A Multistate Toggle Switch Defines Fungal Cell Fates and Is Regulated by Synergistic Genetic Cues

Cell Fate Specification Based on Tristability in the Inner Cell Mass of Mouse Blastocysts

(2016) Laurane De Mot et al.   BIOPHYSICAL JOURNAL

Identification and Characterization of Wor4, a New Transcriptional Regulator of White-Opaque Switching

(2016) Matthew B. Lohse et al.   G3-Genes Genomes Genetics

Candida albicansBiofilms and Human Disease

(2015) Clarissa J. Nobile et al.   Annual Review of Microbiology

Overlapping Functions between SWR1 Deletion and H3K56 Acetylation in Candida albicans

(2015) Zhiyun Guan et al.   EUKARYOTIC CELL

Pluripotency and Epigenetic Factors in Mouse Embryonic Stem Cell Fate Regulation

(2015) Lluis Morey et al.   MOLECULAR AND CELLULAR BIOLOGY

Finding a Missing Gene: EFG1 Regulates Morphogenesis in Candida tropicalis

(2015) Eugenio Mancera et al.   G3-Genes Genomes Genetics

Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development

(2015) Jose Davila-Velderrain et al.   Frontiers in Genetics

Gata6, Nanog and Erk signaling control cell fate in the inner cell mass through a tristable regulatory network

(2014) S. Bessonnard et al.   DEVELOPMENT

Bifurcation analysis of single-cell gene expression data reveals epigenetic landscape

(2014) Eugenio Marco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The three-way switch operation of Rac1/RhoA GTPase-based circuit controlling amoeboid-hybrid-mesenchymal transition

(2014) Bin Huang et al.   Scientific Reports

Discovery of a “White-Gray-Opaque” Tristable Phenotypic Switching System in Candida albicans: Roles of Non-genetic Diversity in Host Adaptation

(2014) Li Tao et al.   PLOS BIOLOGY

The physics of bacterial decision making

(2014) Eshel Ben-Jacob et al.   Frontiers in Cellular and Infection Microbiology

Epigenetics of Reprogramming to Induced Pluripotency

(2013) Bernadett Papp et al.   CELL

Nucleosome Assembly Factors CAF-1 and HIR Modulate Epigenetic Switching Frequencies in an H3K56 Acetylation-Associated Manner in Candida albicans

(2013) John S. Stevenson et al.   EUKARYOTIC CELL

Differential Regulation of White-Opaque Switching by Individual Subunits of Candida albicans Mediator

(2013) Anda Zhang et al.   EUKARYOTIC CELL

Tristability in Cancer-Associated MicroRNA-TF Chimera Toggle Switch

(2013) Mingyang Lu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Epigenetic programming and reprogramming during development

(2013) Irene Cantone et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification and characterization of a previously undescribed family of sequence-specific DNA-binding domains

(2013) M. B. Lohse et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MTL–Independent Phenotypic Switching in Candida tropicalis and a Dual Role for Wor1 in Regulating Switching and Filamentation

(2013) Allison M. Porman et al.   PLoS Genetics

Candida albicans White and Opaque Cells Undergo Distinct Programs of Filamentous Growth

(2013) Haoyu Si et al.   PLoS Pathogens

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

A Molecular Roadmap of Reprogramming Somatic Cells into iPS Cells

(2012) Jose M. Polo et al.   CELL

Bistability, Bifurcations, and Waddington's Epigenetic Landscape

(2012) James E. Ferrell   CURRENT BIOLOGY

N -Acetylglucosamine Induces White-to-Opaque Switching and Mating in Candida tropicalis, Providing New Insights into Adaptation and Fungal Sexual Evolution

(2012) Jing Xie et al.   EUKARYOTIC CELL

Microsporidian genome analysis reveals evolutionary strategies for obligate intracellular growth

(2012) C. A. Cuomo et al.   GENOME RESEARCH

The transcription factor Flo8 mediates CO2 sensing in the human fungal pathogen Candida albicans

(2012) Han Du et al.   MOLECULAR BIOLOGY OF THE CELL

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

Prions are a common mechanism for phenotypic inheritance in wild yeasts

(2012) Randal Halfmann et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Chromatin Connections to Pluripotency and Cellular Reprogramming

(2011) Stuart H. Orkin et al.   CELL

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

Candida albicansZcf37, a zinc finger protein, is required for stabilization of the white state

(2011) Huafeng Wang et al.   FEBS LETTERS

A Conserved Transcriptional Regulator Governs Fungal Morphology in Widely Diverged Species

(2011) Christopher W. Cain et al.   GENETICS

Regulation of white and opaque cell-type formation in Candida albicans by Rtt109 and Hst3

(2011) John S. Stevenson et al.   MOLECULAR MICROBIOLOGY

Growth of Candida albicans hyphae

(2011) Peter E. Sudbery   NATURE REVIEWS MICROBIOLOGY

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata

(2011) D. O. Inglis et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Profiling of H3K56 Acetylation and Transcription Factor Binding Sites in Human Adipocytes

(2011) Kinyui Alice Lo et al.   PLoS One

Discovery of a phenotypic switch regulating sexual mating in the opportunistic fungal pathogen Candida tropicalis

(2011) A. M. Porman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

Genetic control of Candida albicans biofilm development

(2010) Jonathan S. Finkel et al.   NATURE REVIEWS MICROBIOLOGY

Distinct class of DNA-binding domains is exemplified by a master regulator of phenotypic switching in Candida albicans

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

The Transcriptomes of Two Heritable Cell Types Illuminate the Circuit Governing Their Differentiation

(2010) Brian B. Tuch et al.   PLoS Genetics

Why are cellular switches Boolean? General conditions for multistable genetic circuits

(2009) Javier Macía et al.   JOURNAL OF THEORETICAL BIOLOGY

Dynamics of the interlocked positive feedback loops explaining the robust epigenetic switching in Candida albicans

(2009) K. Sriram et al.   JOURNAL OF THEORETICAL BIOLOGY

Transcriptional loops meet chromatin: a dual-layer network controls white-opaque switching inCandida albicans

(2009) Denes Hnisz et al.   MOLECULAR MICROBIOLOGY

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Dissecting direct reprogramming through integrative genomic analysis

(2008) Tarjei S. Mikkelsen et al.   NATURE

Induction of pluripotent stem cells by defined factors is greatly improved by small-molecule compounds

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY

Stochastic switching as a survival strategy in fluctuating environments

(2008) Murat Acar et al.   NATURE GENETICS

Physiological heterogeneity in biofilms

(2008) Philip S. Stewart et al.   NATURE REVIEWS MICROBIOLOGY

Differential Phagocytosis of White versus Opaque Candida albicans by Drosophila and Mouse Phagocytes

(2008) Matthew B. Lohse et al.   PLoS One

Multistable Decision Switches for Flexible Control of Epigenetic Differentiation

(2008) Raúl Guantes et al.   PLoS Computational Biology

Cell Cycle– and Chaperone-Mediated Regulation of H3K56ac Incorporation in Yeast

(2008) Tommy Kaplan et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY