Knoechel, Birgit, Gillespie, Shawn M., Rheinbay, Esther, Boulay, Gaylor, Suvà, Mario L., Rossetti, Nikki E., Boonseng, Wannaporn E., Oksuz, Ozgur, Cook, Edward B., Formey, Aurélie, Patel, Anoop, Gymrek, Melissa, Thapar, Vishal, Deshpande, Vikram, Ting, David T., Hornicek, Francis J., Nielsen, G. Petur, Stamenkovic, Ivan, Aryee, Martin J., Bernstein, Bradley E., Rivera, Miguel N.

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