Caleb Lareau: Publications

Caleb Lareau: Publications


C.A. Lareau+, et al. (2023) Latent human herpesvirus 6 is reactivated in CAR T cells. Nature. DOI: 10.1038/s41586-023-06704-2

C.A. Lareau+, et al. (2023) Single-cell multi-omics reveals dynamics of purifying selection of pathogenic mitochondrial DNA across human immune cells. Nature Genetics. DOI: 10.1038/s41588-023-01433-8.

C.A. Lareau+, et al. (2023) Mitochondrial single cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nature Protocols. DOI: 10.1038/s41596-022-00795-3.

A.M Tousley, M.C. Rotiroti, L Labanieh, L.W. Rysavy, W. Kim, C.A. Lareau, et al. (2023). Co-opting T cell proximal signaling molecules enables Boolean logic-gated CAR T cell control. Nature. DOI: 10.1038/s41586-023-05778-2.

C.A. Lareau+. (2023). Resolving subtle cell states in sparse single-cell data. Nature Biotechnology DOI:10.1038/s41587-023-01797-6.

T. Ruckert, C.A. Lareau, et al. (2022) Clonal expansion and epigenetic inheritance of long-lasting NK cell memory. Nature Immunology. DOI: 10.1038/s41590-022-01327-7.

T. Miller, C.A. Lareau, et al. (2022) Mitochondrial variant enrichment from high-throughput single-cell RNA-seq resolves clonal populations. Nature Biotechnology. DOI: 10.1101/2021.03.08.434450v1.

L.S. Ludwig,* C.A. Lareau,* et al. (2022) A Congenital Anemia Dissociates the Pleiotropic Functions of Master Transcription Factor GATA1. Blood. DOI: 10.1182/blood.2021013753.

E.P. Mimitou+, P. Smibert+, and C.A. Lareau+ (2022) Massively parallel profiling of accessible chromatin and proteins with ASAP-seq. Methods in Molecular Biology - Chromatin Accessibility: Methods and Protocols. DOI: 10.1007/978-1-0716-2899-7_13.

L.S. Ludwig and C.A. Lareau+ (2022) Concomitant sequencing of accessible chromatin and mitochondrial genomes in single cells using mtscATAC-seq. Methods in Molecular Biology - Chromatin Accessibility: Methods and Protocols. DOI: 10.1007/978-1-0716-2899-7_14.

L. Penter, E. ten Hacken, J. Southard, C.A. Lareau, et al. (2022) Mitochondrial DNA mutations as natural barcodes for lineage tracing of murine tumor models. Cancer Research. DOI: 10.1158/0008-5472.CAN-22-0275.

C.A. Lareau+, et al.(2021) Charting the tumor antigen maps drawn by single-cell genomics. Cancer Cell. DOI: 10.1016/j.ccel.2021.11.005.

C.A. Lareau+, L.S. Ludwig,*+, et al. (2021) Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling. Nature Biotechnology. DOI: 10.1038/s41587-020-0645-6.

J. Wang*, C.A. Lareau*, et al. (2021) Single-Cell Multiomics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium. Science Immunology. DOI: 10.1126/sciimmunol.abl5053.

E. Mimitou*, C.A. Lareau*, K.Y. Chen* et al. (2021) Scalable, multimodal profiling of chromatin accessibility, RNA, and protein levels in single cells. Nature Biotechnology. DOI: 10.1038/s41587-021-00927-2

N. Schmidt*, C.A. Lareau*, H. Keshishian* et al. (2021) A direct RNA-protein interaction atlas of the SARS-CoV-2 RNA in infected human cells. Nature Microbiology. DOI: 10.1101/2020.07.15.204404.

E. Fiskin, C.A. Lareau, et al. (2021) Single-cell multimodal profiling of proteins and chromatin accessibility using PHAGE-ATAC. Nature Biotechnology. DOI: 10.1038/s41587-021-01065-5.

T. Stuart, A. Srivastava, S. Madad, C.A. Lareau, R. Satija. (2021) Multimodal single-cell chromatin analysis with Signac. Nature Methods. DOI: 10.1101/2020.11.09.373613.

L. Penter, S. Gohil, C.A. Lareau, et al. (2021) Longitudinal single-cell dynamics of chromatin accessibility and mitochondrial mutations in chronic lymphocytic leukemia mirror disease history. Cancer Discovery. DOI: 10.1158/2159-8290.CD-21-0276

C.A. Lareau+, S. Ma, F.M. Duarte, J.D. Buenrostro+. (2020) Inference and effects of barcode multipets in droplet-based single-cell assays. Nature Communications. DOI: 10.1038/s41467-020-14667-5

C.A. Lareau and A.T. Satpathy. (2020) An old BATF’s new T-ricks. Nature Immunology. DOI: 10.1038/s41590-020-0796-0

M. A. Walker,* C.A. Lareau,* L.S. Ludwig,* et al. (2020) Purifying Selection against Pathogenic Mitochondrial DNA in Human T cells. New England Journal of Medicine. DOI: 10.1056/NEJMoa2001265.

D. Vuckovic*, E. Bao*, P. Akbari*, C.A. Lareau*, et al. (2020) The Polygenic and Monogenic Basis of Blood Traits and Diseases. Cell. DOI: 10.1101/2020.02.02.20020065.

J. Grünewald, R. Zhao, C.A. Lareau, et al. (2020) A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nature Biotechnology. DOI: 10.1038/s41587-020-0535-y.

A.L. Basak, M. Munschauer, C.A. Lareau, et al. (2020) Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation. Nature Genetics. DOI: 10.1038/s41588-019-0568-7.

J. Ray, C. de Boer, C. Fulco, C.A. Lareau, et al. (2020) Prioritizing disease and trait causal variants at the TNFAIP3 locus using functional and genomic features. Nature Communications. DOI: 10.1038/s41467-020-15022-4.

C.A. Lareau,* F.M. Duarte,* J.G. Chew,* et al. (2019) Droplet-based combinatorial indexing for massive-scale single-cell chromatin accessibility. Nature Biotechnology. DOI: 10.1038/s41587-019-0147-6.

L.S. Ludwig,*, C.A. Lareau,* J.C. Ulirsch*, et al. (2019) Lineage tracing in humans enabled by mitochondrial mutations and single cell genomics. Cell. DOI: 10.1016/j.cell.2019.01.022.

C.A. Lareau, L.S. Ludwig, V.G. Sankaran. (2019) Longitudinal assessment of clonal mosaicism in human hematopoiesis via mitochondrial mutation tracking. Blood Advances. DOI: 10.1182/bloodadvances.2019001196.

J.C. Ulirsch,* C.A. Lareau,* E.L. Bao,* et al. (2019) Interrogation of human hematopoiesis at single-cell and single-variant resolution. Nature Genetics. DOI: 10.1038/s41588-019-0362-6.

C.A. Lareau, et al. (2019) Preprocessing and computational analysis of single-cell epigenomic datasets. Methods in Molecular Biology - Computational Methods for Single-Cell Data Analysis. DOI: 10.1007/978-1-4939-9057-3.

E.L. Bao,* C.A. Lareau,* et al. (2019) Heritability of fetal hemoglobin, white cell count, and other clinical traits from a sickle cell disease family cohort. American Journal of Hematology. DOI: 10.1002/ajh.25421.

L.S. Ludwig,*, C.A. Lareau,* et al. (2019) Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis. Cell Reports. DOI: 10.1016/j.celrep.2019.05.046

H. Yoshida, C.A. Lareau, R.N. Ramirez, S.A. Rose, et al. (2019) The cis-regulatory atlas of the mouse immune system. Cell. DOI: 10.1016/j.cell.2018.12.036.

J. Grünewald, R. Zhao, S. Garcia,* S. Iyer,* C.A. Lareau,* et al. (2019) Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors. Nature. DOI: 10.1038/s41586-019-1161-z.

H. Chen, C.A. Lareau, T. Andreani, et al. (2019) Assessment of computational methods for the analysis of single-cell ATAC-seq data. Genome Biology. DOI: 10.1186/s13059-019-1854-5.

J. Grünewald, R. Zhao, S. Iyer,* C.A. Lareau,* S. Garcia,* et al. (2019) CRISPR adenine and cytosine base editors with reduced RNA off-target activities. Nature Biotechnology. DOI: 10.1038/s41587-019-0236-6.

S.K. Nandakumar, S.K. McFarland, L.M. Mateyka,* C.A. Lareau,* et al. (2019) Gene-centric functional dissection of human genetic variation uncovers regulators of hematopoiesis. eLife: DOI: 10.7554/eLife.44080.

J. Pan, Z. McKenzie, A. D’Avino, N. Mashtalir, C.A. Lareau, et al. (2019) The ATPase module of mammalian SWI/SNF family complexes mediates subcomplex identity and catalytic activity-independent genomic targeting. Nature Genetics. DOI: 10.1038/s41588-019-0363-5.

J.D. Buenrostro, M.R. Corces, C.A. Lareau, et al. (2018) Integrated Single-Cell Analysis Maps the Continuous Regulatory Landscape of Human Hematopoietic Differentiation. Cell. DOI: 10.1016/j.cell.2018.03.074.

C.A. Lareau,* K. Clement,* J.Y. Hsu,* et al. (2018) Response to “Unexpected mutations after CRISPR-Cas9 editing in vivo.” Nature Methods. DOI: 10.1038/nmeth.4541.

C.A. Lareau and M.J. Aryee. (2018) hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data. Nature Methods. DOI: 10.1038/nmeth.4583.

C.A. Lareau, C.F. DeWeese et al. (2017) Polygenic risk assessment reveals pleiotropy between sarcoidosis and inflammatory disorders in the context of genetic ancestry. Genes and Immunity. DOI: 10.1038/gene.2017.3

C.A. Lareau and M.J. Aryee. (2017) diffloop: a novel computational framework for identifying and functionalizing differential topological features in DNA. Bioinformatics. DOI: 10.1093/bioinformatics/btx623.

J.C. Ulirsch, C.A. Lareau, et al. (2017) Confounding in ex vivo models of Diamond-Blackfan anemia. Blood. DOI:10.1182/blood-2017-05-783191.

C.A. Lareau, B.C. White, et al. (2016) An interaction quantitative trait loci tool implicates epistatic functional variants in an apoptosis pathway in smallpox vaccine eQTL data. Genes and Immunity. DOI: 10.1038/gene.2016.15.

C.A. Lareau, B.C. White, C.G. Montgomery, and B.A. McKinney. (2015) Common Variants Modulate Differential Correlation Structures in Gene Expression Data. Frontiers in Genetics. DOI: 10.3389/fgene.2015.00312.

C.A. Lareau, I.A. Adrianto, et al. (2015) Fine mapping of Chromosome 15q25 in Sarcoidosis Implicates Zinc Finger Protein 592 in Patients with Neurological Involvement. Annals of Translational and Clinical Neurology. DOI: 10.1002/acn3.229.

C.A. Lareau, B.C. White, A.L. Oberg, and B.A. McKinney. (2015) Differential co-expression network centrality and machine learning feature selection for identifying susceptibility hubs in networks with scale-free structure. BioData Mining, DOI: 10.1186/s13040-015-0040-x.

C.A. Lareau and B.A. McKinney. (2014) Network Theory for Data-Driven Epistasis Networks. Methods in Molecular Biology– Epistasis: Methods and Protocols, DOI: 10.1007/978-1-4939-2155-3.

N.A. Davis,* C.A. Lareau,* et al. (2013) Encore: Genetic association interaction network centrality pipeline and application to SLE exome data. Genetic Epidemiology. DOI: 10.1002/gepi.21739