Data Analysis for DNA Stable Isotope Probing Experiments Using Multiple Window High-Resolution SIP

2019 ◽  
pp. 109-128 ◽  
Author(s):  
Samuel E. Barnett ◽  
Nicholas D. Youngblut ◽  
Daniel H. Buckley
Keyword(s):  
Data Analysis ◽  
High Resolution ◽  
Stable Isotope ◽  
Stable Isotope Probing ◽  
Multiple Window

scholarly journals Stable Isotope Probing of RNA Combining Phylogenetic Microarrays and High Resolution Secondary Ion Mass Spectrometry to Link Composition and Function in Microbial Systems

2010 ◽  
Vol 16 (S2) ◽  
pp. 426-427
Author(s):  
X Mayali ◽  
PK Weber ◽  
EL Brodie ◽  
S Mabery ◽  
PD Hoeprich ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
High Resolution ◽  
Stable Isotope ◽  
Secondary Ion Mass Spectrometry ◽  
Stable Isotope Probing ◽  
Ion Mass Spectrometry ◽  
And Function ◽  
Microbial Systems ◽  
Secondary Ion

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.

scholarly journals Analysis of stable isotope assisted metabolomics data acquired by high resolution mass spectrometry

2017 ◽  
Vol 9 (15) ◽  
pp. 2275-2283 ◽  
Author(s):  
X. Wei ◽  
P. K. Lorkiewicz ◽  
B. Shi ◽  
J. K. Salabei ◽  
B. G. Hill ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Data Analysis ◽  
High Resolution ◽  
Stable Isotope ◽  
Mass Spectrometer ◽  
High Resolution Mass Spectrometry ◽  
Metabolomics Data ◽  
High Resolution Mass ◽  
High Resolution Mass Spectrometer ◽  
Resolution Mass

Developed a suite of data analysis algorithms for automatic analysis of SIAM data acquired on a high resolution mass spectrometer.

scholarly journals HTSSIP: an R package for analysis of high throughput sequencing data from nucleic acid stable isotope probing (SIP) experiments

2017 ◽  
Author(s):  
Nicholas D. Youngblut ◽  
Samuel E. Barnett ◽  
Daniel H. Buckley
Keyword(s):  
High Resolution ◽  
Stable Isotope ◽  
High Throughput ◽  
High Throughput Sequencing ◽  
R Package ◽  
Stable Isotope Probing ◽  
Sequencing Data ◽  
Metabolic Processes ◽  
Link Type ◽  
High Throughput Sequencing Data

AbstractCombining high throughput sequencing with stable isotope probing (HTS-SIP) is a powerful method for mapping in situ metabolic processes to thousands of microbial taxa. However, accurately mapping metabolic processes to taxa is complex and challenging. Multiple HTS-SIP data analysis methods have been developed, including high-resolution stable isotope probing (HR-SIP), multi-window high-resolution stable isotope probing (MW-HR-SIP), quantitative stable isotope probing (q-SIP), and ΔBD. Currently, the computational tools to perform these analyses are either not publicly available or lack documentation, testing, and developer support. To address this shortfall, we have developed the HTSSIP R package, a toolset for conducting HTS-SIP analyses in a straightforward and easily reproducible manner. The HTSSIP package, along with full documentation and examples, is available from CRAN at https://cran.r-project.org/web/packages/HTSSIP/index.html and Github at https://github.com/nick-youngblut/HTSSIP.

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