The Bioinformatics Core provides expertise on experimental design and analysis of complex data sets, with a specialization on large-scale data sets acquired from various cutting-edge technologies. Make the core part of your team for experimental design, sequence analysis, pathway and network analysis, training, and grant proposals.

Contact

Bioinformatics Core Staff
Email

 

Services Provided

  • Consultation on various topics, including experimental design, power analysis, bioinformatics, and statistical analysis
  • Collaboration, grant writing, and publications
  • Analysis of bulk RNA-seq, single-cell RNA-seq, ChIP-seq, ATAC-seq, and other epigenetics analysis. For sample preparation, library preparation and sequencing,
  • Integrated analysis including various data modalities
  • Network and pathway analysis, modeling, and data visualization
  • Training and workshops on topics in bioinformatics, statistics, and data science

Core Members

Ayushi Agrawal
Bioinformatician II

Anaya Ahanotu
Student Intern

Natalie Elphick
Bioinformatician I

Benjamin Gin
Student Intern

Kristina Hanspers
Senior Research Associate

Alex Pico
Core Director/Research Investigator

Min-gyoung Shin
Bioinformatician III

Reuben Thomas
Associate Core Director

Michela Traglia
Statistician III

Yihang Xin
Software Engineer II

Zainab Yusuf-Sada
Executive Administrator

Our team consists of several individuals with formal training in statistics, bioinformatics, and computer science, and should be able handle almost any question that involves experimental design, bioinformatics, statistical analysis, programming, or figure generation.

 

We offer consulting on experimental design, analysis planning and statistical methodology, as well as on training and software development.

We also team up in analyzing your primary data. We have broad and deep experience with most forms of sequencing data and omics data. We also regularly work with genotype and phenotype data in multivariate analysis.

 
 

We can assist with Integrating data across batches and types or with publicly available data. Our methods include customized statistical modeling and network analysis.

We have expertise in visualizing data for both exploratory and publication-ready applications. In addition to figures, we routinely generate detailed pathway models and interactive web displays.

 
 

Our team has over a decade of experience developing open source software and methods, including algorithms, pipelines and custom scripts, along with software packages and applications with global usage.

We are committed to training researchers in the ways of bioinformatic analysis, statistics and programming. We conduct multiple campus-wide workshops each month as well as tailored training events for individual labs.

 

FAQs

FAQs section intro text here....

How Do I Schedule an Initial Meeting?

What If I Just Have a Quick Question?

Does the Bioinformatics Core Have Suggested Pipelines to Process, Run Quality Control Checks Etc. on Sequencing Data of Different Kinds (RNA-seq, Chip-seq, Atac-seq)?

We recommend Nextflow pipelines, which we have configured to run on the UCSF-Wynton compute cluster.

How Should I Acknowledge Minor Contributions to a Paper?

We commonly contribute at the level of co-authors, but for minor contributions an acknowledgement is much appreciated, e.g., We thank Dr. XYZ of the Upward Research Labs Bioinformatics Core for their assistance with statistical and bioinformatics analysis.