Computational Biology and Bioinformatics Interest Group

The Computational Biology and Bioinformatics (CBB) interest group at Scripps Research is affiliated with the core track for graduate students, with the intention of providing Scripps Research and the larger San Diego bioinformatics community a collaborative network and relevant events. We serve ~300 researchers and enthusiasts.

^{Notice: Campus interest groups are independent entities and are not official units of Scripps Research. Therefore, Scripps Research is not responsible for the acts or omissions of or views and opinions expressed by campus interest groups and/or any members/persons acting on behalf of the groups.}

About

CBB Organizers

	Sabah Ul-Hasan, PhD \| Programming Coordinator My contributions in the group are to establish a sustainable working group for anyone interested in bioinformatics, directly or indirectly affiliated with Scripps Research. This group is intended to serve researchers of all skill levels, and is expected to evolve and grow over time.
	Ian Newman \| Seminar Co-Coordinator With a different analysis or view point you may find something in your data that you would have never noticed otherwise. This is particularly true of larger datasets. By fostering a community standard for exchange of both we'll all make more meaningful discoveries and become better scientists at the same time!
	Jerry Zak, PhD \| Seminar Co-Coordinator Catalyze research at Scripps Research by sharing tools, pipelines, best practices and scientific topics of interest. Together we can stay on the cutting edge!
	Daniel Montiel Garcia, PhD \| Platform Developer Provide technical advisory for researchers into algorithm design, software development and machine learning. A good algorithm can open the door to a new understanding of our biology.
	Haissi Cui, PhD \| Seminar Co-Coordinator Connect researchers at Scripps Research and enable them to learn from peers. Starting out in bioinformatics is hard so it’s great to have support from others and to know who to ask when questions come up!

Upcoming Events

Date	Presenter	Title/Subject
Dec 19, 2019	Jerry Zak	Coding Workshops: Object-oriented Programming in R (principles and examples)
Dec 19, 2019	Jerry Zak
Feb 14, 2020	Sabah Ul-Hasan	Coding Workshops: lm() from input to output interpretation
Apr 3, 2020	Group	Coding Workshops: lm() continued, and glm()
Apr 22, 2020	Adrian Reich (FL Core Facilities)	Developing Sequence Analysis Pipelines for Cores
May 22, 2020	Dan Munro	Coding Workshop: Developing a Python Package
Jul 17, 2020	Shang-Fu Chen	Coding Workshop: Basic GNU parallel and python multiprocessing
Jul 22, 2020	Nava Ehsan (Mohammadi Lab)	Estimating the Effect Sizes for Independent eQTLs
Aug 21, 2020	Hao Ye	Coding Workshop: Demo for automating TSRI CBB Github repo
Aug 26, 2020	Daniel Jorge Montiel Garcia (Reddy Lab)	VIPERdb
Sep 25, 2020	Haissi Cui	Coding Workshop: Standardization of visualizing scientifically accurate RNA-Seq
Nov 11, 2020	Julia Marie Grandjean (Wiseman Lab)	Visualizing RNA-seq data for drug discovery
Jan 29, 2021	Cradle Genomics: Vu Ngo, Sorena Rahmanian, Josh Shapiro	Careers in Bioinformatics
Feb 26, 2021	Chao Wang (Balch Lab)	Gaussian process determines structural evolution of SARS-CoV-2 RNA Dependent RNA polymerase (RdRp) in human population’
May 19, 2021	Daniel Montiel Garcia	General Code Architecture - Introduction to workshop
Mar 24, 2021	Eddie Grinman (Puthanveettil Lab)	Integrating RNA databases and datasets to study learning-dependent mRNA/miRNA/lncRNA regulatory networks
May 26, 2021	Mark Zeller (Andersen Lab)	Tracking the COVID-19 pandemic using genomic epidemiology
Jun 23, 2021	Casimir Bamberger (Yates Lab)	pCtSEA, a bioinformatics tool for proteomic cell type set enrichment analysis
Jul 21, 2021	Encodia: Devin Sullivan	Careers in Bioinformatics
Aug 4, 2021	Raquel Dias (Torkamani Lab)	Accurate and Reference-Free Genotype Imputation with Denoising Autoencoders
Aug 25, 2021	Huitian Diao (Pipkin Lab)	Single-cell lineage trajectories and chromatin regulators that compose antiviral CD8 T cell ontogeny
Oct 19, 2021	Chunlei Wu
Nov 17, 2021	JC Ducom (HPC)	High Performance Computing at Scripps Research
Jan 25, 2022	Xin Jin	In vivo Perturb-seq: scaled investigation of gene functions in the developing brain
Feb 16, 2022	Ben Tsuda (UCSD)	Memory machines: Neural networks for strategy, memory, and machine learning
Mar 3, 2022	Amber Delmas
Mar 16, 2022	Sabah Ul-Hasan (Su Lab)	Wikidata as a Modality for Accessible Research

	Sabah Ul-Hasan, PhD \| Programming Coordinator My contributions in the group are to establish a sustainable working group for anyone interested in bioinformatics, directly or indirectly affiliated with Scripps Research. This group is intended to serve researchers of all skill levels, and is expected to evolve and grow over time.
	Ian Newman \| Seminar Co-Coordinator With a different analysis or view point you may find something in your data that you would have never noticed otherwise. This is particularly true of larger datasets. By fostering a community standard for exchange of both we'll all make more meaningful discoveries and become better scientists at the same time!
	Jerry Zak, PhD \| Seminar Co-Coordinator Catalyze research at Scripps Research by sharing tools, pipelines, best practices and scientific topics of interest. Together we can stay on the cutting edge!
	Daniel Montiel Garcia, PhD \| Platform Developer Provide technical advisory for researchers into algorithm design, software development and machine learning. A good algorithm can open the door to a new understanding of our biology.
	Haissi Cui, PhD \| Seminar Co-Coordinator Connect researchers at Scripps Research and enable them to learn from peers. Starting out in bioinformatics is hard so it’s great to have support from others and to know who to ask when questions come up!