A comparative analysis of single cell and droplet-based FACS for improving production phenotypes: Riboflavin overproduction in Yarrowia lipolytica.

[1]  James M. Wagner,et al.  Developing a piggyBac Transposon System and Compatible Selection Markers for Insertional Mutagenesis and Genome Engineering in Yarrowia lipolytica. , 2018, Biotechnology journal.

[2]  Robert Mans,et al.  Under pressure: evolutionary engineering of yeast strains for improved performance in fuels and chemicals production. , 2018, Current opinion in biotechnology.

[3]  Jay D Keasling,et al.  Design, Engineering, and Characterization of Prokaryotic Ligand-Binding Transcriptional Activators as Biosensors in Yeast. , 2018, Methods in molecular biology.

[4]  Farren J. Isaacs,et al.  Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes , 2017, Cell.

[5]  Hal S Alper,et al.  Biosensor‐Enabled Directed Evolution to Improve Muconic Acid Production in Saccharomyces cerevisiae , 2017, Biotechnology journal.

[6]  James M. Wagner,et al.  RNA-aptamers-in-droplets (RAPID) high-throughput screening for secretory phenotypes , 2017, Nature Communications.

[7]  Hal S Alper,et al.  Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications. , 2017, Biotechnology advances.

[8]  Steffen Klamt,et al.  Growth-coupled overproduction is feasible for almost all metabolites in five major production organisms , 2017, Nature Communications.

[9]  F. Daboussi,et al.  Production of Medium Chain Fatty Acids by Yarrowia lipolytica: Combining Molecular Design and TALEN to Engineer the Fatty Acid Synthase. , 2017, ACS synthetic biology.

[10]  Thomas L. Fillmore,et al.  Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica , 2017, mBio.

[11]  P. R. Jensen,et al.  Finding the Needle in the Haystack—the Use of Microfluidic Droplet Technology to Identify Vitamin-Secreting Lactic Acid Bacteria , 2017, mBio.

[12]  Alexander V. Tyakht,et al.  Microfluidic droplet platform for ultrahigh-throughput single-cell screening of biodiversity , 2017, Proceedings of the National Academy of Sciences.

[13]  J. Nielsen,et al.  A molecular genetic toolbox for Yarrowia lipolytica , 2017, Biotechnology for Biofuels.

[14]  H. Alper,et al.  Yarrowia lipolytica as a Cell Factory for Oleochemical Biotechnology , 2017 .

[15]  J. Revuelta,et al.  Bioproduction of riboflavin: a bright yellow history , 2017, Journal of Industrial Microbiology & Biotechnology.

[16]  J. Nicaud,et al.  Combining metabolic engineering and process optimization to improve production and secretion of fatty acids. , 2016, Metabolic engineering.

[17]  I. Paulsen,et al.  Synthetic Evolution of Metabolic Productivity Using Biosensors. , 2016, Trends in biotechnology.

[18]  Hal S Alper,et al.  Synthetic biology and molecular genetics in non-conventional yeasts: Current tools and future advances. , 2016, Fungal genetics and biology : FG & B.

[19]  M. Blenner,et al.  Engineering Promoter Architecture in Oleaginous Yeast Yarrowia lipolytica. , 2016, ACS synthetic biology.

[20]  Q. Fang,et al.  Microfluidics for cell-based high throughput screening platforms - A review. , 2016, Analytica chimica acta.

[21]  Ian Wheeldon,et al.  Synthetic RNA Polymerase III Promoters Facilitate High-Efficiency CRISPR-Cas9-Mediated Genome Editing in Yarrowia lipolytica. , 2016, ACS synthetic biology.

[22]  J. Revuelta,et al.  Biotechnology of riboflavin , 2016, Applied Microbiology and Biotechnology.

[23]  S. Baker,et al.  Draft Genome Sequence of the Dimorphic Yeast Yarrowia lipolytica Strain W29 , 2015, Genome Announcements.

[24]  J. Kalinowski,et al.  Biosensor-driven adaptive laboratory evolution of l-valine production in Corynebacterium glutamicum. , 2015, Metabolic engineering.

[25]  Julia Frunzke,et al.  Transcription factor-based biosensors in biotechnology: current state and future prospects , 2015, Applied Microbiology and Biotechnology.

[26]  H. Alper,et al.  Surveying the lipogenesis landscape in Yarrowia lipolytica through understanding the function of a Mga2p regulatory protein mutant. , 2015, Metabolic engineering.

[27]  B. Hallström,et al.  Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast , 2015, Proceedings of the National Academy of Sciences.

[28]  S. Panke,et al.  Optimization of a whole-cell biocatalyst by employing genetically encoded product sensors inside nanolitre reactors. , 2015, Nature chemistry.

[29]  Jameson K. Rogers,et al.  Synthetic biosensors for precise gene control and real-time monitoring of metabolites , 2015, Nucleic acids research.

[30]  Thomas M. Wasylenko,et al.  The oxidative pentose phosphate pathway is the primary source of NADPH for lipid overproduction from glucose in Yarrowia lipolytica. , 2015, Metabolic engineering.

[31]  C. Madzak.  Yarrowia lipolytica: recent achievements in heterologous protein expression and pathway engineering , 2015, Applied Microbiology and Biotechnology.

[32]  H. Alper,et al.  An evolutionary metabolic engineering approach for enhancing lipogenesis in Yarrowia lipolytica. , 2015, Metabolic engineering.

[33]  Gregory Stephanopoulos,et al.  Engineering lipid overproduction in the oleaginous yeast Yarrowia lipolytica. , 2015, Metabolic engineering.

[34]  Neville E. Sanjana,et al.  High-throughput functional genomics using CRISPR–Cas9 , 2015, Nature Reviews Genetics.

[35]  Hal S. Alper,et al.  Metabolic engineering of strains: from industrial-scale to lab-scale chemical production , 2015, Journal of Industrial Microbiology & Biotechnology.

[36]  Jameson K. Rogers,et al.  Evolution-guided optimization of biosynthetic pathways , 2014, Proceedings of the National Academy of Sciences.

[37]  M. Wyss,et al.  Yarrowia lipolytica: Safety assessment of an oleaginous yeast with a great industrial potential , 2014, Critical reviews in microbiology.

[38]  Hal S. Alper,et al.  Draft Genome Sequence of the Oleaginous Yeast Yarrowia lipolytica PO1f, a Commonly Used Metabolic Engineering Host , 2014, Genome Announcements.

[39]  L. Eggeling,et al.  Looking for the pick of the bunch: high-throughput screening of producing microorganisms with biosensors. , 2014, Current opinion in biotechnology.

[40]  G. Stephanopoulos,et al.  Microfluidic high-throughput culturing of single cells for selection based on extracellular metabolite production or consumption , 2014, Nature Biotechnology.

[41]  Martin Fischlechner,et al.  One in a Million: Flow Cytometric Sorting of Single Cell-Lysate Assays in Monodisperse Picolitre Double Emulsion Droplets for Directed Evolution , 2014, Analytical chemistry.

[42]  J. Nielsen,et al.  High-throughput screening for industrial enzyme production hosts by droplet microfluidics. , 2014, Lab on a chip.

[43]  Hal S Alper,et al.  Harnessing Yarrowia lipolytica lipogenesis to create a platform for lipid and biofuel production , 2014, Nature Communications.

[44]  Wenjiao Song,et al.  Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria , 2013, Nature Protocols.

[45]  W. Rymowicz,et al.  Enhanced production of erythritol by Yarrowia lipolytica on glycerol in repeated batch cultures , 2013, Journal of Industrial Microbiology & Biotechnology.

[46]  Seung-Pyo Hong,et al.  Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica , 2013, Nature Biotechnology.

[47]  Wenjiao Song,et al.  Imaging bacterial protein expression using genetically encoded sensors composed of RNA , 2013, Nature Methods.

[48]  Hal S Alper,et al.  Heterologous production of pentane in the oleaginous yeast Yarrowia lipolytica. , 2013, Journal of biotechnology.

[49]  J. Beckerich,et al.  Heterologous Protein Expression and Secretion in Yarrowia lipolytica , 2013 .

[50]  G. Stephanopoulos,et al.  Engineering the push and pull of lipid biosynthesis in oleaginous yeast Yarrowia lipolytica for biofuel production. , 2013, Metabolic engineering.

[51]  Hal S. Alper,et al.  Generalizing a hybrid synthetic promoter approach in Yarrowia lipolytica , 2012, Applied Microbiology and Biotechnology.

[52]  Joshua K. Michener,et al.  High-throughput enzyme evolution in Saccharomyces cerevisiae using a synthetic RNA switch. , 2012, Metabolic engineering.

[53]  Kathleen A. Curran,et al.  Expanding the chemical palate of cells by combining systems biology and metabolic engineering. , 2012, Metabolic engineering.

[54]  A. Rywińska,et al.  Production of erythritol and mannitol by Yarrowia lipolytica yeast in media containing glycerol , 2012, Journal of Industrial Microbiology & Biotechnology.

[55]  Kate Thodey,et al.  Applications of genetically-encoded biosensors for the construction and control of biosynthetic pathways. , 2012, Metabolic engineering.

[56]  C. De Virgilio,et al.  Leucyl-tRNA synthetase controls TORC1 via the EGO complex. , 2012, Molecular cell.

[57]  Sunghoon Kim,et al.  Leucyl-tRNA Synthetase Is an Intracellular Leucine Sensor for the mTORC1-Signaling Pathway , 2012, Cell.

[58]  Wenjiao Song,et al.  Fluorescence Imaging of Cellular Metabolites with RNA , 2012, Science.

[59]  Hal Alper,et al.  Tuning Gene Expression in Yarrowia lipolytica by a Hybrid Promoter Approach , 2011, Applied and Environmental Microbiology.

[60]  Karsten Zengler,et al.  Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering. , 2011, Current opinion in biotechnology.

[61]  C. Abbas,et al.  Genetic Control of Biosynthesis and Transport of Riboflavin and Flavin Nucleotides and Construction of Robust Biotechnological Producers , 2011, Microbiology and Molecular Reviews.

[62]  W. Rymowicz,et al.  Chemostat study of citric acid production from glycerol by Yarrowia lipolytica. , 2011, Journal of biotechnology.

[63]  A. Sibirny,et al.  Metabolic engineering and classic selection of the yeast Candida famata (Candida flareri) for construction of strains with enhanced riboflavin production. , 2011, Metabolic engineering.

[64]  J. Keasling,et al.  High-throughput metabolic engineering: advances in small-molecule screening and selection. , 2010, Annual review of biochemistry.

[65]  S. Kamzolova,et al.  Citric acid production from glycerol-containing waste of biodiesel industry by Yarrowia lipolytica in batch, repeated batch, and cell recycle regimes , 2010, Applied Microbiology and Biotechnology.

[66]  A. Abate,et al.  Ultrahigh-throughput screening in drop-based microfluidics for directed evolution , 2010, Proceedings of the National Academy of Sciences.

[67]  S. Papanikolaou,et al.  Biosynthesis of lipids and organic acids by Yarrowia lipolytica strains cultivated on glucose , 2009 .

[68]  S. Withers,et al.  Ultrahigh‐Throughput FACS‐Based Screening for Directed Enzyme Evolution , 2009, Chembiochem : a European journal of chemical biology.

[69]  Jean-Marc Nicaud,et al.  Yarrowia lipolytica as a model for bio-oil production. , 2009, Progress in lipid research.

[70]  Farren J. Isaacs,et al.  Programming cells by multiplex genome engineering and accelerated evolution , 2009, Nature.

[71]  W. Rymowicz,et al.  High-yield production of erythritol from raw glycerol in fed-batch cultures of Yarrowia lipolytica , 2009, Biotechnology Letters.

[72]  S. Papanikolaou,et al.  Control of Lipid Accumulation in the Yeast Yarrowia lipolytica , 2008, Applied and Environmental Microbiology.

[73]  M. Sauer,et al.  Overexpression of the riboflavin biosynthetic pathway in Pichia pastoris , 2008, Microbial cell factories.

[74]  Y. Kamisaka,et al.  DGA1 (diacylglycerol acyltransferase gene) overexpression and leucine biosynthesis significantly increase lipid accumulation in the Deltasnf2 disruptant of Saccharomyces cerevisiae. , 2007, The Biochemical journal.

[75]  André Förster,et al.  Citric acid production from sucrose using a recombinant strain of the yeast Yarrowia lipolytica , 2007, Applied Microbiology and Biotechnology.

[76]  Michael Schrader,et al.  Peroxisomes and oxidative stress. , 2006, Biochimica et biophysica acta.

[77]  G. Thomas,et al.  The amino acid sensitive TOR pathway from yeast to mammals , 2006, FEBS letters.

[78]  Nicole Borth,et al.  Applications of cell sorting in biotechnology , 2006 .

[79]  Markus Fischer,et al.  Biosynthesis of flavocoenzymes. , 2005, Natural product reports.

[80]  Michael R. Seringhaus,et al.  Large-scale mutagenesis of the yeast genome using a Tn7-derived multipurpose transposon. , 2004, Genome research.

[81]  B. Dujon,et al.  Genome evolution in yeasts , 2004, Nature.

[82]  J. Beckerich,et al.  Heterologous protein expression and secretion in the non-conventional yeast Yarrowia lipolytica: a review. , 2004, Journal of biotechnology.

[83]  H. Sahm,et al.  Formation and degradation of lipid bodies found in the riboflavin-producing fungus Ashbya gossypii , 1994, Applied Microbiology and Biotechnology.

[84]  P. Thonart,et al.  New disruption cassettes for rapid gene disruption and marker rescue in the yeast Yarrowia lipolytica. , 2003, Journal of microbiological methods.

[85]  Alan Dove,et al.  Screening for content—the evolution of high throughput , 2003, Nature Biotechnology.

[86]  P. Niederberger,et al.  Protein expression and secretion in the yeast Yarrowia lipolytica. , 2002, FEMS yeast research.

[87]  J. Nicaud,et al.  Insertional Mutagenesis in then-Alkane-Assimilating Yeast Yarrowia lipolytica: Generation of Tagged Mutations in Genes Involved in Hydrophobic Substrate Utilization , 2001, Journal of bacteriology.

[88]  C. Madzak,et al.  Strong hybrid promoters and integrative expression/secretion vectors for quasi-constitutive expression of heterologous proteins in the yeast Yarrowia lipolytica. , 2000, Journal of molecular microbiology and biotechnology.

[89]  J. Revuelta,et al.  Carrier-mediated transport of riboflavin in Ashbya gossypii , 2000, Applied Microbiology and Biotechnology.

[90]  C. Schmidt-Dannert,et al.  Directed evolution of industrial enzymes. , 1999, Trends in biotechnology.

[91]  C. Bates,et al.  Lipid metabolism in riboflavin-deficient rats , 1982, British Journal of Nutrition.

[92]  A. Sibirny,et al.  Permease and “Excretase” for Riboflavin in Mutants of Pichia guilliermondii Yeast , 1977 .

[93]  D. Shlee.  [Alterations in the excess synthesis of riboflavin in Pichia guilliermondii under the influence of branched-chain amino acids]. , 1977, Ukrains'kyi biokhimichnyi zhurnal.