New semester, new members–Sept 2024

Hannah, Shah, and Sean are the newest members in the lab. Welcome!

Kavya, Phydena, and Lauren will continue to work remotely on their projects, with Alyssa

ISI 2024 Retreat–Aug 9th

ISI 2023 Retreat--Aug 11th @ Avery Point. 

The ISI retreat aims to enhance collaborative discoveries with cross-disciplinary strengths from Immunology (UCONN Health Center) and Computer Science (Storrs, UCONN), to develop innovative solutions to address critical biomedical challenges in applied immunological systems.

High School Team in the lab Gabo, Phydena and Lauren will share their research on the ISI2024!

Mentored by Alyssa and Keaton: Lauren from Darien High School,  Gabo and Phydena from Avon High School will share their research project at the ISI 2024.

 

 

 

 

Our New Member of Hannah to the Lab!

Hannah is our newest member to the lab, she will pursue her PhD degree at the Immunology Graduate Program.

Welcome to Stephen to the lab for a summer rotation!

 

 

 

 

 

Welcome to the lab, Kavya! Kavya will perform her Holster Scholar project in the lab this Summer

Kavya will perform her project in the lab this Summer as a Holster Scholar!

 

 

 

 

Our New Member of 2024. Welcome Aish to our team!

Our newest member Aish has started her exploration since Feb, 2024

Congratulations! Alyssa and Keaton CHARGing to the CHARGE 2023

Congratulations to Keaton Karlinsey and  Alyssa Matz for receiving invitations to give short oral presentations at the CHARGE 2023! We will join the conference on October 10-12, 2023, in San Antonio, Texas.

Keaton’s project relates to developing a risk assessment model for cardiovascular diseases using novel computer algorithms.

Alyssa received a competitive travel award to present her exciting discovery on aging B cell response to vaccination using an innovative computational program, B-RAY.

We are hiring (postdoc, graduate and undergraduate researchers) !!!!! Science is fun; the team is cool, Join us! contact us  (bzhou@uchc.edu). !!!!!

Science is fun; the team is cool, Join us! please contact us  (bzhou@uchc.edu). 

 
You will join a dynamic group instilled with curiosity and equipped with innovative minds and tools to tackle critical questions with innovative strategies.

It is also a team of achievement (checkout our news and recent highlights)

You can join us to answer questions like the following:

a) How do immune cells impact diabetes-derived health risks, such as cardiovascular diseases?

b) How do B cells respond to obesity stress with skewed programming?

c) How to capture high-resolution immune cell actions under stress?

 

 

 

 

Recent Highlights

Welcome Ivy, bye to Lili

Welcome Ivy to join our group

Thanks to Lili for the great contributions over the past 5 years. Best wishes for your future endeavors!

 

 

Keaton has been awarded NIH F30 Fellowship–CONGRATS!

MD/PhD Candidate Keaton Karlinsey awarded NIH F30 Fellowship

Ready to be a member of CASE

I am so humbled and honored to be elected to CASE (Connecticut Academy of Science and Engineering)

Beiyan Zhou Elected to Connecticut Academy of Science and Engineering (CASE)

    Awarded! Alyssa and Keaton from AHA 2023

    • Congratulations to Alyssa and Keaton for being awarded the Predoctoral Awards from AHA with impressive 1 and 2 percentiles!!
    • https://health.uconn.edu/immunology/2023/02/07/alyssa-matz-and-keaton-karlinsey-receive-aha-predoctoral-research-awards/

      Not all foam cells are bad!—AtheroSpectrum story on Circulation, January 18, 2022

      News from UConn Today

      UConn Researchers Improve Prediction of Heart Attacks

        NiCir–To predict therapeutic response in immunotherapy Patients (JEM, January 2022)

        Exciting story published on JEM (2021) and a story on UConn Today--Congratulations, Team!

        Which Patients Benefit Most from Immunotherapy? This Tool Can Tell

        A high OXPHOS CD8 T cell subset is predictive of immunotherapy resistance in melanoma patients.

        Li C, Phoon YP, Karlinsey K, Tian YF, Thapaliya S, Thongkum A, Qu L, Matz AJ, Cameron M, Cameron C, Menoret A, Funchain P, Song JM, Diaz-Montero CM, Tamilselvan B, Golden JB, Cartwright M, Rodriguez A, Bonin C, Vella A, Zhou B, Gastman BR.J Exp Med. 2022 Jan 3;219(1):e20202084. doi: 10.1084/jem.20202084. Epub 2021 Nov 22.PMID: 34807232

        A journal of 2022

        Announcements

           

          • Alyssa and Keaton are now the awardees of Predoc Awards from AHA with impressive 1 and 2 percentiles, respectively
          • Kudos to Alyssa and Li for wining the travel awards from the 18th SCBA International Conference at Boston, July 2022!
          • Congratulations to Alyssa, Lili, and Chuan for your abstracts accepted for presentation at the Scientific Sessions 2020 by the American Heart Association in Nov, 2020. Chuan was selected for an oral presentation on this new research revealed by AtheroSpectrum. Lili and Alyssa were selected for their poster presentation on dynamic B cell function in obesity (Alyssa) and T subset in atherosclerosis (Lili).
          • We are glad to be part of an important study of fatty liver using single-cell seq with Dr. Jiandie Lin's team at U Michigan. Landscape of Intercellular Crosstalk in Healthy and NASH Liver Revealed by Single-Cell Secretome Gene Analysis. Mol Cell. 2019 Aug 8;75(3):644-660.e5
          • Chuan's presentation at ATVB 2019 received top score and was invited by AHA Scientific Sessions 2019 for re-presentation in Nov, 2019 at Phili.
          • Congratulations on the acceptance of our new publication, "Single-cell transcriptomics based-MacSpectrum reveals novel macrophage activation signatures in diseases," by JCI Insight!
          • Congratulations to Chuan Li and Lili Qu to present at ATVB 2019, Boston MA Chuan also won the competitive Travel Award for Young Scientists (ATVB 2019). Bravo!

          MacSpectrum and MacBrowser

          Macrophage Annotation Programs–MacSpectrum, MacBrowser, AtheroSpectrum

          MacSpectrum (R package)

          MacSpectrum is a macrophage annotation system that allows comprehensive analysis of heterogeneous subpopulations and their multifaceted activation states under various in vitro and in vivo conditions, including the identification of condition-specific signature genes. Each subpopulation identified by MacSpectrum can be further analyzed for cell function and intracellular signaling networks in conjunction with other programs, such as Ingenuity Pathway Analysis by Qiagen, NIH DAVID, and others.

          Citation: Chuan Li, Antoine Menoret, Cullen Farragher, Zhengqing Ouyang, Christopher Bonin, Paul Holvoet, Anthony T. Vella, Beiyan Zhou.  Single cell transcriptomics-based MacSpectrum reveals novel macrophage activation signatures in diseases. JCI insight.  April 16 2019. PMID: 30990466

           

          MacBrowser 

          You can check the MPI/AMDI plots and gene expressions of murine bone marrow derived macrophages that were not stimulated (“M0”), or stimulated LPS+IFNγ (“M1”) or IL4+IL13 (“M2”). You can see their MPI/AMDI distributions and expression patterns of any genes. Please refer to our JCI insight publication (PMID: 30990466) for more details of the dataset.

           

          AtheroSpectrum (Coming soon)

          AtheroSpectrum Reveals Novel Macrophage Foam Cell Gene Signatures Associated With Atherosclerotic Cardiovascular Disease Risk

          Chuan Li*,  Lili Qu*, Alyssa J. Matz*, Patrick A. Murphy, Yongmei Liu, Ani W. Manichaikul, Derek Aguiar, Stephen S. Rich, David M. Herrington, David Vu, W. Craig ohnson, Jerome I. Rotter, Wendy S. Post, Anthony T. Vella, Annabelle Rodriguez-Oquendo, and  Beiyan Zhou#   Originally published 16 Dec 2021 https://doi.org/10.1161/CIRCULATIONAHA.121.054285  Circulation. 2022;145:206–218

          To request an R package--please contact us.

          Due to server issues, We have changed the venue for those who want to use MacSpectrum for their research--request the R package.

          Email: bzhou@uchc.edu

          You can check out your gene of interest using MacBrowser using the BMDM single cell seq data from our lab. MacSpectrum is a macrophage annotation system that allows comprehensive analysis of heterogeneous subpopulations and their multifaceted activation states under various in vitro and in vivo conditions, including the identification of condition-specific signature genes. Each subpopulation identified by MacSpectrum can be further analyzed for cell function and intracellular signaling networks in conjunction with other programs, such as Ingenuity Pathway Analysis by Qiagen, NIH DAVID, and others. Further information can be accessed on MacSpectrum with step-by-step instructions. For other functions, and specific questions, please contact us.