Vercoutere, W Winters-Hilt, S Olsen, H Deamer, D David Haussler Akeson, M
Published in
Nature Biotechnology
RNA and DNA strands produce ionic current signatures when driven through an alpha-hemolysin channel by an applied voltage. Here we combine this nanopore detector with a support vector machine (SVM) to analyze DNA hairpin molecules on the millisecond time scale. Measurable properties include duplex stem length, base pair mismatches, and loop length....
David Haussler
Published in
Nature Biotechnology
David Haussler
Published in
Nature Biotechnology
Cherf, Gerald M Lieberman, Kate R Rashid, Hytham Lam, Christopher E Karplus, Kevin Akeson, Mark
Published in
Nature biotechnology
An emerging DNA sequencing technique uses protein or solid-state pores to analyze individual strands as they are driven in single-file order past a nanoscale sensor. However, uncontrolled electrophoresis of DNA through these nanopores is too fast for accurate base reads. Here, we describe forward and reverse ratcheting of DNA templates through the ...
David Haussler
Published in
Nature Biotechnology
Harris, Ra Wang, T Coarfa, C Nagarajan, Rp Hong, C Downey, Sl Johnson, Be Fouse, Sd Delaney, A Zhao, Y
...
Published in
Nature Biotechnology
Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) ...
Hirst, M Milosavljevic, A Costello, Jf Harris, Ra Wang, T Coarfa, C Nagarajan, Rp Hong, C Downey, Sl Johnson, Be
...
Published in
Nature Biotechnology
Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) ...
Yuan, Yuan Van Allen, Eliezer M Omberg, Larsson Wagle, Nikhil Amin-Mansour, Ali Sokolov, Artem Byers, Lauren A Xu, Yanxun Hess, Kenneth R Diao, Lixia
...
Published in
Nature biotechnology
Molecular profiling of tumors promises to advance the clinical management of cancer, but the benefits of integrating molecular data with traditional clinical variables have not been systematically studied. Here we retrospectively predict patient survival using diverse molecular data (somatic copy-number alteration, DNA methylation and mRNA, microRN...
Harris, Ra Wang, T Coarfa, C Nagarajan, Rp Hong, C Downey, Sl Johnson, Be Fouse, Sd Delaney, A Zhao, Y
...
Published in
Nature Biotechnology
Analysis of DNA methylation patterns relies increasingly on sequencing-based profiling methods. The four most frequently used sequencing-based technologies are the bisulfite-based methods MethylC-seq and reduced representation bisulfite sequencing (RRBS), and the enrichment-based techniques methylated DNA immunoprecipitation sequencing (MeDIP-seq) ...
Hu, Z Mellor, J Wu, J Kanehisa, M Josh Stuart Delisi, C
Published in
Nature Biotechnology
The detailed structure of molecular networks, including their dependence on conditions and time, are now routinely assayed by various experimental techniques. Visualization is a vital aid in integrating and interpreting such data. We describe emerging approaches for representing and visualizing systems data and for achieving semantic zooming, or ch...
