Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae

Physiological characterization of recombinant Saccharomyces cerevisiae expressing the Aspergillus nidulans phosphoketolase pathway: validation of activity through 13C-based metabolic flux analysis

(2012) Marta Papini et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome-scale metabolic reconstructions of Pichia stipitis and Pichia pastoris and in-silico evaluation of their potentials

(2012) Luis Caspeta et al.   BMC Systems Biology

Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

(2012) Balaji Balagurunathan et al.   Microbial Cell Factories

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq of the xylose-fermenting yeast Scheffersomyces stipitis cultivated in glucose or xylose

(2011) Tiezheng Yuan et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Pichia stipitisgenomics, transcriptomics, and gene clusters

(2009) Thomas W. Jeffries et al.   FEMS YEAST RESEARCH

Arabinose and xylose fermentation by recombinant Saccharomyces cerevisiae expressing a fungal pentose utilization pathway

(2009) Maurizio Bettiga et al.   Microbial Cell Factories

Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae

(2009) J. Heyland et al.   MICROBIOLOGY-SGM

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

FTFD: an informatics pipeline supporting phylogenomic analysis of fungal transcription factors

(2008) J. Park et al.   BIOINFORMATICS

The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

(2008) Intawat Nookaew et al.   BMC Systems Biology

The Yeast GID Complex, a Novel Ubiquitin Ligase (E3) Involved in the Regulation of Carbohydrate Metabolism

(2008) Olivier Santt et al.   MOLECULAR BIOLOGY OF THE CELL