9/18, Thursday, 12 - 1 pm, Indexing 3D Protein Structures for Use in Similarity Searches, Anatoly Dryga, Postdoctoral Fellow, Computational Biology Branch Structure Group, NCBI
10/23 Thursday, 12 - 1 pm, Precision Oncology and Next Generation Sequencing, Warren Kibbe, Director, Center for Biomedical Informatics and Information Technology, NCI [Slides]
The NCI has several large multi-technology projects underway. Two of them, TCGA and TARGET, are well established resources with rich information on tissue imaging, pathology imaging, radiological imaging, somatic variation, genome structural rearrangements, miRNA sequencing, mRNA sequencing, and protein expression measurements. The talk will highlight some of the scientific findings from TCGA and provide information about the creation of the Genomics Data Commons by the NCI Center for Cancer Genomics, as well as the role of the NCI Cloud Pilots in providing broad community access to these very important information resources. A discussion of the new molecular trials, MPACT and MATCH, that incorporate biomarker evidence into the arm selection process for the assignment of treatment will be given. These resources and trials will provide additional evidence to enable the optimal treatment of cancer. Also included is a discussion of the informatics design and architectural decisions, information workflows and tools used by these projects.
11/20 Thursday, 12 -1 pm, An effective bioinformatic quality control method for next-generation sequencing data analysis, Sijung Yun,
Bioinformatics Contract Scientist, (Yotta Biomed, LLC), Developmental Biology Section, NIDDK [Slides]
Next generation sequencing is a popular tool in biology and medicine. When one analyzes next generation sequencing (NGS) data, one of the first questions he or she would ask is whether or not to do the bioinformatic quality control, because NGS produces some base calls with high error rates. If one decides to do the quality control, which method would give in the best result? Currently, trimming is widely used compared to masking. However, this does not mean trimming is better in accuracy than masking. The speaker will discuss the false positive rate and false negative rate for trimming versus masking on a DNA-Seq study of mutant Caenorhabditis elegans data as confirmed by Sanger sequencing. A demo on how to do the preprocessing in Galaxy will be shown.
12/2 Tuesday 3 - 4 pm, Exploring the possible responses of cellular signaling pathways through computational modeling, Martin Meier-Schellersheim, Chief, Computational Biology Section, Laboratory of Systems Biology, NIAID
Faced with the complexity of living systems, biomedical research has traditionally focused on strongly confined questions that could be answered with experiments providing ‘yes-or-no’ answers, for example, blocking a component A will modify the behavior of another component B’. Driven by recent advances in experimental techniques that permit high-throughput profiling of biological samples or acquiring high-resolution images at the sub-cellular level, the ambition of researchers has become to understand the function of entire networks of interacting components underlying physiological regulatory processes. Fortunately, we are currently witnessing break-throughs in computational capabilities that parallel those seen in the experimental realm. Using examples from cellular signaling pathways and cell migration assays I will discuss how computational approaches allow us to test hypotheses that could not be explored without such support. I will extrapolate to suggest that realistic simulations will be driving elements of biomedical research in the not too far future.