List of works - Zizhen Yao

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

scientific article

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development.

scientific article published on 27 October 2016

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

scientific article published on 01 July 2018

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes

scientific article

A coupled autoencoder approach for multi-modal analysis of cell types ⬇️

scientific article published in January 2019

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

scientific article

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

scientific article published on 31 March 2020

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

scientific article published on 17 May 2021

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

scientific article

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

scientific article

Alternating sources of perisomatic inhibition during behavior

scientific article published on 01 February 2021

Antagonistic regulation of p57kip2 by Hes/Hey downstream of Notch signaling and muscle regulatory factors regulates skeletal muscle growth arrest

scientific article published in July 2014

Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

scientific article published in 2022

Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.

scientific article

CMfinder--a covariance model based RNA motif finding algorithm

scientific article

Canonical genetic signatures of the adult human brain

scientific article

Comparative cellular analysis of motor cortex in human, marmoset and mouse

scientific article published on 06 October 2021

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

scientific article

Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

scientific article published on 8 April 2013

Comparison of genome-wide binding of MyoD in normal human myogenic cells and rhabdomyosarcomas identifies regional and local suppression of promyogenic transcription factors.

scientific article published on 10 December 2012

Conserved cell types with divergent features in human versus mouse cortex

scientific article published in 2019 in Nature

Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage

scientific article published on 19 March 2015

DICER/AGO-dependent epigenetic silencing of D4Z4 repeats enhanced by exogenous siRNA suggests mechanisms and therapies for FSHD.

scientific article published on 3 June 2015

DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.

scientific article

DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis

scientific article

DUX4 promotes transcription of FRG2 by directly activating its promoter in facioscapulohumeral muscular dystrophy

scientific article

DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle

scientific article

De novo prediction of structured RNAs from genomic sequences

scientific article

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

scientific article

Discriminative motif analysis of high-throughput dataset.

scientific article published on 25 October 2013

Distinct Activities of Myf5 and MyoD Indicate Separate Roles in Skeletal Muscle Lineage Specification and Differentiation

scientific article published on February 2016

Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis

scientific article published on 01 May 2020

Distinct descending motor cortex pathways and their roles in movement

scientific article published in Nature

Enhancer viruses for combinatorial cell-subclass-specific labeling

scientific article published on 30 March 2021

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

scientific article published in April 2020

Fixed single-cell transcriptomic characterization of human radial glial diversity.

scientific article published on 26 October 2015

Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer

scientific article published on 09 October 2013

Genetic and epigenetic determinants of neurogenesis and myogenesis.

scientific article

Genome engineering of isogenic human ES cells to model autism disorders

scientific article published on 11 March 2015

Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas

scientific article

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

scientific article published on April 2010

Genome-wide binding of the basic helix-loop-helix myogenic inhibitor musculin has substantial overlap with MyoD: implications for buffering activity.

scientific article published on November 2013

Human neocortical expansion involves glutamatergic neuron diversification

scientific article

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

scientific article

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells ⬇️

scientific article published on 01 November 2020

Intrinsic epigenetic regulation of the D4Z4 macrosatellite repeat in a transgenic mouse model for FSHD

scientific article

Isoform cell-type specificity in the mouse primary motor cortex

scientific article published on 06 October 2021

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex.

scientific article published on 23 January 2017

MYOD1 functions as a clock amplifier as well as a critical co-factor for downstream circadian gene expression in muscle

article

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

scientific article published in December 2023

Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

scientific article published on 12 October 2023

Morphological diversity of single neurons in molecularly defined cell types

scientific article

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

scientific article published on 01 October 2019

MyoD directly up-regulates premyogenic mesoderm factors during induction of skeletal myogenesis in stem cells.

scientific article

Myod and H19-Igf2 locus interactions are required for diaphragm formation in the mouse.

scientific article

Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish

scientific article

Phenotypic variation of transcriptomic cell types in mouse motor cortex

scientific article published on 12 November 2020

Polycomb-mediated repression during terminal differentiation: what don't you want to be when you grow up?

scientific article published in May 2011

SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes

scientific article published on 6 June 2017

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.

scientific article published on March 2017

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.

scientific article published in November 2017

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

scientific article

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks

scientific article published on 11 November 2019

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

scientific article published in PLoS ONE

Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures

scientific article published on 01 August 2018

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

scientific article

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches

scientific article

The identification and functional annotation of RNA structures conserved in vertebrates.

scientific article published on 9 May 2017

Tissue-specific splicing of a ubiquitously expressed transcription factor is essential for muscle differentiation

scientific article published on 30 May 2013

Transcriptomic evidence for dense peptidergic neuromodulation networks in mouse cortex

miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells

scientific article published on 29 April 2012

List of works by Zizhen Yao

A Marfan syndrome gene expression phenotype in cultured skin fibroblasts

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development.

A Suite of Transgenic Driver and Reporter Mouse Lines with Enhanced Brain-Cell-Type Targeting and Functionality

A computational pipeline for high- throughput discovery of cis-regulatory noncoding RNA in prokaryotes

A coupled autoencoder approach for multi-modal analysis of cell types ⬇️

A multimodal cell census and atlas of the mammalian primary motor cortex

A regression-based K nearest neighbor algorithm for gene function prediction from heterogeneous data.

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

Alternating sources of perisomatic inhibition during behavior

Antagonistic regulation of p57kip2 by Hes/Hey downstream of Notch signaling and muscle regulatory factors regulates skeletal muscle growth arrest

Author Correction: Human neocortical expansion involves glutamatergic neuron diversification

Bone morphogenetic protein 4: potential regulator of shear stress-induced graft neointimal atrophy.

CMfinder--a covariance model based RNA motif finding algorithm

Canonical genetic signatures of the adult human brain

Comparative cellular analysis of motor cortex in human, marmoset and mouse

Comparative genomics beyond sequence-based alignments: RNA structures in the ENCODE regions

Comparison of endogenous and overexpressed MyoD shows enhanced binding of physiologically bound sites.

Comparison of genome-wide binding of MyoD in normal human myogenic cells and rhabdomyosarcomas identifies regional and local suppression of promyogenic transcription factors.

Conserved cell types with divergent features in human versus mouse cortex

Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage

DICER/AGO-dependent epigenetic silencing of D4Z4 repeats enhanced by exogenous siRNA suggests mechanisms and therapies for FSHD.

DUX4 activates germline genes, retroelements, and immune mediators: implications for facioscapulohumeral dystrophy.

DUX4 binding to retroelements creates promoters that are active in FSHD muscle and testis

DUX4 promotes transcription of FRG2 by directly activating its promoter in facioscapulohumeral muscular dystrophy

DUX4-induced gene expression is the major molecular signature in FSHD skeletal muscle

De novo prediction of structured RNAs from genomic sequences

Differential genomic targeting of the transcription factor TAL1 in alternate haematopoietic lineages

Discriminative motif analysis of high-throughput dataset.

Distinct Activities of Myf5 and MyoD Indicate Separate Roles in Skeletal Muscle Lineage Specification and Differentiation

Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis

Distinct descending motor cortex pathways and their roles in movement

Enhancer viruses for combinatorial cell-subclass-specific labeling

Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse

Fixed single-cell transcriptomic characterization of human radial glial diversity.

Fundamental differences in promoter CpG island DNA hypermethylation between human cancer and genetically engineered mouse models of cancer

Genetic and epigenetic determinants of neurogenesis and myogenesis.

Genome engineering of isogenic human ES cells to model autism disorders

Genome-wide DNA methylation studies suggest distinct DNA methylation patterns in pediatric embryonal and alveolar rhabdomyosarcomas

Genome-wide MyoD binding in skeletal muscle cells: a potential for broad cellular reprogramming.

Genome-wide binding of the basic helix-loop-helix myogenic inhibitor musculin has substantial overlap with MyoD: implications for buffering activity.

Human neocortical expansion involves glutamatergic neuron diversification

Identification of 22 candidate structured RNAs in bacteria using the CMfinder comparative genomics pipeline

Integrated Morphoelectric and Transcriptomic Classification of Cortical GABAergic Cells ⬇️

Intrinsic epigenetic regulation of the D4Z4 macrosatellite repeat in a transgenic mouse model for FSHD

Isoform cell-type specificity in the mouse primary motor cortex

Layer-specific chromatin accessibility landscapes reveal regulatory networks in adult mouse visual cortex.

MYOD1 functions as a clock amplifier as well as a critical co-factor for downstream circadian gene expression in muscle

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

Morphoelectric and transcriptomic divergence of the layer 1 interneuron repertoire in human versus mouse neocortex

Morphological diversity of single neurons in molecularly defined cell types

Multimodal Analysis of Cell Types in a Hypothalamic Node Controlling Social Behavior

MyoD directly up-regulates premyogenic mesoderm factors during induction of skeletal myogenesis in stem cells.

Myod and H19-Igf2 locus interactions are required for diaphragm formation in the mouse.

Pbx and Prdm1a transcription factors differentially regulate subsets of the fast skeletal muscle program in zebrafish

Phenotypic variation of transcriptomic cell types in mouse motor cortex

Polycomb-mediated repression during terminal differentiation: what don't you want to be when you grow up?

SMCHD1 regulates a limited set of gene clusters on autosomal chromosomes

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.

Single-Cell Profiling of an In Vitro Model of Human Interneuron Development Reveals Temporal Dynamics of Cell Type Production and Maturation.

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding.

Single-cell transcriptomic evidence for dense intracortical neuropeptide networks

Single-nucleus and single-cell transcriptomes compared in matched cortical cell types

Small noncoding RNAs in FSHD2 muscle cells reveal both DUX4- and SMCHD1-specific signatures

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

The aptamer core of SAM-IV riboswitches mimics the ligand-binding site of SAM-I riboswitches

The identification and functional annotation of RNA structures conserved in vertebrates.

Tissue-specific splicing of a ubiquitously expressed transcription factor is essential for muscle differentiation

Transcriptomic evidence for dense peptidergic neuromodulation networks in mouse cortex

miR-206 integrates multiple components of differentiation pathways to control the transition from growth to differentiation in rhabdomyosarcoma cells