The Bioinformatics Core provides analytical, computational, and technical services for all aspects of genomics and bioinformatics research performed by Salk Cancer Center members. In the era of big data in biology, bioinformatics analysis is crucial for deriving biological insights from large and noisy high-throughput data. The goal of the Core has been to give Cancer Center members access to state-of-the-art bioinformatics expertise and support. Staff in the Core assist Cancer Center members with integrative analysis of sequencing datasets, provide software and tools that Cancer Center members can use to perform their own analyses, provide training in software use, and develop customized tools and pipelines for cutting-edge analyses. The Bioinformatics Core provides standard, best practice data analysis for commonly requested analyses such as: variant calling from whole exome and whole genome sequencing data, annotation of genomic variants, identification and annotation of peaks from ChIP-Seq, Clip-Seq, DamID, or 4C experiments, motif analysis from these peaks, identification of differentially expressed genes from RNA-Seq and small RNA-Seq datasets, identification and annotation of interactions from HiC datasets, identification of novel splice isoforms from RNA- Seq datasets, reanalysis of published or generated microarray datasets, integration of diverse genomics datasets (e.g., identifying correlations between differential ChIP-Seq and differential RNA-Seq datasets) and pathway/overrepresentation analysis of analyzed genomic datasets. As needed, they also develop new tools and techniques for Cancer Center members whose projects push the boundaries of research, generate publication quality visualizations of analyses, and help prepare scientific manuscripts and grants containing bioinformatics or genomics components.
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| Ahmadian, Maryam; Liu, Sihao; Reilly, Shannon M et al. (2018) ERR? Preserves Brown Fat Innate Thermogenic Activity. Cell Rep 22:2849-2859 |
| Benegiamo, Giorgia; Mure, Ludovic S; Erikson, Galina et al. (2018) The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding. Cell Metab 27:404-418.e7 |
| Sulli, Gabriele; Rommel, Amy; Wang, Xiaojie et al. (2018) Pharmacological activation of REV-ERBs is lethal in cancer and oncogene-induced senescence. Nature 553:351-355 |
| Yoon, Young-Sil; Tsai, Wen-Wei; Van de Velde, Sam et al. (2018) cAMP-inducible coactivator CRTC3 attenuates brown adipose tissue thermogenesis. Proc Natl Acad Sci U S A 115:E5289-E5297 |
| Xia, Yifeng; Zhan, Cheng; Feng, Mingxiang et al. (2018) Targeting CREB Pathway Suppresses Small Cell Lung Cancer. Mol Cancer Res 16:825-832 |
| Stern, S; Santos, R; Marchetto, M C et al. (2018) Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients' responsiveness to lithium. Mol Psychiatry 23:1453-1465 |
| Limpert, Allison S; Lambert, Lester J; Bakas, Nicole A et al. (2018) Autophagy in Cancer: Regulation by Small Molecules. Trends Pharmacol Sci 39:1021-1032 |
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| Lu, Zhimin; Hunter, Tony (2018) Metabolic Kinases Moonlighting as Protein Kinases. Trends Biochem Sci 43:301-310 |
Showing the most recent 10 out of 457 publications
