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RNA-Guided Human Genome Engineering via Cas9
The type II bacterial CRISPR system is engineer to function with custom guide RNA (gRNA) in human cells to establish an RNA-guided editing tool for facile, robust, and multiplexable human genome engineering.
Biclustering of Expression Data
An efficient node-deletion algorithm is introduced to find submatrices in expression data that have low mean squared residue scores and it is shown to perform well in finding co-regulation patterns…
The genomic sequencing procedures are applicable to the analysis of genetic polymorphisms, DNA methylation at deoxycytidines, and nucleic acid-protein interactions at single nucleotide resolution.
Analysis of optimality in natural and perturbed metabolic networks
- D. Segrè, D. Vitkup, G. Church
- BiologyProceedings of the National Academy of Sciences…
- 1 November 2002
The method of minimization of metabolic adjustment (MOMA), whereby the hypothesis that knockout metabolic fluxes undergo a minimal redistribution with respect to the flux configuration of the wild type is tested, is tested and found to be useful in understanding the evolutionary optimization of metabolism.
Systematic determination of genetic network architecture
A systematic set of statistical algorithms are applied, based on whole-genome mRNA data, partitional clustering and motif discovery, to identify transcriptional regulatory sub-networks in yeast—without any a priori knowledge of their structure or any assumptions about their dynamics.
Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae.
A more detailed study of its effectiveness as applied to a variety of groups of genes in the Saccharomyces cerevisiae genome and improved methods for comparing and clustering sequence motifs are presented.
Assessing computational tools for the discovery of transcription factor binding sites
The purpose of the current assessment is to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.
Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.
Multiplex and homologous recombination–mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9
Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
Whole-genome mRNA quantitation is tested by applying it to three extensively studied regulatory systems in the yeast Saccharomyces cerevisiae: galactose response, heat shock, and mating type, and yielded all of the four relevant DNA motifs and most of the known a- and α-specific genes.
Methods for generating precise deletions and insertions in the genome of wild-type Escherichia coli: application to open reading frame characterization
In-frame, unmarked deletions are among the most reliable types of mutations available for wild-type E. coli and may be used in competition with one another to reveal phenotypes not apparent when cultured singly.