LSRII flow cell lasers: photo by David Parks
2021
December | talk on SuPERR-seq
Eliver is presenting our work on integrating and analyzing multi-omics single-cell sequencing data (SuPERR-seq pipeline) at the International Conference on Computational Advances in Biomedical Sciences (ICCABS) in the CASCODA workshop (Computational Advances for Single-Cell Omics Data Analysis). Register for the conference here. Eliver’s talk is on December 17th at 4 pm (EST).
December | He is a doctor now!
Congratulations to Dr. Devon Eddins for the outstanding defense of his Ph.D. thesis on December 15th! Devon is the first Ph.D. student to graduate from the Ghosn Lab! Good luck with your next endeavors, Dr. Eddins! We will miss you in the lab, but we are excited and rooting for you!
December | cover art and top read!
Our study on the dual origin of tissue-resident macrophages was selected for the cover art of the December 15th issue of The Journal of Immunology! The same study was selected by the Editors as the Top Read! #JI_TopRead
Congratulations to the co-first authors Devon Eddins and Astrid Kosters, and to all our fantastic collaborators at Stanford and Calgary!
November | NIH grant awarded
We were awarded an NIAID R21 grant to further develop and apply our new high-parameter technology flowBEAT to determine the breadth of antibody responses that correlate with efficient recovery from COVID-19.
We will post more about the various applications of the flowBEAT technology soon. Stay tuned!
November | Black in Immuno Week
Devon Eddins is giving a talk on Nov. 17th in the Translational Immunology session of Black in Immuno Week! Devon will be discussing our new findings on lung immune responses in Black/African-American patients with severe COVID-19 in ICU beds here in the Atlanta area.
Register for the event here!
October | SARS-CoV-2 and COVID-19 sample inactivation for contemporary assays
We have developed optimized protocols to inactivate SARS-CoV-2 and COVID-19 patient samples without affecting downstream assays, including scRNA-seq, hi-d flow cytometry, and metabolomics. The results from this study, which was led by Devon Eddins and our collaborators at Emory, are now in a preprint in bioRxiv.
Congratulations, Devon!
October | manuscript accepted!
Our studies on the (dual) origins of tissue-resident macrophages got accepted for publication in The Journal of Immunology.
Congratulations to Devon Eddins and Astrid Kosters (co-first authors), and to all our collaborators!
We will post the JI link here once the article goes live on the journal website.
September | Ghosn Lab recognized by the school of Medicine
The Ghosn Lab was honored with the 2021 Research Appreciation Day in recognition of the frontier research in immunology and related cutting-edge technologies. We sincerely thank our peers and colleagues in the SOM for nominating us for this recognition!
Ben Babcock (left), Junkai Yang (middle), and Eliver Ghosn.
August | poster session at Georgia Tech
Ben and Junkai prepared a poster summarizing some of the current research projects in our lab for the incoming class of Bioinformatics students at Georgia Tech during orientation day. It was a fun day!
august | batch correction and single-cell data integration
We developed a new metric system and an analysis framework to minimize batch effects in single-cell data integration. Our new Cell Misclassification Statistic (CMS) score directly quantifies the loss of biological signal by taking into account the fidelity of cell-type identity before and after data integration and provides a new framework by which to consider batch effects.
This work, now posted in bioRxiv, was led by our graduate student Ben Babcock in collaboration with Astrid Kosters, Junkai Yang, and Landi White.
Congratulations, Ben and team!
August | SuPERR-seq
Our new single-cell multi-omics data analysis workflow, SuPERR-seq, is now posted in bioRxiv! We implemented gold-standard approaches of high-dimensional flow cytometry to develop a novel data analysis workflow that 1) accurately assigns a biological identity to each cell barcode, 2) removes undesirable cell doublets, 3) prevents cell-type misclassifications that often occurs in conventional workflows, and 4) provides higher clustering resolution that allows for the discovery of new cell types.
This work was led by our bioinformatician Junkai Yang together with (co-first author) Congmin Xu from Peng Qiu’s group at Georgia Tech. Astrid Kosters and Ben Babcock were second and third authors, respectively.
Congratulations, Junkai and team!
August | in the news… laser-induced whisper
Our nanomedicine study in collaboration with Bryan Smith’s group (Michigan State) was highlighted in the Emory blog Lab Land. We used ultra-selective carbon nanotubes and photoacoustic imaging to locate inflamed atherosclerotic plaques.
Congratulations, Devon and team!
July | In the news…
Our studies profiling the immune responses in the lungs and blood of COVID-19 patients in ICU were profiled in the Emory blog Lab Land. The science writer Quinn Eastman nicely summarized our key findings to a broad audience.
Congratulations to all members of the Ghosn Lab! Great teamwork!
July | fellowship award
Congratulations to Jinyoung Eum for being selected as a 2021 GRA fellow! Jin is a master’s student at Georgia Tech’s Bioinformatics Program and he has been awarded the Computational Biology Faculty Research Award to continue his studies in the Ghosn Lab on optimizing cell trajectory algorithms for single-cell RNA-seq datasets.
Congratulations, Jin!
June | T cells predict recovery from COVID-19
Our study in collaboration with Nadia Roan (Gladstone Institutes), Kara Lynch (UCSF), and Sulggi Lee (UCSF) is now published in Cell Reports. See the press release from Gladstone here.
Junkai contributed with the analysis of the single-cell RNA-seq datasets from the lung samples (BALF) of severe and mild COVID-19 patients. Congratulations, team!
Left to right: Ben Babcock, Landi White, Junkai Yang, Devon Eddins, Jinyoung Eum, Astrid Kosters, Fathma Abdulkhader, Eliver Ghosn.
June | he passed the quals!
Ben presented his thesis proposal and did extremely well on his qualifying exam. He now is officially a doctoral candidate!
We celebrated with caramel cake, allegedly his favorite. Congratulations, Ben!
June | Pathogenic neutrophilia drives acute respiratory distress syndrome in severe COVID-19 patients
Our PROATECT studies employing multi-omics single-cell assays to dissect the immune responses in the lungs and matching blood of severe COVID-19 patients are now in a preprint in bioRxiv. This study focuses on Black/African-American patients, who have been disproportionally affected by COVID-19.
This is the result of major efforts from all the members of the Ghosn Lab in collaboration with our superb colleagues at Emory University and Genentech. The studies were led by Devon Eddins (first author), Astrid Kosters (second author), and Junkai Yang (second author). Congratulations, team!
June | cover art!
Our studies on ultra-selective carbon nanotubes in collaboration with Dr. Bryan Smith and Mahsa Gifani from Michigan State and Nori Kosuge from Japan got accepted in Advanced Functional Materials. And it was selected for the magazine cover art!
Devon performed the hi-d flow cytometry studies to identify the nanoparticle-loaded monocytes and macrophages in the atherosclerotic plaques.
Congratulations, Devon!
May | Global Immunology Symposium
Eliver presented our recent findings on applying multi-omics single-cell approaches to study the immune responses in the lung and matching blood of severe COVID-19 patients during the Annual Global Immunology Symposium organized by 10x Genomics.
You can access the recordings by registering here.
The talk is titled: Systems immunology approach reveals novel mechanisms of lung pathology in severe COVID-19
May | Gut cell-dissociation protocols for multi-omics studies
As part of our collaboration with the Gut Cell Atlas, Astrid and Landi developed and published new protocols to generate a single-cell suspension of intestinal tissues for downstream single-cell multi-omics assays. Here are the links for the HUMAN and MOUSE protocols. Junkai generated the scRNA-seq data to validate the performance of the protocols.
Congratulations, Astrid, Landi, and Junkai!
April | Undergraduate Research Symposium
Our undergraduate student, Landi, gave a fantastic oral presentation on her honors thesis project on generating new humanized mice to study the development and function of the human immune system during prenatal life.
Congratulations, Landi!
April | Coordinated T- and B- cell responses during COVID-19 convalescence
Another study in collaboration with Nadia Roan and Sulggi Lee (UCSF/Gladstone Institutes) is now in a preprint in bioRxiv and currently under peer review.
Ben Babcock generated and analyzed the data on antibody responses using our new technology flowBEAT.
Congratulations, Ben!
April | on the origins of tissue-resident macrophages
Devon’s and Astrid’s manuscript on the dual origin of tissue-resident macrophages (HSC-independent and HSC-dependent) is now posted in bioRxiv and is currently under peer review.
The manuscript was also selected for review by the Oxford-Mount Sinai Preprint Journal Club.
Congratulations, Devon and Astrid!
February | bioinformatics master’s student
Jinyoung (Jin) Eum is a first-year Bioinformatics student at Georgia Tech pursuing his master’s degree. Jin’s project aims to improve and implement trajectory algorithms to understand immune cell development and cell differentiation.
Outside of grad school, Jin enjoys exercising and playing sports, particularly basketball. He also plays video games.
Welcome to the team, Jin!
February | rotating graduate student - imp
Cody Elkins is joining our team as a rotating graduate student from the IMP (Immunology and Molecular Pathogenesis) Program. Cody is taking on the task of characterizing the human plasma cell development in a new humanized mouse model developed by our lab member Astrid Kosters. Cody will learn to develop, apply, and analyze high-dimensional flow cytometry data to characterize the various human B-cell subsets.
In his free time, Cody enjoys hiking and playing fingerstyle guitar! I hope we will have a chance to hear him play…
Welcome to the team, Cody!
FEBRUARY | elucidating severe COVID-19
Devon Eddins has been selected to give a talk at Memorial Sloan Kettering for the MSKView Day: A diversity recruitment event for MSK scientific laboratories. Devon will share some of his recent findings on the innate immune responses to SARS-CoV-2 using multi-omics single-cell analysis of airways and blood specimens of severe COVID-19 patients in the Atlanta/Emory hospitals. Devon also just presented his research in progress for the Emory IMP graduate program.
Congratulations Devon!
January | on the origins of mast cells
Astrid Kosters, in collaboration with our colleagues from the University of Texas Health Science Center at Houston - Yoshimoto & Kobayashi - submitted an abstract to the 2021 AAI Conference. Astrid has been working on elucidating the immune lineages that develop independently of the Blood Stem Cell (aka, Hematopoietic Stem Cells).
Congratulations Astrid!
January | distinctive features of T cells can predict survival from severe COVID-19
The results from our studies in collaboration with UCSF and Gladstone Institute has just been posted in medRxiv. Jason Neidleman (Roan lab) et al. performed 38-parameter CyTOF on total and SARS-CoV-2-specific T cells from longitudinal specimens spanning the entire spectrum of COVID-19 and show that fatal COVID-19 is characterized by escalating activation of bystander CXCR4+ T cells.
Junkai Yang in our lab performed the analysis of the scRNAseq datasets from BALF samples that revealed increased bystander CXCR4hi T cells in the lungs of severe, but not mild, COVID-19 patients.
Congratulations Junkai!