May 3, 2018  |  Announcements

New Release 6.3.0: Do More with Exploratory Data Analysis

viSNE is a powerful tool for exploratory data analysis. Samples or cells are visible in one view or “map” based on their similarity across the n-dimensions used to generate the map. Cytobank’s latest release introduces features to facilitate data exploration and the reproducibility of your results.

Our new expanded features can help investigators use viSNE in translational or clinical research studies to both uncover new discoveries and repeat these exciting findings.

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December 20, 2017  |  Conferences, viSNE

ASH Annual Meeting Report: Key Takeaways and Developments

We were excited to attend the American Society of Hematology meeting this month in Atlanta. Despite the conference beginning with the arrival of an unexpected winter storm, many leading scientists and clinicians congregated to present and discuss cutting-edge research in hematology.

The Cytobank platform was used by many who attended and presented and we were proud to contribute to these scientific advances. Highlights for us were:

  1. A multiparametric approach, “pharmacoscopy:” (a single-cell drug-response profiling approach that utilizes IF, automated microscopy, and image analysis, as detailed by Vladimer, Snijder et al., Nat. Chem. Biol. 2017) identified targetable drug pathways in CLL patients. Interestingly, the way that these authors use image morphology to quantify cell death is similar to what Ross Marklein from the FDA’s Center for Biologics Evaluation and Research (CBER) presented at BMES using Cytobank on imaging morphology data. In our consulting services, we’re excited to work with our customers on projects that integrate multiple data types, such as this work presented at ASH.
  2. Next Generation Sequencing (NGS) and its application in the clinic today was widely discussed. Similar to high dimensional cytometry analyses, developing reproducible and efficient bioinformatics analysis pipelines was identified as a major challenge to dissecting the large volume of data generated by NGS. During the late breaking abstract session, Dr. Tim Grob, presented data from a large prospective clinical trial demonstrating that NGS MRD detection can predict relapse and survival in newly diagnosed AML.
    Challenges for clinical use of Whole Exome Sequencing presented by Dr. Haferlach
    Challenges for clinical use of Whole Exome Sequencing presented by Dr. Haferlach.

     

  3.  Cytobank in action: Numerous posters and presentations used Cytobank to investigate immune system response to cancer, dysplasia, and other blood disorders. Some examples include:

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Tanaya Shree, Stanford University Medical Center, presenting “
Altered Peripheral Immune Phenotypes in Mantle Cell Lymphoma Survivors”. Here, CITRUS helped identify alterations of T cell subsets on MCL PBMC samples as compared to healthy donor samples.

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Bita Sahaf:
“Ibrutinib Inhibits cGVHD Pathogenic Pre-Germinal center B-cells and Follicular Helper Cells While Preserving Immune Memory and Th1 T-cells”

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Thomas Coats:
Neoantigens in MDS Are Associated with Two Novel CD4+ T Cell Subsets and Improved Overall Survival”

Learn more about how you can:

 

February 23, 2017  |  Education, Flow Cytometry, viSNE

Five Key Takeaways from Our Latest viSNE Webinar

We recently hosted a very popular webinar, “Placing viSNE in Your Toolbox” featuring special guest Dr. Anna Belkina of Boston University School of Medicine. More than 500 investigators registered for our event to learn about cutting-edge tools and techniques for optimizing results from high-dimensional cytometry datasets.

Cytobank screenshots from Bendall et.al. Science 2011
Cytobank screenshots on Bendall et.al. Science 2011 data

Missed our latest viSNE presentation?
View the webinar recording here:
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September 29, 2016  |  Announcements, User Stories

Customer Story: Reema Baskar, Stanford Medicine

Welcome to Cytobank User Stories, a series featuring interviews with Cytobank users on their research, scientific vision, and use of fluorescence and mass cytometry.

This week we interview Reema Baskar, a graduate student in the Cancer Biology Department at Stanford University, co-mentored by Sean Bendall and Sylvia Plevritis. We asked Reema about how she uses Cytobank’s high-dimensional tools to help elucidate mechanisms of drug resistance in cancer, and her early experience beta-testing our new CITRUS implementation.

What is an important problem in human health and/or fundamental biology that you’d like to address? What is your scientific vision?
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Reema Baskar
Cancer Biology Dept.
Stanford University

My vision is to develop high-dimensional techniques and computational tools to address the challenge of ‘big data.’ My hope is that these tools may be broadly applied to aid our understanding of the human condition. Technology, such as mass cytometry (CyTOF), has made it possible to capture different facets of biology such as cell function, epigenetic traits, and transcriptional readouts with infinitesimal single-cell granularity. More »