Metabolic network remodelling enhances yeast’s fitness on xylose using aerobic glycolysis

Yeast Systems Biology: Model organism and Cell Factory

(2019) Jens Nielsen   Biotechnology Journal

Harnessing xylose pathways for biofuels production

(2019) Xiaowei Li et al.   CURRENT OPINION IN BIOTECHNOLOGY

Expanding the Dynamic Range of a Transcription Factor-Based Biosensor in Saccharomyces cerevisiae

(2019) Yasaman Dabirian et al.   ACS Synthetic Biology

Rewiring carbon metabolism in yeast for high level production of aromatic chemicals

(2019) Quanli Liu et al.   Nature Communications

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

(2018) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

(2018) Tao Yu et al.   CELL

Production of fuels and chemicals from xylose by engineered Saccharomyces cerevisiae: a review and perspective

(2017) Suryang Kwak et al.   Microbial Cell Factories

Molecular mechanism of environmental d-xylose perception by a XylFII-LytS complex in bacteria

(2017) Jianxu Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Composition and Function of Mutant Swi/Snf Complexes

(2017) Arnob Dutta et al.   Cell Reports

Engineering Cellular Metabolism

(2016) Jens Nielsen et al.   CELL

Mutation of a regulator Ask10p improves xylose isomerase activity through up-regulation of molecular chaperones in Saccharomyces cerevisiae

(2016) Jin Hou et al.   METABOLIC ENGINEERING

PHO13 deletion-induced transcriptional activation prevents sedoheptulose accumulation during xylose metabolism in engineered Saccharomyces cerevisiae

(2016) Haiqing Xu et al.   METABOLIC ENGINEERING

Model-based transcriptome engineering promotes a fermentative transcriptional state in yeast

(2016) Drew G. Michael et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Warburg Effect: How Does it Benefit Cancer Cells?

(2016) Maria V. Liberti et al.   TRENDS IN BIOCHEMICAL SCIENCES

Metabolic Engineering of TCA Cycle for Production of Chemicals

(2016) Kiira S. Vuoristo et al.   TRENDS IN BIOTECHNOLOGY

Production of fatty acid-derived oleochemicals and biofuels by synthetic yeast cell factories

(2016) Yongjin J. Zhou et al.   Nature Communications

Directed Evolution Reveals Unexpected Epistatic Interactions That Alter Metabolic Regulation and Enable Anaerobic Xylose Use by Saccharomyces cerevisiae

(2016) Trey K. Sato et al.   PLoS Genetics

Evolved hexose transporter enhances xylose uptake and glucose/xylose co-utilization in Saccharomyces cerevisiae

(2016) Amanda Reider Apel et al.   Scientific Reports

Unraveling the genetic basis of xylose consumption in engineered Saccharomyces cerevisiae strains

(2016) Leandro Vieira dos Santos et al.   Scientific Reports

CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae

(2015) Robert Mans et al.   FEMS YEAST RESEARCH

Cloning and characterization of heterologous transporters in Saccharomyces cerevisiae and identification of important amino acids for xylose utilization

(2015) Chengqiang Wang et al.   METABOLIC ENGINEERING

Rapid Evolution of Recombinant Saccharomyces cerevisiae for Xylose Fermentation through Formation of Extra-chromosomal Circular DNA

(2015) Mekonnen M. Demeke et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Temporal system-level organization of the switch from glycolytic to gluconeogenic operation in yeast

(2013) G. G. Zampar et al.   Molecular Systems Biology

Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods

(2013) Leif Väremo et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Directed Evolution of Xylose Isomerase for Improved Xylose Catabolism and Fermentation in the Yeast Saccharomyces cerevisiae

(2012) Sun-Mi Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Functional expression of Burkholderia cenocepacia xylose isomerase in yeast increases ethanol production from a glucose–xylose blend

(2012) Leonardo de Figueiredo Vilela et al.   BIORESOURCE TECHNOLOGY

Modular Pathway Engineering of Diterpenoid Synthases and the Mevalonic Acid Pathway for Miltiradiene Production

(2012) Yongjin J. Zhou et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Microbial production of indolylglucosinolate through engineering of a multi-gene pathway in a versatile yeast expression platform

(2012) Michael Dalgaard Mikkelsen et al.   METABOLIC ENGINEERING

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functional Survey for Heterologous Sugar Transport Proteins, Using Saccharomyces cerevisiae as a Host

(2011) Eric Young et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Xylitol does not inhibit xylose fermentation by engineered Saccharomyces cerevisiae expressing xylA as severely as it inhibits xylose isomerase reaction in vitro

(2011) Suk-Jin Ha et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Unraveling condition-dependent networks of transcription factors that control metabolic pathway activity in yeast

(2010) Sarah-Maria Fendt et al.   Molecular Systems Biology

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Structural and Functional Study of Yer067w, a New Protein Involved in Yeast Metabolism Control and Drug Resistance

(2010) Tatiana Domitrovic et al.   PLoS One

Bulk Segregant Analysis by High-Throughput Sequencing Reveals a Novel Xylose Utilization Gene from Saccharomyces cerevisiae

(2010) Jared W. Wenger et al.   PLoS Genetics

Functional Expression of a Bacterial Xylose Isomerase in Saccharomyces cerevisiae

(2009) D. Brat et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

(2008) Ana Oliveira et al.   BMC Systems Biology