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2024

Single-Cell Technologies for Studying the Evolution and Function of Mitochondrial DNA Heteroplasmy in Cancer
Single-Cell Technologies for Studying the Evolution and Function of Mitochondrial DNA Heteroplasmy in Cancer
Sonia Boscenco, Erin M. Cumming, Minsoo Kim, Caleb Lareau, Ed Reznik
Annual Review of Cancer Biology   ·   12 Nov 2024   ·   10.1146/annurev-cancerbio-080124-102241
Identifying optimal tumor-associated antigen combinations with single-cell genomics to enable multi-targeting therapies
Identifying optimal tumor-associated antigen combinations with single-cell genomics to enable multi-targeting therapies
Matthew A. Nix, Caleb A. Lareau, Jeffrey Verboon, David G. Kugler
Frontiers in Immunology   ·   07 Nov 2024   ·   10.3389/fimmu.2024.1492782
Concepts and new developments in droplet-based single cell multi-omics
Concepts and new developments in droplet-based single cell multi-omics
Arthur Chow, Caleb A. Lareau
Trends in Biotechnology   ·   01 Nov 2024   ·   doi:10.1016/j.tibtech.2024.07.006
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Retinoic acid and TGF-β orchestrate organ-specific programs of tissue residency
Retinoic acid and TGF-β orchestrate organ-specific programs of tissue residency
Andreas Obers, Tobias Poch, Grace Rodrigues, Susan N. Christo, Luke C. Gandolfo, ..., Tri Giang Phan, Christoph Wilhelm, Colby Zaph, Maximilien Evrard, Laura K. Mackay
Immunity   ·   01 Oct 2024   ·   doi:10.1016/j.immuni.2024.09.015
Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations
Tracking rare single donor and recipient immune and leukemia cells after allogeneic hematopoietic cell transplantation using mitochondrial DNA mutations
Livius Penter, Nicoletta Cieri, Katie Maurer, Marwan Kwok, Haoxiang Lyu, ..., Gad Getz, Jacqueline S. Garcia, Robert J. Soiffer, Kenneth J. Livak, Catherine J. Wu
Blood Cancer Discovery   ·   05 Sep 2024   ·   doi:10.1158/2643-3230.BCD-23-0138
Deciphering the impact of genomic variation on function
Deciphering the impact of genomic variation on function
Jesse M. Engreitz, Heather A. Lawson, Harinder Singh, Lea M. Starita, Gary C. Hon, ..., Stephanie Calluori, Daniel A. Gilchrist, Carolyn M. Hutter, Stephanie A. Morris, Ella K. Samer
Nature   ·   04 Sep 2024   ·   doi:10.1038/s41586-024-07510-0
Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation
Distinct epigenomic landscapes underlie tissue-specific memory T cell differentiation
Frank A. Buquicchio, Raissa Fonseca, Patrick K. Yan, Fangyi Wang, Maximilien Evrard, ..., Flora M. Tierney, Michael R. Howitt, Caleb A. Lareau, Ansuman T. Satpathy, Laura K. Mackay
Immunity   ·   01 Sep 2024   ·   doi:10.1016/j.immuni.2024.06.014
Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference
Artifacts in single-cell mitochondrial DNA mutation analyses misinform phylogenetic inference
Caleb A. Lareau, Michael S. Chapman, Livius Penter, Tal Nawy, Dana Pe’er, Leif S. Ludwig
Cold Spring Harbor Laboratory   ·   29 Jul 2024   ·   doi:10.1101/2024.07.28.605517
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Mitochondrial genetics through the lens of single-cell multi-omics
Mitochondrial genetics through the lens of single-cell multi-omics
Lena Nitsch, Caleb A. Lareau, Leif S. Ludwig
Nature Genetics   ·   01 Jul 2024   ·   doi:10.1038/s41588-024-01794-8
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A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification
A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification
Chunhong Liu, Hiroyuki Nagashima, Nilisha Fernando, Victor Bass, Jaanam Gopalakrishnan, ..., Martin J. Aryee, Aleksandra Pękowska, Yasmine Belkaid, John O’Shea, Han-Yu Shih
Immunity   ·   01 May 2024   ·   doi:10.1016/j.immuni.2024.04.007
Convergent epigenetic evolution drives relapse in acute myeloid leukemia
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
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
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 Chaligné, Ansuman T. Satpathy, Caleb A. Lareau
Cold Spring Harbor Laboratory   ·   27 Mar 2024   ·   doi:10.1101/2024.03.27.587039
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Regulation of immune signal integration and memory by inflammation-induced chromosome conformation
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

2023

Latent human herpesvirus 6 is reactivated in CAR T cells
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
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Multi-modal skin atlas identifies a multicellular immune-stromal community associated with altered cornification and specific T cell expansion in atopic dermatitis
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
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
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
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Subtle cell states resolved in single-cell data
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
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
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Co-opting signalling molecules enables logic-gated control of CAR T cells
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
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
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Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq
Concomitant Sequencing of Accessible Chromatin and Mitochondrial Genomes in Single Cells Using mtscATAC-Seq
Leif S. Ludwig, Caleb A. Lareau
Methods in Molecular Biology   ·   01 Jan 2023   ·   doi:10.1007/978-1-0716-2899-7_14
Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq
Massively Parallel Profiling of Accessible Chromatin and Proteins with ASAP-Seq
Eleni P. Mimitou, Peter Smibert, Caleb A. Lareau
Methods in Molecular Biology   ·   01 Jan 2023   ·   doi:10.1007/978-1-0716-2899-7_13

2022

Mitochondrial DNA Mutations as Natural Barcodes for Lineage Tracing of Murine Tumor Models
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
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
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
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Editorial: Lineage tracing, hematopoietic stem cell and immune cell dynamics
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
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
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
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
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
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
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Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations
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
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
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

2021

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
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
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
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
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
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
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
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
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
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
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STAG2 loss rewires oncogenic and developmental programs to promote metastasis in Ewing sarcoma
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
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

2020

The SARS-CoV-2 RNA–protein interactome in infected human cells
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation
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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2019

Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking
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
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
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
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
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
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
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
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
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
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
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
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Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics
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
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Heritability of fetal hemoglobin, white cell count, and other clinical traits from a sickle cell disease family cohort
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
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
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

2018

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

2017

Common genes associated with antidepressant response in mouse and man identify key role of glucocorticoid receptor sensitivity
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
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
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Caleb A Lareau, Martin J Aryee
Bioinformatics   ·   29 Sep 2017   ·   doi:10.1093/bioinformatics/btx623
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing
Dissecting hematopoietic and renal cell heterogeneity in adult zebrafish at single-cell resolution using RNA sequencing
Qin Tang, Sowmya Iyer, Riadh Lobbardi, John C. Moore, Huidong Chen, ..., Andre Bernards, Martin Aryee, Luca Pinello, Iain A. Drummond, David M. Langenau
Journal of Experimental Medicine   ·   06 Sep 2017   ·   doi:10.1084/jem.20170976
Confounding in ex vivo models of Diamond-Blackfan anemia
Confounding in ex vivo models of Diamond-Blackfan anemia
Jacob C. Ulirsch, Caleb Lareau, Leif S. Ludwig, Narla Mohandas, David G. Nathan, Vijay G. Sankaran
Blood   ·   31 Aug 2017   ·   doi:10.1182/blood-2017-05-783191
Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry
Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry
C A Lareau, C F DeWeese, I Adrianto, C J Lessard, P M Gaffney, M C Iannuzzi, B A Rybicki, A M Levin, C G Montgomery
Genes & Immunity   ·   01 Mar 2017   ·   doi:10.1038/gene.2017.3

2016

The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine
The Integration of Epistasis Network and Functional Interactions in a GWAS Implicates RXR Pathway Genes in the Immune Response to Smallpox Vaccine
Brett A. McKinney, Caleb Lareau, Ann L. Oberg, Richard B. Kennedy, Inna G. Ovsyannikova, Gregory A. Poland
PLOS ONE   ·   11 Aug 2016   ·   doi:10.1371/journal.pone.0158016
An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data
An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data
C A Lareau, B C White, A L Oberg, R B Kennedy, G A Poland, B A McKinney
Genes & Immunity   ·   07 Apr 2016   ·   doi:10.1038/gene.2016.15

2015

dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data
dcVar: a method for identifying common variants that modulate differential correlation structures in gene expression data
Caleb A. Lareau, Bill C. White, Courtney G. Montgomery, Brett A. McKinney
Frontiers in Genetics   ·   19 Oct 2015   ·   doi:10.3389/fgene.2015.00312
Fine mapping of chromosome 15q25 implicates <scp>ZNF</scp>592 in neurosarcoidosis patients
Fine mapping of chromosome 15q25 implicates ZNF592 in neurosarcoidosis patients
Caleb A. Lareau, Indra Adrianto, Albert M. Levin, Michael C. Iannuzzi, Benjamin A. Rybicki, Courtney G. Montgomery
Annals of Clinical and Translational Neurology   ·   31 Jul 2015   ·   doi:10.1002/acn3.229
Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure
Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure
Caleb A Lareau, Bill C White, Ann L Oberg, Brett A McKinney
BioData Mining   ·   03 Feb 2015   ·   doi:10.1186/s13040-015-0040-x

2014

Network Theory for Data-Driven Epistasis Networks
Network Theory for Data-Driven Epistasis Networks
Caleb A. Lareau, Brett A. McKinney
Methods in Molecular Biology   ·   03 Nov 2014   ·   doi:10.1007/978-1-4939-2155-3_15

2013

Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data
Encore: Genetic Association Interaction Network Centrality Pipeline and Application to SLE Exome Data
Nicholas A. Davis, Caleb A. Lareau, Bill C. White, Ahwan Pandey, Graham Wiley, Courtney G. Montgomery, Patrick M. Gaffney, B. A. McKinney
Genetic Epidemiology   ·   05 Jun 2013   ·   doi:10.1002/gepi.21739