Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection

In‐depth and 3‐dimensional exploration of the budding yeast phosphoproteome

(2021) Michael C Lanz et al.   EMBO REPORTS

Bayesian genome scale modelling identifies thermal determinants of yeast metabolism

(2021) Gang Li et al.   Nature Communications

A novel yeast hybrid modeling framework integrating Boolean and enzyme-constrained networks enables exploration of the interplay between signaling and metabolism

(2021) Linnea Österberg et al.   PLoS Computational Biology

Random Transfer of Ogataea polymorpha Genes into Saccharomyces cerevisiae Reveals a Complex Background of Heat Tolerance

(2021) Taisuke Seike et al.   Journal of Fungi

Beat the heat: correlates, compounds, and mechanisms involved in fungal thermotolerance

(2021) Ellie Rose Mattoon et al.   Fungal Biology Reviews

Metabolic and genetic basis for auxotrophies in Gram-negative species

(2020) Yara Seif et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Wickerhamiella/Starmerella clade – a treasure trove for the study of the evolution of yeast metabolism

(2020) Paula Gonçalves et al.   YEAST

Contribution of Complex I NADH dehydrogenase to respiratory energy coupling in glucose-grown cultures of Ogataea parapolymorpha

(2020) Hannes Juergens et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Pyruvate kinase variant of fission yeast tunes carbon metabolism, cell regulation, growth and stress resistance

(2020) Stephan Kamrad et al.   Molecular Systems Biology

Pan‐Genome‐Scale Network Reconstruction: Harnessing Phylogenomics Increases the Quantity and Quality of Metabolic Models

(2020) Kevin Correia et al.   Biotechnology Journal

Convergent evolution and structural adaptation to the deep ocean in the protein folding chaperonin CCTα

(2020) Alexandra A-T Weber et al.   Genome Biology and Evolution

Yeast Systems Biology: Model organism and Cell Factory

(2019) Jens Nielsen   Biotechnology Journal

Environment-dependent fitness gains can be driven by horizontal gene transfer of transporter-encoding genes

(2019) David S. Milner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

(2019) Laurent Heirendt et al.   Nature Protocols

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

HyPhy 2.5—A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies

(2019) Sergei L Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Energy metabolism controls phenotypes by protein efficiency and allocation

(2019) Yu Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multilayered horizontal operon transfers from bacteria reconstruct a thiamine salvage pathway in yeasts

(2019) Carla Gonçalves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

(2019) Hongzhong Lu et al.   Nature Communications

The Heat Shock Response in Yeast Maintains Protein Homeostasis by Chaperoning and Replenishing Proteins

(2019) Moritz Mühlhofer et al.   Cell Reports

Identification and characterization of EYD1 , encoding an erythritol dehydrogenase in Yarrowia lipolytica and its application to bioconvert erythritol into erythrulose

(2018) Frédéric Carly et al.   BIORESOURCE TECHNOLOGY

Factors driving metabolic diversity in the budding yeast subphylum

(2018) Dana A. Opulente et al.   BMC BIOLOGY

Deciphering the Underlying Metabolomic and Lipidomic Patterns Linked to Thermal Acclimation in Saccharomyces cerevisiae

(2018) Francesc Puig-Castellví et al.   JOURNAL OF PROTEOME RESEARCH

Fast automated reconstruction of genome-scale metabolic models for microbial species and communities

(2018) Daniel Machado et al.   NUCLEIC ACIDS RESEARCH

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

Erythritol production by yeasts: a snapshot of current knowledge

(2018) Frédéric Carly et al.   YEAST

Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

(2018) Carla Gonçalves et al.   eLife

Reprogramming Yeast Metabolism from Alcoholic Fermentation to Lipogenesis

(2018) Tao Yu et al.   CELL

Genome evolution across 1,011 Saccharomyces cerevisiae isolates

(2018) Jackson Peter et al.   NATURE

Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum

(2018) Xing-Xing Shen et al.   CELL

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

PomBase 2018: user-driven reimplementation of the fission yeast database provides rapid and intuitive access to diverse, interconnected information

(2018) Antonia Lock et al.   NUCLEIC ACIDS RESEARCH

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Each of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment

(2018) Tin Yau Pang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional and evolutionary characterization of a secondary metabolite gene cluster in budding yeasts

(2018) David J. Krause et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A single Gal4-like transcription factor activates the Crabtree effect in Komagataella phaffii

(2018) Özge Ata et al.   Nature Communications

Construction and characterization of a Saccharomyces cerevisiae strain able to grow on glucosamine as sole carbon and nitrogen source

(2018) Carmen-Lisset Flores et al.   Scientific Reports

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor

(2018) Hao Wang et al.   PLoS Computational Biology

Identifying bacterial essential genes based on a feature-integrated method

(2017) Yan Lin et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans

(2017) J.T. Daub et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the phenotype predictions of a yeast genome‐scale metabolic model by incorporating enzymatic constraints

(2017) Benjamín J Sánchez et al.   Molecular Systems Biology

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

(2017) Petri-Jaan Lahtvee et al.   Cell Systems

mutation3D: Cancer Gene Prediction Through Atomic Clustering of Coding Variants in the Structural Proteome

(2016) Michael J. Meyer et al.   HUMAN MUTATION

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Causes of evolutionary rate variation among protein sites

(2016) Julian Echave et al.   NATURE REVIEWS GENETICS

Control of the negative IREStrans-acting factor KHSRP by ubiquitination

(2016) Yu-An Kung et al.   NUCLEIC ACIDS RESEARCH

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Independent Evolution of Winner Traits without Whole Genome Duplication in Dekkera Yeasts

(2016) Yi-Cheng Guo et al.   PLoS One

Comparative genomics of biotechnologically important yeasts

(2016) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase

(2016) Avlant Nilsson et al.   Scientific Reports

Using Genome-scale Models to Predict Biological Capabilities

(2015) Edward J. O’Brien et al.   CELL

Less Is More: An Adaptive Branch-Site Random Effects Model for Efficient Detection of Episodic Diversifying Selection

(2015) Martin D. Smith et al.   MOLECULAR BIOLOGY AND EVOLUTION

An expanded regulatory network temporally controlsCandida albicansbiofilm formation

(2015) Emily P. Fox et al.   MOLECULAR MICROBIOLOGY

GUIDANCE2: accurate detection of unreliable alignment regions accounting for the uncertainty of multiple parameters

(2015) Itamar Sela et al.   NUCLEIC ACIDS RESEARCH

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2015) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Comprehensive assessment of cancer missense mutation clustering in protein structures

(2015) Atanas Kamburov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis of Yeast Metabolic Network Models Highlights Progress, Opportunities for Metabolic Reconstruction

(2015) Benjamin D. Heavner et al.   PLoS Computational Biology

Expression of multiple horizontally acquired genes is a hallmark of both vertebrate and invertebrate genomes

(2015) Alastair Crisp et al.   GENOME BIOLOGY

A Study on the Fundamental Mechanism and the Evolutionary Driving Forces behind Aerobic Fermentation in Yeast

(2015) Arne Hagman et al.   PLoS One

Why, when, and how did yeast evolve alcoholic fermentation?

(2014) Sofia Dashko et al.   FEMS YEAST RESEARCH

Predicting bacterial essential genes using only sequence composition information

(2014) L.W. Ning et al.   GENETICS AND MOLECULAR RESEARCH

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Altered sterol composition renders yeast thermotolerant

(2014) L. Caspeta et al.   SCIENCE

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

DEG 10, an update of the database of essential genes that includes both protein-coding genes and noncoding genomic elements: Table 1.

(2013) Hao Luo et al.   NUCLEIC ACIDS RESEARCH

Yeast “Make-Accumulate-Consume” Life Strategy Evolved as a Multi-Step Process That Predates the Whole Genome Duplication

(2013) Arne Hagman et al.   PLoS One

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

(2012) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Gene transfer into the fungi

(2011) Thomas A. Richards et al.   Fungal Biology Reviews

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

(2010) Chris A. Brown et al.   CURRENT BIOLOGY

Intracellular characterization of aerobic glucose metabolism in seven yeast species by 13C flux analysis and metabolomics

(2010) Stefan Christen et al.   FEMS YEAST RESEARCH

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Acquisition of prokaryotic genes by fungal genomes

(2009) Marina Marcet-Houben et al.   TRENDS IN GENETICS

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE