Zhenglong Gu Laboratory: Publications

Gu Laboratory: people

Selected Publications:

See the full list of publications and citations from Google Scholar: https://scholar.google.com/citations?user=4ghczSgAAAAJ&hl=en

Association of mitochondrial DNA variants with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) symptoms

MR Hanson, Z Gu, A Keinan, K Ye, A Germain, P Billing-Ross

Journal of Translational Medicine 14 (1), 342


Genetic Evidence for Elevated Pathogenicity of Mitochondrial DNA Heteroplasmy in Autism Spectrum Disorder

Y Wang, M Picard, Z Gu

PLoS Genet 12 (10), e1006391


Coordinated Evolution of Transcriptional and Post-Transcriptional Regulation for Mitochondrial Functions in Yeast Strains

X Sun, Z Wang, X Guo, H Li, Z Gu

PloS one 11 (4), e0153523


RNA Sequencing: A Novel FADS2 Isoform Identified in Milk Fat Globule Suppresses FADS2 Mediated Delta 6-Desaturation of Omega-3 Fatty Acids

KSD Kothapalli, HG Park, X Guo, X Sun, J Zou, SS Hyon, X Qin, ...

The FASEB Journal 30 (1 Supplement), 684.12-684.12


Positive selection on a regulatory insertion-deletion polymorphism in FADS2 influences apparent endogenous synthesis of arachidonic acid

KSD Kothapalli, K Ye, MS Gadgil, SE Carlson, KO O’Brien, JY Zhang, ...

Molecular biology and evolution, msw049


Mitochondrial DNA variants correlate with symptoms in myalgic encephalomyelitis/chronic fatigue syndrome

P Billing-Ross, A Germain, K Ye, A Keinan, Z Gu, MR Hanson

Journal of translational medicine 14 (1), 19


Very Short Mitochondrial DNA Fragments and Heteroplasmy in Human Plasma

R Zhang, K Nakahira, X Guo, AMK Choi, Z Gu

Scientific Reports 6


MBE Advance Access published March 29, 2016

KSD Kothapalli, K Ye, MS Gadgil, SE Carlson, KO O’Brien, JY Zhang, ...


A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data

BE Barker, N Sadagopan, Y Wang, K Smallbone, CR Myers, H Xi, ...

Computational biology and chemistry 59, 98-112


Natural selection on HFE in Asian populations contributes to enhanced non-heme iron absorption

K Ye, C Cao, X Lin, KO O’Brien, Z Gu

BMC genetics 16 (1), 61


Evolution of gene regulation during transcription and translation

Z Wang, X Sun, Y Zhao, X Guo, H Jiang, H Li, Z Gu

Genome biology and evolution 7 (4), 1155-1167


Diminishing returns in next-generation sequencing (NGS) transcriptome data

R Lei, K Ye, Z Gu, X Sun

Gene 557 (1), 82-87


Dynamic Epistasis under Varying Environmental Perturbations

B Barker, L Xu, Z Gu

PloS one 10 (1), e0114911


Coordinating expression of RNA binding proteins with their mRNA targets

H Jiang, L Xu, Z Wang, J Keene, Z Gu

Scientific reports 4, 7175


Reply to Just et al.: Mitochondrial DNA heteroplasmy could be reliably detected with massively parallel sequencing technologies

K Ye, J Lu, F Ma, A Keinan, Z Gu

Proceedings of the National Academy of Sciences 111 (43), E4548-E4550


Nutritional Genomics

Z Gu, K Ye, PJ Stover

Genomic Medicine: Principles and Practice, 180


Extensive pathogenicity of mitochondrial heteroplasmy in healthy human individuals

K Ye, J Lu, F Ma, A Keinan, Z Gu

Proceedings of the National Academy of Sciences 111 (29), 10654-10659


Genome structure and dynamics of the yeast pathogen Candida glabrata

KM Ahmad, J Kokošar, X Guo, Z Gu, OP Ishchuk, J Piškur

FEMS yeast research 14 (4), 529-535


Alternative transcripts in the human milk fat globule proteinogenic RNA transcriptome with emphasis on desaturases (818.8)

K Kothapalli, X Guo, X Sun, S Hyon, R Ran-Ressler, J Zou, Z Gu, ...

The FASEB Journal 28 (1 Supplement), 818.8


Computational approaches for understanding energy metabolism

AA Shestov, B Barker, Z Gu, JW Locasale

Wiley Interdisciplinary Reviews: Systems Biology and Medicine 5 (6), 733-750


Human expression QTLs are enriched in signals of environmental adaptation

K Ye, J Lu, SM Raj, Z Gu

Genome biology and evolution 5 (9), 1689-1701


High-resolution view of bacteriophage lambda gene expression by ribosome profiling

X Liu, H Jiang, Z Gu, JW Roberts

Proceedings of the National Academy of Sciences 110 (29), 11928-11933


Rewiring of posttranscriptional RNA regulons: Puf4p in fungi as an example

H Jiang, X Guo, L Xu, Z Gu

Molecular biology and evolution 29 (9), 2169-2176


Dynamic epistasis for different alleles of the same gene

L Xu, B Barker, Z Gu

Proceedings of the National Academy of Sciences 109 (26), 10420-10425


A mutation in intracellular loop 4 affects the drug-efflux activity of the yeast multidrug resistance ABC transporter Pdr5p

X Guo, J Li, T Wang, Z Liu, X Chen, Y Li, Z Gu, X Mao, W Guan, Y Li

PloS one 7 (1), e29520


Recent advances in understanding the role of nutrition in human genome evolution

K Ye, Z Gu

Advances in Nutrition: An International Review Journal 2 (6), 486-496


A conserved structural determinant located at the interdomain region of mammalian inositol-requiring enzyme 1α

Z Xue, Y He, K Ye, Z Gu, Y Mao, L Qi

Journal of Biological Chemistry 286 (35), 30859-30866


Predominant gain of promoter TATA box after gene duplication associated with stress responses

Y Zou, W Huang, Z Gu, X Gu

Molecular biology and evolution, msr116


Genetic architecture of growth traits revealed by global epistatic interactions

L Xu, H Jiang, H Chen, Z Gu

Genome biology and evolution 3, 909-914


Growth of novel epistatic interactions by gene duplication

H Jiang, L Xu, Z Gu

Genome Biology and Evolution 3, 295-301


Detection of heterozygous mutations in the genome of mismatch repair defective diploid yeast using a Bayesian approach

S Zanders, X Ma, A RoyChoudhury, RD Hernandez, A Demogines, ...

Genetics 186 (2), 493


The baker's yeast diploid genome is remarkably stable in vegetative growth and meiosis

KT Nishant, W Wei, E Mancera, JL Argueso, A Schlattl, N Delhomme, ...

PLoS Genet 6 (9), e1001109


Tinkering evolution of post-transcriptional RNA regulons: puf3p in fungi as an example

H Jiang, W Guan, Z Gu

PLoS Genet 6 (7), e1001030


Antagonistic changes in sensitivity to antifungal drugs by mutations of an important ABC transporter gene in a fungal pathogen

W Guan, H Jiang, X Guo, E Mancera, L Xu, Y Li, L Steinmetz, Y Li, Z Gu

PLoS One 5 (6), e11309


Detecting positive selection in the budding yeast genome

YD LI, H Liang, Z Gu, Z Lin, W Guan, L Zhou, YQ LI, WH LI

Journal of evolutionary biology 22 (12), 2430-2437


Origins of digestive RNases in leaf monkeys are an open question

Z Su, L Xu, Z Gu, X Gu

Molecular Phylogenetics and Evolution 53 (2), 610-611


Yeasts as models in evolutionary biology

Z Gu, S Oliver

Genome Biology 10 (3), 304


Evolution of RNases in leaf monkeys: being parallel gene duplications or parallel gene conversions is a problem of molecular phylogeny

L Xu, Z Su, Z Gu, X Gu

Mol Phylogenet Evol 50, 397-400


Differential selection on gene translation efficiency between the filamentous fungus Ashbya gossypii and yeasts

H Jiang, Y Zhang, J Sun, W Wang, Z Gu

BMC evolutionary biology 8 (1), 343


Regulation dynamics of WGD genes during yeast metabolic oscillation

H Chen, L Xu, Z Gu

Molecular biology and evolution 25 (12), 2513-2516


Relaxation of yeast mitochondrial functions after whole-genome duplication

H Jiang, W Guan, D Pinney, W Wang, Z Gu

Genome research 18 (9), 1466-1471


Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

W Wei, JH McCusker, RW Hyman, T Jones, Y Ning, Z Cao, Z Gu, D Bruno, ...

Proceedings of the National Academy of Sciences 104 (31), 12825


Rapid evolution in a pair of recent duplicate segments of rice

H Jiang, D Liu, Z Gu, W Wang

Journal of Experimental Zoology Part B: Molecular and Developmental ...


Molecular mechanisms involved in robustness of yeast central metabolism against null mutations

N Maltsev, EM Glass, G Ovchinnikova, Z Gu

Journal of biochemistry 137 (2), 177


Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiae

Z Gu, L David, D Petrov, T Jones, RW Davis, LM Steinmetz

Proceedings of the National Academy of Sciences of the United States of ...


Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data

TH Oakley, Z Gu, E Abouheif, NH Patel, WH Li

Molecular biology and evolution 22 (1), 40-50


Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli

E Marland, A Prachumwat, N Maltsev, Z Gu, WH Li

Journal of molecular evolution 59 (6), 806-814


Duplicate genes increase gene expression diversity within and between species

Z Gu, SA Rifkin, KP White, WH Li

Nature genetics 36 (6), 577


Different evolutionary patterns between young duplicate genes in the human genome

P Zhang, Z Gu, WH Li

Genome biology 4 (9), R56


Rate of protein evolution versus fitness effect of gene deletion

J Yang, Z Gu, WH Li

Molecular biology and evolution 20 (5), 772-774


Detection of gene duplications and block duplications in eukaryotic genomes

WH Li, Z Gu, ARO Cavalcanti, A Nekrutenko

Journal of Structural and Functional Genomics 3 (1), 27-34


Role of duplicate genes in genetic robustness against null mutations

Z Gu, LM Steinmetz, X Gu, C Scharfe, RW Davis, WH Li

Nature 421 (6918), 63-66


Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans

ARO Cavalcanti, R Ferreira, Z Gu, WH Li

Journal of molecular evolution 56 (1), 28-37


Rapid divergence in expression between duplicate genes inferred from microarray data

Z Gu, D Nicolae, HHS Lu, WH Li

Trends in genetics 18 (12), 609-613


Extent of gene duplication in the genomes of Drosophila, nematode, and yeast

Z Gu, A Cavalcanti, FC Chen, P Bouman, WH Li

Molecular biology and evolution 19 (3), 256-262


Evolutionary analyses of the human genome

WH Li, Z Gu, H Wang, A Nekrutenko

Nature 409 (6822), 847-849


Densities, length proportions, and other distributional features of repetitive sequences in the human genome estimated from 430 megabases of genomic sequence

Z Gu, H Wang, A Nekrutenko, WH Li

Gene 259 (1-2), 81-88