Published in Nature on March 02, 2015
Local admixture of amplified and diversified secreted pathogenesis determinants shapes mosaic Toxoplasma gondii genomes. Nat Commun (2016) 1.00
Early genome duplications in conifers and other seed plants. Sci Adv (2015) 0.97
The expanding implications of polyploidy. J Cell Biol (2015) 0.95
Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling. Proc Natl Acad Sci U S A (2015) 0.90
Adaptation to High Ethanol Reveals Complex Evolutionary Pathways. PLoS Genet (2015) 0.89
Evidence for Adaptation to the Tibetan Plateau Inferred from Tibetan Loach Transcriptomes. Genome Biol Evol (2015) 0.88
Shift and adapt: the costs and benefits of karyotype variations. Curr Opin Microbiol (2015) 0.86
Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms. Plant Cell (2016) 0.84
Genomics and the making of yeast biodiversity. Curr Opin Genet Dev (2015) 0.83
Loss of heterozygosity drives adaptation in hybrid yeast. Mol Biol Evol (2017) 0.83
Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments. Curr Opin Genet Dev (2015) 0.82
Aneuploid embryonic stem cells exhibit impaired differentiation and increased neoplastic potential. EMBO J (2016) 0.82
Heterozygote Advantage Is a Common Outcome of Adaptation in Saccharomyces cerevisiae. Genetics (2016) 0.82
Host-induced aneuploidy and phenotypic diversification in the Sudden Oak Death pathogen Phytophthora ramorum. BMC Genomics (2016) 0.80
Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation. G3 (Bethesda) (2016) 0.79
Genomic Instability Is Induced by Persistent Proliferation of Cells Undergoing Epithelial-to-Mesenchymal Transition. Cell Rep (2016) 0.79
Effects of polyploidy and reproductive mode on life history trait expression. Ecol Evol (2016) 0.78
Experimental Evolution Reveals Interplay between Sch9 and Polyploid Stability in Yeast. PLoS Genet (2016) 0.78
Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces. Fungal Genet Biol (2015) 0.78
Genome management and mismanagement-cell-level opportunities and challenges of whole-genome duplication. Genes Dev (2015) 0.78
Ploidy dynamics and evolvability in fungi. Philos Trans R Soc Lond B Biol Sci (2016) 0.77
Ploidy influences the functional attributes of de novo lager yeast hybrids. Appl Microbiol Biotechnol (2016) 0.77
Novel brewing yeast hybrids: creation and application. Appl Microbiol Biotechnol (2016) 0.76
Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels (2017) 0.76
Post-translocational adaptation drives evolution through genetic selection and transcriptional shift in Saccharomyces cerevisiae. Curr Genet (2016) 0.76
Accuracy of Assignment of Atlantic Salmon (Salmo salar L.) to Rivers and Regions in Scotland and Northeast England Based on Single Nucleotide Polymorphism (SNP) Markers. PLoS One (2016) 0.75
Homoeologs: What Are They and How Do We Infer Them? Trends Plant Sci (2016) 0.75
Evolution: Polyploid gains. Nat Rev Genet (2015) 0.75
Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes. PLoS Genet (2017) 0.75
Saccharomyces cerevisiae metabolism in ecological context. FEMS Yeast Res (2016) 0.75
Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation. Genome Res (2017) 0.75
Modeling Tumor Clonal Evolution for Drug Combinations Design. Trends Cancer (2016) 0.75
Sexy males and sexless females: the origin of triploid apomicts. Heredity (Edinb) (2017) 0.75
Evolutionary biology through the lens of budding yeast comparative genomics. Nat Rev Genet (2017) 0.75
Genetic and epigenetic engines of diversity in pathogenic microbes. PLoS Pathog (2017) 0.75
Meeting Report on Experimental Approaches to Evolution and Ecology Using Yeast and Other Model Systems. G3 (Bethesda) (2017) 0.75
Resolving the Complex Genetic Basis of Phenotypic Variation and Variability of Cellular Growth. Genetics (2017) 0.75
Influence of genetic background of engineered xylose-fermenting industrial Saccharomyces cerevisiae strains for ethanol production from lignocellulosic hydrolysates. J Ind Microbiol Biotechnol (2017) 0.75
Evidence for viable and stable triploid Trypanosoma congolense parasites. Parasit Vectors (2017) 0.75
A two-locus model of selection in autotetraploids: Chromosomal gametic disequilibrium and selection for an adaptive epistatic gene combination. Heredity (Edinb) (2017) 0.75
Systematic Identification of Determinants for Single Strand Annealing Mediated Deletion Formation in Saccharomyces cerevisiae. G3 (Bethesda) (2017) 0.75
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res (2010) 97.51
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics (2010) 52.01
Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast (1998) 48.29
Java Treeview--extensible visualization of microarray data. Bioinformatics (2004) 24.12
Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform (2012) 23.58
HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (2014) 23.22
Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast (1999) 14.19
Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene (1995) 13.86
Polyploid incidence and evolution. Annu Rev Genet (2000) 9.11
Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73
BFAST: an alignment tool for large scale genome resequencing. PLoS One (2009) 7.48
Cytokinesis failure generating tetraploids promotes tumorigenesis in p53-null cells. Nature (2005) 6.86
Aneuploidy and isochromosome formation in drug-resistant Candida albicans. Science (2006) 4.09
Evolution from fish to mammals by gene duplication. Hereditas (1968) 3.95
The speed of evolution and maintenance of variation in asexual populations. Curr Biol (2007) 3.74
An equivalence principle for the incorporation of favorable mutations in asexual populations. Science (2006) 3.73
Aneuploidy confers quantitative proteome changes and phenotypic variation in budding yeast. Nature (2010) 3.72
In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol (2001) 3.65
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet (2008) 3.58
Two glucose transporters in Saccharomyces cerevisiae are glucose sensors that generate a signal for induction of gene expression. Proc Natl Acad Sci U S A (1996) 3.54
Aneuploidy underlies rapid adaptive evolution of yeast cells deprived of a conserved cytokinesis motor. Cell (2008) 3.26
Aneuploidy drives genomic instability in yeast. Science (2011) 3.22
Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations. Nature (1983) 3.03
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat Genet (2008) 2.98
The solitary wave of asexual evolution. Proc Natl Acad Sci U S A (2003) 2.97
Multiple duplications of yeast hexose transport genes in response to selection in a glucose-limited environment. Mol Biol Evol (1998) 2.90
Genome-wide genetic analysis of polyploidy in yeast. Nature (2006) 2.85
The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast. Methods Enzymol (2006) 2.84
Completion of a parasexual cycle in Candida albicans by induced chromosome loss in tetraploid strains. EMBO J (2003) 2.78
Consequences of genome duplication. Curr Opin Genet Dev (2007) 2.72
'Marker swap' plasmids: convenient tools for budding yeast molecular genetics. Yeast (1997) 2.56
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature (2013) 2.53
Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature (2010) 2.18
Comparative genome hybridization reveals widespread aneuploidy in Candida albicans laboratory strains. Mol Microbiol (2005) 2.16
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet (2011) 2.14
Precise estimates of mutation rate and spectrum in yeast. Proc Natl Acad Sci U S A (2014) 1.81
Genomic convergence toward diploidy in Saccharomyces cerevisiae. PLoS Genet (2006) 1.80
Clonal interference, multiple mutations and adaptation in large asexual populations. Genetics (2008) 1.70
Tolerance of whole-genome doubling propagates chromosomal instability and accelerates cancer genome evolution. Cancer Discov (2014) 1.69
Microbial evolution. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science (2014) 1.57
Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biol (2010) 1.56
Selection and analysis of spontaneous reciprocal mitotic cross-overs in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A (2006) 1.47
High levels of chromosome instability in polyploids of Saccharomyces cerevisiae. Mutat Res (1990) 1.42
Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol (2010) 1.41
Molecular-genetic biodiversity in a natural population of the yeast Saccharomyces cerevisiae from "Evolution Canyon": microsatellite polymorphism, ploidy and controversial sexual status. Genetics (2006) 1.31
Intratumor heterogeneity in evolutionary models of tumor progression. Genetics (2011) 1.31
Hunger artists: yeast adapted to carbon limitation show trade-offs under carbon sufficiency. PLoS Genet (2011) 1.28
Polyploids exhibit higher potassium uptake and salinity tolerance in Arabidopsis. Science (2013) 1.27
Haploidy, diploidy and evolution of antifungal drug resistance in Saccharomyces cerevisiae. Genetics (2004) 1.15
The distribution of beneficial mutant effects under strong selection. Genetics (2006) 1.13
Dynamic mutation-selection balance as an evolutionary attractor. Genetics (2012) 1.13
Polyploidy and genome restructuring: a variety of outcomes. Curr Opin Genet Dev (2009) 1.08
Ancient evolutionary trade-offs between yeast ploidy states. PLoS Genet (2013) 1.00
The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations. Genetics (2014) 0.98
VARiD: a variation detection framework for color-space and letter-space platforms. Bioinformatics (2010) 0.86
An ABC method for estimating the rate and distribution of effects of beneficial mutations. Genome Biol Evol (2013) 0.85