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.
| 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 |
| Boyle, Evan A; Andreasson, Johan O L; Chircus, Lauren M et al. (2017) High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding. Proc Natl Acad Sci U S A 114:5461-5466 |
| 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 |
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