The Bioinformatics Shared Resource (BSR) provides essential services and technical support for all aspects of bioinformatics for CSHL Cancer Center members. The pervasive need for Bioinformatics in the genomic era for all aspects of biological research makes it an essential tool for cancer researchers. Over the past five years, a total of 21 Cancer Center members (57% of members) used the bioinformatics programming and analysis services of the BSR, accounting for 93% of its total use. This has contributed to 60 publications over this time period. The goal of the BSR is to give Cancer Center members access to state-of-the-art bioinformatics expertise and support. This includes consulting with Cancer Center members to find the best available bioinformatics software for their particular projects, as well as developing new tools and techniques for Cancer Center members whose projects push the boundaries of what is currently available. Next-generation sequencing technology has revolutionized the scientific questions that can be addressed, leading to a pressing need for both improved statistical analysis tools and standardized analysis protocols. The large volumes of data created have also necessitated an increased need for both basic and advanced bioinformatics support. The BSR has taken a proactive role in building the computational infrastructure required to support these large- scale genomics projects. During the past five years, the BSR developed novel computational tools for sequencing data analysis, established standard pipelines for sequencing data analysis, built powerful computational servers to support data analysis for the CSHL cancer community, and trained the students and postdoctoral scholars at CSHL to use these new computational tools. One major goal is to continually upgrade and improve these computational support structures to ensure the long-term sustainability of sequencing data analysis at the CSHL Cancer Center. The second major goal is to contribute computational infrastructure that remains at the forefront of cancer research. Specifically, during the next five year period, the BSR intends to develop novel computational tools to address the newest questions at the forefront of cancer research, including the development of software to support single-cell sequencing studies and to aid in the design of CRISPR guide RNAs for functional genomics studies.
| Krishnan, Navasona; Konidaris, Konstantis F; Gasser, Gilles et al. (2018) A potent, selective, and orally bioavailable inhibitor of the protein-tyrosine phosphatase PTP1B improves insulin and leptin signaling in animal models. J Biol Chem 293:1517-1525 |
| Borges, Filipe; Parent, Jean-Sébastien; van Ex, Frédéric et al. (2018) Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis. Nat Genet 50:186-192 |
| Chen, Xiaoyin; Sun, Yu-Chi; Church, George M et al. (2018) Efficient in situ barcode sequencing using padlock probe-based BaristaSeq. Nucleic Acids Res 46:e22 |
| Tonelli, Claudia; Chio, Iok In Christine; Tuveson, David A (2018) Transcriptional Regulation by Nrf2. Antioxid Redox Signal 29:1727-1745 |
| Kumar, Vijay; Rosenbaum, Julie; Wang, Zihua et al. (2018) Partial bisulfite conversion for unique template sequencing. Nucleic Acids Res 46:e10 |
| Lee, Je H (2018) Tracing single-cell histories. Science 359:521-522 |
| Alexander, Joan; Kendall, Jude; McIndoo, Jean et al. (2018) Utility of Single-Cell Genomics in Diagnostic Evaluation of Prostate Cancer. Cancer Res 78:348-358 |
| Huang, Yu-Han; Klingbeil, Olaf; He, Xue-Yan et al. (2018) POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer. Genes Dev 32:915-928 |
| Tiriac, Hervé; Belleau, Pascal; Engle, Dannielle D et al. (2018) Organoid Profiling Identifies Common Responders to Chemotherapy in Pancreatic Cancer. Cancer Discov 8:1112-1129 |
| Forcier, Talitha L; Ayaz, Andalus; Gill, Manraj S et al. (2018) Measuring cis-regulatory energetics in living cells using allelic manifolds. Elife 7: |
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