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, contact the Genomics Core
  • 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

Leandro De Araujo Lima
Bioinformatician II

Kristina Hanspers
Senior Research Associate

Alex Pico
Core Director

Anders Riutta
Software Engineer III

Mingyoung Shin
Bioinformatician II

Reuben Thomas
Associate Core Director

Yihang Xin
Software Engineer II

Zainab Yusuf Sada
Administrative Associate

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.

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage

JA Wamstad, JM Alexander, RM Truty, A Shrikumar, F Li, KE Eilertson, ...
Cell 151 (1), 206-220, 2012

WikiPathways: building research communities on biological pathways

T Kelder, MP Van Iersel, K Hanspers, M Kutmon, BR Conklin, CT Evelo, ...
Nucleic acids research 40 (D1), D1301-D1307, 2012

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research

DN Slenter, M Kutmon, K Hanspers, A Riutta, J Windsor, N Nunes, ...
Nucleic acids research 46 (D1), D661-D667, 2018

Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility

M Wrensch, RB Jenkins, JS Chang, RF Yeh, Y Xiao, PA Decker, ...
Nature genetics 41 (8), 905-908, 2009

WikiPathways: capturing the full diversity of pathway knowledge

M Kutmon, A Riutta, N Nunes, K Hanspers, EL Willighagen, A Bohler, ...
Nucleic acids research 44 (D1), D488-D494, 2016

Presenting and exploring biological pathways with PathVisio

MP van Iersel, T Kelder, AR Pico, K Hanspers, S Coort, BR Conklin, ...
BMC bioinformatics 9 (1), 1-9, 2008

Direct reprogramming of human fibroblasts toward a cardiomyocyte-like state

JD Fu, NR Stone, L Liu, CI Spencer, L Qian, Y Hayashi, P Delgado-Olguin, ...
Stem cell reports 1 (3), 235-247, 2013

PathVisio 3: an extendable pathway analysis toolbox

M Kutmon, MP van Iersel, A Bohler, T Kelder, N Nunes, AR Pico, CT Evelo
PLoS computational biology 11 (2), e1004085, 2015

Genome-wide analyses identify KIF5A as a novel ALS gene

A Nicolas, KP Kenna, AE Renton, N Ticozzi, F Faghri, R Chia, ...
Neuron 97 (6), 1268-1283. e6, 2018

Cytoscape Automation: empowering workflow-based network analysis

D Otasek, JH Morris, J Bouças, AR Pico, B Demchak
Genome biology 20 (1), 1-15, 2019

GO-Elite: a flexible solution for pathway and ontology over-representation

AC Zambon, S Gaj, I Ho, K Hanspers, K Vranizan, CT Evelo, BR Conklin, ...
Bioinformatics 28 (16), 2209-2210, 2012

Epigenetic repression of cardiac progenitor gene expression by Ezh2 is required for postnatal cardiac homeostasis

P Delgado-Olguín, Y Huang, X Li, D Christodoulou, CE Seidman, ...
Nature genetics 44 (3), 343-347, 2012

Alternative splicing regulates mouse embryonic stem cell pluripotency and differentiation

N Salomonis, CR Schlieve, L Pereira, C Wahlquist, A Colas, AC Zambon, ...
Proceedings of the National Academy of Sciences 107 (23), 10514-10519, 2010

Ketogenic diet reduces midlife mortality and improves memory in aging mice

JC Newman, AJ Covarrubias, M Zhao, X Yu, P Gut, CP Ng, Y Huang, ...
Cell metabolism 26 (3), 547-557. e8, 2017

Chromatin remodelling complex dosage modulates transcription factor function in heart development

JK Takeuchi, X Lou, JM Alexander, H Sugizaki, P Delgado-Olguín, ...
Nature communications 2 (1), 1-11, 2011

Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors

JE Eckel-Passow, DH Lachance, AM Molinaro, KM Walsh, PA Decker, ...
New England Journal of Medicine 372 (26), 2499-2508, 2015

A travel guide to Cytoscape plugins

R Saito, ME Smoot, K Ono, J Ruscheinski, PL Wang, S Lotia, AR Pico, ...
Nature methods 9 (11), 1069-1076, 2012

A high-resolution map of human evolutionary constraint using 29 mammals

K Lindblad-Toh, M Garber, O Zuk, MF Lin, BJ Parker, S Washietl, ...
Nature 478 (7370), 476-482, 2011

Targeted degradation of CTCF decouples local insulation of chromosome domains from genomic compartmentalization

EP Nora, A Goloborodko, AL Valton, JH Gibcus, A Uebersohn, ...
Cell 169 (5), 930-944. e22, 2017

WikiPathways: pathway editing for the people

AR Pico, T Kelder, MP Van Iersel, K Hanspers, BR Conklin, C Evelo
PLoS biology 6 (7), e184, 2008

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.