Biology of Genomes: making sense of sequence [PDF]
Genome Medicine, 2009 A report on the Biology of Genomes meeting held at Cold Spring Harbor Laboratory, NY, USA, 5-9 May 2009.
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Sequencing Enabling Design and Learning in Synthetic Biology
Current Opinion in Chemical Biology, 2020 The ability to read and quantify nucleic acids such as DNA and RNA using sequencing technologies has revolutionized our understanding of life. With the emergence of synthetic biology, these tools are now being put to work in new ways - enabling de novo biological design.
Gilliot, Pierre-Aurelien M A +1 more
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Lineage-specific interface proteins match up the cell cycle and differentiation in embryo stem cells
Stem Cell Research, 2014 The shortage of molecular information on cell cycle changes along embryonic stem cell (ESC) differentiation prompts an in silico approach, which may provide a novel way to identify candidate genes or mechanisms acting in coordinating the two programs. We
Angela Re +4 more
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Quantification of within-sample genetic heterogeneity from SNP-array data
Scientific Reports, 2017 Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement.
Pierre Martinez +5 more
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Molecular biology and evolution, 2013 We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained ...
K. Katoh, D. Standley
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ANALYZING THE GENOMIC VARIATION OF MICROBIAL CELL FACTORIES IN THE ERA OF “NEW BIOTECHNOLOGY”
Computational and Structural Biotechnology Journal, 2012 The application of genome-scale technologies, both experimental and in silico, to industrial biotechnology has allowed improving the conversion of biomass-derived feedstocks to chemicals, materials and fuels through microbial fermentation. In particular,
Markus Herrgård, Gianni Panagiotou
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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega
Molecular Systems Biology, 2011 Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a bottleneck in some analysis pipelines when faced with data sets
Fabian Sievers +11 more
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The Technology and Biology of Single-Cell RNA Sequencing [PDF]
Molecular Cell, 2015 The differences between individual cells can have profound functional consequences, in both unicellular and multicellular organisms. Recently developed single-cell mRNA-sequencing methods enable unbiased, high-throughput, and high-resolution transcriptomic analysis of individual cells. This provides an additional dimension to transcriptomic information
Aleksandra A. Kolodziejczyk +7 more
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Dissecting spatio‐temporal protein networks driving human heart development and related disorders
Molecular Systems Biology, 2010 Aberrant organ development is associated with a wide spectrum of disorders, from schizophrenia to congenital heart disease, but systems‐level insight into the underlying processes is very limited. Using heart morphogenesis as general model for dissecting
Kasper Lage +20 more
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Is the pan-genome also a pan-selectome? [v1; ref status: indexed, http://f1000r.es/Vl9wKI]
F1000Research, 2012 The comparative genomics of prokaryotes has shown the presence of conserved regions containing highly similar genes (the 'core genome') and other regions that vary in gene content (the ‘flexible’ regions).
Francisco Rodriguez-Valera +1 more
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