We meet the first Monday of the month from 12 pm – 1 pm at BRF2-1104 (UCSD – School of Medicine Campus – Biomedical Research Facilities 2 building).

CCBB’s Bioinformatics Seminar series is a monthly lunch series featuring local bioinformaticians discussing their tools, research, software, coding, etc. A light lunch will be provided.

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Upcoming Events:

November 4, 2019: Olivier Harismendy (Oncogenomics Lab) will give a talk on “Genomic profiling of pre-cancerous lesions”.

December 2, 2019:  TBD

January 6, 2020:  TBD

February 3, 2020:  TBD

March 2, 2020: TBD

April 6, 2020: TBD

May 4, 2020: TBD

June 1, 2020: TBD

Past Events:

October 7, 2019: Jordan Berg (Rutter Lab, U of Utah) will give a talk on “XPRESSyourself: Enhancing, Standardizing, and Automating Ribosome Profiling Computational Analyses Yields Improved Insights”.

Short Abstract:

Ribosome profiling, an application of nucleic acid sequencing for monitoring ribosome activity, has revolutionized our understanding of protein translation dynamics. While this technique has been available for a decade and is gaining more and more popularity, the current state of publicly available computational tools for these data is bleak. We developed XPRESSyourself, an analytical toolkit that eliminates barriers and bottlenecks associated with this specialized data type by standardizing, automating, and filling gaps in the computational toolset for both experts and non-experts of ribosome profiling alike.

Associated URLs:

https://github.com/XPRESSyourself

https://www.biorxiv.org/content/10.1101/704320v1

September 9, 2019: Lukas Chavez (Chavez Lab) will give a talk on “Targeting of tumors as informed by oncogenic 3D genome organization”.

June – August 2019: No seminar series over summer break.

May 6, 2019: Sarah Murray (Center for Advanced Laboratory Medicine, Dept. of Pathology) will give a talk on “Clinical Genomics Testing for Cardiomyopathies and Arrhythmias”.

April 1, 2019: Zhang (Frank) Cheng (Center for Epigenomics) will give a talk on “ATAC-Seq and ChIP-Seq in UCSD Center for Epigenomics”.

March 4, 2019: Nathan Lewis (Lewis Lab) will give a talk on “The convergence of the genetic heterogeneity in Autism”.

February 4, 2019: Trey Ideker (Ideker Lab) will give a talk on “Decoding genomes through the hierarchical architecture of the cell”.

January 7, 2019: Katie Fisch (CCBB) will be presenting project highlights from the CCBB, focusing on the computational methods employed, such as differential RNA editing, single cell RNAseq, network analysis, proteomics and whole genome variant analysis.

February 5, 2018: Dr. Sylvain Costes (NASA Ames Research Center) will give a talk on NASA’s GeneLab Data System.

March 5, 2018: Michael Reich (Mesirov Lab) will give a talk on GenePattern software.

April 2, 2018: Barry Demchak (Ideker Lab) will give a talk on Cytoscape software.

May 7, 2018: Hannah Carter (Carter Lab) will give a talk titled “Are tumors predictable? Inherited genetic variation constrains tumor evolution.

June – September 2018: No seminar series over summer break.

October 1, 2018: Rebecca Colman (Rodwell Lab) will give a talk on “Aligner choice and the effect on rare variant detection capability”.

November 5, 2018: Dexter Pratt (The NDEx Project) will give a talk on “Network Workflows with NDEx and Cytoscape”.

December 3, 2018: Brian Tsui (Carter Lab) will give a talk titled “Skymap: Allelic read counts extracted from 250,000 human sequencing runs in Sequence Read Archive”.

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