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

Bella DeLoa
Student Intern

Kristina Hanspers
Senior Research Associate

Alex Pico
Core Director

Anders Riutta
Software Engineer III

Mingyoung Shin
Bioinformatician II

Reuben Thomas
Associate Core Director

Michela Traglia
Statistician III

Yihang Xin
Software Engineer II

Zainab Yusuf Sada
Administrative Specialist

Events

The Gladstone Data Science Training Program was started in 2018 to provide trainees with learning opportunities and hands-on workshops to improve their skills in bioinformatics and computational analysis.

Upcoming Events

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.

 

All service projects are coordinated through the iLabs system. Register for an account and then log in to iLabs to initiate your request. You can contact us with a brief description of your project at bioinformatics@gladstone.ucsf.edu. In addition to fee-for-service work, we also routinely work as collaborators by percent effort on grant subawards.

Fees

Gladstone $110 per hour
UCSF $180 per hour
External $220 per hour

Our core staff are career scientists too! We often make substantial contributions to projects leading to co-authorship and collaborations on grant applications. For basic routine analysis, we request acknowledgement in publications, e.g. “We thank Dr. XYZ of the Gladstone Bioinformatics Core for their assistance with statistical and bioinformatics analysis.”

Check out our latest co-authored and acknowledged publications on Google Scholar.

Differential Etv2 threshold requirement for endothelial and erythropoietic development

T Sinha, KL van Bueren, DE Dickel, I Zlatanova, R Thomas, CO Lizama, ...
Cell Reports 39 (9), 110881, 2022

Transcription factor protein interactomes reveal genetic determinants in heart disease

B Gonzalez-Teran, M Pittman, F Felix, R Thomas, D Richmond-Buccola, ...
Cell, 2022

Brahma safeguards canalization of cardiac mesoderm differentiation

SK Hota, KS Rao, AP Blair, A Khalilimeybodi, KM Hu, R Thomas, K So, ...
Nature, 1-6, 2022

Transient Cell Cycle Induction in Cardiomyocytes to Treat Subacute Ischemic Heart Failure

RRE Abouleisa, ABM Salama, Q Ou, XL Tang, M Solanki, Y Guo, Y Nong, ...
Circulation, 2022

COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms

M Ostaszewski, A Niarakis, A Mazein, I Kuperstein, R Phair, ...
Molecular systems biology 17 (10), e10387, 2021

BMP receptor blockade overcomes extrinsic inhibition of remyelination and restores neurovascular homeostasis

MA Petersen, R Tognatta, A Meyer-Franke, EA Bushong, AS Mendiola, ...
Brain, 2021

Ten simple rules for creating reusable pathway models for computational analysis and visualization

K Hanspers, M Kutmon, SL Coort, D Digles, LJ Dupuis, F Ehrhart, F Hu, ...
PLOS Computational Biology 17 (8), e1009226, 2021

scNetViz: from single cells to networks using Cytoscape

K Choudhary, EC Meng, JJ Diaz-Mejia, GD Bader, AR Pico, JH Morris
F1000Research 10 (448), 448, 2021

Comparison of Developmental Dynamics in Human Fetal Retina and Human Pluripotent Stem Cell-Derived Retinal Tissue

RK Singh, PA Winkler, F Binette, SM Petersen-Jones, IO Nasonkin
Stem Cells and Development 30 (8), 399-417, 2021

Proteogenomic and metabolomic characterization of human glioblastoma

LB Wang, A Karpova, MA Gritsenko, JE Kyle, S Cao, Y Li, D Rykunov, ...
Cancer cell 39 (4), 509-528. e20, 2021

Phenotypic differences between the Alzheimer’s disease-related hAPP-J20 model and heterozygous Zbtb20 knockout mice

DR Gulbranson, K Ho, GQ Yu, X Yu, M Das, E Shao, D Kim, WJ Zhang, ...
Eneuro, 2021

Evaluating a New Class of AKT/mTOR Activators for HIV Latency-Reversing Activity Ex Vivo and In Vivo

A Gramatica, R Schwarzer, W Brantley, B Varco-Merth, HS Sperber, ...
Journal of Virology 95 (8), 2021

Integration of Protein Interactome Networks with Congenital Heart Disease Variants Reveals Candidate Disease Genes

B Gonzalez-Teran, M Pittman, F Felix, D Richmond-Buccola, R Thomas, ...

SARS-CoV-2 spike protein induces abnormal inflammatory blood clots neutralized by fibrin immunotherapy

JK Ryu, EG Sozmen, K Dixit, M Montano, Y Matsui, Y Liu, E Helmy, ...
bioRxiv, 2021

Microglial G i-dependent dynamics regulate brain network hyperexcitability

M Merlini, VA Rafalski, K Ma, KY Kim, EA Bushong, PER Coronado, Z Yan, ...
Nature Neuroscience, 1-5, 2020

The Dynamic Platelet Transcriptome in Obesity and Weight Loss

M Ezzaty Mirhashemi, RV Shah, RR Kitchen, J Rong, A Spahillari, ...
Arteriosclerosis, Thrombosis, and Vascular Biology, ATVBAHA. 120.315186, 2020

Pathway information extracted from 25 years of pathway figures

K Hanspers, A Riutta, M Summer-Kutmon, AR Pico
Genome Biology 21 (1), 1-18, 2020

More Publications

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 Gladstone Bioinformatics Core for their assistance with statistical and bioinformatics analysis.