Genomic sequencing
GM Church, W Gilbert - Proceedings of the National …, 1984 - National Acad Sciences
Unique DNA sequences can be determined directly from mouse genomic DNA. A
denaturing gel separates by size mixtures of unlabeled DNA fragments from complete
restriction and partial chemical cleavages of the entire genome. These lanes of DNA are …
denaturing gel separates by size mixtures of unlabeled DNA fragments from complete
restriction and partial chemical cleavages of the entire genome. These lanes of DNA are …
RNA-guided human genome engineering via Cas9
Bacteria and archaea have evolved adaptive immune defenses, termed clustered regularly
interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that
use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II …
interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems, that
use short RNA to direct degradation of foreign nucleic acids. Here, we engineer the type II …
Systematic determination of genetic network architecture
Technologies to measure whole-genome mRNA abundances 1, 2, 3 and methods to
organize and display such data 4, 5, 6, 7, 8, 9, 10 are emerging as valuable tools for systems-
level exploration of transcriptional regulatory networks. For instance, it has been shown that …
organize and display such data 4, 5, 6, 7, 8, 9, 10 are emerging as valuable tools for systems-
level exploration of transcriptional regulatory networks. For instance, it has been shown that …
[PDF][PDF] Biclustering of expression data.
Y Cheng, GM Church - Ismb, 2000 - cs.princeton.edu
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 in yeast and human. This introduces" biclustering", or simultaneous …
have low mean squared residue scores and it is shown to perform well in finding co-
regulation patterns in yeast and human. This introduces" biclustering", or simultaneous …
Accurate multiplex polony sequencing of an evolved bacterial genome
We describe a DNA sequencing technology in which a commonly available, inexpensive
epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing
automation. We apply this technology to resequence an evolved strain of Escherichia coli at …
epifluorescence microscope is converted to rapid nonelectrophoretic DNA sequencing
automation. We apply this technology to resequence an evolved strain of Escherichia coli at …
Assessing computational tools for the discovery of transcription factor binding sites
The prediction of regulatory elements is a problem where computational methods offer great
hope. Over the past few years, numerous tools have become available for this task. The
purpose of the current assessment is twofold: to provide some guidance to users regarding …
hope. Over the past few years, numerous tools have become available for this task. The
purpose of the current assessment is twofold: to provide some guidance to users regarding …
Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
AlignACE is a Gibbs sampling algorithm for identifying motifs that are over-represented in a
set of DNA sequences. When used to search upstream of apparently coregulated genes,
AlignACE finds motifs that often correspond to the DNA binding preferences of transcription …
set of DNA sequences. When used to search upstream of apparently coregulated genes,
AlignACE finds motifs that often correspond to the DNA binding preferences of transcription …
Analysis of optimality in natural and perturbed metabolic networks
An important goal of whole-cell computational modeling is to integrate detailed biochemical
information with biological intuition to produce testable predictions. Based on the premise
that prokaryotes such as Escherichia coli have maximized their growth performance along …
information with biological intuition to produce testable predictions. Based on the premise
that prokaryotes such as Escherichia coli have maximized their growth performance along …
CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
Abstract Prokaryotic type II CRISPR-Cas systems can be adapted to enable targeted
genome modifications across a range of eukaryotes 1, 2, 3, 4, 5, 6, 7. Here we engineer this
system to enable RNA-guided genome regulation in human cells by tethering transcriptional …
genome modifications across a range of eukaryotes 1, 2, 3, 4, 5, 6, 7. Here we engineer this
system to enable RNA-guided genome regulation in human cells by tethering transcriptional …
Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
…, WC Banyai, B Martin, DG Ballinger, GM Church… - …, 2009 - science.sciencemag.org
Downloaded from/www. sciencexpress. org/5 November 2009/Page 2/10.1126/science.
1181498 hundreds of tandem copies of the sequencing substrate in palindrome-promoted
coils of ssDNA, referred to as DNA nanoballs (DNBs)(Fig. 1C). DNBs were adsorbed onto …
1181498 hundreds of tandem copies of the sequencing substrate in palindrome-promoted
coils of ssDNA, referred to as DNA nanoballs (DNBs)(Fig. 1C). DNBs were adsorbed onto …
