Dissecting cell identity via network inference and in silico gene perturbation

Current insights into the role of Fli-1 in hematopoiesis and malignant transformation

(2022) Yaacov Ben-David et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Inferring and perturbing cell fate regulomes in human brain organoids

(2022) Jonas Simon Fleck et al.   NATURE

Gene regulatory network reconfiguration in direct lineage reprogramming

(2022) Kenji Kamimoto et al.   Stem Cell Reports

Localized EMT reprograms glial progenitors to promote spinal cord repair

(2021) Dana Klatt Shaw et al.   DEVELOPMENTAL CELL

The coding and long noncoding single-cell atlas of the developing human fetal striatum

(2021) Vittoria Dickinson Bocchi et al.   SCIENCE

Machine learning for perturbational single-cell omics

(2021) Yuge Ji et al.   Cell Systems

Benchmarking algorithms for gene regulatory network inference from single-cell transcriptomic data

(2020) Aditya Pratapa et al.   NATURE METHODS

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

An ATAC-seq atlas of chromatin accessibility in mouse tissues

(2019) Chuanyu Liu et al.   Scientific Data

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

scGen predicts single-cell perturbation responses

(2019) Mohammad Lotfollahi et al.   NATURE METHODS

Highly Efficient CRISPR-Cas9-Based Methods for Generating Deletion Mutations and F0 Embryos that Lack Gene Function in Zebrafish

(2019) Kazuyuki Hoshijima et al.   DEVELOPMENTAL CELL

A single-cell hematopoietic landscape resolves 8 lineage trajectories and defects in Kit mutant mice

(2018) Joakim S. Dahlin et al.   BLOOD

Mapping gene regulatory networks from single-cell omics data

(2018) Mark W E J Fiers et al.   Briefings in Functional Genomics

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

(2018) Jason D. Buenrostro et al.   CELL

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

(2018) Hannah A. Pliner et al.   MOLECULAR CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

ChIP‐Atlas: a data‐mining suite powered by full integration of public ChIP‐seq data

(2018) Shinya Oki et al.   EMBO REPORTS

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Nonlinear Network Reconstruction from Gene Expression Data Using Marginal Dependencies Measured by DCOL

(2016) Haodong Liu et al.   PLoS One

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Easy quantitative assessment of genome editing by sequence trace decomposition

(2014) Eva K. Brinkman et al.   NUCLEIC ACIDS RESEARCH

ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software

(2014) Mathieu Jacomy et al.   PLoS One

Elucidation of the role of LMO2 in human erythroid cells

(2013) Ai Inoue et al.   EXPERIMENTAL HEMATOLOGY

Structural and dynamical analysis of biological networks

(2012) Cecilia Klein et al.   Briefings in Functional Genomics

Spatiotemporal resolution of the Ntla transcriptome in axial mesoderm development

(2012) Ilya A Shestopalov et al.   Nature Chemical Biology

A Large Gene Network in Immature Erythroid Cells Is Controlled by the Myeloid and B Cell Transcriptional Regulator PU.1

(2011) Sandeep N. Wontakal et al.   PLoS Genetics

FoxA transcription factors are essential for the development of dorsal axial structures

(2010) Sophie Dal-Pra et al.   DEVELOPMENTAL BIOLOGY

The role of PU.1 and GATA-1 transcription factors during normal and leukemogenic hematopoiesis

(2010) P Burda et al.   LEUKEMIA

Gfi1 and Gfi1b: key regulators of hematopoiesis

(2010) L T van der Meer et al.   LEUKEMIA

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

Long-range gene regulation links genomic type 2 diabetes and obesity risk regions to HHEX, SOX4, and IRX3

(2009) A. Ragvin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hematopoiesis: An Evolving Paradigm for Stem Cell Biology

(2008) Stuart H. Orkin et al.   CELL

High-resolution in situ hybridization to whole-mount zebrafish embryos

(2007) Christine Thisse et al.   Nature Protocols