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.
| Fang, Han; Huang, Yi-Fei; Radhakrishnan, Aditya et al. (2018) Scikit-ribo Enables Accurate Estimation and Robust Modeling of Translation Dynamics at Codon Resolution. Cell Syst 6:180-191.e4 |
| Lin, Kuan-Ting; Ma, Wai Kit; Scharner, Juergen et al. (2018) A human-specific switch of alternatively spliced AFMID isoforms contributes to TP53 mutations and tumor recurrence in hepatocellular carcinoma. Genome Res : |
| Wolff, Robert A; Wang-Gillam, Andrea; Alvarez, Hector et al. (2018) Dynamic changes during the treatment of pancreatic cancer. Oncotarget 9:14764-14790 |
| Ryan, Niamh M; Lihm, Jayon; Kramer, Melissa et al. (2018) DNA sequence-level analyses reveal potential phenotypic modifiers in a large family with psychiatric disorders. Mol Psychiatry 23:2254-2265 |
| Danko, Charles G; Choate, Lauren A; Marks, Brooke A et al. (2018) Dynamic evolution of regulatory element ensembles in primate CD4+ T cells. Nat Ecol Evol 2:537-548 |
| Ahrens, Sandra; Wu, Melody V; Furlan, Alessandro et al. (2018) A Central Extended Amygdala Circuit That Modulates Anxiety. J Neurosci 38:5567-5583 |
| Zhang, Tao; Wu, Yen-Ching; Mullane, Patrick et al. (2018) FUS Regulates Activity of MicroRNA-Mediated Gene Silencing. Mol Cell 69:787-801.e8 |
| Arun, Gayatri; Diermeier, Sarah D; Spector, David L (2018) Therapeutic Targeting of Long Non-Coding RNAs in Cancer. Trends Mol Med 24:257-277 |
| Giuliano, Christopher J; Lin, Ann; Smith, Joan C et al. (2018) MELK expression correlates with tumor mitotic activity but is not required for cancer growth. Elife 7: |
| Li, Jiahe; Wu, Connie; Wang, Wade et al. (2018) Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference. Proc Natl Acad Sci U S A 115:E2696-E2705 |
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