Yeast gene order browser
Other names: yeast_gene_order_browser
Tool for visualising the syntenic context of any gene from several yeast genomes.
Description
More detailed information about this field from each metasource.
Tool for visualising the syntenic context of any gene from several yeast genomes.
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:40.876907
Webpage:
http://ygob.ucd.ie/Webpage
More detailed information about this field from each metasource.
Publications:
Publications
More detailed information about this field from each metasource.
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
PMID: 16169922
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:40.876907
Publications
More detailed information about this field from each metasource.
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
PMID: 16169922
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:40.876907
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The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
PubMed citations: 355.
355 articles citing: The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species
IAGS: Inferring Ancestor Genome Structure under a Wide Range of Evolutionary Scenarios. PMID:35176153
SWI/SNF senses carbon starvation with a pH-sensitive low-complexity sequence. PMID:35129437
Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy. PMID:34909054
The Role of Ancestral Duplicated Genes in Adaptation to Growth on Lactate, a Non-Fermentable Carbon Source for the Yeast Saccharomyces cerevisiae. PMID:34830177
The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating proteins. PMID:34791214
Sex without crossing over in the yeast Saccharomycodes ludwigii. PMID:34732243
A Markerless CRISPR-Mediated System for Genome Editing in Candida auris Reveals a Conserved Role for Cas5 in the Caspofungin Response. PMID:34730409
A functionally divergent intrinsically disordered region underlying the conservation of stochastic signaling. PMID:34506483
Yeast Ssd1 is a non-enzymatic member of the RNase II family with an alternative RNA recognition site. PMID:34302485
Retention of duplicated genes in evolution. PMID:34294428
Oxidative stress induces coordinated remodeling of RNA-enzyme interactions. PMID:34278261
Molecular and structural mechanisms of ZZ domain-mediated cargo selection by Nbr1. PMID:34169534
BLAST from the Past: Impacts of Evolving Approaches on Studies of Evolution by Gene Duplication. PMID:34164667
Conservation of a DNA Replication Motif among Phylogenetically Distant Budding Yeast Species. PMID:34132803
Whole-genome microsynteny-based phylogeny of angiosperms. PMID:34108452
The Role of Structural Variation in Adaptation and Evolution of Yeast and Other Fungi. PMID:34066718
The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. PMID:34065948
Yeast cell fate control by temporal redundancy modulation of transcription factor paralogs. PMID:34035307
Identification of novel pentose transporters in Kluyveromyces marxianus using a new screening platform. PMID:33890624
Evolution of the complex transcription network controlling biofilm formation in Candida species. PMID:33825680
Analysis of Fungal Genomes Reveals Commonalities of Intron Gain or Loss and Functions in Intron-Poor Species. PMID:33772558
Genome sequencing, annotation and exploration of the SO2-tolerant non-conventional yeast Saccharomycodes ludwigii. PMID:33622260
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. PMID:33616531
Translation machinery reprogramming in programmed cell death in Saccharomyces cerevisiae. PMID:33462193
SUMOylation in fungi: A potential target for intervention. PMID:33294142
Giant GAL gene clusters for the melibiose-galactose pathway in Torulaspora. PMID:33141945
Many, but not all, lineage-specific genes can be explained by homology detection failure. PMID:33137085
GWideCodeML: A Python Package for Testing Evolutionary Hypotheses at the Genome-Wide Level. PMID:33093185
Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast. PMID:33062452
A large accessory protein interactome is rewired across environments. PMID:32924934
Determining the interaction status and evolutionary fate of duplicated homomeric proteins. PMID:32853212
In Kluyveromyces lactis a Pair of Paralogous Isozymes Catalyze the First Committed Step of Leucine Biosynthesis in Either the Mitochondria or the Cytosol. PMID:32849440
Uptake of exogenous serine is important to maintain sphingolipid homeostasis in Saccharomyces cerevisiae. PMID:32845888
Mitochondrial HMG-Box Containing Proteins: From Biochemical Properties to the Roles in Human Diseases. PMID:32824374
Identification of Essential Genes and Fluconazole Susceptibility Genes in Candida glabrata by Profiling Hermes Transposon Insertions. PMID:32819971
Transcriptional Rewiring, Adaptation, and the Role of Gene Duplication in the Metabolism of Ethanol of Saccharomyces cerevisiae. PMID:32788405
Recurrent sequence evolution after independent gene duplication. PMID:32770961
Independent evolution of transcript abundance and gene regulatory dynamics. PMID:32699020
New Aspects of Invasive Growth Regulation Identified by Functional Profiling of MAPK Pathway Targets in Saccharomyces cerevisiae. PMID:32665277
Exploring whole-genome duplicate gene retention with complex genetic interaction analysis. PMID:32586993
Stress-induced expression is enriched for evolutionarily young genes in diverse budding yeasts. PMID:32358542
The functional study of human proteins using humanized yeast. PMID:32342338
The lasting after-effects of an ancient polyploidy on the genomes of teleosts. PMID:32298330
Evolution of Distinct Responses to Low NAD+ Stress by Rewiring the Sir2 Deacetylase Network in Yeasts. PMID:32071196
Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes. PMID:32066524
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. PMID:32064787
Loss of centromere function drives karyotype evolution in closely related Malassezia species. PMID:31958060
A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program. PMID:31757755
A Novel cis Element Achieves the Same Solution as an Ancestral cis Element During Thiamine Starvation in Candida glabrata. PMID:31732505
Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance. PMID:31589316
Analysis of the protein composition of the spindle pole body during sporulation in Ashbya gossypii. PMID:31581259
Regulation of Skn7-dependent, oxidative stress-induced genes by the RNA polymerase II-CTD phosphatase, Fcp1, and Mediator kinase subunit, Cdk8, in yeast. PMID:31506296
Endogenous RNAi pathway evolutionarily shapes the destiny of the antisense lncRNAs transcriptome. PMID:31462400
The role of structural pleiotropy and regulatory evolution in the retention of heteromers of paralogs. PMID:31454312
The Methylotroph Gene Order Browser (MGOB) reveals conserved synteny and ancestral centromere locations in the yeast family Pichiaceae. PMID:31397853
MCHM Acts as a Hydrotrope, Altering the Balance of Metals in Yeast. PMID:31392542
Genome and transcriptome evolve separately in recently hybridized Trichosporon fungi. PMID:31341962
Proteome-wide signatures of function in highly diverged intrinsically disordered regions. PMID:31264965
Functional link between mitochondria and Rnr3, the minor catalytic subunit of yeast ribonucleotide reductase. PMID:31172013
Recent trends in molecular diagnostics of yeast infections: from PCR to NGS. PMID:31158289
Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima. PMID:31081214
Pervasive and dynamic transcription initiation in Saccharomyces cerevisiae. PMID:31076411
YeasTSS: an integrative web database of yeast transcription start sites. PMID:31032841
Suppression of respiratory growth defect of mitochondrial phosphatidylserine decarboxylase deficient mutant by overproduction of Sfh1, a Sec14 homolog, in yeast. PMID:30958856
Comparative Genomics Between Saccharomyces kudriavzevii and S. cerevisiae Applied to Identify Mechanisms Involved in Adaptation. PMID:30930934
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. PMID:30893420
Cell Wall Surface Properties of Kluyveromyces marxianus Strains From Dairy-Products. PMID:30766524
Identification of Suppressor of Clathrin Deficiency-1 (SCD1) and Its Connection to Clathrin-Mediated Endocytosis in Saccharomyces cerevisiae. PMID:30679249
Discovery and Evolution of New Domains in Yeast Heterochromatin Factor Sir4 and Its Partner Esc1. PMID:30668669
Conservation of location of several specific inhibitory codon pairs in the Saccharomyces sensu stricto yeasts reveals translational selection. PMID:30576464
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). PMID:30535146
Gene Essentiality Analyzed by In Vivo Transposon Mutagenesis and Machine Learning in a Stable Haploid Isolate of Candida albicans. PMID:30377286
A Transcriptomics Approach To Unveiling the Mechanisms of In Vitro Evolution towards Fluconazole Resistance of a Candida glabrata Clinical Isolate. PMID:30348666
Oxidative stress-induced structural changes in the microtubule-associated flavoenzyme Irc15p from Saccharomyces cerevisiae. PMID:30267443
Intrinsic cooperativity potentiates parallel cis-regulatory evolution. PMID:30198843
Whole Genome Sequencing, de Novo Assembly and Phenotypic Profiling for the New Budding Yeast Species Saccharomyces jurei. PMID:30097472
Implications of maintenance of mother-bud neck size in diverse vital processes of Saccharomyces cerevisiae. PMID:30066140
Tracing the De Novo Origin of Protein-Coding Genes in Yeast. PMID:30065088
Genetics of trans-regulatory variation in gene expression. PMID:30014850
Decoding the chromatin proteome of a single genomic locus by DNA sequencing. PMID:30005073
Genome analysis of the yeast Diutina catenulata, a member of the Debaryomycetaceae/Metschnikowiaceae (CTG-Ser) clade. PMID:29944657
Overexpression of SNF4 and deletions of REG1- and REG2-enhanced maltose metabolism and leavening ability of baker's yeast in lean dough. PMID:29936578
Systematic Identification, Characterization, and Conservation of Adjacent-Gene Coregulation in the Budding Yeast Saccharomyces cerevisiae. PMID:29898982
Evolutionary instability of CUG-Leu in the genetic code of budding yeasts. PMID:29760453
Gene dosage effects in yeast support broader roles for the LOG1, HAM1 and DUT1 genes in detoxification of nucleotide analogues. PMID:29738539
Surveying alignment-free features for Ortholog detection in related yeast proteomes by using supervised big data classifiers. PMID:29724166
Signature pathway expression of xylose utilization in the genetically engineered industrial yeast Saccharomyces cerevisiae. PMID:29621349
Preferential retention of genes from one parental genome after polyploidy illustrates the nature and scope of the genomic conflicts induced by hybridization. PMID:29590103
Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications. PMID:29566222
Dal81 Regulates Expression of Arginine Metabolism Genes in Candida parapsilosis. PMID:29564399
A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. PMID:29525204
Gene regulation in Kluyveromyces marxianus in the context of chromosomes. PMID:29346402
Introns provide a platform for intergenic regulatory feedback of RPL22 paralogs in yeast. PMID:29304067
A Novel Sterol-Signaling Pathway Governs Azole Antifungal Drug Resistance and Hypoxic Gene Repression in Saccharomyces cerevisiae. PMID:29263028
Unique molecular mechanisms for maintenance and alteration of genetic information in the budding yeast Saccharomyces cerevisiae. PMID:29213342
The Effect of Nonreversibility on Inferring Rooted Phylogenies. PMID:29149300
Reconstructing Yeasts Phylogenies and Ancestors from Whole Genome Data. PMID:29123238
Can Interspecies Hybrid Zygosaccharomyces rouxii Produce an Allohaploid Gamete? PMID:29079616
A CRISPR-Cas9-based gene drive platform for genetic interaction analysis in Candida albicans. PMID:29062088
Genetic Interaction Network as an Important Determinant of Gene Order in Genome Evolution. PMID:29029158
A Comprehensive Analysis of Transcript-Supported De Novo Genes in Saccharomyces sensu stricto Yeasts. PMID:28981695
Diversification of Transcriptional Regulation Determines Subfunctionalization of Paralogous Branched Chain Aminotransferases in the Yeast Saccharomyces cerevisiae. PMID:28912343
Glycolytic Functions Are Conserved in the Genome of the Wine Yeast Hanseniaspora uvarum, and Pyruvate Kinase Limits Its Capacity for Alcoholic Fermentation. PMID:28887422
Mechanism for Restoration of Fertility in Hybrid Zygosaccharomyces rouxii Generated by Interspecies Hybridization. PMID:28842546
The Yeast Heterochromatin Protein Sir3 Experienced Functional Changes in the AAA+ Domain After Gene Duplication and Subfunctionalization. PMID:28827288
Hormesis enables cells to handle accumulating toxic metabolites during increased energy flux. PMID:28826004
Evolutionary biology through the lens of budding yeast comparative genomics. PMID:28714481
Expression properties exhibit correlated patterns with the fate of duplicated genes, their divergence, and transcriptional plasticity in Saccharomycotina. PMID:28633360
DNA replication timing influences gene expression level. PMID:28539386
Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch. PMID:28510588
Insight into the Recent Genome Duplication of the Halophilic Yeast Hortaea werneckii: Combining an Improved Genome with Gene Expression and Chromatin Structure. PMID:28500048
Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway. PMID:28485712
Genome Mutational and Transcriptional Hotspots Are Traps for Duplicated Genes and Sources of Adaptations. PMID:28459980
Parallel reorganization of protein function in the spindle checkpoint pathway through evolutionary paths in the fitness landscape that appear neutral in laboratory experiments. PMID:28410373
From Lipid Homeostasis to Differentiation: Old and New Functions of the Zinc Cluster Proteins Ecm22, Upc2, Sut1 and Sut2. PMID:28379181
Genome urbanization: clusters of topologically co-regulated genes delineate functional compartments in the genome of Saccharomyces cerevisiae. PMID:28369650
Meta-analytic framework for liquid association. PMID:28334340
Gene regulatory network plasticity predates a switch in function of a conserved transcription regulator. PMID:28327289
Growth condition dependency is the major cause of non-responsiveness upon genetic perturbation. PMID:28257504
The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism. PMID:28250014
Differential paralog divergence modulates genome evolution across yeast species. PMID:28196070
Predicted RNA Binding Proteins Pes4 and Mip6 Regulate mRNA Levels, Translation, and Localization during Sporulation in Budding Yeast. PMID:28193845
Selection maintains signaling function of a highly diverged intrinsically disordered region. PMID:28167781
Increased rates of protein evolution and asymmetric deceleration after the whole-genome duplication in yeasts. PMID:28166720
The Zygosaccharomyces bailii transcription factor Haa1 is required for acetic acid and copper stress responses suggesting subfunctionalization of the ancestral bifunctional protein Haa1/Cup2. PMID:28086780
Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast. PMID:28072816
Eukaryotic stand-alone pseudouridine synthases - RNA modifying enzymes and emerging regulators of gene expression? PMID:28045575
A genome wide dosage suppressor network reveals genomic robustness. PMID:27899637
Diversification of the kinetic properties of yeast NADP-glutamate-dehydrogenase isozymes proceeds independently of their evolutionary origin. PMID:27864882
The Phenotypic Plasticity of Duplicated Genes in Saccharomyces cerevisiae and the Origin of Adaptations. PMID:27799339
Building a Regulatory Network with Short Linear Sequence Motifs: Lessons from the Degrons of the Anaphase-Promoting Complex. PMID:27716480
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. PMID:27690225
Exploring Quantitative Yeast Phenomics with Single-Cell Analysis of DNA Damage Foci. PMID:27617677
Transcriptional rewiring over evolutionary timescales changes quantitative and qualitative properties of gene expression. PMID:27614020
Sequence Assembly of Yarrowia lipolytica Strain W29/CLIB89 Shows Transposable Element Diversity. PMID:27603307
Prioritized Expression of BTN2 of Saccharomyces cerevisiae under Pronounced Translation Repression Induced by Severe Ethanol Stress. PMID:27602028
Sporadic Gene Loss After Duplication Is Associated with Functional Divergence of Sirtuin Deacetylases Among Candida Yeast Species. PMID:27543294
The Nuts and Bolts of Transcriptionally Silent Chromatin in Saccharomyces cerevisiae. PMID:27516616
A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference. PMID:27492233
Global deceleration of gene evolution following recent genome hybridizations in fungi. PMID:27440871
A Phylogenetic Approach Finds Abundant Interlocus Gene Conversion in Yeast. PMID:27297467
GenFamClust: an accurate, synteny-aware and reliable homology inference algorithm. PMID:27260514
CRISPR-directed mitotic recombination enables genetic mapping without crosses. PMID:27230379
Independent Evolution of Winner Traits without Whole Genome Duplication in Dekkera Yeasts. PMID:27152421
SimpleSynteny: a web-based tool for visualization of microsynteny across multiple species. PMID:27141960
Springing into Action: Reg2 Negatively Regulates Snf1 Protein Kinase and Facilitates Recovery from Prolonged Glucose Starvation in Saccharomyces cerevisiae. PMID:27107116
History of chromosome rearrangements reflects the spatial organization of yeast chromosomes. PMID:27021249
Origin and evolution of GATA2a and GATA2b in teleosts: insights from tongue sole, Cynoglossus semilaevis. PMID:27019782
Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi. PMID:27018804
VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity. PMID:27006949
From one to many: expanding the Saccharomyces cerevisiae reference genome panel. PMID:26989152
Inferring Orthologs: Open Questions and Perspectives. PMID:26966373
Massive Amplification at an Unselected Locus Accompanies Complex Chromosomal Rearrangements in Yeast. PMID:26945028
Evolution and Functional Trajectory of Sir1 in Gene Silencing. PMID:26811328
Saccharomyces cerevisiae Forms D-2-Hydroxyglutarate and Couples Its Degradation to D-Lactate Formation via a Cytosolic Transhydrogenase. PMID:26774271
An Effective Big Data Supervised Imbalanced Classification Approach for Ortholog Detection in Related Yeast Species. PMID:26605337
Atg41/Icy2 regulates autophagosome formation. PMID:26565778
SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand. PMID:26560340
Patterns of Gene Conversion in Duplicated Yeast Histones Suggest Strong Selection on a Coadapted Macromolecular Complex. PMID:26560339
Identification of Saccharomyces cerevisiae Genes Whose Deletion Causes Synthetic Effects in Cells with Reduced Levels of the Nuclear Pif1 DNA Helicase. PMID:26483010
Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response. PMID:26446933
Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae. PMID:26399295
Experimental Evidence for a Revision in the Annotation of Putative Pyridoxamine 5'-Phosphate Oxidases P(N/M)P from Fungi. PMID:26327315
Regulation of Telomere Length Requires a Conserved N-Terminal Domain of Rif2 in Saccharomyces cerevisiae. PMID:26294668
Origin of the Yeast Whole-Genome Duplication. PMID:26252643
Beyond the Whole-Genome Duplication: Phylogenetic Evidence for an Ancient Interspecies Hybridization in the Baker's Yeast Lineage. PMID:26252497
The Evolutionary Potential of Phenotypic Mutations. PMID:26244544
Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres. PMID:26166782
Proteny: discovering and visualizing statistically significant syntenic clusters at the proteome level. PMID:26116928
A Minimal Set of Glycolytic Genes Reveals Strong Redundancies in Saccharomyces cerevisiae Central Metabolism. PMID:26071034
Clade- and species-specific features of genome evolution in the Saccharomycetaceae. PMID:26066552
The Structure of an NDR/LATS Kinase-Mob Complex Reveals a Novel Kinase-Coactivator System and Substrate Docking Mechanism. PMID:25966461
Plasma Membrane Proteolipid 3 Protein Modulates Amphotericin B Resistance through Sphingolipid Biosynthetic Pathway. PMID:25965669
Maintenance and Loss of Duplicated Genes by Dosage Subfunctionalization. PMID:25908670
Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae. PMID:25860149
Interaction between the RNA-dependent ATPase and poly(A) polymerase subunits of the TRAMP complex is mediated by short peptides and important for snoRNA processing. PMID:25589546
Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory sequences. PMID:25474245
GenomicusPlants: a web resource to study genome evolution in flowering plants. PMID:25432975
The GCKIII kinase Sps1 and the 14-3-3 isoforms, Bmh1 and Bmh2, cooperate to ensure proper sporulation in Saccharomyces cerevisiae. PMID:25409301
Distance-based assessment of the localization of functional annotations in 3D genome reconstructions. PMID:25407917
The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. PMID:25399418
Targeting and plasticity of mitochondrial proteins revealed by proximity-specific ribosome profiling. PMID:25378625
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
Intron evolution in Saccharomycetaceae. PMID:25364803
The Hsp90-dependent proteome is conserved and enriched for hub proteins with high levels of protein-protein connectivity. PMID:25316598
The yeast enzyme Eht1 is an octanoyl-CoA:ethanol acyltransferase that also functions as a thioesterase. PMID:25308280
TORC2-dependent protein kinase Ypk1 phosphorylates ceramide synthase to stimulate synthesis of complex sphingolipids. PMID:25279700
The small GTP-binding proteins AgRho2 and AgRho5 regulate tip-branching, maintenance of the growth axis and actin-ring-integrity in the filamentous fungus Ashbya gossypii. PMID:25171205
Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae. PMID:25149527
Orthology detection combining clustering and synteny for very large datasets. PMID:25137074
Relationship between gene duplicability and diversifiability in the topology of biochemical networks. PMID:25005725
Conservation and divergence of transcriptional coregulations between box C/D snoRNA and ribosomal protein genes in Ascomycota. PMID:25002674
Evaluating synteny for improved comparative studies. PMID:24932010
Inferring gene family histories in yeast identifies lineage specific expansions. PMID:24921666
Mlh2 is an accessory factor for DNA mismatch repair in Saccharomyces cerevisiae. PMID:24811092
Histidine degradation via an aminotransferase increases the nutritional flexibility of Candida glabrata. PMID:24728193
SearchDOGS bacteria, software that provides automated identification of potentially missed genes in annotated bacterial genomes. PMID:24659774
Vhs2 is a novel regulator of septin dynamics in budding yeast. PMID:24646733
Yeast telomere maintenance is globally controlled by programmed ribosomal frameshifting and the nonsense-mediated mRNA decay pathway. PMID:24563826
Plus ça change - evolutionary sequence divergence predicts protein subcellular localization signals. PMID:24438075
The cellular roles of Ccr4-NOT in model and pathogenic fungi-implications for fungal virulence. PMID:24391665
A visual screen of protein localization during sporulation identifies new components of prospore membrane-associated complexes in budding yeast. PMID:24390141
Detecting and locating whole genome duplications on a phylogeny: a probabilistic approach. PMID:24361993
The deacetylase Sir2 from the yeast Clavispora lusitaniae lacks the evolutionarily conserved capacity to generate subtelomeric heterochromatin. PMID:24204326
The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny. PMID:24185697
The basis for evolution of DNA-binding specificity of the Aft1 transcription factor in yeasts. PMID:24172132
Yeast metabolic and signaling genes are required for heat-shock survival and have little overlap with the heat-induced genes. PMID:24167267
Comparative genomics of emerging pathogens in the Candida glabrata clade. PMID:24034898
Distinct SUMO ligases cooperate with Esc2 and Slx5 to suppress duplication-mediated genome rearrangements. PMID:23935535
Extensive intra-kingdom horizontal gene transfer converging on a fungal fructose transporter gene. PMID:23818872
Evolutionary principles of modular gene regulation in yeasts. PMID:23795289
All or nothing: protein complexes flip essentiality between distantly related eukaryotes. PMID:23661563
Inferring ancient divergences requires genes with strong phylogenetic signals. PMID:23657258
Identifying cis-regulatory changes involved in the evolution of aerobic fermentation in yeasts. PMID:23650209
Alternative splicing and subfunctionalization generates functional diversity in fungal proteomes. PMID:23516382
Comparative genome analysis and gene finding in Candida species using CGOB. PMID:23486613
Role of glutathione in the oxidative stress response in the fungal pathogen Candida glabrata. PMID:23455613
Evolutionary mobility of the ribosomal DNA array in yeasts. PMID:23419706
High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. PMID:23368932
JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison. PMID:23324080
The roles of whole-genome and small-scale duplications in the functional specialization of Saccharomyces cerevisiae genes. PMID:23300483
A flexible ancestral genome reconstruction method based on gapped adjacencies. PMID:23281872
Mitotic exit and separation of mother and daughter cells. PMID:23212898
Genomicus: five genome browsers for comparative genomics in eukaryota. PMID:23193262
A model system for mitochondrial biogenesis reveals evolutionary rewiring of protein import and membrane assembly pathways. PMID:23151513
The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes. PMID:23051624
Paralogous ALT1 and ALT2 retention and diversification have generated catalytically active and inactive aminotransferases in Saccharomyces cerevisiae. PMID:23049841
The SWI/SNF KlSnf2 subunit controls the glucose signaling pathway to coordinate glycolysis and glucose transport in Kluyveromyces lactis. PMID:23002104
A pipeline for automated annotation of yeast genome sequences by a conserved-synteny approach. PMID:22984983
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species. PMID:22904089
Polyploidy and the evolution of complex traits. PMID:22900230
cis- and trans-acting localization determinants of pH response regulator Rim13 in Saccharomyces cerevisiae. PMID:22865500
An independent genome duplication inferred from Hox paralogs in the American paddlefish--a representative basal ray-finned fish and important comparative reference. PMID:22851613
Candida albicans scavenges host zinc via Pra1 during endothelial invasion. PMID:22761575
Maintaining replication origins in the face of genomic change. PMID:22665441
Genome and transcriptome analysis of the food-yeast Candida utilis. PMID:22629373
Functional analysis of the single Est1/Ebs1 homologue in Kluyveromyces lactis reveals roles in both telomere maintenance and rapamycin resistance. PMID:22544908
Diverse forms of RPS9 splicing are part of an evolving autoregulatory circuit. PMID:22479208
Network evolution: rewiring and signatures of conservation in signaling. PMID:22438796
Rewiring of posttranscriptional RNA regulons: Puf4p in fungi as an example. PMID:22438588
Charting the travels of copper in eukaryotes from yeast to mammals. PMID:22387373
Genome evolution in the eremothecium clade of the Saccharomyces complex revealed by comparative genomics. PMID:22384365
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. PMID:22384314
A model for biased fractionation after whole genome duplication. PMID:22369177
Evaluation and properties of the budding yeast phosphoproteome. PMID:22286756
LCGbase: A Comprehensive Database for Lineage-Based Co-regulated Genes. PMID:22267903
Candida albicans Dicer (CaDcr1) is required for efficient ribosomal and spliceosomal RNA maturation. PMID:22173636
Fractionation statistics. PMID:22152148
Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function. PMID:22141333
Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents. PMID:22123960
Yeast: an experimental organism for 21st Century biology. PMID:22084421
Local synteny and codon usage contribute to asymmetric sequence divergence of Saccharomyces cerevisiae gene duplicates. PMID:21955875
Putatively noncoding transcripts show extensive association with ribosomes. PMID:21948395
Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom. PMID:21938499
IONS: Identification of Orthologs by Neighborhood and Similarity-an Automated Method to Identify Orthologs in Chromosomal Regions of Common Evolutionary Ancestry and its Application to Hemiascomycetous Yeasts. PMID:21918595
Orthology prediction methods: a quality assessment using curated protein families. PMID:21853451
An iron homeostasis regulatory circuit with reciprocal roles in Candida albicans commensalism and pathogenesis. PMID:21843869
The GAL10 gene is located 40 kbp away from the GAL7-GAL1 region in the yeast Kazachstania naganishii. PMID:21822965
Mechanisms of chromosome number evolution in yeast. PMID:21811419
Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments. PMID:21791067
Reinventing heterochromatin in budding yeasts: Sir2 and the origin recognition complex take center stage. PMID:21764908
Coexpression of linked gene pairs persists long after their separation. PMID:21737396
Positional orthology: putting genomic evolutionary relationships into context. PMID:21705766
The duplicated deacetylases Sir2 and Hst1 subfunctionalized by acquiring complementary inactivating mutations. PMID:21690292
Computational methods for Gene Orthology inference. PMID:21690100
Minimal regulatory spaces in yeast genomes. PMID:21679449
Evaluating ortholog prediction algorithms in a yeast model clade. PMID:21533202
The peroxin Pex34p functions with the Pex11 family of peroxisomal divisional proteins to regulate the peroxisome population in yeast. PMID:21441307
Protein complexes are central in the yeast genetic landscape. PMID:21390331
Ectopic gene conversions in the genome of ten hemiascomycete yeast species. PMID:21350633
On the PATHGROUPS approach to rapid small phylogeny. PMID:21342571
Gene clustering pattern, promoter architecture, and gene expression stability in eukaryotic genomes. PMID:21300882
Genetic, genomic, and molecular tools for studying the protoploid yeast, L. waltii. PMID:21246627
Ancient gene duplication provided a key molecular step for anaerobic growth of Baker's yeast. PMID:21245414
Novel genes exhibit distinct patterns of function acquisition and network integration. PMID:21187012
OMA 2011: orthology inference among 1000 complete genomes. PMID:21113020
Endogenous ribosomal frameshift signals operate as mRNA destabilizing elements through at least two molecular pathways in yeast. PMID:21109528
Genetic interactions reveal the evolutionary trajectories of duplicate genes. PMID:21081923
Conflict between noise and plasticity in yeast. PMID:21079670
Nonrandom survival of gene conversions among yeast ribosomal proteins duplicated through genome doubling. PMID:20966100
Expansion of hexose transporter genes was associated with the evolution of aerobic fermentation in yeasts. PMID:20660490
Gene duplication and environmental adaptation within yeast populations. PMID:20660110
Nuclear-localized tiny RNAs are associated with transcription initiation and splice sites in metazoans. PMID:20622877
The evolutionary rate variation among genes of HOG-signaling pathway in yeast genomes. PMID:20618989
Structural and functional study of YER067W, a new protein involved in yeast metabolism control and drug resistance. PMID:20567505
Yeast evolutionary genomics. PMID:20559329
Ordered structure of the transcription network inherited from the yeast whole-genome duplication. PMID:20525287
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PMID:20485561
The collapse of gene complement following whole genome duplication. PMID:20482863
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. PMID:20459735
Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis. PMID:20412590
Fragile genomic sites are associated with origins of replication. PMID:20333204
Gene duplication and the evolution of ribosomal protein gene regulation in yeast. PMID:20212107
Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. PMID:20185404
Evolution and regulation of cellular periodic processes: a role for paralogues. PMID:20168326
Enrichment of homologs in insignificant BLAST hits by co-complex network alignment. PMID:20152020
Posttranslational regulation impacts the fate of duplicated genes. PMID:20080574
A phenotypic profile of the Candida albicans regulatory network. PMID:20041210
Alpha3, a transposable element that promotes host sexual reproduction. PMID:20008928
Rapid reorganization of the transcriptional regulatory network after genome duplication in yeast. PMID:19923128
The Sir2-Sum1 complex represses transcription using both promoter-specific and long-range mechanisms to regulate cell identity and sexual cycle in the yeast Kluyveromyces lactis. PMID:19893609
Gene responses to oxygen availability in Kluyveromyces lactis: an insight on the evolution of the oxygen-responding system in yeast. PMID:19855843
Combined phylogeny and neighborhood analysis of the evolution of the ABC transporters conferring multiple drug resistance in hemiascomycete yeasts. PMID:19796374
A screen for spore wall permeability mutants identifies a secreted protease required for proper spore wall assembly. PMID:19779569
RNAi in budding yeast. PMID:19745116
Enhancer of decapping proteins 1 and 2 are important for translation during heat stress in Saccharomyces cerevisiae. PMID:19682251
Variation in gene duplicates with low synonymous divergence in Saccharomyces cerevisiae relative to Caenorhabditis elegans. PMID:19594930
KlAft, the Kluyveromyces lactis ortholog of Aft1 and Aft2, mediates activation of iron-responsive transcription through the PuCACCC Aft-type sequence. PMID:19581449
Comparative genomics of protoploid Saccharomycetaceae. PMID:19525356
Family classification without domain chaining. PMID:19478015
Knockout of the DNA ligase IV homolog gene in the sphingoid base producing yeast Pichia ciferrii significantly increases gene targeting efficiency. PMID:19468735
Protein phosphatase type 1-interacting protein Ysw1 is involved in proper septin organization and prospore membrane formation during sporulation. PMID:19465564
Reconstructing the history of yeast genomes. PMID:19436717
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PMID:19436716
Dynamic reprogramming of transcription factors to and from the subtelomere. PMID:19372386
Candida glabrata PHO4 is necessary and sufficient for Pho2-independent transcription of phosphate starvation genes. PMID:19332882
Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. PMID:19299507
Specialized sugar sensing in diverse fungi. PMID:19249212
Complex fate of paralogs. PMID:19094234
SynteBase/SynteView: a tool to visualize gene order conservation in prokaryotic genomes. PMID:19087285
SNUGB: a versatile genome browser supporting comparative and functional fungal genomics. PMID:19055845
A multispecies-based taxonomic microarray reveals interspecies hybridization and introgression in Saccharomyces cerevisiae. PMID:19054123
Age-dependent evolution of the yeast protein interaction network suggests a limited role of gene duplication and divergence. PMID:19043579
Network hubs buffer environmental variation in Saccharomyces cerevisiae. PMID:18986213
Transcriptional regulators of seven yeast species: comparative genome analysis. Review. PMID:18759110
Preservation of duplicate genes by originalization. PMID:18726163
Elusive origins of the extra genes in Aspergillus oryzae. PMID:18725939
Relaxation of yeast mitochondrial functions after whole-genome duplication. PMID:18669479
MNL1 regulates weak acid-induced stress responses of the fungal pathogen Candida albicans. PMID:18653474
Pervasive and persistent redundancy among duplicated genes in yeast. PMID:18604285
Guided genome halving: hardness, heuristics and the history of the Hemiascomycetes. PMID:18586750
Probabilistic cross-species inference of orthologous genomic regions created by whole-genome duplication in yeast. PMID:18562662
The evolution of combinatorial gene regulation in fungi. PMID:18303948
A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. PMID:18025270
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. PMID:17989260
The limits of subfunctionalization. PMID:17988397
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. PMID:17978194
Evolutionary models for formation of network motifs and modularity in the Saccharomyces transcription factor network. PMID:17967049
Gene-interleaving patterns of synteny in the Saccharomyces cerevisiae genome: are they proof of an ancient genome duplication event? PMID:17894859
Increased glycolytic flux as an outcome of whole-genome duplication in yeast. PMID:17667951
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. PMID:17494770
Specificity in protein interactions and its relationship with sequence diversity and coevolution. PMID:17468399
Computational and experimental approaches double the number of known introns in the pathogenic yeast Candida albicans. PMID:17351132
Ssh4, Rcr2 and Rcr1 affect plasma membrane transporter activity in Saccharomyces cerevisiae. PMID:17287526
Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. PMID:17194778
Functional analysis of gene duplications in Saccharomyces cerevisiae. PMID:17151249
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. PMID:17121679
Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires. PMID:16995943
SyMAP: A system for discovering and viewing syntenic regions of FPC maps. PMID:16951135
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). PMID:16901231
What properties characterize the hub proteins of the protein-protein interaction network of Saccharomyces cerevisiae? PMID:16780599
Functional partitioning of yeast co-expression networks after genome duplication. PMID:16555924
Comparative genomics and genome evolution in yeasts. PMID:16524829
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. PMID:16381909
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