Yi Liu

发表

FRQ-CK1 interaction determines the period of circadian rhythms in Neurospora

Christian I. Hong, Sookkyung Lim, Angélica Caicedo-Casso, 2019, Nature Communications.

Nonoptimal codon usage influences protein structure in intrinsically disordered regions

Guanghua Xiao, Tao Wang, Mian Zhou, 2015, Molecular microbiology.

Methods to study molecular mechanisms of the Neurospora circadian clock.

Yi Liu, Mian Zhou, J. Cha, 2015, Methods in enzymology.

The Neurospora crassa circadian clock.

Yi Liu, Christian Heintzen, Yi Liu, 2007, Advances in genetics.

The COP9 signalosome regulates the Neurospora circadian clock by controlling the stability of the SCFFWD-1 complex.

Qun He, Yi Liu, P. Cheng, 2005, Genes & development.

Light-independent Phosphorylation of WHITE COLLAR-1 Regulates Its Function in the Neurospora Circadian Negative Feedback Loop*

H. Shu, She Chen, Yi Liu, 2005, Journal of Biological Chemistry.

Distinct roles for PP1 and PP2A in the Neurospora circadian clock.

Yuhong Yang, O. Yarden, Qun He, 2004, Genes & development.

Molecular Mechanisms of Entrainment in the Neurospora Circadian Clock

Yi Liu, Yi Liu, 2003, Journal of biological rhythms.

Functional conservation of light, oxygen, or voltage domains in light sensing

Yi Liu, Yuhong Yang, Yi Liu, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Phosphorylation of FREQUENCY Protein by Casein Kinase II Is Necessary for the Function of the Neurospora Circadian Clock

Yuhong Yang, Yi Liu, P. Cheng, 2003, Molecular and Cellular Biology.

and Yi Clock Circadian Neurospora Function of the Casein Kinase II Is Necessary for the Phosphorylation of FREQUENCY Protein

Yuhong Yang, Yi Liu, P. Cheng, 2003 .

WHITE COLLAR-1, a Multifunctional NeurosporaProtein Involved in the Circadian Feedback Loops, Light Sensing, and Transcription Repression of wc-2*

Yuhong Yang, Yi Liu, P. Cheng, 2003, The Journal of Biological Chemistry.

Regulation of the Neurospora circadian clock by casein kinase II.

Yuhong Yang, Yi Liu, P. Cheng, 2002, Genes & development.

PAS Domain-Mediated WC-1/WC-2 Interaction Is Essential for Maintaining the Steady-State Level of WC-1 and the Function of Both Proteins in Circadian Clock and Light Responses of Neurospora

K. Gardner, Yuhong Yang, Yi Liu, 2002, Molecular and Cellular Biology.

Neurospora Clock and Light Responses of Function of Both Proteins in Circadian Steady-State Level of WC-1 and the Interaction Is Essential for Maintaining the PAS Domain-Mediated WC-1 / WC2

K. Gardner, Yuhong Yang, Yi Liu, 2001 .

Alternative Initiation of Translation and Time-Specific Phosphorylation Yield Multiple Forms of the Essential Clock Protein FREQUENCY

Yi Liu, Jennifer J. Loros, Jay C. Dunlap, 1997, Cell.

Thermally Regulated Translational Control of FRQ Mediates Aspects of Temperature Responses in the Neurospora Circadian Clock

Yi Liu, Jay C Dunlap, J. Dunlap, 1997, Cell.

Diverse small non-coding RNAs in RNA interference pathways.

Yi Liu, Liande Li, Yi Liu, 2011, Methods in molecular biology.

Reconstitution of an Argonaute-dependent small RNA biogenesis pathway reveals a handover mechanism involving the RNA exosome and the exonuclease QIP.

Yi Liu, Zhihong Xue, Yi Liu, 2012, Molecular cell.

The N‐terminal region of the Neurospora NDR kinase COT1 regulates morphology via its interactions with MOB2A/B

She Chen, O. Yarden, Yi Liu, 2013, Molecular microbiology.

The DNA/RNA-Dependent RNA Polymerase QDE-1 Generates Aberrant RNA and dsRNA for RNAi in a Process Requiring Replication Protein A and a DNA Helicase

D. Bamford, Yi Liu, J. Cha, 2010, PLoS biology.

The Neurospora RNA polymerase II kinase CTK negatively regulates Catalase expression in a chromatin context dependent manner.

Xiao Liu, Qun He, Yi Liu, 2019, Environmental microbiology.

Codon Usage Influences the Local Rate of Translation Elongation to Regulate Co-translational Protein Folding.

Matthew S. Sachs, Cheng Wu, M. Sachs, 2015, Molecular cell.

A code within the genetic code: codon usage regulates co-translational protein folding

Yi Liu, 2020, Cell Communication and Signaling.

A role for the mitotic proteins Bub3 and BuGZ in transcriptional regulation of catalase-3 expression

Qun He, Yi Liu, Ying Wang, 2022, PLoS genetics.

Antisense transcription licenses nascent transcripts to mediate transcriptional gene silencing

Yi Liu, Jiasen Cheng, Xianyun Sun, 2016, Genes & development.

Molecular mechanism of light responses in Neurospora: from light-induced transcription to photoadaptation.

Yi Liu, Qiyang He, 2005, Genes & development.

IMITATION SWITCH is required for normal chromatin structure and gene repression in PRC2 target domains

Robert J. Schmitz, Mojgan Amirebrahimi, R. Schmitz, 2021, Proceedings of the National Academy of Sciences.

Synonymous but not Silent: The Codon Usage Code for Gene Expression and Protein Folding.

Yi Liu, Fangzhou Zhao, Qian Yang, 2021, Annual review of biochemistry.

A role for the ribosome-associated complex in activation of the IRE1 branch of UPR.

P. Thomas, Yi Liu, W. Skach, 2020, Cell reports.

Histone H3K56 Acetylation Is Required for Quelling-induced Small RNA Production through Its Role in Homologous Recombination*

She Chen, Shaojie Li, Qun He, 2014, The Journal of Biological Chemistry.

Highly conserved shifts in ubiquitin-proteasome system (UPS) activity drive mitochondrial remodeling during quiescence

Yi Liu, G. Demartino, Matthew Sieber, 2022, Nature Communications.

Decoupling PER phosphorylation, stability and rhythmic expression from circadian clock function by abolishing PER-CK1 interaction

Yi Liu, Yue Gu, Baoshi Yuan, 2022, Nature Communications.

Codon usage is an important determinant of gene expression levels largely through its effects on transcription

Mian Zhou, Yi Liu, She Chen, 2016, Proceedings of the National Academy of Sciences.

Reply to Qian and Zhang: Demonstration of the effect of codon usage on transcription by multiple approaches from fungi to animal cells

Yi Liu, Fangzhou Zhao, 2021, Proceedings of the National Academy of Sciences.

White Collar-1, a Circadian Blue Light Photoreceptor, Binding to the frequency Promoter

J. Dunlap, J. Loros, Yi Liu, 2002, Science.

The nutrient-sensing GCN2 signaling pathway is essential for circadian clock function by regulating histone acetylation under amino acid starvation

Yulin Yang, Xiao Liu, Qun He, 2022, bioRxiv.

RNA interference pathways in fungi: mechanisms and functions.

Yi Liu, Shwu-shin Chang, Zhenyu Zhang, 2012, Annual review of microbiology.

Diverse pathways generate microRNA-like RNAs and Dicer-independent small interfering RNAs in fungi.

C. Mello, A. Pertsemlidis, E. Selker, 2010, Molecular cell.

Small RNA-mediated gene silencing in neurospora

Yi Liu, Yunkun Dang, Zhenyu Zhang, 2014 .

RNA interference pathways in filamentous fungi

Yi Liu, Liande Li, Shwu-shin Chang, 2010, Cellular and Molecular Life Sciences.

A code within the genetic code: codon usage regulates co-translational protein folding

Yi Liu, 2020, Cell communication and signaling : CCS.

RNA Interference in Fungi: Pathways, Functions, and Applications

Yi Liu, Zhihong Xue, Qiuying Yang, 2011, Eukaryotic Cell.

MINIREVIEWS RNA Interference in Fungi: Pathways, Functions, and Applications

Yi Liu, Zhihong Xue, Qiuying Yang, 2011 .

Codon usage regulates protein structure and function by affecting translation elongation speed in Drosophila cells

Yi Liu, Chien-Hung Yu, Fangzhou Zhao, 2017, Nucleic acids research.

Codon usage affects the structure and function of the Drosophila circadian clock protein PERIOD

J. Chiu, Yi Liu, Mian Zhou, 2016, Genes & development.

Guanosine triphosphate links MYC-dependent metabolic and ribosome programs in small cell lung cancer.

R. Deberardinis, J. Minna, L. Girard, 2020, The Journal of clinical investigation.

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality

Antonis Rokas, Yi Liu, Peijun Ma, 2013, Nature.

Mechanism of siRNA production from repetitive DNA

Yi Liu, Qiuying Yang, Qiaohong Ye, 2015, Genes & development.

Homologous recombination as a mechanism to recognize repetitive DNA sequences in an RNAi pathway.

Shaojie Li, Yi Liu, Zhihong Xue, 2013, Genes & development.

qiRNA is a new type of small interfering RNA induced by DNA damage

Yi Liu, Swati Choudhary, D. Bamford, 2009, Nature.

Convergent Transcription Induces Dynamic DNA Methylation at disiRNA Loci

Wei Guo, Yi Liu, Liande Li, 2013, PLoS genetics.

Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Yi Liu, Mian Zhou, Haiyan Yuan, 2018, eLife.

A Double-Stranded-RNA Response Program Important for RNA Interference Efficiency

Qinghua Liu, Qun He, Yi Liu, 2007, Molecular and Cellular Biology.

QIP, a putative exonuclease, interacts with the Neurospora Argonaute protein and facilitates conversion of duplex siRNA into single strands.

Yi Liu, Heng-Chi Lee, Mekhala Maiti, 2007, Genes & development.

Transcription of the Major Neurospora crassa microRNA–Like Small RNAs Relies on RNA Polymerase III

Shaojie Li, Yi Liu, Liande Li, 2013, PLoS genetics.

Codon usage and protein length-dependent feedback from translation elongation regulates translation initiation and elongation speed

Yi Liu, Xueliang Lyu, Fangzhou Zhao, 2021, Nucleic acids research.

Adaptation of codon usage to tRNA I34 modification controls translation kinetics and proteome landscape

She Chen, Lin Li, Yi Liu, 2020, PLoS genetics.

eRF1 mediates codon usage effects on mRNA translation efficiency through premature termination at rare codons

M. Sachs, Cheng Wu, Yi Liu, 2019, Nucleic acids research.

Non-optimal codon usage affects expression , structure and function of clock protein FRQ

Matthew S. Sachs, Mian Zhou, Yi Liu, 2013 .

Human-specific gene CT47 blocks PRMT5 degradation to lead to meiosis arrest

Chengji J. Zhou, Chao Li, A. Vidal-Puig, 2022, Cell Death Discovery.

Role for Protein Kinase A in the Neurospora Circadian Clock by Regulating White Collar-Independent frequency Transcription through Phosphorylation of RCM-1

Hongda Li, Xiao Liu, Qun He, 2015, Molecular and Cellular Biology.

Mechanism of the Neurospora Circadian Clock, a FREQUENCY-centric View

Yi Liu, Mian Zhou, J. Cha, 2014, Biochemistry.

Transcriptional interference by antisense RNA is required for circadian clock function

D. Kowbel, Guanghua Xiao, Jichen Yang, 2014, Nature.

Codon usage regulates human KRAS expression at both transcriptional and translational levels

C. Counter, Yi Liu, Jingjing Fu, 2018, The Journal of Biological Chemistry.

Genome-wide role of codon usage on transcription and identification of potential regulators

I. Grigoriev, A. Lipzen, Yi Liu, 2021, Proceedings of the National Academy of Sciences.

Effects of codon usage on gene expression are promoter context dependent

Yi Liu, Xueliang Lyu, Fangzhou Zhao, 2021, Nucleic acids research.

Nonoptimal Codon Usage Is Critical for Protein Structure and Function of the Master General Amino Acid Control Regulator CPC-1

Yi Liu, Xueliang Lyu, 2020, mBio.

Non-optimal codon usage affects expression, structure and function of FRQ clock protein

Matthew S. Sachs, Mian Zhou, Yi Liu, 2013, Nature.

Circadian Rhythms in Neurospora crassa and Other Filamentous Fungi

D. Bell-Pedersen, Yi Liu, 2006, Eukaryotic Cell.

DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition.

C. Hong, Xiao Liu, Qun He, 2017, Molecular cell.

FWD1‐mediated degradation of FREQUENCY in Neurospora establishes a conserved mechanism for circadian clock regulation

Hongtao Yu, Qun He, Yi Liu, 2003, The EMBO journal.

Distinct Roles of HDAC3 in the Core Circadian Negative Feedback Loop Are Critical for Clock Function.

Yi Liu, Yi Liu, Guoqiang Xu, 2016, Cell reports.

White Collar-1, a DNA Binding Transcription Factor and a Light Sensor

K. Gardner, Yuhong Yang, Yi Liu, 2002, Science.

High-throughput discovery of genetic determinants of circadian misalignment

Steve D. M. Brown, A. Flenniken, M. Angelis, 2020, PLoS genetics.

Dual roles of FBXL3 in the mammalian circadian feedback loops are important for period determination and robustness of the clock

L. Ptáček, Yi Liu, Ying Xu, 2013, Proceedings of the National Academy of Sciences.

Regulation of the Neurospora circadian clock by an RNA helicase.

Qun He, Yi Liu, P. Cheng, 2005, Genes & development.

The Exosome Regulates Circadian Gene Expression in a Posttranscriptional Negative Feedback Loop

Yi Liu, P. Cheng, Haiyan Yuan, 2009, Cell.

Molecular mechanism of the Neurospora circadian oscillator

Yi Liu, Jinhu Guo, 2010, Protein & Cell.

Biochemical methods used to study the gene expression and protein complexes in the filamentous fungus Neurospora crassa.

Yi Liu, J. Cha, Jinhu Guo, 2010, Methods in molecular biology.

Control of WHITE COLLAR localization by phosphorylation is a critical step in the circadian negative feedback process

Yi Liu, J. Cha, P. Cheng, 2008, The EMBO journal.

Protein kinase A and casein kinases mediate sequential phosphorylation events in the circadian negative feedback loop.

She Chen, Shaojie Li, Chengzu Long, 2007, Genes & development.

CKI and CKII mediate the FREQUENCY-dependent phosphorylation of the WHITE COLLAR complex to close the Neurospora circadian negative feedback loop.

Yuhong Yang, Qun He, Yi Liu, 2006, Genes & development.

FRQ-CK1 Interaction Underlies Temperature Compensation of the Neurospora Circadian Clock

Yulin Yang, Yue Hu, Xiao Liu, 2021, mBio.

FRQ-CK1 Interaction Underlies Temperature Compensation of the Neurospora Circadian Clock

Yulin Yang, Yue Hu, Qun He, 2021 .

Transcription factor CBF-1 is critical for circadian gene expression by modulating WHITE COLLAR complex recruitment to the frq locus

Hongda Li, Xiao Liu, Qun He, 2018, PLoS genetics.

Setting the pace of the Neurospora circadian clock by multiple independent FRQ phosphorylation events

She Chen, Shaojie Li, Chengzu Long, 2009, Proceedings of the National Academy of Sciences.

Eukaryotic circadian systems: cycles in common

J. Dunlap, J. Loros, Yi Liu, 1999, Genes to cells : devoted to molecular & cellular mechanisms.

The Translin-TRAX complex/C3PO is a ribonuclease in tRNA processing

C. Mello, Qinghua Liu, Yi Liu, 2012, Nature Structural &Molecular Biology.

Regulation of the Activity and Cellular Localization of the Circadian Clock Protein FRQ*

Yi Liu, J. Cha, Haiyan Yuan, 2011, The Journal of Biological Chemistry.

Analysis of posttranslational regulations in the Neurospora circadian clock.

Yi Liu, 2005, Methods in enzymology.

Functional Significance of FRH in Regulating the Phosphorylation and Stability of Neurospora Circadian Clock Protein FRQ*

Yi Liu, P. Cheng, Jinhu Guo, 2010, The Journal of Biological Chemistry.

Coiled‐coil domain‐mediated FRQ–FRQ interaction is essential for its circadian clock function in Neurospora

Yi Liu, C. Heintzen, P. Cheng, 2001, The EMBO journal.

Impaired function of the suprachiasmatic nucleus rescues the loss of body temperature homeostasis caused by time-restricted feeding.

Yi Liu, Qiaocheng Zhai, Yue Gu, 2020, Science bulletin.

Non-optimal codon usage is critical for protein structure and function of the master general amino acid control regulator CPC-1

Yi Liu, Xueliang Lyu, 2020 .

The Ccr4-Not Protein Complex Regulates the Phase of the Neurospora Circadian Clock by Controlling WHITE COLLAR Protein Stability and Activity*

Yi Liu, J. Cha, Qiyang He, 2013, The Journal of Biological Chemistry.

! ! " ! The Ccr 4-Not complex regulates the phase of the Neurospora circadian clock by controlling WHITE COLLAR protein stability and activity

Yi Liu, J. Cha, Qiyang He, 2013 .

Author response: Codon usage biases co-evolve with transcription termination machinery to suppress premature cleavage and polyadenylation

Yi Liu, Mian Zhou, Haiyan Yuan, 2018 .

CATP is a critical component of the Neurospora circadian clock by regulating the nucleosome occupancy rhythm at the frequency locus

Yi Liu, Mian Zhou, J. Cha, 2013, EMBO reports.

DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition.

C. Hong, Xiao Liu, Qun He, 2017, Molecular cell.

Suppression of WC-independent frequency transcription by RCO-1 is essential for Neurospora circadian clock

Xiao Liu, Qun He, Yi Liu, 2013, Proceedings of the National Academy of Sciences.

Molecular mechanism of suppression of circadian rhythms by a critical stimulus

Yi Liu, Lixin Wang, Guocun Huang, 2006, The EMBO journal.

Two NDR kinase–MOB complexes function as distinct modules during septum formation and tip extension in Neurospora crassa

S. Seiler, O. Yarden, Yi Liu, 2009, Molecular microbiology.

Functional Significance of FRH in Regulating the Phosphorylation and Stability of Neurospora Circadian Clock Protein FRQ*

Yi Liu, P. Cheng, Jinhu Guo, 2010, The Journal of Biological Chemistry.

A role for the ribosome-associated complex in activation of the IRE1 branch of UPR

P. Thomas, Yi Liu, W. Skach, 2021, Cell reports.

Erratum: CATP is a critical component of the Neurospora circadian clock by regulating the nucleosome occupancy rhythm at the frequency locus (EMBO reports (2013) 14 (923-930) DOI: 10.1038/embor.2013.131)

Yi Liu, Mian Zhou, J. Cha, 2014 .