May 10, 2017  |  API, CITRUS, Cytobank, User Stories

Two Disciplines, One Analysis Pipeline:
Leveraging the Cytobank API to Find Biological Insights

This week we interview scientists from two different disciplines to hear how they worked together and used the Cytobank API to develop an automated pipeline to find biomarkers for several chronic Graft-versus-host disease (GVHD) outcomes.  We asked bioinformatician and Cytobank consultant Ashu Sethi to share with us her experience using the API, and Cytobank’s own Hannah Polikowsky, on behalf of Vanderbilt, how this pipeline improved her analysis workflow.

AshuHannah2 More »

September 29, 2016  |  Announcements, Cytobank, 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?
ReemaBaskar_userstoryphoto400px
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 »

March 20, 2015  |  User Stories

User Stories: Claude Chew and his experience with Cytobank 4.2 release

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 Claude Chew, a Flow Cytometry Specialist Senior at University of Virginia in
Charlottesville, VA.  We asked Claude to share with us his favorite features from our 4.2 release and to describe how this release has helped to improve his scientific workflow.

What are you excited about in science? What is your scientific vision?
Claude Chew

Claude Chew
Flow Cytometry Specialist Senior at University of Virginia

My vision is to try to bring together the technical aspects of flow/mass cytometry with biology. My experience is that there is often a disconnect between the two. Hopefully there is a way to more fully integrate these aspects to make a fully-functioning unit that will be a powerful tool for looking into how life works at the single cell level! I’m particularly excited about recent developments in the field of high-dimensional analysis with the advent of the CyTOF and the data analysis platforms that have and continue to be generated to meet the challenge of ‘big data’.
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March 16, 2015  |  Cytobank, User Stories

User Stories: Erica Alvendia and her experience with Cytobank 4.2 release

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 time we interview Erica Alvendia, a Research Associate at Primity Bio in Fremont, California.  We asked Erica to share with us her favorite features from our 4.2 release and to describe how this release has helped to improve her scientific workflow.

What are you excited about in science? What is your scientific vision?
Erica Alvendia

Erica Alvendia
Research Associate at Primity Bio

Science has such a broad subject range that there is always something new to learn. The knowledge you can obtain seems endless and that’s what I find exciting. More specifically, I’m fascinated with reading up on the pathogenesis of various diseases (especially the rare ones) and learning about the different treatments available for them. With that said, it’s my scientific vision to find treatment options for diseases that have none. Primarily any disease that results in either a physical or mental disability.
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February 5, 2015  |  Announcements, Publications, User Stories

New Breakthrough Method in Mass Cytometry

Zunder and Finck et al., from the Nolan Lab at Stanford University report new cell barcoding reagents for mass cytometry that incorporate the previously unused element palladium, expanding the number of mass cytometry measurement parameters by six. Leveraging this methodology, they present a new barcoding scheme which can be used to identify and remove cell doublets, as well as provide software that deconvolves barcoded datasets via a “single-cell debarcode” algorithm [1].

The dataset for this paper is hosted and publicly available on Cytobank Community; a free resource for the analysis, workflow, and protocols represented in this paper. Cytobank is the cloud-based analytics platform for single cell analysis. In Cytobank you can easily access and analyze multi-parameter data, visualize findings, produce high-impact graphics, and securely connect and collaborate with colleagues around the world.

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November 10, 2014  |  Announcements, User Stories

Behbehani et al. Transient Partial Permeabilization with Saponin Enables Cellular Barcoding Prior to Surface Marker Staining.

Greg BehbehaniGreg Behbehani, a physician scientist, is focused on translational research, leveraging his work treating patients in clinical trials for high-risk hematologic malignancies towards the ultimate goal of utilizing data generated in the laboratory to predict ideal chemotherapy regimens and optimal novel agents for individual patients.

Most recently Dr. Behbehani has contributed to a published paper surrounding research of new protocols for barcoding on mass and fluorescence cytometry [1]. The dataset is hosted and publicly available on Community Cytobank; a free resource for individuals interested in the analysis, workflow, and protocols represented in this paper.

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September 24, 2014  |  User Stories

Cytobank User Stories: Gabi Fragiadakis

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 time we interview Gabi Fragiadakis, Ph.D. candidate in the Nolan Lab at Stanford University School of Medicine.

What are you excited about in science? What is your scientific vision?
Gabi Fragiadakis

Gabi Fragiadakis
Ph.D. candidate at Stanford University School of Medicine

We are in a particularly exciting time for immunology—with the advent of new technologies, we have the potential to profile the immune system as a dynamic set of interactions as opposed to looking at one piece at a time.

I believe that the ability to examine the immune system as a system will lead to vast improvements in patient monitoring and treatment.
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July 21, 2014  |  User Stories

Cytobank User Stories: Marianne Enger

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 time we interview Marianna Enger, the flow cytometry core facility manager at University of Bergen.

What are you excited about in science? What is your scientific vision?
Marianna Enger

Marianna Enger
Flow Cytometry Core Facility Manager at University of Bergen

My vision as a flow cytometry core facility manager is to make flow cytometry available and affordable to anyone interested. The ambition is to provide research groups with the specialized resources and the expertise they need to produce the best possible scientific output in a cost effective way.

Cell signaling pathways interact with one another to form networks and my special interest is in hematopietic stem cells and signaling pathways. Flow cytometry is great for exploring signaling networks which I find very challenging and exciting and my wishes for the future include a CyTOF. My focus for the last two years has been on normal hematopoietic cellular responses and their potential disregulation in disease.

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