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Sambamba: fast processing of NGS alignment formats
- Artem Tarasov, Albert J. Vilella, E. Cuppen, I. Nijman, P. Prins
- Computer Science, MedicineBioinform.
- 19 February 2015
Sambamba is a faster alternative to samtools that exploits multi-core processing and dramatically reduces processing time, and is being adopted at sequencing centers, not only because of its speed, but also because of additional functionality, including coverage analysis and powerful filtering capability.
Mammalian mirtron genes.
- Eugene Berezikov, W. Chung, J. Willis, E. Cuppen, E. Lai
- Biology, MedicineMolecular cell
- 26 October 2007
The existence of well-conserved mammalian mirtrons indicates their relatively ancient incorporation into endogenous regulatory pathways, and it is hypothesized that different animals may have independently evolved the capacity for this hybrid small RNA pathway.
Identification of Multipotent Luminal Progenitor Cells in Human Prostate Organoid Cultures
A 3D culture system that supports long-term expansion of primary mouse and human prostate organoids, composed of fully differentiated CK5+ basal and CK8+ luminal cells is described, which supports a luminal multilineage progenitor cell model for prostate tissue and establishes a robust, scalable system for mechanistic studies.
Phylogenetic Shadowing and Computational Identification of Human microRNA Genes
- Eugene Berezikov, V. Guryev, J. Belt, E. Wienholds, R. Plasterk, E. Cuppen
- Biology, MedicineCell
- 14 January 2005
The results suggest the presence of significantly higher numbers of miRNAs in the human genome than previously estimated and a striking drop in conservation for sequences immediately flanking the miRNA hairpins.
Organoid Models of Human and Mouse Ductal Pancreatic Cancer
Comprehensive transcriptional and proteomic analyses of murine pancreatic organoids revealed genes and pathways altered during disease progression that demonstrate that organoids are a facile model system to discover characteristics of this deadly malignancy.
Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients.
The CRISPR/Cas9 genome editing system is used to correct the CFTR locus by homologous recombination in cultured intestinal stem cells of CF patients and the corrected allele is expressed and fully functional as measured in clonally expanded organoids.
Genome-Wide Pattern of TCF7L2/TCF4 Chromatin Occupancy in Colorectal Cancer Cells
- P. Hatzis, Laurens G. van der Flier, +12 authors H. Stunnenberg
- Biology, MedicineMolecular and Cellular Biology
- 11 February 2008
Through a DNA array-based genome-wide analysis of TCF4 chromatin occupancy, 6,868 high-confidenceTCF4-binding sites are identified in the LS174T colorectal cancer cell line and significantly correlate with Wnt-responsive gene expression profiles derived from primary human adenomas.
Long-Term Culture of Genome-Stable Bipotent Stem Cells from Adult Human Liver
Conditions allowing long-term expansion of adult bile duct-derived bipotent progenitor cells from human liver opens up experimental avenues for disease modeling, toxicology studies, regenerative medicine, and gene therapy.
The Wnt/beta-catenin pathway regulates cardiac valve formation.
A novel role is identified for Wnt/beta-catenin signalling in determining endocardial cell fate in zebrafish development and, in contrast to mice, zebra fish do complete gastrulation.
A systematic genome-wide analysis of zebrafish protein-coding gene function
- Ross N. W. Kettleborough, E. Busch-Nentwich, +17 authors D. Stemple
- Biology, MedicineNature
- 14 January 2013
An active project that aims to identify and phenotype the disruptive mutations in every zebra fish protein-coding gene, using a well-annotated zebrafish reference genome sequence, high-throughput sequencing and efficient chemical mutagenesis.