Publications

Convergent epigenetic evolution drives relapse in acute myeloid leukemia

Kevin Nuno, Armon Azizi, Thomas Koehnke, Caleb Lareau, Asiri Ediriwickrema, M Ryan Corces, Ansuman T Satpathy, Ravindra Majeti

eLife · 22 Apr 2024 · doi:10.7554/eLife.93019

FOXO1 is a master regulator of memory programming in CAR T cells

Alexander E. Doan, Katherine P. Mueller, Andy Y. Chen, Geoffrey T. Rouin, Yingshi Chen, ..., Joseph A. Fraietta, Elena Sotillo, Ansuman T. Satpathy, Crystal L. Mackall, Evan W. Weber

Nature · 10 Apr 2024 · doi:10.1038/s41586-024-07300-8

Transcript-specific enrichment enables profiling rare cell states via scRNA-seq

Tsion Abay, Robert R. Stickels, Meril T. Takizawa, Benan N. Nalbant, Yu-Hsin Hsieh, ..., Viviane Tabar, Leif S. Ludwig, Ronan Chaligne, Ansuman T. Satpathy, Caleb A. Lareau

Cold Spring Harbor Laboratory · 27 Mar 2024 · doi:10.1101/2024.03.27.587039

Regulation of immune signal integration and memory by inflammation-induced chromosome conformation

Bence Daniel, Andy Y. Chen, Katalin Sandor, Wenxi Zhang, Zhuang Miao, Caleb A. Lareau, Kathryn E. Yost, Howard Y. Chang, Ansuman T. Satpathy

Cold Spring Harbor Laboratory · 04 Mar 2024 · doi:10.1101/2024.02.29.582872

bioRxiv

Latent human herpesvirus 6 is reactivated in CAR T cells

Caleb A. Lareau, Yajie Yin, Katie Maurer, Katalin D. Sandor, Bence Daniel, ..., Theodore L. Roth, Marie J. Kersten, Catherine J. Wu, Robbie G. Majzner, Ansuman T. Satpathy

Nature · 08 Nov 2023 · doi:10.1038/s41586-023-06704-2

Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis

Evgenij Fiskin, Gökcen Eraslan, Maria B Alora-Palli, Juan Manuel Leyva-Castillo, Sean Kim, ..., Jacques Deguine, Gideon P Smith, Raif Geha, Aviv Regev, Ramnik Xavier

Cold Spring Harbor Laboratory · 30 Oct 2023 · doi:10.1101/2023.10.29.563503

bioRxiv

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9

Nora Schmidt, Sabina Ganskih, Yuanjie Wei, Alexander Gabel, Sebastian Zielinski, ..., Andreas Pichlmair, Steven A. Carr, Petr Chlanda, Florian Erhard, Mathias Munschauer

Cell · 01 Oct 2023 · doi:10.1016/j.cell.2023.09.002

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells

Caleb A. Lareau, Sonia M. Dubois, Frank A. Buquicchio, Yu-Hsin Hsieh, Kopal Garg, ..., Ansuman T. Satpathy, Aviv Regev, Vijay G. Sankaran, Suneet Agarwal, Leif S. Ludwig

Nature Genetics · 29 Jun 2023 · doi:10.1038/s41588-023-01433-8

Subtle cell states resolved in single-cell data

Caleb Lareau

Nature Biotechnology · 17 May 2023 · doi:10.1038/s41587-023-01797-6

Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness

Caleb A. Lareau, Yajie Yin, Jacob C. Gutierrez, Ryan S. Dhindsa, Anne-Sophie Gribling-Burrer, ..., William J. Greenleaf, Anshul Kundaje, Mathias Munschauer, Leif S. Ludwig, Ansuman T. Satpathy

Cold Spring Harbor Laboratory · 23 Apr 2023 · doi:10.1101/2023.04.23.537997

Co-opting signalling molecules enables logic-gated control of CAR T cells

Aidan M. Tousley, Maria Caterina Rotiroti, Louai Labanieh, Lea Wenting Rysavy, Won-Ju Kim, ..., Eva L. de la Serna, Alexander R. Dunn, Ansuman T. Satpathy, Crystal L. Mackall, Robbie G. Majzner

Nature · 08 Mar 2023 · doi:10.1038/s41586-023-05778-2

Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility

Caleb A. Lareau, Vincent Liu, Christoph Muus, Samantha D. Praktiknjo, Lena Nitsch, ..., Karin Pelka, Ansuman T. Satpathy, Aviv Regev, Vijay G. Sankaran, Leif S. Ludwig

Nature Protocols · 15 Feb 2023 · doi:10.1038/s41596-022-00795-3

Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq

Leif S. Ludwig, Caleb A. Lareau

Chromatin Accessibility · 01 Jan 2023 · doi:10.1007/978-1-0716-2899-7_14

Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq

Eleni P. Mimitou, Peter Smibert, Caleb A. Lareau

Chromatin Accessibility · 01 Jan 2023 · doi:10.1007/978-1-0716-2899-7_13

The Impact of Genomic Variation on Function (IGVF) Consortium

IGVF Consortium

arXiv · 01 Jan 2023 · doi:10.48550/arXiv.2307.13708

bioRxiv

Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models

Livius Penter, Elisa ten Hacken, Jackson Southard, Caleb A. Lareau, Leif S. Ludwig, Shuqiang Li, Donna S. Neuberg, Kenneth J. Livak, Catherine J. Wu

Cancer Research · 05 Dec 2022 · doi:10.1158/0008-5472.CAN-22-0275

BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma

Eshini Panditharatna, Joana G. Marques, Tingjian Wang, Maria C. Trissal, Ilon Liu, ..., Charles D. Stiles, Michelle Monje, Todd R. Golub, Jun Qi, Mariella G. Filbin

Cancer Discovery · 11 Nov 2022 · doi:10.1158/2159-8290.CD-21-1491

Clonal expansion and epigenetic inheritance of long-lasting NK cell memory

Timo Rückert, Caleb A. Lareau, Mir-Farzin Mashreghi, Leif S. Ludwig, Chiara Romagnani

Nature Immunology · 26 Oct 2022 · doi:10.1038/s41590-022-01327-7

Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics

Caleb A. Lareau, Chiara Romagnani, Leif S. Ludwig

Frontiers in Immunology · 18 Oct 2022 · doi:10.3389/fimmu.2022.1062415

A RORγt+ cell instructs gut microbiota-specific Treg cell differentiation

Ranit Kedmi, Tariq A. Najar, Kailin R. Mesa, Allyssa Grayson, Lina Kroehling, ..., Paul M. Allen, Helena Paidassi, James M. Gardner, Marlon Stoeckius, Dan R. Littman

Nature · 07 Sep 2022 · doi:10.1038/s41586-022-05089-y

Functional inference of gene regulation using single-cell multi-omics

Vinay K. Kartha, Fabiana M. Duarte, Yan Hu, Sai Ma, Jennifer G. Chew, ..., Andrew Earl, Zach D. Burkett, Andrew S. Kohlway, Ronald Lebofsky, Jason D. Buenrostro

Cell Genomics · 01 Sep 2022 · doi:10.1016/j.xgen.2022.100166

Advancing T cell–based cancer therapy with single-cell technologies

Samantha L. Bucktrout, Nicholas E. Banovich, Lisa H. Butterfield, Cansu Cimen-Bozkus, Josephine R. Giles, ..., Deena M. Maurer, Paul V. Munson, Mike Stubbington, Sarah Taylor, Abbey Cutchin

Nature Medicine · 01 Sep 2022 · doi:10.1038/s41591-022-01986-x

Runx3 drives a CD8+ T cell tissue residency program that is absent in CD4+ T cells

Raíssa Fonseca, Thomas N. Burn, Luke C. Gandolfo, Sapna Devi, Simone L. Park, ..., Terence P. Speed, Ansuman T. Satpathy, Scott N. Mueller, Francis R. Carbone, Laura K. Mackay

Nature Immunology · 26 Jul 2022 · doi:10.1038/s41590-022-01273-4

Congenital anemia reveals distinct targeting mechanisms for master transcription factor GATA1

Leif S. Ludwig, Caleb A. Lareau, Erik L. Bao, Nan Liu, Taiju Utsugisawa, ..., Stuart H. Orkin, Aviv Regev, Timothy L. McCavit, Hitoshi Kanno, Vijay G. Sankaran

Blood · 21 Apr 2022 · doi:10.1182/blood.2021013753

Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations

Tyler E. Miller, Caleb A. Lareau, Julia A. Verga, Erica A. K. DePasquale, Vincent Liu, ..., Andrew A. Lane, J. Christopher Love, Bradley E. Bernstein, Vijay G. Sankaran, Peter van Galen

Nature Biotechnology · 24 Feb 2022 · doi:10.1038/s41587-022-01210-8

Functional dissection of inherited non-coding variation influencing multiple myeloma risk

Ram Ajore, Abhishek Niroula, Maroulio Pertesi, Caterina Cafaro, Malte Thodberg, ..., Unnur Thorsteinsdottir, Vijay G. Sankaran, Kari Stefansson, Richard Houlston, Björn Nilsson

Nature Communications · 10 Jan 2022 · doi:10.1038/s41467-021-27666-x

JAK inhibition in a patient with a STAT1 gain-of-function variant reveals STAT1 dysregulation as a common feature of aplastic anemia

Jacob M. Rosenberg, Joshua M. Peters, Travis Hughes, Caleb A. Lareau, Leif S. Ludwig, ..., Yi-Bin Chen, Aviv Regev, Alex K. Shalek, Sarah M. Fortune, David B. Sykes

Med · 01 Jan 2022 · doi:10.1016/j.medj.2021.12.003

Differential Requirement of 3D Genomic Organization for the  <i>Mdm1-Il22-Ifng</i> Locus Regulation in Adaptive Versus Innate Responses

Chunhong Liu, Hiroyuki Nagashima, Nilisha Fernando, Sadie Signorella, Will Montgomery, ..., Martin J. Aryee, Aleksandra Pekowska, Yasmine Belkaid, John O’Shea, Han-Yu Shih

SSRN Electronic Journal · 01 Jan 2022 · doi:10.2139/ssrn.4271102

CPSP

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues

Tongtong Zhao, Zachary D. Chiang, Julia W. Morriss, Lindsay M. LaFave, Evan M. Murray, ..., Andrew S. Earl, Evan Z. Macosko, Tyler Jacks, Jason D. Buenrostro, Fei Chen

Nature · 15 Dec 2021 · doi:10.1038/s41586-021-04217-4

Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History

Livius Penter, Satyen H. Gohil, Caleb Lareau, Leif S. Ludwig, Erin M. Parry, ..., Matthew S. Davids, Donna S. Neuberg, Kenneth J. Livak, Vijay G. Sankaran, Catherine J. Wu

Cancer Discovery · 01 Dec 2021 · doi:10.1158/2159-8290.CD-21-0276

Charting the tumor antigen maps drawn by single-cell genomics

Caleb A. Lareau, Kevin R. Parker, Ansuman T. Satpathy

Cancer Cell · 01 Dec 2021 · doi:10.1016/j.ccell.2021.11.005

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Single-cell multiomics defines tolerogenic extrathymic Aire-expressing populations with unique homology to thymic epithelium

Jiaxi Wang, Caleb A. Lareau, Jhoanne L. Bautista, Alexander R. Gupta, Katalin Sandor, ..., Fang Xie, Vasilis Ntranos, Ansuman T. Satpathy, Mark S. Anderson, James M. Gardner

Science Immunology · 26 Nov 2021 · doi:10.1126/sciimmunol.abl5053

Single-cell chromatin state analysis with Signac

Tim Stuart, Avi Srivastava, Shaista Madad, Caleb A. Lareau, Rahul Satija

Nature Methods · 01 Nov 2021 · doi:10.1038/s41592-021-01282-5

Integrated single-cell transcriptomics and epigenomics reveals strong germinal center–associated etiology of autoimmune risk loci

Hamish W. King, Kristen L. Wells, Zohar Shipony, Arwa S. Kathiria, Lisa E. Wagar, ..., Robson Capasso, Mark M. Davis, Lars M. Steinmetz, Louisa K. James, William J. Greenleaf

Science Immunology · 29 Oct 2021 · doi:10.1126/sciimmunol.abh3768

Single-cell profiling of proteins and chromatin accessibility using PHAGE-ATAC

Evgenij Fiskin, Caleb A. Lareau, Leif S. Ludwig, Gökcen Eraslan, Feimei Liu, Aaron M. Ring, Ramnik J. Xavier, Aviv Regev

Nature Biotechnology · 21 Oct 2021 · doi:10.1038/s41587-021-01065-5

Transient dendritic cell activation diversifies the T cell response to acute infection

Kamir J. Hiam-Galvez, Rachel DeBarge, Caleb A. Lareau, Nam Woo Cho, Jacqueline L. Yee, Trine Line H. Okholm, Matthew H. Spitzer

Cold Spring Harbor Laboratory · 27 Sep 2021 · doi:10.1101/2021.09.26.461821

bioRxiv

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

Eleni P. Mimitou, Caleb A. Lareau, Kelvin Y. Chen, Andre L. Zorzetto-Fernandes, Yuhan Hao, ..., Shimon Sakaguchi, Leif S. Ludwig, Vijay G. Sankaran, Aviv Regev, Peter Smibert

Nature Biotechnology · 03 Jun 2021 · doi:10.1038/s41587-021-00927-2

STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma

Biniam Adane, Gabriela Alexe, Bo Kyung A. Seong, Diana Lu, Elizabeth E. Hwang, ..., Steven A. Carr, Martin J. Aryee, Richard A. Young, Brian D. Crompton, Kimberly Stegmaier

Cancer Cell · 01 Jun 2021 · doi:10.1016/j.ccell.2021.05.007

Distinct Foxp3 enhancer elements coordinate development, maintenance, and function of regulatory T cells

Ryoji Kawakami, Yohko Kitagawa, Kelvin Y. Chen, Masaya Arai, Daiya Ohara, ..., Hitomi Watanabe, Gen Kondoh, Keiji Hirota, Naganari Ohkura, Shimon Sakaguchi

Immunity · 01 May 2021 · doi:10.1016/j.immuni.2021.04.005

The SARS-CoV-2 RNA–protein interactome in infected human cells

Nora Schmidt, Caleb A. Lareau, Hasmik Keshishian, Sabina Ganskih, Cornelius Schneider, ..., Utz Fischer, Jörg Vogel, Steven A. Carr, Jochen Bodem, Mathias Munschauer

Nature Microbiology · 21 Dec 2020 · doi:10.1038/s41564-020-00846-z

Single Cell Transcriptomics Implicate Novel Monocyte and T Cell Immune Dysregulation in Sarcoidosis

Lori Garman, Richard C. Pelikan, Astrid Rasmussen, Caleb A. Lareau, Kathryn A. Savoy, ..., Harini Bagavant, Albert M. Levin, Salim Daouk, Wonder P. Drake, Courtney G. Montgomery

Frontiers in Immunology · 08 Dec 2020 · doi:10.3389/fimmu.2020.567342

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin

Sai Ma, Bing Zhang, Lindsay M. LaFave, Andrew S. Earl, Zachary Chiang, ..., Travis Law, Caleb Lareau, Ya-Chieh Hsu, Aviv Regev, Jason D. Buenrostro

Cell · 01 Nov 2020 · doi:10.1016/j.cell.2020.09.056

Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells

Melissa A. Walker, Caleb A. Lareau, Leif S. Ludwig, Amel Karaa, Vijay G. Sankaran, Aviv Regev, Vamsi K. Mootha

New England Journal of Medicine · 15 Oct 2020 · doi:10.1056/NEJMoa2001265

Inherited myeloproliferative neoplasm risk affects haematopoietic stem cells

Erik L. Bao, Satish K. Nandakumar, Xiaotian Liao, Alexander G. Bick, Juha Karjalainen, ..., Christopher J. O’Donnell, Mark J. Daly, Michael Milyavsky, Sekar Kathiresan, Vijay G. Sankaran

Nature · 14 Oct 2020 · doi:10.1038/s41586-020-2786-7

An old BATF’s new T-ricks

Caleb A. Lareau, Ansuman T. Satpathy

Nature Immunology · 28 Sep 2020 · doi:10.1038/s41590-020-0796-0

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer

Sarah E. Johnstone, Alejandro Reyes, Yifeng Qi, Carmen Adriaens, Esmat Hegazi, ..., Nir Hacohen, Rafael A. Irizarry, Bin Zhang, Martin J. Aryee, Bradley E. Bernstein

Cell · 01 Sep 2020 · doi:10.1016/j.cell.2020.07.030

Trans-ethnic and Ancestry-Specific Blood-Cell Genetics in 746,667 Individuals from 5 Global Populations

Ming-Huei Chen, Laura M. Raffield, Abdou Mousas, Saori Sakaue, Jennifer E. Huffman, ..., Nicole Soranzo, Andrew D. Johnson, Alexander P. Reiner, Paul L. Auer, Guillaume Lettre

Cell · 01 Sep 2020 · doi:10.1016/j.cell.2020.06.045

The Polygenic and Monogenic Basis of Blood Traits and Diseases

Dragana Vuckovic, Erik L. Bao, Parsa Akbari, Caleb A. Lareau, Abdou Mousas, ..., Adam S. Butterworth, Willem H. Ouwehand, Guillaume Lettre, Vijay G. Sankaran, Nicole Soranzo

Cell · 01 Sep 2020 · doi:10.1016/j.cell.2020.08.008

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling

Caleb A. Lareau, Leif S. Ludwig, Christoph Muus, Satyen H. Gohil, Tongtong Zhao, ..., Nir Hacohen, Catherine J. Wu, Martin J. Aryee, Aviv Regev, Vijay G. Sankaran

Nature Biotechnology · 12 Aug 2020 · doi:10.1038/s41587-020-0645-6

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Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma

Lindsay M. LaFave, Vinay K. Kartha, Sai Ma, Kevin Meli, Isabella Del Priore, ..., Haley Hauck, Annalisa Okimoto, Aviv Regev, Jason D. Buenrostro, Tyler Jacks

Cancer Cell · 01 Aug 2020 · doi:10.1016/j.ccell.2020.06.006

ImmGen at 15

Stephanie Vargas Aguilar, Oscar Aguilar, Rhys Allan, El Ad David Amir, Veronique Angeli, ..., Hideyuki Yoshida, Bingfei Yu, Yan Zhou, Yanan Zhu, Caroline Ziemkiewicz

Nature Immunology · 23 Jun 2020 · doi:10.1038/s41590-020-0687-4

A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing

Julian Grünewald, Ronghao Zhou, Caleb A. Lareau, Sara P. Garcia, Sowmya Iyer, Bret R. Miller, Lukas M. Langner, Jonathan Y. Hsu, Martin J. Aryee, J. Keith Joung

Nature Biotechnology · 01 Jun 2020 · doi:10.1038/s41587-020-0535-y

Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features

John P. Ray, Carl G. de Boer, Charles P. Fulco, Caleb A. Lareau, Masahiro Kanai, ..., Robbyn Issner, Hilary K. Finucane, Eric S. Lander, Aviv Regev, Nir Hacohen

Nature Communications · 06 Mar 2020 · doi:10.1038/s41467-020-15022-4

Inference and effects of barcode multiplets in droplet-based single-cell assays

Caleb A. Lareau, Sai Ma, Fabiana M. Duarte, Jason D. Buenrostro

Nature Communications · 13 Feb 2020 · doi:10.1038/s41467-020-14667-5

Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation

Anindita Basak, Mathias Munschauer, Caleb A. Lareau, Kara E. Montbleau, Jacob C. Ulirsch, ..., Steven A. Carr, Jane-Jane Chen, Stuart H. Orkin, Eric S. Lander, Vijay G. Sankaran

Nature Genetics · 20 Jan 2020 · doi:10.1038/s41588-019-0568-7

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Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking

Caleb A. Lareau, Leif S. Ludwig, Vijay G. Sankaran

Blood Advances · 16 Dec 2019 · doi:10.1182/bloodadvances.2019001196

Activity-by-contact model of enhancer–promoter regulation from thousands of CRISPR perturbations

Charles P. Fulco, Joseph Nasser, Thouis R. Jones, Glen Munson, Drew T. Bergman, ..., Caleb A. Lareau, Elena K. Stamenova, Erez Lieberman Aiden, Eric S. Lander, Jesse M. Engreitz

Nature Genetics · 29 Nov 2019 · doi:10.1038/s41588-019-0538-0

Assessment of computational methods for the analysis of single-cell ATAC-seq data

Huidong Chen, Caleb Lareau, Tommaso Andreani, Michael E. Vinyard, Sara P. Garcia, Kendell Clement, Miguel A. Andrade-Navarro, Jason D. Buenrostro, Luca Pinello

Genome Biology · 18 Nov 2019 · doi:10.1186/s13059-019-1854-5

CRISPR DNA base editors with reduced RNA off-target and self-editing activities

Julian Grünewald, Ronghao Zhou, Sowmya Iyer, Caleb A. Lareau, Sara P. Garcia, Martin J. Aryee, J. Keith Joung

Nature Biotechnology · 01 Sep 2019 · doi:10.1038/s41587-019-0236-6

Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility

Caleb A. Lareau, Fabiana M. Duarte, Jennifer G. Chew, Vinay K. Kartha, Zach D. Burkett, ..., Dmitry Pokholok, Martin J. Aryee, Frank J. Steemers, Ronald Lebofsky, Jason D. Buenrostro

Nature Biotechnology · 24 Jun 2019 · doi:10.1038/s41587-019-0147-6

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Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis

Leif S. Ludwig, Caleb A. Lareau, Erik L. Bao, Satish K. Nandakumar, Christoph Muus, ..., Narla Mohandas, Xiuli An, Martin J. Aryee, Aviv Regev, Vijay G. Sankaran

Cell Reports · 01 Jun 2019 · doi:10.1016/j.celrep.2019.05.046

Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis

Satish K Nandakumar, Sean K McFarland, Laura M Mateyka, Caleb A Lareau, Jacob C Ulirsch, ..., John G Doench, Jaroslaw P Maciejewski, Benjamin L Ebert, David E Root, Vijay G Sankaran

eLife · 09 May 2019 · doi:10.7554/eLife.44080

Single-cell trajectories reconstruction, exploration and mapping of omics data with STREAM

Huidong Chen, Luca Albergante, Jonathan Y. Hsu, Caleb A. Lareau, Giosuè Lo Bosco, ..., David M. Langenau, Andrei Zinovyev, Jason D. Buenrostro, Guo-Cheng Yuan, Luca Pinello

Nature Communications · 23 Apr 2019 · doi:10.1038/s41467-019-09670-4

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors

Julian Grünewald, Ronghao Zhou, Sara P. Garcia, Sowmya Iyer, Caleb A. Lareau, Martin J. Aryee, J. Keith Joung

Nature · 17 Apr 2019 · doi:10.1038/s41586-019-1161-z

Impaired human hematopoiesis due to a cryptic intronic <i>GATA1</i> splicing mutation

Impaired human hematopoiesis due to a cryptic intronic GATA1 splicing mutation

Nour J. Abdulhay, Claudia Fiorini, Jeffrey M. Verboon, Leif S. Ludwig, Jacob C. Ulirsch, ..., Rami N. Khoriaty, Philip Ancliff, Hanna T. Gazda, Marcin W. Wlodarski, Vijay G. Sankaran

Journal of Experimental Medicine · 26 Mar 2019 · doi:10.1084/jem.20181625

The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity–independent genomic targeting

Joshua Pan, Zachary M. McKenzie, Andrew R. D’Avino, Nazar Mashtalir, Caleb A. Lareau, Roodolph St. Pierre, Lu Wang, Ali Shilatifard, Cigall Kadoch

Nature Genetics · 11 Mar 2019 · doi:10.1038/s41588-019-0363-5

Interrogation of human hematopoiesis at single-cell and single-variant resolution

Jacob C. Ulirsch, Caleb A. Lareau, Erik L. Bao, Leif S. Ludwig, Michael H. Guo, ..., Joel N. Hirschhorn, Hilary K. Finucane, Martin J. Aryee, Jason D. Buenrostro, Vijay G. Sankaran

Nature Genetics · 11 Mar 2019 · doi:10.1038/s41588-019-0362-6

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

Leif S. Ludwig, Caleb A. Lareau, Jacob C. Ulirsch, Elena Christian, Christoph Muus, ..., Orit Rozenblatt-Rosen, Martin J. Aryee, Jason D. Buenrostro, Aviv Regev, Vijay G. Sankaran

Cell · 01 Mar 2019 · doi:10.1016/j.cell.2019.01.022

Heritability of fetal hemoglobin, white cell count, and other clinical traits from a sickle cell disease family cohort

Erik L. Bao, Caleb A. Lareau, Carlo Brugnara, Isabel R. Fulcher, Caroline Barau, ..., Pablo Bartolucci, Frédéric Galactéros, Orah S. Platt, Michael Mahaney, Vijay G. Sankaran

American Journal of Hematology · 06 Feb 2019 · doi:10.1002/ajh.25421

The cis-Regulatory Atlas of the Mouse Immune System

Hideyuki Yoshida, Caleb A. Lareau, Ricardo N. Ramirez, Samuel A. Rose, Barbara Maier, ..., Stephen L. Nutt, Brian D. Brown, Sara Mostafavi, Jason D. Buenrostro, Christophe Benoist

Cell · 01 Feb 2019 · doi:10.1016/j.cell.2018.12.036

Preprocessing and Computational Analysis of Single-Cell Epigenomic Datasets

Caleb Lareau, Divy Kangeyan, Martin J. Aryee

Methods in Molecular Biology · 01 Jan 2019 · doi:10.1007/978-1-4939-9057-3_13

A non-canonical SWI/SNF complex is a synthetic lethal target in cancers driven by BAF complex perturbation

Brittany C. Michel, Andrew R. D’Avino, Seth H. Cassel, Nazar Mashtalir, Zachary M. McKenzie, ..., Nora Fortoul, Nathanael S. Gray, James E. Bradner, Ho Man Chan, Cigall Kadoch

Nature Cell Biology · 05 Nov 2018 · doi:10.1038/s41556-018-0221-1

Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks

Richard C. Pelikan, Jennifer A. Kelly, Yao Fu, Caleb A. Lareau, Kandice L. Tessneer, ..., Joel M. Guthridge, Judith A. James, Martin J. Aryee, Courtney Montgomery, Patrick M. Gaffney

Nature Communications · 25 Jul 2018 · doi:10.1038/s41467-018-05328-9

Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation

Jason D. Buenrostro, M. Ryan Corces, Caleb A. Lareau, Beijing Wu, Alicia N. Schep, Martin J. Aryee, Ravindra Majeti, Howard Y. Chang, William J. Greenleaf

Cell · 01 May 2018 · doi:10.1016/j.cell.2018.03.074

Transcript-indexed ATAC-seq for precision immune profiling

Ansuman T. Satpathy, Naresha Saligrama, Jason D. Buenrostro, Yuning Wei, Beijing Wu, ..., Youn H. Kim, Paul A. Khavari, William J. Greenleaf, Mark M. Davis, Howard Y. Chang

Nature Medicine · 23 Apr 2018 · doi:10.1038/S41591-018-0008-8

Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types

Hilary K. Finucane, Yakir A. Reshef, Verneri Anttila, Kamil Slowikowski, Alexander Gusev, ..., Bradley E. Bernstein, Soumya Raychaudhuri, Steven McCarroll, Benjamin M. Neale, Alkes L. Price

Nature Genetics · 01 Apr 2018 · doi:10.1038/s41588-018-0081-4

Response to “Unexpected mutations after CRISPR–Cas9 editing in vivo”

Caleb A Lareau, Kendell Clement, Jonathan Y Hsu, Vikram Pattanayak, J Keith Joung, Martin J Aryee, Luca Pinello

Nature Methods · 30 Mar 2018 · doi:10.1038/nmeth.4541

hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

Caleb A Lareau, Martin J Aryee

Nature Methods · 28 Feb 2018 · doi:10.1038/nmeth.4583

Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity

Tania Carrillo-Roa, Christiana Labermaier, Peter Weber, David P. Herzog, Caleb Lareau, ..., Manfred Uhr, Florian Holsboer, Inge Sillaber, Elisabeth B. Binder, Marianne B. Müller

PLOS Biology · 28 Dec 2017 · doi:10.1371/journal.pbio.2002690

A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas

Russell J.H. Ryan, Jelena Petrovic, Dylan M. Rausch, Yeqiao Zhou, Caleb A. Lareau, ..., David M. Weinstock, Robert B. Faryabi, Bradley E. Bernstein, Jon C. Aster, Warren S. Pear

Cell Reports · 01 Oct 2017 · doi:10.1016/j.celrep.2017.09.066

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