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:

  • Genomic NGS data analysis

    •       WGS, WES, targeted panel


  • Transcriptomic NGS data analysis

    •       Bulk RNA-seq, single-cell RNA-seq


  • Epigenomic NGS data analysis

    •       WGBS, ChIP-seq, ATAC-seq, Hi-C, HiChIP;


  • Statistical consulting

  • Customized workflow development

  • Web tool development and hosting for data visualization

    • 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: 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 the internal price information first; 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

  • Bioinformatics in Biology Seminars [2021]

    • 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


  • New Technology Seminars [2022]

    • 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
  • Please email fgao@caltech.edu to subscribe to the mailing list.

    • Workshops

  • Annual Bioinformatics Symposium [02/14/2019] Click for online material

  • Symposium on the Analysis of Single Cell RNA-Seq Data [02/10/2020] Click for workshop information


    • Resources

    A list of commonly used NGS bioinformatics tools:

  • Genome:

    •       BWA

          BOWTIE

          SAMTOOLS

          MINIMAP2


  • Transcriptome:

    •       TOPHAT

          CUFFLINKS

          KALLISTO

          SLEUTH


  • Epigenome:

    •       MACS2

          HOMER

          GENRICH

          HIC-PRO


  • Misc:

    •       The Network Data Exchange

          Gene Information eXtension

          Single cell RNASeq tools

          Gene ontology g:Profiler

          Metascape

          String

          WebGestalt

          MetaboAnalyst

          The Connectivity Map

          VisANT Biological Network

          Deep learning in biology

          A guide to machine learning for biologists

          Machine Learning Packages


    Publications co-authored by our staff

    2019

  • Modular and efficient pre-processing of single-cell RNA-seq. BioRxiv
  • The BUS Format for Single-Cell RNA-Seq Processing and Analysis. Journal of Biomolecular Techniques: JBT 30 (Suppl), S62

    • 2020

  • Genome-wide In Vivo CNS Screening Identifies Genes that Modify CNS Neuronal Survival and mHTT Toxicity. Neuron 106 (1), 76-89. e8
  • HDAC1 modulates OGG1-initiated oxidative DNA damage repair in the aging brain and Alzheimer's disease. Nature Communications 11 (1), 1-17
  • Secondary single-cell transcriptomic analysis reveals common molecular signatures of cerebrovascular injury between traumatic brain injury and aging. BioRxiv
  • Odd-paired is a pioneer-like factor that coordinates with Zelda to control gene expression in embryos. Elife 9, e59610
  • Non-canonical, potassium-driven cerebrospinal fluid clearance. BioRxiv
  • Cell type-specific transcriptomics reveals that mutant huntingtin leads to mitochondrial RNA release and neuronal innate immune activation. Neuron 107 (5), 891-908. e8

    • 2021

  • Choroid plexus NKCC1 mediates cerebrospinal fluid clearance during mouse early postnatal development. Nature Communications 12 (1), 1-16
  • Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nature Biotechnology s41587-021-00870-2
  • Blockade of the CD93 pathway normalizes tumor vasculature to facilitate drug delivery and immunotherapy. Science Translational Medicine 13 (604)
  • Single-cell perturbation dissects transcription factor control of progression speed and trajectory choice in early T-cell development. BioRxiv
  • Whole-animal multiplexed single-cell RNA-seq reveals transcriptional shifts across Clytia medusa cell types. Science Advances 7 (48), eabh1683
  • Efficient pre-processing of Single-cell ATAC-seq data. BioRxiv

    • 2022

  • Single-cell deletion analyses show control of pro–T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b. Science Immunology 7 (71)
  • A multi-omics analysis of blood-brain barrier and synaptic dysfunction in APOE4 mice. Journal of Experimental Medicine 219 (11)
  • 1027 – Relinquishing stemness in early T cells through gene regulatory networks and epigenetic control. Experimental Hematology 111 (S28)
  • Runx factors launch T-cell and innate lymphoid programs via direct and gene network-based mechanisms. BioRxiv
  • Cell-specific occupancy dynamics between the pioneer-like factor Opa/ZIC and Ocelliles/OTX regulate early head development in embryos. BioRxiv

    • News

  • 06/18/2019 Beckman Institute at Caltech decided to fund CBRC as a resource center for Caltech.

  • 09/20/2019 CBRC received bioinformatics service contract from Keck School of Medicine of USC.

  • 10/01/2019 According to the Beckman Institute at Caltech, CBRC will serve as a rechargeable center.

  • 12/02/2019 CBRC received bioinformatics service contract from MIT.

  • 01/31/2020 CBRC received CES grant from Caltech (work with Parker Group) to establish local web interfaces to visualize genomic data.

  • 05/11/2020 CBRC received Rosen grant from Caltech (work with Stathopoulos Group) to analyze drosophila epigenomic and transcriptomic data.

  • 03/31/2021 CBRC received a sub-award of 1RF1NS122060 grant from NIH/NINDS to study TMEM252-dependent microvascular endophenotype in Alzheimer's Disease.

  • 07/01/2021 CBRC received bioinformatics service contract from DGIST of South Korea.

  • 09/01/2022 CBRC received bioinformatics service contract from University of Texas.

    • 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

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