Publications

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

I Setliff et al.

Resolving sub-clonal heterogeneity within cell-line growths by single cell sequencing genomic DNA

Velazquez-Villarreal EI et al. Biorxiv. 2019 Sept 5; preprint.

Stochastic cell-cycle entry and cell-state-dependent fate outputs of injury-reactivated tectal radial glia in zebrafish

Yu S et al. Elife. 2019 Aug 23;8. pii: e48660. doi: 10.7554/eLife.48660. PMID: 31442201.

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

Howick VM et al. Science. 2019 Aug 23;365(6455). pii: eaaw2619. doi: 10.1126/science.aaw2619. PMID: 31439762.

Systematic Immunotherapy Target Discovery Using Genome-Scale In Vivo CRISPR Screens in CD8 T Cells

Dong MB et al. Cell. 2019 Aug 22;178(5):1189-1204.e23. doi: 10.1016/j.cell.2019.07.044. PMID: 31442407.

B1 oligomerization regulates PML nuclear body biogenesis and leukemogenesis

Li Y et al. Nat Commun. 2019 Aug 22;10(1):3789. doi: 10.1038/s41467-019-11746-0. PMID: 31439836.

A single-cell transcriptome atlas of the adult human retina

Lukowski SW et al. EMBO J. 2019 Aug 22:e100811. doi: 10.15252/embj.2018100811. PMID: 31436334.

Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes

Elyahu Y et al. Sci Adv. 2019 Aug 21;5(8):eaaw8330. doi: 10.1126/sciadv.aaw8330. PMID: 31457092.

IL-2 production by self-reactive CD4 thymocytes scales regulatory T cell generation in the thymus

Hemmers S et al. J Exp Med. 2019 Aug 21. pii: jem.20190993. doi: 10.1084/jem.20190993. PMID: 31434685.

Activation of Hedgehog Signaling Promotes Development of Mouse and Human Enteric Neural Crest Cells, Based on single-cell Transcriptome Analyses

Lau ST et al. Gastroenterology. 2019 Aug 20. pii: S0016-5085(19)41233-X. doi: 10.1053/j.gastro.2019.08.019. PMID: 31442438.

Global prediction of chromatin accessibility using small-cell-number and single-cell RNA-seq

Zhou W et al. Nucleic Acids Res. 2019 Aug 20. pii: gkz716. doi: 10.1093/nar/gkz716. PMID: 31428792.

Integrated single-cell transcriptomics and chromatin accessibility analysis reveals novel regulators of mammary epithelial cell identity

Pervolarakis N et al. Biorxiv. 2019 Aug 20; preprint. biorxiv: 10.1101/740746v1.

Glucose-Dependent Insulinotropic Polypeptide Receptor-Expressing Cells in the Hypothalamus Regulate Food Intake

Adriaenssens AE et al. Cell Metab. 2019 Aug 19. pii: S1550-4131(19)30386-9. doi: 10.1016/j.cmet.2019.07.013. PMID: 31447324.

Dissecting the heterogeneity of DENV vaccine elicited cellular immunity using single-cell RNA sequencing and metabolic profiling

Waickman AT et al. Nat Commun. 2019 Aug 14; 10(1):3666. doi: 10.1038/s41467-019-11634-7.

TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation

Campbell SA et al. Cell Rep. 2019 Aug 13;28(7):1830-1844.e6. doi: 10.1016/j.celrep.2019.07.035. PMID: 31412250.

TrxG Complex Catalytic and Non-catalytic Activity Play Distinct Roles in Pancreas Progenitor Specification and Differentiation

Campbell SA et al. Cell Rep. 2019 Aug 13;28(7):1830-1844.e6. doi: 10.1016/j.celrep.2019.07.035. PMID: 31412250.

m⁶A RNA Methylation Maintains Hematopoietic Stem Cell Identity and Symmetric Commitment

Cheng Y et al. Cell Rep. 2019 Aug 13;28(7):1703-1716.e6. doi: 10.1016/j.celrep.2019.07.032. PMID: 31412241.

Single-cell RNA sequencing reveals cell type-specific HPV expression in hyperplastic skin lesions

Devitt K et al. Virology. 2019 Aug 13;537:14-19. doi: 10.1016/j.virol.2019.08.007. PMID: 31425970.

Single-cell landscape in mammary epithelium reveals bipotent-like cells associated with breast cancer risk and outcome

Chen W et al. Commun Biol. 2019 Aug 9;2:306. doi: 10.1038/s42003-019-0554-8. PMID: 31428694.

Massively parallel single-cell B-cell receptor sequencing enables rapid discovery of diverse antigen-reactive antibodies

Goldstein LD et al. Commun Biol. 2019 Aug 9; 2:304. doi: 10.1038/s42003-019-0551-y.

MsPAC: A tool for haplotype-phased structural variant detection

Rodriguez OL et al. Bioinformatics. 2019 Aug 9. pii: btz618. doi: 10.1093/bioinformatics/btz618. PMID: 31397844.

Syndecan-1 promotes lung fibrosis by regulating epithelial reprogramming through extracellular vesicles

Parimon T et al. JCI Insight. 2019 Aug 8;5. pii: 129359. doi: 10.1172/jci.insight.129359. PMID: 31393853.

Opposing Functions of Interferon Coordinate Adaptive and Innate Immune Responses to Cancer Immune Checkpoint Blockade

Benci JL et al. Cell. 2019 Aug 8;178(4):933-948.e14. doi: 10.1016/j.cell.2019.07.019. PMID: 31398344.

Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades

Hiltunen M et al. Curr Biol. 2019 Aug 8. pii: S0960-9822(19)30870-X. doi: 10.1016/j.cub.2019.07.025. PMID: 31402298.

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

Norman TM et al. Science. 2019 Aug 8. pii: eaax4438. doi: 10.1126/science.aax4438. PMID: 31395745.

Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis

Xiong X et al. Mol Cell. 2019 Aug 8;75(3):644-660.e5. doi: 10.1016/j.molcel.2019.07.028. PMID: 31398325.

BORIS promotes chromatin regulatory interactions in treatment-resistant cancer cells

Debruyne DN et al. Nature. 2019 Aug 7; online. doi: 10.1038/s41586-019-1472-0. PMID: 31391581.

Locally renewing resident synovial macrophages provide a protective barrier for the joint

Culemann S et al. Nature. 2019 Aug 7; online. doi: 10.1038/s41586-019-1471-1. PMID: 31391580.

LTMG: a novel statistical modeling of transcriptional expression states in single-cell RNA-Seq data

Wan C et al. Nucleic Acids Res. 2019 Aug 2. pii: gkz655. doi: 10.1093/nar/gkz655. PMID: 31372654.

Massively parallel single-cell chromatin landscapes of human immune cell development and intratumoral T cell exhaustion

Satpathy AT et al. Nat Biotechnol. 2019 Aug 2; online. doi: 10.1038/s41587-019-0206-z.

A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana)

Wang L et al. Gigascience. 2019 Aug 1;8(8). pii: giz098. doi: 10.1093/gigascience/giz098. PMID: 31437279.

Single-Cell Survey of Human Lymphatics Unveils Marked Endothelial Cell Heterogeneity and Mechanisms of Homing for Neutrophils

Takeda A et al. Immunity. 2019 Aug 1. pii: S1074-7613(19)30297-3. doi: 10.1016/j.immuni.2019.06.027. PMID: 31402260.

Modeling Monogenic Diabetes using Human ESCs Reveals Developmental and Metabolic Deficiencies Caused by Mutations in HNF1A

Cardenas-Diaz FL et al. Cell Stem Cell. 2019 Aug 1;25(2):273-289.e5. doi: 10.1016/j.stem.2019.07.007. PMID: 31374199.

Identification of a T follicular helper cell subset that drives anaphylactic IgE

Gowthaman U et al. Science. 2019 Aug 1. pii: eaaw6433. doi: 10.1126/science.aaw6433. PMID: 31371561.

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

Lind AL et al. Nat Ecol Evol. 2019 Aug;3(8):1241-1252. doi: 10.1038/s41559-019-0945-8. PMID: 31358948.

The transcription factor TCF-1 enforces commitment to the innate lymphoid cell lineage

Harly C et al. Nat Immunol. 2019 Jul 29; online. doi: 10.1038/s41590-019-0445-7. PMID: 31358996.

Atheroprotective roles of smooth muscle cell phenotypic modulation and the TCF21 disease gene as revealed by single-cell analysis

Wirka RC et al. Nat Med. 2019 Jul 29; online. doi: 10.1038/s41591-019-0512-5. PMID: 31359001.

ACTINN: Automated Identification of Cell Types in Single Cell RNA Sequencing

Ma F et al. Bioinformatics. 2019 Jul 29. pii: btz592. doi: 10.1093/bioinformatics/btz592. PMID: 31359028.

Clonal replacement of tumor-specific T cells following PD-1 blockade

Yost KE et al. Nat Med. 2019 Jul 29; online. doi: 10.1038/s41591-019-0522-3. PMID: 31359002.

Single-Cell RNA-Sequencing and Metabolomics Analyses Reveal the Contribution of Perivascular Adipose Tissue Stem Cells to Vascular Remodeling

Gu W et al. Arterioscler Thromb Vasc Biol. 2019 Jul 25:ATVBAHA119312732. doi: 10.1161/ATVBAHA.119.312732. PMID: 31340667.

Anti-idiotypic antibodies elicit anti-HIV-1-specific B cell responses

Dosenovic P et al. J Exp Med. 2019 Jul 25. pii: jem.20190446. doi: 10.1084/jem.20190446. PMID: 31345931.

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

Smillie CS et al. Cell. 2019 Jul 25;178(3):714-730.e22. doi: 10.1016/j.cell.2019.06.029. PMID: 31348891.

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects

de Soysa TY et al. Nature. 2019 Jul 24; online. doi: 10.1038/s41586-019-1414-x. PMID: 31341279.

Resolving medulloblastoma cellular architecture by single-cell genomics

Hovestadt V et al. Nature. 2019 Jul 24; online. doi: 10.1038/s41586-019-1434-6. PMID: 31341285.

DMSO cryopreservation is the method of choice to preserve cells for droplet-based single-cell RNA sequencing

Wohnhaas CT et al. Sci Rep. 2019 Jul 23;9(1):10699. doi: 10.1038/s41598-019-46932-z. PMID: 31337793.

Noncoding CGG repeat expansions in neuronal intranuclear inclusion disease, oculopharyngodistal myopathy and an overlapping disease

Ishiura H et al. Nat Genet. 2019 Jul 22; online. doi: 10.1038/s41588-019-0458-z. PMID: 31332380.

Predicting bacterial infection outcomes using single cell RNA-sequencing analysis of human immune cells

Bossel Ben-Moshe N et al. Nat Commun. 2019 Jul 22;10(1):3266. doi: 10.1038/s41467-019-11257-y. PMID: 31332193.

Single-cell reconstruction of follicular remodeling in the human adult ovary

Fan X et al. Nat Commun. 2019 Jul 18;10(1):3164. doi: 10.1038/s41467-019-11036-9. PMID: 31320652.

Neuronal vulnerability and multilineage diversity in multiple sclerosis

Schirmer L et al. Nature. 2019 Jul 17; online. doi: 10.1038/s41586-019-1404-z. PMID: 31316211.

Single-cell RNA sequencing profiling of the effects of aging on alveolar stem cells

Lv T et al. Sci China Life Sci. 2019 Jul 17; online. doi: 10.1007/s11427-019-9583-9. PMID: 31321669.

Sensitization to immune checkpoint blockade through activation of a STAT1/NK axis in the tumor microenvironment

Zemek RM et al. Sci Transl Med. 2019 Jul 17;11(501). pii: eaav7816. doi: 10.1126/scitranslmed.aav7816. PMID: 31316010.

Neuropeptide CGRP Limits Group 2 Innate Lymphoid Cell Responses and Constrains Type 2 Inflammation

Nagashima H et al. Immunity. 2019 Jul 16. pii: S1074-7613(19)30279-1. doi: 10.1016/j.immuni.2019.06.009. PMID: 31353223.

Conversion of Astrocytes and Fibroblasts into Functional Noradrenergic Neurons

Li S et al. Cell Rep. 2019 Jul 16;28(3):682-697.e7. doi: 10.1016/j.celrep.2019.06.042. PMID: 31315047.

Joint analysis of heterogeneous single-cell RNA-seq dataset collections

Barkas N et al. Nat Methods. 2019 Jul 15; online. doi: 10.1038/s41592-019-0466-z. PMID: 31308548.

Treg Cells Promote the SREBP1-Dependent Metabolic Fitness of Tumor-Promoting Macrophages via Repression of CD8+ T Cell-Derived Interferon-γ

Liu C et al. Immunity. 2019 Jul 13. pii: S1074-7613(19)30287-0. doi: 10.1016/j.immuni.2019.06.017. PMID: 31350177.

Transcriptomic Profiling of the Developing Cardiac Conduction System at Single-Cell Resolution

Goodyer WR et al. Circ Res. 2019 Jul 9; online. doi: 10.1161/CIRCRESAHA.118.314578. PMID: 31284824.

Metabolic Changes in Lymphangioleiomyomatosis Patients Treated with Sirolimus and Hydroxychloroquine

Tang Y et al. Chest. 2019 Jul 9. pii: S0012-3692(19)31310-8. doi: 10.1016/j.chest.2019.05.038. PMID: 31299246.

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma

Neftel C et al. Cell. 2019 Jul 9. pii: S0092-8674(19)30687-7. doi: 10.1016/j.cell.2019.06.024. PMID: 31327527.

A single cell framework for multi-omic analysis of disease identifies malignant 2 regulatory signatures in mixed phenotype acute leukemia

Granja JM et al. Biorxiv. 2019 Jul 9; preprint. biorxiv: 10.1101/696328v1.

MCPyV Large T antigen induced atonal homolog 1 (ATOH1) is a lineage-dependency oncogene in Merkel cell carcinoma

Fan K et al. J Invest Dermatol. 2019 Jul 5. pii: S0022-202X(19)31853-6. doi: 10.1016/j.jid.2019.06.135. PMID: 31283928.

Genome assembly provides insights into the genome evolution and flowering regulation of orchardgrass

Huang L et al. Plant Biotechnol J. 2019 Jul 5; online. doi: 10.1111/pbi.13205. PMID: 31276273.

A draft genome for Spatholobus suberectus

Qin S et al. Sci Data. 2019 Jul 4;6(1):113. doi: 10.1038/s41597-019-0110-x. PMID: 31273216.

Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming

Stone NR et al. Cell Stem Cell. 2019 Jul 3;25(1):87-102.e9. doi: 10.1016/j.stem.2019.06.012. PMID: 31271750.

Somatic mutations and cell identity linked by Genotyping of Transcriptomes

Nam AS et al. Nature. 2019 Jul 3; online. doi: 10.1038/s41586-019-1367-0. PMID: 31270458.

Single-cell analysis reveals T cell infiltration in old neurogenic niches

Dulken BW et al. Nature. 2019 Jul 3; online. doi: 10.1038/s41586-019-1362-5. PMID: 31270459.

Generation of Human PSC-Derived Kidney Organoids with Patterned Nephron Segments and a De Novo Vascular Network

Low JH et al. Cell Stem Cell. 2019 Jul 2. pii: S1934-5909(19)30273-5. doi: 10.1016/j.stem.2019.06.009. PMID: 31303547.

R-spondin-3 induces secretory, antimicrobial Lgr5+ cells in the stomach

Sigal M et al. Nat Cell Biol. 2019 Jul;21(7):812-823. doi: 10.1038/s41556-019-0339-9. PMID: 31235935.

Long-read sequencing unveils IGH-DUX4 translocation into the silenced IGH allele in B-cell acute lymphoblastic leukemia

Tian L et al. Nat Commun. 2019 Jun 26;10(1):2789. doi: 10.1038/s41467-019-10637-8. PMID: 31243274.

Developmental kinetics and transcriptome dynamics of stem cell specification in the spermatogenic lineage

Law NC et al. Nat Commun. 2019 Jun 26;10(1):2787. doi: 10.1038/s41467-019-10596-0. PMID: 31243281.

Lipid-Associated Macrophages Control Metabolic Homeostasis in a Trem2-Dependent Manner

Jaitin DA et al. Cell. 2019 Jun 26. pii: S0092-8674(19)30625-7. doi: 10.1016/j.cell.2019.05.054. PMID: 31257031.

T cell receptor gene therapy targeting WT1 prevents acute myeloid leukemia relapse post-transplant

Chapuis AG et al. Nat Med. 2019 Jun 24; online. doi: 10.1038/s41591-019-0472-9. PMID: 31235963.

Loss of the interleukin-6 receptor causes immunodeficiency, atopy, and abnormal inflammatory responses

Spencer S et al. J Exp Med. 2019 Jun 24. pii: jem.20190344. doi: 10.1084/jem.20190344. PMID: 31235509.

Immature excitatory neurons develop during adolescence in the human amygdala

Sorrells SF et al. Nat Commun. 2019 Jun 21;10(1):2748. doi: 10.1038/s41467-019-10765-1. PMID: 31227709.

Enhancement of LIN28B-induced hematopoietic reprogramming by IGF2BP3

Wang S et al. Genes Dev. 2019 Jun 20; online. doi: 10.1101/gad.325100.119. PMID: 31221665.

Targeting enhancer switching overcomes non-genetic drug resistance in acute myeloid leukaemia

Bell CC et al. Nat Commun. 2019 Jun 20;10(1):2723. doi: 10.1038/s41467-019-10652-9. PMID: 31222014.

Identification of dicarbonyl and L-xylulose reductase as a therapeutic target in human chronic kidney disease

Perco P et al. JCI Insight. 2019 Jun 20;4(12). pii: 128120. doi: 10.1172/jci.insight.128120. PMID: 31217356.

MRLR: unraveling high-resolution meiotic recombination by linked reads

Xu P et al. Bioinformatics. 2019 Jun 19. pii: btz503. doi: 10.1093/bioinformatics/btz503. PMID: 31214684.

Single-Cell RNA-Seq Analysis of Retinal Development Identifies NFI Factors as Regulating Mitotic Exit and Late-Born Cell Specification

Clark BS et al. Neuron. 2019 Jun 19;102(6):1111-1126.e5. doi: 10.1016/j.neuron.2019.04.010. PMID: 31128945.

Aquatic adaptation and depleted diversity: a deep dive into the genomes of the sea otter and giant otter

Beichman AC et al. Mol Biol Evol. 2019 Jun 18. pii: msz101. doi: 10.1093/molbev/msz101. PMID: 31212313.

Fcmr regulates mononuclear phagocyte control of anti-tumor immunity

Kubli SP et al. Nat Commun. 2019 Jun 18;10(1):2678. doi: 10.1038/s41467-019-10619-w. PMID: 31213601.

Tissue-Resident Group 2 Innate Lymphoid Cells Differentiate by Layered Ontogeny and In Situ Perinatal Priming

Schneider C et al. Immunity. 2019 Jun 18;50(6):1425-1438.e5. doi: 10.1016/j.immuni.2019.04.019. PMID: 31128962.

The immune cell landscape in kidneys of patients with lupus nephritis

Arazi A et al. Nat Immunol. 2019 Jun 17; online. doi: 10.1038/s41590-019-0398-x. PMID: 31209404.

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

McGinnis CS et al. Nat Methods. 2019 Jun 17; online. doi: 10.1038/s41592-019-0433-8. PMID: 31209384.

Single-cell RNA-seq reveals TOX as a key regulator of CD8+ T cell persistence in chronic infection

Yao C et al. Nat Immunol. 2019 Jun 17; online. doi: 10.1038/s41590-019-0403-4. PMID: 31209400.

Subsets of ILC3-ILC1-like cells generate a diversity spectrum of innate lymphoid cells in human mucosal tissues

Cella M et al. Nat Immunol. 2019 Jun 17; online. doi: 10.1038/s41590-019-0425-y. PMID: 31209406.

A cellular census of human lungs identifies novel cell states in health and in asthma

Vieira Braga FA et al. Nat Med. 2019 Jun 17; online. doi: 10.1038/s41591-019-0468-5. PMID: 31209336.

Agouti-Related Protein 2 Is a New Player in the Teleost Stress Response System

Shainer I et al. Curr Biol. 2019 Jun 17;29(12):2009-2019.e7. doi: 10.1016/j.cub.2019.05.021. PMID: 31178320.

Single-cell RNA-Seq analysis identifies a putative epithelial stem cell population in human primary prostate cells in monolayer and organoid culture conditions

McCray T et al. Am J Clin Exp Urol. 2019 Jun 15;7(3):123-138. PMID: 31317052.

A cellular atlas of Pitx2-dependent cardiac development

Hill MC et al. Development. 2019 Jun 14;146(12). pii: dev180398. doi: 10.1242/dev.180398. PMID: 31201182.

SSCC: A Novel Computational Framework for Rapid and Accurate Clustering Large-scale Single Cell RNA-seq Data

Ren X et al. Genomics Proteomics Bioinformatics. 2019 Jun 13. pii: S1672-0229(18)30108-6. doi: 10.1016/j.gpb.2018.10.003. PMID: 31202000.

Simulating multiple faceted variability in single cell RNA sequencing

Zhang X et al. Nat Commun. 2019 Jun 13;10(1):2611. doi: 10.1038/s41467-019-10500-w. PMID: 31197158.

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

Welch JD et al. Cell. 2019 Jun 13;177(7):1873-1887.e17. doi: 10.1016/j.cell.2019.05.006. PMID: 31178122.

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia

Baryawno N et al. Cell. 2019 Jun 13;177(7):1915-1932.e16. doi: 10.1016/j.cell.2019.04.040. PMID: 31130381.

Migrant memory B cells secrete luminal antibody in the vagina

Oh JE et al. Nature. 2019 Jun 12; online. doi: 10.1038/s41586-019-1285-1. PMID: 31189952.

Single-cell RNA sequencing unveils the shared and the distinct cytotoxic hallmarks of human TCRVδ1 and TCRVδ2 γδ T lymphocytes

Pizzolato G et al. Proc Natl Acad Sci U S A. 2019 Jun 11;116(24):11906-11915. doi: 10.1073/pnas.1818488116. PMID: 31118283.

Comprehensive genomic characterization of breast tumors with BRCA1 and BRCA2 mutations

Lal A et al. BMC Med Genomics. 2019 Jun 10;12(1):84. doi: 10.1186/s12920-019-0545-0. PMID: 31182087.

Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue

Kono N et al. Sci Rep. 2019 Jun 10;9(1):8380. doi: 10.1038/s41598-019-44775-2. PMID: 31182776.

Regulatory T-cells regulate neonatal heart regeneration by potentiating cardiomyocyte proliferation in a paracrine manner

Li J et al. Theranostics. 2019 Jun 9;9(15):4324-4341. doi: 10.7150/thno.32734. PMID: 31285764.

Reactive microglia and IL1β/IL-1R1-signaling mediate neuroprotection in excitotoxin-damaged mouse retina

Todd L et al. J Neuroinflammation. 2019 Jun 6;16(1):118. doi: 10.1186/s12974-019-1505-5. PMID: 31170999.

Individual brain organoids reproducibly form cell diversity of the human cerebral cortex

Velasco S et al. Nature. 2019 Jun 5; online. doi: 10.1038/s41586-019-1289-x. PMID: 31168097.

Single-cell imaging and transcriptomic analyses of endogenous cardiomyocyte dedifferentiation and cycling

Zhang Y et al. Cell Discov. 2019 Jun 4;5:30. doi: 10.1038/s41421-019-0095-9. PMID: 31231540.

Robust hematopoietic specification requires the ubiquitous Sp1 and Sp3 transcription factors

Gilmour J et al. Epigenetics Chromatin. 2019 Jun 4;12(1):33. doi: 10.1186/s13072-019-0282-9. PMID: 31164147.

De Novo Sequencing, Assembly, and Annotation of Four Threespine Stickleback Genomes Based on Microfluidic Partitioned DNA Libraries

Berner D et al. Genes (Basel). 2019 Jun 3;10(6). pii: E426. doi: 10.3390/genes10060426. PMID: 31163709.

A chromosome-scale genome assembly of cucumber (Cucumis sativus L.)

Li Q et al. Gigascience. 2019 Jun 1;8(6). pii: giz072. doi: 10.1093/gigascience/giz072. PMID: 31216035.

Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement

Yang N et al. Nat Genet. 2019 Jun;51(6):1052-1059. doi: 10.1038/s41588-019-0427-6. PMID: 31152161.

High-throughput single-cell ChIP-seq identifies heterogeneity of chromatin states in breast cancer

Grosselin K et al. Nat Genet. 2019 Jun;51(6):1060-1066. doi: 10.1038/s41588-019-0424-9. PMID: 31152164.

Distinct fibroblast subsets drive inflammation and damage in arthritis

Croft AP et al. Nature. 2019 Jun;570(7760):246-251. doi: 10.1038/s41586-019-1263-7. PMID: 31142839.

Single-Cell Profiles and Clinically Useful Properties of Human Mesenchymal Stem Cells of Adipose and Bone Marrow Origin

Zhou W et al. Am J Sports Med. 2019 Jun;47(7):1722-1733. doi: 10.1177/0363546519848678. PMID: 31100005.

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

Hie B et al. Nat Biotechnol. 2019 Jun;37(6):685-691. doi: 10.1038/s41587-019-0113-3. PMID: 31061482.

A single-cell atlas of mouse brain macrophages reveals unique transcriptional identities shaped by ontogeny and tissue environment.

Van Hove H et al. Nat Neurosci. 2019 Jun;22(6):1021-1035. doi: 10.1038/s41593-019-0393-4. PMID: 31061494.

Single-cell transcriptomic analysis of Alzheimer’s disease

Mathys H et al. Nature. 2019 Jun;570(7761):332-337.. doi: 10.1038/s41586-019-1195-2. PMID: 31042697.

Single-cell transcriptomes of murine bone marrow stromal cells reveal niche-associated heterogeneity

Addo RK et al. Eur J Immunol. 2019 May 31; online. doi: 10.1002/eji.201848053. PMID: 31149730.

Single Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations

Kalluri AS et al. Circulation. 2019 May 31; online. doi: 10.1161/CIRCULATIONAHA.118.038362. PMID: 31146585.

Defective Tmprss3-Associated Hair Cell Degeneration in Inner Ear Organoids

Tang PC et al. Stem Cell Reports. 2019 May 29. pii: S2213-6711(19)30181-X. doi: 10.1016/j.stemcr.2019.05.014. PMID: 31204303.

Transient multifocal genomic crisis creating chromothriptic and non-chromothriptic rearrangements in prezygotic testicular germ cells

Hattori A et al. BMC Med Genomics. 2019 May 28;12(1):77. doi: 10.1186/s12920-019-0526-3. PMID: 31138192.

Rare variant phasing using paired tumor:normal sequence data

Buckley AR et al. BMC Bioinformatics. 2019 May 27;20(1):265. doi: 10.1186/s12859-019-2753-1. PMID: 31132991.

Clonal replacement of tumor-specific T cells following PD-1 blockade

Yost et al. Biorxiv. 2019 May 24; pre-print. biorxiv: 648899v1.

An Atlas of Vagal Sensory Neurons and Their Molecular Specialization

Kupari J et al. Cell Rep. 2019 May 21;27(8):2508-2523.e4. doi: 10.1016/j.celrep.2019.04.096. PMID: 31116992.

Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight

Ebbert MTW et al. Genome Biol. 2019 May 20;20(1):97. doi: 10.1186/s13059-019-1707-2. PMID: 31104630.

Single-cell genomics identifies cell type-specific molecular changes in autism

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From Pine Cones to Read Clouds: Rescaffolding the Megagenome of Sugar Pine (Pinus lambertiana)

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