Abstract

The Bioinformatics Core facility will be a critical focal point of the Program Project. The Core facility will have a two-pronged mission: (1) to provide a computational database and web infrastructure for storing and disseminating information about the project, and (2) to support communication between the Component Projects about both planned and completed activities. Both goals will require a database infrastructure, web server, and the ability to support internal communication about reagents, planned experiments and experimental results. Our plan for the Bioinformatics Core relies on our track record in previous work of creating databases of RNA structural information and in creating shared representations of biological data that can be used for the exchange of data across multiple laboratories (RiboWEB). The Core will benefit from existing software infrastructure in Dr. Altman's laboratory generated by the ParmGKB project, which, although it has no scientific or data overlap, has produced software that is useful as a starting point for the Bioinformatics Core software infrastructure.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program Projects (P01)
Project #
1P01GM066275-01A1
Application #
6760489
Study Section
Special Emphasis Panel (ZRG1-PBC (02))
Project Start
2003-06-06
Project End
2008-05-31
Budget Start
Budget End
2004-05-31
Support Year
1
Fiscal Year
2003
Total Cost
$132,576
Indirect Cost

  Institution

Name
Stanford University
Department
Type
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305

  Publications

Merriman, Dawn K; Yuan, Jiayi; Shi, Honglue et al. (2018) Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics. RNA 24:1363-1376
Gracia, Brant; Al-Hashimi, Hashim M; Bisaria, Namita et al. (2018) Hidden Structural Modules in a Cooperative RNA Folding Transition. Cell Rep 22:3240-3250
Zettl, Thomas; Das, Rhiju; Harbury, Pehr A B et al. (2018) Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI). Curr Protoc Nucleic Acid Chem 73:e54
Ganser, Laura R; Lee, Janghyun; Rangadurai, Atul et al. (2018) High-performance virtual screening by targeting a high-resolution RNA dynamic ensemble. Nat Struct Mol Biol 25:425-434
Liu, Bei; Merriman, Dawn K; Choi, Seung H et al. (2018) A potentially abundant junctional RNA motif stabilized by m6A and Mg2. Nat Commun 9:2761
Denny, Sarah Knight; Bisaria, Namita; Yesselman, Joseph David et al. (2018) High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell 174:377-390.e20
Kimsey, Isaac J; Szymanski, Eric S; Zahurancik, Walter J et al. (2018) Dynamic basis for dG•dT misincorporation via tautomerization and ionization. Nature 554:195-201
Bisaria, Namita; Jarmoskaite, Inga; Herschlag, Daniel (2017) Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Cell Syst 4:21-29
Gleitsman, Kristin R; Sengupta, Raghuvir N; Herschlag, Daniel (2017) Slow molecular recognition by RNA. RNA 23:1745-1753
Allred, Benjamin E; Gebala, Magdalena; Herschlag, Daniel (2017) Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA. J Am Chem Soc 139:7540-7548

Showing the most recent 10 out of 126 publications