Caltech Bioinformatics Resource Center
Professor Lior Pachter, Faculty Adviser Google Scholar
Dr. Fan Gao, Center Director Google Scholar
Dr. Ingileif Hallgrimsdottir, Statistical Consultant
Caltech Bioinformatics Resource Center (CBRC) provides pipeline development, benchmarking, bioinformatics consulting, and general training to all Caltech researchers. This Resource Center bridges the gap between biological research and up-to-date NGS information technology (e.g., single-cell RNA-seq data workflow), and supports both technology development and novel biology discoveries in a collaborative manner.
This facility utilizes on-campus computational resources for pipeline development, data processing and bioinformatics analysis. Caltech and external customers are welcome to contact the center for bioinformatics consulting services.
Office hours are provided to the Caltech community to introduce the latest in-house bioinformatics technology.
About Caltech Bioinformatics Resource Center (CBRC)
CBRC is affiliated with the Beckman Institute at Caltech and provides bioinformatics services to the community.
Technology development
As a Beckman Institute Resource Center, CBRC is involved in developing and benchmarking new bioinformatics tools for genomic, transcriptomic and epigenomic data processing. (YouTube video from Professor Lior Pachter Lab).
Customized bioinformatics services
CBRC works with Caltech and external groups to study basic biological systems and to tackle biomedical problems. Fee-based bioinformatics services are provided for NGS workflow development and NGS data analysis.
Seminars, workshops and office hours
CBRC supports bioinformatics seminars and hands-on workshops. Our staff also provide free-of-charge office hours to Caltech groups (appointment required).
Bioinformatics Services
CBRC provides the following services:
WGS, WES, targeted panel
Bulk RNA-seq, single-cell RNA-seq
WGBS, ChIP-seq, ATAC-seq, Hi-C, HiChIP;
As part of our mission, CBRC is designed to provide bioinformatics consultations that assist grants and service contracts. Therefore, our staff prioritize their time to support those efforts. Also noted, customers from Caltech always have the priority to be served.
Occasional external customers: For 2020-2021 School Year, our academic rate is $125/hr (industry rate $160/hr). Please contact fgao@caltech.edu to get an estimated cost for your project first. After a technical services agreement (provided by Beckman Institute Administration) is signed, CBRC can start working on your project.
Occasional Caltech customers: Please contact fgao@caltech.edu to get an estimated cost first (For 2020-2021 School Year, our internal rate is $75/hr); a valid PTA number is required before CBRC can start working on your project.
Authorship guidelines: Informatics projects that require significant intellectual contribution to the work described are considered collaborative efforts and merit co-authorship; the order of authorship is not of concern. Placing our staff on publications significantly increases our ability to obtain financial support through grants and is helpful in the renewal process for BI core grant.
Notes to our customers:
CBRC is supported by the Beckman Institute (BI) at Caltech. It is a BI policy that publications resulting from our services need to include ...Bioinformatics Resource Center in the Beckman Institute at Caltech... in the acknowledgement. We appreciate your understanding and support!
Seminars
| Date | Time | Presenter | Location | Title/Topic |
|---|---|---|---|---|
| 04/22 | 1PM | Sina Booeshaghi - Lior Pachter Lab, Caltech | Zoom | Pre-processing single-cell RNA-seq data using Kallisto |
| 05/13 | 1PM | Shashank Gandhi - Marianne Bronner Lab, Caltech | Zoom | Seq your destiny - Neural crest plasticity and determination of cell fate |
| 05/27 | 1PM | Yaping Liu - Assistant Professor, Cincinnati Children's Hospital | Zoom | De novo characterization of cell-free DNA fragmentation hotspots in early-stage cancer |
| 06/03 | 1PM | Eduardo Beltrame - Paul Sternberg Lab, Caltech | Zoom | WormBase single cell tools - https://wormbase.github.io/single-cell/ |
| 06/10 | 1PM | Xin Jin - Paola Arlotta Lab, Harvard | Zoom | How Genes and Environment Shape Brain Development: in vivo Perturb-seq and Beyond |
| 06/17 | 1PM | Abolfazl Doostparast - Research Scientist, Children's Hospital of Philadelphia | Zoom | Network models for precision targeting of risk genes in brain diseases |
| 07/01 | 1PM | David Brown - Viviana Gradinaru Lab, Caltech | Zoom | Parallel characterization of AAV tropism via single-cell RNA sequencing |
| 07/08 | 1PM | Tatyana Dobreva - Matt Thomson Lab, Caltech | Zoom | Single-cell profiling of capillary blood enables out of clinic human immunity studies |
| Summer Break | ||||
| 09/09 | 1PM | Mary Arrastia - Rustem Ismagilov Lab, Caltech | Zoom | Development of scSPRITE as a single-cell genomic tool |
| 09/23 | 1PM | Tara Chari - Lior Pachter Lab, Caltech | Zoom | Whole Animal Multiplexed Single-Cell RNA-Seq Reveals Transcriptional Shifts Across Clytia Medusa Cell Types |
| 10/07 | 9AM | Asaf Marco - Assistant Professor, The Hebrew University of Jerusalem | Zoom | Mapping the epigenomic and transcriptomic interplay during memory formation and recall in the hippocampal engram ensemble |
| 10/28 | 1PM | Boyoung Shin - Ellen Rothenberg Lab, Caltech | Zoom | Who moved Runx? – dynamic binding site shifts during T-lineage commitment and its dose-dependent role in development speed |
| 11/04 | 1PM | Prashant Bhat - Mitchell Guttman Lab, Caltech | Zoom | Right Place at the Right Time: a role for nuclear compartmentalization in RNA splicing |
| 11/18 | 1PM | Peiwei Chen - Alexei Aravin Lab, Caltech | Zoom | Treasure hunt in the repetitive junk DNA: Genetic innovation of small non-coding piRNA |
| Date | Time | Presenter | Location | Title/Topic |
|---|---|---|---|---|
| 08/10 | 2PM | Dr. Yuan Jiang & Dr. Shan Yang - BGI Complete Genomics | Zoom | Stereo-seq, a spatial omics tool with nanoscale resolution |
| 09/06 | 10AM | Dr. Julie Laliberte - Singleron Biotechnologies | Zoom | Make every cell count: novel single cell multi-omics solutions |
Workshops
Resources
A list of commonly used NGS bioinformatics tools:
A guide to machine learning for biologists
Publications co-authored by our staff
2019
2020
2021
2022
News
Contact
Caltech Bioinformatics Resource Center
Beckman Institute Campus map
BI Room 340, Caltech, Pasadena CA 91125
Service Hours
Monday - Wednesday: 9:00 AM to 5:30 PM, Thursday: 9:00AM to 1:00PM, Friday: 9:00AM to 1:00PM
Office Hours
Thursday: 1:30 PM to 5:30 PM, Friday: 1:30 PM to 5:30 PM
Bioinformatics Email: fgao@caltech.edu
Biostatistics Email: ingileif@caltech.edu