Robust discovery of gene regulatory networks from single-cell gene expression data by Causal Inference Using Composition of Transactions

Dissecting cell identity via network inference and in silico gene perturbation

(2023) Kenji Kamimoto et al.   NATURE

Benchmarking integration of single-cell differential expression

(2023) Hai C. T. Nguyen et al.   Nature Communications

High performance single-cell gene regulatory network inference at scale: The Inferelator 3.0

(2022) Claudia Skok Gibbs et al.   BIOINFORMATICS

Network inference with Granger causality ensembles on single-cell transcriptomics

(2022) Atul Deshpande et al.   Cell Reports

A comprehensive overview and critical evaluation of gene regulatory network inference technologies

(2021) Mengyuan Zhao et al.   BRIEFINGS IN BIOINFORMATICS

Evaluating the Reproducibility of Single-Cell Gene Regulatory Network Inference Algorithms

(2021) Yoonjee Kang et al.   Frontiers in Genetics

DeepDRIM: a deep neural network to reconstruct cell-type-specific gene regulatory network using single-cell RNA-seq data

(2021) Jiaxing Chen et al.   BRIEFINGS IN BIOINFORMATICS

Potentials of single-cell genomics in deciphering cellular phenotypes

(2021) Abbas Shojaee et al.   CURRENT OPINION IN PLANT BIOLOGY

A new concordant partial AUC and partial c statistic for imbalanced data in the evaluation of machine learning algorithms

(2020) André M. Carrington et al.   BMC Medical Informatics and Decision Making

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

(2020) Aditya Pratapa et al.   NATURE METHODS

Inferring Causal Gene Regulatory Networks from Coupled Single-Cell Expression Dynamics Using Scribe

(2020) Xiaojie Qiu et al.   Cell Systems

A comprehensive survey of regulatory network inference methods using single cell RNA sequencing data

(2020) Hung Nguyen et al.   BRIEFINGS IN BIOINFORMATICS

SERGIO: A Single-Cell Expression Simulator Guided by Gene Regulatory Networks

(2020) Payam Dibaeinia et al.   Cell Systems

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Benchmark and integration of resources for the estimation of human transcription factor activities

(2019) Luz Garcia-Alonso et al.   GENOME RESEARCH

Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state

(2019) Jelena Tosic et al.   NATURE CELL BIOLOGY

Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data

(2018) Anna Marco-Ramell et al.   BMC BIOINFORMATICS

SCNS: a graphical tool for reconstructing executable regulatory networks from single-cell genomic data

(2018) Steven Woodhouse et al.   BMC Systems Biology

Integrative analysis of single-cell genomics data by coupled nonnegative matrix factorizations

(2018) Zhana Duren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-cell full-length total RNA sequencing uncovers dynamics of recursive splicing and enhancer RNAs

(2018) Tetsutaro Hayashi et al.   Nature Communications

Efficient differentiation of human pluripotent stem cells into skeletal muscle cells by combining RNA-based MYOD1-expression and POU5F1-silencing

(2018) Tomohiko Akiyama et al.   Scientific Reports

Extensive evaluation of the generalized relevance network approach to inferring gene regulatory networks

(2018) Vladimir Kuzmanovski et al.   GigaScience

GRNBoost2 and Arboreto: efficient and scalable inference of gene regulatory networks

(2018) Thomas Moerman et al.   BIOINFORMATICS

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

(2018) Shinya Oki et al.   EMBO REPORTS

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions

(2017) Heonjong Han et al.   NUCLEIC ACIDS RESEARCH

MYBL2 (B-Myb): a central regulator of cell proliferation, cell survival and differentiation involved in tumorigenesis

(2017) Julian Musa et al.   Cell Death & Disease

Gene Regulatory Network Inference from Single-Cell Data Using Multivariate Information Measures

(2017) Thalia E. Chan et al.   Cell Systems

LEAP: constructing gene co-expression networks for single-cell RNA-sequencing data using pseudotime ordering

(2016) Alicia T. Specht et al.   BIOINFORMATICS

A single-cell resolution map of mouse hematopoietic stem and progenitor cell differentiation

(2016) S. Nestorowa et al.   BLOOD

A Myc-driven self-reinforcing regulatory network maintains mouse embryonic stem cell identity

(2016) Luca Fagnocchi et al.   Nature Communications

Integrating heterogeneous genomic data to accurately identify disease subtypes

(2015) Xianwen Ren et al.   BMC Medical Genomics

RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse

(2015) Zhi-Ping Liu et al.   Database-The Journal of Biological Databases and Curation

The Precision-Recall Plot Is More Informative than the ROC Plot When Evaluating Binary Classifiers on Imbalanced Datasets

(2015) Takaya Saito et al.   PLoS One

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Otx2 and Oct4 Drive Early Enhancer Activation during Embryonic Stem Cell Transition from Naive Pluripotency

(2014) Shen-Hsi Yang et al.   Cell Reports

Incorporating prior knowledge into Gene Network Study

(2013) Zixing Wang et al.   BIOINFORMATICS

Insm1 controls development of pituitary endocrine cells and requires a SNAG domain for function and for recruitment of histone-modifying factors

(2013) J. E. Welcker et al.   DEVELOPMENT

Embryonic fibroblasts represent a connecting link between mesenchymal and embryonic stem cells

(2013) Batul Yusuf et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Dax1 Associates with Esrrb and Regulates Its Function in Embryonic Stem Cells

(2013) K. Uranishi et al.   MOLECULAR AND CELLULAR BIOLOGY

Minireview: The Diverse Roles of Nuclear Receptors in the Regulation of Embryonic Stem Cell Pluripotency

(2013) Ryan T. Wagner et al.   MOLECULAR ENDOCRINOLOGY

ESCAPE: database for integrating high-content published data collected from human and mouse embryonic stem cells

(2013) Huilei Xu et al.   Database-The Journal of Biological Databases and Curation

Two-factor reprogramming of somatic cells to pluripotent stem cells reveals partial functional redundancy of Sox2 and Klf4

(2012) A Nemajerova et al.   CELL DEATH AND DIFFERENTIATION

Esrrb Is a Pivotal Target of the Gsk3/Tcf3 Axis Regulating Embryonic Stem Cell Self-Renewal

(2012) Graziano Martello et al.   Cell Stem Cell

ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

(2010) Alexander Lachmann et al.   BIOINFORMATICS

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

B-Myb is Critical for Proper DNA Duplication During an Unperturbed S Phase in Mouse Embryonic Stem Cells

(2010) Maëlle Lorvellec et al.   STEM CELLS

PRC2 Complexes with JARID2, MTF2, and esPRC2p48 in ES Cells to Modulate ES Cell Pluripotency and Somatic Cell Reprograming

(2010) Zhuo Zhang et al.   STEM CELLS

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

EsrrbActivatesOct4Transcription and Sustains Self-renewal and Pluripotency in Embryonic Stem Cells

(2008) Xiaofei Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Retinoic acid-stimulated sequential phosphorylation, PML recruitment, and SUMOylation of nuclear receptor TR2 to suppress Oct4 expression

(2008) P. Gupta et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

AUC: a misleading measure of the performance of predictive distribution models

(2007) Jorge M. Lobo et al.   GLOBAL ECOLOGY AND BIOGEOGRAPHY