Using data science and a health equity lens to identify long-COVID sequelae among medically underserved populations

Md Nasir, Nicole Cook, Daniel Parras, Sumit Mukherjee, Geralyn Miller, Juan M. Lavista Ferres, Katherine Chung-Bridges

Journal of Health Care for the Poor and Underserved | May 2023

Publication Project

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Boonyaratanakornkit J, Wald A, Selke S, Wener Mh, Morishima C, Greninger Al, Michael Gale, Tien-Ying Hsiang, Lichen Jing, Holbrook Mr, Ian M. Kaplan, Damon H May, H. Jabran Zahid, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S Robins, David M Koelle

JCI Insight | April 2022, Vol 7(10)

DOI Preprint Publication Project Project

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H. Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Andrea Crisanti, Giovanni Tonon

JCI Insight | April 2022, Vol 7(10)

DOI Publication Project

Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2

Shuyuan Zhang, Qingtai Liang, Xinheng He, Chongchong Zhao, Wenlin Ren, Ziqing Yang, Ziyi Wang, Qiang Ding, Haiteng Deng, Tong Wang, Linqi Zhang, Xinquan Wang

Cell Research | January 2022

Publication

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.

Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

PLOS ONE | April 2021, Vol 16(4): pp. e0250780

DOI Publication Publication Publication Publication Publication Publication Publication Project

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project

A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N Dines, Ian M Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitch Pesesky, Rachel M Gittelman, Thomas M Snyder, Christopher J Gooley, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D Goldman, James R Heath, Luigi D Notarangelo, Jonathan M. Carlson, Joaquin Martinez-Lopez, Harlan S Robins

August 2020

DOI Publication Publication Publication Publication Project

Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines

Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine

Nature Biomedical Engineering | May 2020, Vol 4(6): pp. 636-648

DOI

Using data science and a health equity lens to identify long-COVID sequelae among medically underserved populations

Md Nasir, Nicole Cook, Daniel Parras, Sumit Mukherjee, Geralyn Miller, Juan M. Lavista Ferres, Katherine Chung-Bridges

Journal of Health Care for the Poor and Underserved | May 2023

Publication Project

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project

Using data science and a health equity lens to identify long-COVID sequelae among medically underserved populations

Md Nasir, Nicole Cook, Daniel Parras, Sumit Mukherjee, Geralyn Miller, Juan M. Lavista Ferres, Katherine Chung-Bridges

Journal of Health Care for the Poor and Underserved | May 2023

Publication Project

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Boonyaratanakornkit J, Wald A, Selke S, Wener Mh, Morishima C, Greninger Al, Michael Gale, Tien-Ying Hsiang, Lichen Jing, Holbrook Mr, Ian M. Kaplan, Damon H May, H. Jabran Zahid, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S Robins, David M Koelle

JCI Insight | April 2022, Vol 7(10)

DOI Preprint Publication Project Project

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H. Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Andrea Crisanti, Giovanni Tonon

JCI Insight | April 2022, Vol 7(10)

DOI Publication Project

Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2

Shuyuan Zhang, Qingtai Liang, Xinheng He, Chongchong Zhao, Wenlin Ren, Ziqing Yang, Ziyi Wang, Qiang Ding, Haiteng Deng, Tong Wang, Linqi Zhang, Xinquan Wang

Cell Research | January 2022

Publication

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.

Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

PLOS ONE | April 2021, Vol 16(4): pp. e0250780

DOI Publication Publication Publication Publication Publication Publication Publication Project

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project

A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N Dines, Ian M Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitch Pesesky, Rachel M Gittelman, Thomas M Snyder, Christopher J Gooley, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D Goldman, James R Heath, Luigi D Notarangelo, Jonathan M. Carlson, Joaquin Martinez-Lopez, Harlan S Robins

August 2020

DOI Publication Publication Publication Publication Project

Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines

Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine

Nature Biomedical Engineering | May 2020, Vol 4(6): pp. 636-648

DOI

Using data science and a health equity lens to identify long-COVID sequelae among medically underserved populations

Md Nasir, Nicole Cook, Daniel Parras, Sumit Mukherjee, Geralyn Miller, Juan M. Lavista Ferres, Katherine Chung-Bridges

Journal of Health Care for the Poor and Underserved | May 2023

Publication Project

T-cell receptor sequencing identifies prior SARS-CoV-2 infection and correlates with neutralizing antibody titers and disease severity

Rebecca Elyanow, Thomas M. Snyder, Sudeb C. Dalai, Rachel M. Gittelman, Boonyaratanakornkit J, Wald A, Selke S, Wener Mh, Morishima C, Greninger Al, Michael Gale, Tien-Ying Hsiang, Lichen Jing, Holbrook Mr, Ian M. Kaplan, Damon H May, H. Jabran Zahid, Jonathan M. Carlson, Lance Baldo, Thomas Manley, Harlan S Robins, David M Koelle

JCI Insight | April 2022, Vol 7(10)

DOI Preprint Publication Project Project

Longitudinal analysis of T cell receptor repertoires reveals shared patterns of antigen-specific response to SARS-CoV-2 infection

Rachel M Gittelman, Enrico Lavezzo, Thomas M Snyder, H. Jabran Zahid, Cara L Carty, Rebecca Elyanow, Sudeb Dalai, Ilan Kirsch, Lance Baldo, Laura Manuto, Elisa Franchin, Claudia Del Vecchio, Monia Pacenti, Caterina Boldrin, Margherita Cattai, Francesca Saluzzo, Andrea Padoan, Mario Plebani, Fabio Simeoni, Jessica Bordini, Nicola I Lorè, Dejan Lazarević, Daniela M Cirillo, Paolo Ghia, Stefano Toppo, Jonathan M. Carlson, Harlan S Robins, Andrea Crisanti, Giovanni Tonon

JCI Insight | April 2022, Vol 7(10)

DOI Publication Project

Loss of Spike N370 glycosylation as an important evolutionary event for the enhanced infectivity of SARS-CoV-2

Shuyuan Zhang, Qingtai Liang, Xinheng He, Chongchong Zhao, Wenlin Ren, Ziqing Yang, Ziyi Wang, Qiang Ding, Haiteng Deng, Tong Wang, Linqi Zhang, Xinquan Wang

Cell Research | January 2022

Publication

Exploring the Regulatory Function of the N-terminal Domain of SARS-CoV-2 Spike Protein through Molecular Dynamics Simulation

Yao Li, Tong Wang, Juanrong Zhang, Bin Shao, Haipeng Gong, Yusong Wang, Xinheng He, Siyuan Liu, Tie-Yan Liu

Advanced Theory and Simulations | September 2021

"Top Downloaded Article" Award, Cover Story

DOI PDF

Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein.

Debra Van Egeren, Alexander Novokhodko, Madison Stoddard, Uyen Tran, Bruce Zetter, Michael Rogers, Bradley L. Pentelute, Jonathan M. Carlson, Mark Hixon, Diane Joseph-McCarthy, Arijit Chakravarty

PLOS ONE | April 2021, Vol 16(4): pp. e0250780

DOI Publication Publication Publication Publication Publication Publication Publication Project

Pharmacokinetic tuning of protein-antigen fusions enhances the immunogenicity of T-cell vaccines

Naveen K Mehta, Roma V Pradhan, Ava P. Soleimany, Kelly D Moynihan, Adrienne M Rothschilds, Noor Momin, Kavya Rakhra, Jordi Mata-Fink, Sangeeta N Bhatia, K Dane Wittrup, Darrell J Irvine

Nature Biomedical Engineering | May 2020, Vol 4(6): pp. 636-648

DOI

Protein sequence models for prediction and comparative analysis of the SARS-CoV-2 —human interactome

Meghana Kshirsagar, Nure Tasnina, Michael D. Ward, Jeffrey N. Law, T. M. Murali, Juan M. Lavista Ferres, Gregory R. Bowman , Judith Klein-Seetharaman

Pacific Symposium on Biocomputing | January 2021

Publication Project

A large-scale database of T-cell receptor beta (TCRβ) sequences and binding associations from natural and synthetic exposure to SARS-CoV-2

Sean Nolan, Marissa Vignali, Mark Klinger, Jennifer N Dines, Ian M Kaplan, Emily Svejnoha, Tracy Craft, Katie Boland, Mitch Pesesky, Rachel M Gittelman, Thomas M Snyder, Christopher J Gooley, Simona Semprini, Claudio Cerchione, Massimiliano Mazza, Ottavia M Delmonte, Kerry Dobbs, Gonzalo Carreño-Tarragona, Santiago Barrio, Vittorio Sambri, Giovanni Martinelli, Jason D Goldman, James R Heath, Luigi D Notarangelo, Jonathan M. Carlson, Joaquin Martinez-Lopez, Harlan S Robins

August 2020

DOI Publication Publication Publication Publication Project