Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Mapping transcriptomic vector fields of single cells

(2022) Xiaojie Qiu et al.   CELL

Systematic reconstruction of cellular trajectories across mouse embryogenesis

(2022) Chengxiang Qiu et al.   NATURE GENETICS

Hotspot identifies informative gene modules across modalities of single-cell genomics

(2021) David DeTomaso et al.   Cell Systems

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

Molecular logic of cellular diversification in the mouse cerebral cortex

(2021) Daniela J. Di Bella et al.   NATURE

Molecular architecture of the developing mouse brain

(2021) Gioele La Manno et al.   NATURE

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

Embryo-scale, single-cell spatial transcriptomics

(2021) Sanjay R. Srivatsan et al.   SCIENCE

Single-cell chromatin state analysis with Signac

(2021) Tim Stuart et al.   NATURE METHODS

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

(2021) Jian Hu et al.   NATURE METHODS

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

(2021) Tommaso Biancalani et al.   NATURE METHODS

Single-cell chromatin accessibility maps reveal regulatory programs driving early mouse organogenesis

(2020) Blanca Pijuan-Sala et al.   NATURE CELL BIOLOGY

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

(2020) Peng He et al.   NATURE

Huntington’s disease alters human neurodevelopment

(2020) Monia Barnat et al.   SCIENCE

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Genetic mapping of cell type specificity for complex traits

(2019) Kyoko Watanabe et al.   Nature Communications

Molecular architecture of lineage allocation and tissue organization in early mouse embryo

(2019) Guangdun Peng et al.   NATURE

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

LMOD3 -Associated Nemaline Myopathy: Prenatal Ultrasonographic, Pathologic, and Molecular Findings

(2018) Michal Berkenstadt et al.   JOURNAL OF ULTRASOUND IN MEDICINE

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Comprehensive and cell-type-based characterization of the dorsal midbrain during development

(2018) Nariko Arimura et al.   GENES TO CELLS

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Development and Functional Diversification of Cortical Interneurons

(2018) Lynette Lim et al.   NEURON

GRHL2 Is Required for Collecting Duct Epithelial Barrier Function and Renal Osmoregulation

(2017) Christian Hinze et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data

(2017) Alicia N Schep et al.   NATURE METHODS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Addressing challenges in the diagnosis and treatment of rare genetic diseases

(2017) Kym M. Boycott et al.   NATURE REVIEWS DRUG DISCOVERY

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

(2015) Caroline F Wright et al.   LANCET

Spatiotemporal expression and transcriptional perturbations by long noncoding RNAs in the mouse brain

(2015) Loyal A. Goff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Wnt5a regulates growth, patterning, and odontoblast differentiation of developing mouse tooth

(2011) Minkui Lin et al.   DEVELOPMENTAL DYNAMICS

Studies with Wnt genes and nonsyndromic cleft lip and palate

(2010) Renato Menezes et al.   BIRTH DEFECTS RESEARCH PART A-CLINICAL AND MOLECULAR TERATOLOGY

Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

(2009) R. Drmanac et al.   SCIENCE