Center for Computational Biology and Bioinformatics

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Dynamic establishment of recipient resident memory T cell repertoire after human intestinal transplantation

Jiao, W., Martinez, M., Muntnich, C. B., Zuber, J., Parks, C., Obradovic, A., Tian, G., Wang, Z., Long, K. D., Waffarn, E., Frangaj, K., Jones, R., Gorur, A., Shonts, B., Rogers, K., Lv, G., Velasco, M., Ravella, S., Weiner, J., … Sykes, M. (2024). Dynamic establishment of recipient resident memory T cell repertoire after human intestinal transplantation. EBioMedicine, 101, 105028. https://doi.org/10.1016/j.ebiom.2024.105028

Authors:

Wenyu Jiao

Mercedes Martinez

Constanza Bay Muntnich

Julien Zuber

Christopher Parks

Aleksandar Obradovic

Guangyao Tian

Zicheng Wang

Katherine D Long

Elizabeth Waffarn

Kristjana Frangaj

Rebecca Jones

Alaka Gorur

Brittany Shonts

Kortney Rogers

Guoyue Lv

Monica Velasco

Shilpa Ravella

Joshua Weiner

Tomoaki Kato

Yufeng Shen

Jianing Fu

Megan Sykes

Affiliated Authors:

Wenyu Jiao

Mercedes Martinez

Constanza Bay Muntnich

Julien Zuber

Christopher Parks

Aleksandar Obradovic

Zicheng Wang

Katherine D Long

Elizabeth Waffarn

Kristjana Frangaj

Rebecca Jones

Alaka Gorur

Brittany Shonts

Kortney Rogers

Monica Velasco

Shilpa Ravella

Joshua Weiner

Tomoaki Kato

Yufeng Shen

Jianing Fu

Megan Sykes

Columbia Affiliation:

Subjects:

Memory T Cells (MeSH)

Receptors, Antigen, T-Cell (MeSH)

Author Keywords:

tissue resident memory t cells (trm)

human intestinal transplantation (itx)

t cell receptor (tcr) repertoire

tcr beta sequencing

dynamic reconstitution

tcrβ sequencing

Publication Type:

Article

Unique ID:

10.1016/j.ebiom.2024.105028

PMID:

38422982

DOI:

10.1016/j.ebiom.2024.105028

Journal:

EBioMedicine

Publication Date:

2024-02-28

Data Source:

PubMed

Source Link:

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Record Created:

Friday, July 26, 2024 - 14:56

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Golob, J. L., Oskotsky, T. T., Tang, A. S., Roldan, A., Chung, V., Ha, C. W. Y., Wong, R. J., Flynn, K. J., Parraga-Leo, A., Wibrand, C., Minot, S. S., Oskotsky, B., Andreoletti, G., Kosti, I., Bletz, J., Nelson, A., Gao, J., Wei, Z., Chen, G., … Sirota, M. (2024). Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Reports Medicine, 5(1), 101350. https://doi.org/10.1016/j.xcrm.2023.101350

Authors:

Jonathan L Golob

Tomiko T Oskotsky

Alice S Tang

Alennie Roldan

Verena Chung

Connie W Y Ha

Ronald J Wong

Kaitlin J Flynn

Antonio Parraga-Leo

Camilla Wibrand

Samuel S Minot

Boris Oskotsky

Gaia Andreoletti

Idit Kosti

Julie Bletz

Amber Nelson

Jifan Gao

Zhoujingpeng Wei

Guanhua Chen

Zheng-Zheng Tang

Pierfrancesco Novielli

Donato Romano

Ester Pantaleo

Nicola Amoroso

Alfonso Monaco

Mirco Vacca

Maria De Angelis

Roberto Bellotti

Sabina Tangaro

Abigail Kuntzleman

Isaac Bigcraft

Stephen Techtmann

Daehun Bae

Eunyoung Kim

Jongbum Jeon

Soobok Joe

Kevin R Theis

Sherrianne Ng

Yun S Lee

Patricia Diaz-Gimeno

Phillip R Bennett

David A MacIntyre

Gustavo Stolovitzky

Susan V Lynch

Jake Albrecht

Nardhy Gomez-Lopez

Roberto Romero

David K Stevenson

Nima Aghaeepour

Adi L Tarca

James C Costello

Marina Sirota

Affiliated Authors:

Gustavo Stolovitzky

Columbia Affiliation:

Center for Computational Biology and Bioinformatics

Subjects:

Premature Birth (MeSH)

Crowdsourcing (MeSH)

Microbiota (MeSH)

Author Keywords:

16s harmonization

dream challenge

crowdsourced

machine learning

microbiome

predictive modeling

preterm birth

vaginal microbiome

Grants:

P01HD106414 (NIH – Eunice Kennedy Shriver National Institute of Child Health & Human Development)

R01HD105256 (NIH – Eunice Kennedy Shriver National Institute of Child Health & Human Development)

ZIAHD002400 (NIH – Eunice Kennedy Shriver National Institute of Child Health & Human Development)

R01HL139844 (NIH – National Heart, Lung, and Blood Institute)

R01GM140464 (NIH – National Institute of General Medical Sciences)

R35GM138353 (NIH – National Institute of General Medical Sciences)

R61NS114926 (NIH – National Institute of Neurological Disorders and Stroke)

R01AG058417 (NIH – National Institute On Aging)

P30AG066515 (NIH – National Institute On Aging)

F30AG079504 (NIH – National Institute On Aging)

Publication Type:

Article

Unique ID:

10.1016/j.xcrm.2023.101350

PMID:

38134931

DOI:

10.1016/j.xcrm.2023.101350

Journal:

Cell Reports Medicine

Publication Date:

2023-12-23

Data Source:

PubMed

Source Link:

View PubMed Record

Record Created:

Tuesday, December 10, 2024 - 13:55

Plasticity of intragraft alloreactive T cell clones in human gut correlates with transplant outcomes

Fu, J., Wang, Z., Martinez, M., Obradovic, A., Jiao, W., Frangaj, K., Jones, R., Guo, X. V., Zhang, Y., Kuo, W.-I., Ko, H. M., Iuga, A., Bay Muntnich, C., Prada Rey, A., Rogers, K., Zuber, J., Ma, W., Miron, M., Farber, D. L., … Sykes, M. (2023). Plasticity of intragraft alloreactive T cell clones in human gut correlates with transplant outcomes. Journal of Experimental Medicine, 221(1). https://doi.org/10.1084/jem.20230930

Authors:

Jianing Fu

Zicheng Wang

Mercedes Martinez

Aleksandar Obradovic

Wenyu Jiao

Kristjana Frangaj

Rebecca Jones

Xinzheng V Guo

Ya Zhang

Wan-I Kuo

Huaibin M Ko

Alina Iuga

Constanza Bay Muntnich

Adriana Prada Rey

Kortney Rogers

Julien Zuber

Wenji Ma

Michelle Miron

Donna L Farber

Joshua Weiner

Tomoaki Kato

Yufeng Shen

Megan Sykes

Affiliated Authors:

Jianing Fu

Zicheng Wang

Mercedes Martinez

Aleksandar Obradovic

Wenyu Jiao

Kristjana Frangaj

Rebecca Jones

Xinzheng V Guo

Ya Zhang

Wan-I Kuo

Huaibin M Ko

Alina Iuga

Constanza Bay Muntnich

Adriana Prada Rey

Kortney Rogers

Julien Zuber

Wenji Ma

Michelle Miron

Donna L Farber

Joshua Weiner

Tomoaki Kato

Yufeng Shen

Megan Sykes

Columbia Affiliation:

Subjects:

T-Lymphocytes (MeSH)

Immune Tolerance (MeSH)

Grants:

S10RR027050 (NIH – National Center for Research Resources)

P01AI106697 (NIH – National Institute of Allergy and Infectious Diseases)

S10OD020056 (NIH – Office of the Director, National Institutes of Health)

Publication Type:

Article

Unique ID:

10.1084/jem.20230930

PMID:

38091025

DOI:

10.1084/jem.20230930

Journal:

Journal of Experimental Medicine

Publication Date:

2023-12-13

Data Source:

PubMed

Source Link:

View PubMed Record

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Record Created:

Friday, July 26, 2024 - 10:14

2013 – MESENCHYMAL STROMAL CELL MITOCHONDRIAL TRANSFER FUELS MDS TO AML TRANSFORMATION

Labella, R., Ali, A., Mosialou, I., De Angelis, J., Vgenopoulou, P., Zhao, J., Vanderberg, A., Rabadan, R., Raza, A., & Kousteni, S. (2023). 2013 – MESENCHYMAL STROMAL CELL MITOCHONDRIAL TRANSFER FUELS MDS TO AML TRANSFORMATION. Experimental Hematology, 124, S43. https://doi.org/10.1016/j.exphem.2023.06.050

Authors:

Rossella Labella

Abdullah Mahmood Ali

Ioanna Mosialou

Jessica De Angelis

Paraskevi Vgenopoulou

Junfei Zhao

Andrew Vanderberg

Raùl Rabadàn

Azra Raza

Stavroula Kousteni

Affiliated Authors:

Ioanna Mosialou

Jessica De Angelis

Paraskevi Vgenopoulou

Junfei Zhao

Andrew Vanderberg

Raùl Rabadàn

Stavroula Kousteni

Columbia Affiliation:

Subjects:

Acute Myeloid Leukemia (OpenAlex Topic)

Role of Histone Deacetylases in Cellular Regulation (OpenAlex Topic)

Pathogenesis and Treatment of Osteonecrosis (OpenAlex Topic)

Publication Type:

Article

Unique ID:

10.1016/j.exphem.2023.06.050

DOI:

10.1016/j.exphem.2023.06.050

Journal:

Experimental Hematology

Publication Date:

2023-01-01

Data Source:

OpenAlex

Source Link:

View OpenAlex Record

Record Created:

Friday, August 16, 2024 - 12:44

425.3: Single-Cell Immune Profiling of Human Intestinal Allografts Reveals Differential Phenotypes of Alloreactive T-Cell Clones in Quiescent vs Chronically Rejecting Allografts

Fu, J., Wang, Z., Martinez, M., Jiao, W., Frangaj, K., Jones, R., Guo, X. V., Zhang, Y., Kuo, W.-I., Obradovic, A., Ma, W., Rogers, K., Kato, T., Shen, Y., & Sykes, M. (2022). 425.3: Single-Cell Immune Profiling of Human Intestinal Allografts Reveals Differential Phenotypes of Alloreactive T-Cell Clones in Quiescent vs Chronically Rejecting Allografts. Transplantation, 106(9S), S485–S485. https://doi.org/10.1097/01.tp.0000888048.23424.42

Authors:

Jianing Fu

Zicheng Wang

Mercedes Martínez

Wenyu Jiao

Kristjana Frangaj

Rebecca Jones

Xinzheng V. Guo

Ya Zhang

Wan-I Kuo

Aleksandar Z. Obradovic

Wenji Ma

Kortney Rogers

Tomoaki Kato

Yufeng Shen

Megan Sykes

Affiliated Authors:

Jianing Fu

Zicheng Wang

Mercedes Martínez

Wenyu Jiao

Kristjana Frangaj

Rebecca Jones

Xinzheng V. Guo

Ya Zhang

Wan-I Kuo

Aleksandar Z. Obradovic

Wenji Ma

Kortney Rogers

Tomoaki Kato

Yufeng Shen

Megan Sykes

Columbia Affiliation:

Subjects:

Natural Killer Cells in Immunity (OpenAlex Topic)

Provision and Assessment of Nutrition Support Therapy (OpenAlex Topic)

Regulatory T Cell Development and Function (OpenAlex Topic)

Publication Type:

Article

Unique ID:

10.1097/01.tp.0000888048.23424.42

DOI:

10.1097/01.tp.0000888048.23424.42

Journal:

Transplantation

Publication Date:

2022-09-01

Data Source:

OpenAlex

Source Link:

View OpenAlex Record

Record Created:

Wednesday, October 30, 2024 - 11:05

Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia

Lencz, T., Yu, J., Khan, R. R., Flaherty, E., Carmi, S., Lam, M., Ben-Avraham, D., Barzilai, N., Bressman, S., Darvasi, A., Cho, J. H., Clark, L. N., Gümüş, Z. H., Vijai, J., Klein, R. J., Lipkin, S., Offit, K., Ostrer, H., Ozelius, L. J., … Pe’er, I. (2021). Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. Neuron, 109(9), 1465-1478.e4. https://doi.org/10.1016/j.neuron.2021.03.004

Authors:

Todd Lencz

Anil K. Malhotra

Jin Yu

Max Lam

Itsik Pe'er

Raiyan Rashid Khan

Erin Flaherty

Shai Carmi

Danny Ben-Avraham

Nir Barzilai

Gil Atzmon

Susan Bressman

Ariel Darvasi

Judy H. Cho

Zeynep H. Gumus

Robert J. Klein

Inga Peter

Lorraine N. Clark

Joseph Vijai

Kenneth Offit

Steven Lipkin

Harry Ostrer

Laurie J. Ozelius

Tom Maniatis

Affiliated Authors:

Itsik Pe'er

Raiyan Rashid Khan

Erin Flaherty

Lorraine N. Clark

Columbia Affiliation:

Subjects:

Wnt Signaling in Development and Disease (OpenAlex Topic)

Genomic Studies and Association Analyses (OpenAlex Topic)

Genetic Research on BRCA Mutations and Cancer Risk (OpenAlex Topic)

Cadherins (MeSH)

Genetic Predisposition to Disease (MeSH)

Schizophrenia (MeSH)

Author Keywords:

cadherins

exome

founder population

rare variants

schizophrenia

Grants:

U54CA121852 (NIH – National Cancer Institute)

R01DK092235 (NIH – National Institute of Diabetes and Digestive and Kidney Diseases)

U01DK062422 (NIH – National Institute of Diabetes and Digestive and Kidney Diseases)

U24DK062429 (NIH – National Institute of Diabetes and Digestive and Kidney Diseases)

U01DK062429 (NIH – National Institute of Diabetes and Digestive and Kidney Diseases)

R01MH114817 (NIH – National Institute of Mental Health)

R01MH108579 (NIH – National Institute of Mental Health)

R01MH095458 (NIH – National Institute of Mental Health)

R01MH084098 (NIH – National Institute of Mental Health)

RC2MH089964 (NIH – National Institute of Mental Health)

R01NS060113 (NIH – National Institute of Neurological Disorders and Stroke)

P30AG038072 (NIH – National Institute On Aging)

P01AG027734 (NIH – National Institute On Aging)

R01AG042188 (NIH – National Institute On Aging)

Publication Type:

Article

Unique ID:

10.1016/j.neuron.2021.03.004

PMID:

33756103

DOI:

10.1016/j.neuron.2021.03.004

Journal:

Neuron

Publication Date:

2021-05-05

Data Source:

Web of Science

Source Link:

View Web of Science Record

View Scopus Record

View PubMed Record

View OpenAlex Record

Record Created:

Thursday, July 24, 2025 - 08:31

Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation

Fu, J., Zuber, J., Shonts, B., Obradovic, A., Wang, Z., Frangaj, K., Meng, W., Rosenfeld, A. M., Waffarn, E. E., Liou, P., Lau, S., Savage, T. M., Yang, S., Rogers, K., Danzl, N. M., Ravella, S., Satwani, P., Iuga, A., Ho, S., … Sykes, M. (2021). Lymphohematopoietic graft-versus-host responses promote mixed chimerism in patients receiving intestinal transplantation. Journal of Clinical Investigation, 131(8). https://doi.org/10.1172/jci141698

Authors:

Jianing Fu

Julien Zuber

Brittany Shonts

Aleksandar Obradovic

Kristjana Frangaj

Elizabeth E. Waffarn

Sai-ping Lau

Thomas M. Savage

Suxiao Yang

Kortney Rogers

Nichole M. Danzl

Siu-hong Ho

Adam Griesemer

Megan Sykes

Zicheng Wang

Yufeng Shen

Wenzhao Meng

Aaron M. Rosenfeld

Eline T. Luning Prak

Peter Liou

Tomoaki Kato

Shilpa Ravella

Prakash Satwani

Mercedes Martinez

Alina Iuga

Affiliated Authors:

Jianing Fu

Julien Zuber

Brittany Shonts

Aleksandar Obradovic

Kristjana Frangaj

Elizabeth E. Waffarn

Sai-ping Lau

Thomas M. Savage

Suxiao Yang

Kortney Rogers

Nichole M. Danzl

Siu-hong Ho

Adam Griesemer

Megan Sykes

Zicheng Wang

Yufeng Shen

Peter Liou

Tomoaki Kato

Shilpa Ravella

Prakash Satwani

Mercedes Martinez

Alina Iuga

Columbia Affiliation:

Grants:

S10RR027050 (NIH – National Center for Research Resources)

P01AI106697 (NIH – National Institute of Allergy and Infectious Diseases)

S10OD020056 (NIH – Office of the Director, National Institutes of Health)

Publication Type:

Article

Unique ID:

10.1172/JCI141698

PMID:

33630757

DOI:

10.1172/JCI141698

Journal:

Journal of Clinical Investigation

Publication Date:

2021-04-15

Data Source:

Web of Science

Source Link:

View Web of Science Record

View Scopus Record

Record Created:

Thursday, July 24, 2025 - 08:32