BloodGen3Module: blood transcriptional module repertoire analysis and visualization using R

por Rinchai, Darawan, Roelands, Jessica, Toufiq, Mohammed, Hendrickx, Wouter, Altman, Matthew C, Bedognetti, Davide, Chaussabel, Damien
Publicado 2021

Type 2 inflammation reduces SARS-CoV-2 replication in the airway epithelium in allergic asthma through functional alteration of ciliated epithelial cells

por Doni Jayavelu, Naresh, Altman, Matthew C., Benson, Basilin, Dufort, Matthew J., Vanderwall, Elizabeth R., Rich, Lucille M., White, Maria P., Becker, Patrice M., Togias, Alkis, Jackson, Daniel J., Debley, Jason S.
Publicado 2023

Shared and organism-specific host responses to childhood diarrheal diseases revealed by whole blood transcript profiling

por DeBerg, Hannah A., Zaidi, Mussaret B., Altman, Matthew C., Khaenam, Prasong, Gersuk, Vivian H., Campos, Freddy D., Perez-Martinez, Iza, Meza-Segura, Mario, Chaussabel, Damien, Banchereau, Jacques, Estrada-Garcia, Teresa, Linsley, Peter S.
Publicado 2018

DNA methylation signatures in airway cells from adult children of asthmatic mothers reflect subtypes of severe asthma

por Magnaye, Kevin M., Clay, Selene M., Nicodemus-Johnson, Jessie, Naughton, Katherine A., Huffman, Janel, Altman, Matthew C., Jackson, Daniel J., Gern, James E., Hogarth, Douglas K., Naureckas, Edward T., White, Steven R., Ober, Carole
Publicado 2022

Definition of erythroid cell‐positive blood transcriptome phenotypes associated with severe respiratory syncytial virus infection

por Rinchai, Darawan, Altman, Matthew C., Konza, Oceane, Hässler, Signe, Martina, Federica, Toufiq, Mohammed, Garand, Mathieu, Kabeer, Basirudeen Syed Ahamed, Palucka, Karolina, Mejias, Asuncion, Ramilo, Octavio, Bedognetti, Davide, Mariotti‐Ferrandiz, Encarnita, Klatzmann, David, Chaussabel, Damien
Publicado 2020

Fine-mapping studies distinguish genetic risks for childhood- and adult-onset asthma in the HLA region

por Clay, Selene M., Schoettler, Nathan, Goldstein, Andrew M., Carbonetto, Peter, Dapas, Matthew, Altman, Matthew C., Rosasco, Mario G., Gern, James E., Jackson, Daniel J., Im, Hae Kyung, Stephens, Matthew, Nicolae, Dan L., Ober, Carole
Publicado 2022

Kimma: flexible linear mixed effects modeling with kinship covariance for RNA-seq data

por Dill-McFarland, Kimberly A, Mitchell, Kiana, Batchu, Sashank, Segnitz, Richard Max, Benson, Basilin, Janczyk, Tomasz, Cox, Madison S, Mayanja-Kizza, Harriet, Boom, William Henry, Benchek, Penelope, Stein, Catherine M, Hawn, Thomas R, Altman, Matthew C
Publicado 2023

A transcriptomic reporter assay employing neutrophils to measure immunogenic activity of septic patients’ plasma

por Khaenam, Prasong, Rinchai, Darawan, Altman, Matthew C, Chiche, Laurent, Buddhisa, Surachat, Kewcharoenwong, Chidchamai, Suwannasaen, Duangchan, Mason, Michael, Whalen, Elizabeth, Presnell, Scott, Susaengrat, Wattanachai, O’Brien, Kimberly, Nguyen, Quynh-Ahn, Gersuk, Vivian, Linsley, Peter S, Lertmemongkolchai, Ganjana, Chaussabel, Damien
Publicado 2014

A modular framework for the development of targeted Covid-19 blood transcript profiling panels

por Rinchai, Darawan, Syed Ahamed Kabeer, Basirudeen, Toufiq, Mohammed, Tatari-Calderone, Zohreh, Deola, Sara, Brummaier, Tobias, Garand, Mathieu, Branco, Ricardo, Baldwin, Nicole, Alfaki, Mohamed, Altman, Matthew C., Ballestrero, Alberto, Bassetti, Matteo, Zoppoli, Gabriele, De Maria, Andrea, Tang, Benjamin, Bedognetti, Davide, Chaussabel, Damien
Publicado 2020

Multi-omics colocalization with genome-wide association studies reveals a context-specific genetic mechanism at a childhood onset asthma risk locus

por Soliai, Marcus M., Kato, Atsushi, Helling, Britney A., Stanhope, Catherine T., Norton, James E., Naughton, Katherine A., Klinger, Aiko I., Thompson, Emma E., Clay, Selene M., Kim, Soyeon, Celedón, Juan C., Gern, James E., Jackson, Daniel J., Altman, Matthew C., Kern, Robert C., Tan, Bruce K., Schleimer, Robert P., Nicolae, Dan L., Pinto, Jayant M., Ober, Carole
Publicado 2021

Asthma-associated genetic variants induce IL33 differential expression through an enhancer-blocking regulatory region

por Aneas, Ivy, Decker, Donna C., Howard, Chanie L., Sobreira, Débora R., Sakabe, Noboru J., Blaine, Kelly M., Stein, Michelle M., Hrusch, Cara L., Montefiori, Lindsey E., Tena, Juan, Magnaye, Kevin M., Clay, Selene M., Gern, James E., Jackson, Daniel J., Altman, Matthew C., Naureckas, Edward T., Hogarth, Douglas K., White, Steven R., Gomez-Skarmeta, Jose Luis, Schoetler, Nathan, Ober, Carole, Sperling, Anne I., Nóbrega, Marcelo A.
Publicado 2021

Transcriptome networks identify mechanisms of viral and nonviral asthma exacerbations in children

por Altman, Matthew C., Gill, Michelle A., Whalen, Elizabeth, Babineau, Denise C., Shao, Baomei, Liu, Andrew H., Jepson, Brett, Gruchalla, Rebecca S., O’Connor, George T., Pongracic, Jacqueline A., Kercsmar, Carolyn M., Khurana Hershey, Gurjit K., Zoratti, Edward M., Johnson, Christine C., Teach, Stephen J., Kattan, Meyer, Bacharier, Leonard B., Beigelman, Avraham, Sigelman, Steve M., Presnell, Scott, Gern, James E., Gergen, Peter J., Wheatley, Lisa M., Togias, Alkis, Busse, William W., Jackson, Daniel J.
Publicado 2019

Heterogeneity of magnitude, allergen immunodominance, and cytokine polarization of cockroach allergen‐specific T cell responses in allergic sensitized children

por da Silva Antunes, Ricardo, Sutherland, Aaron, Frazier, April, Schulten, Veronique, Pomés, Anna, Glesner, Jill, Calatroni, Agustin, Altman, Matthew C., Wood, Robert A., O'Connor, George T., Pongracic, Jacqueline A., Khurana Hershey, Gurjit K., Kercsmar, Carolyn M., Gruchalla, Rebecca S., Gill, Michelle, Liu, Andrew H., Zoratti, Edward, Kattan, Meyer, Busse, Paula J., Bacharier, Leonard B., Teach, Stephen J., Wheatley, Lisa M., Togias, Alkis, Busse, William W., Jackson, Daniel J., Sette, Alessandro
Publicado 2021

Associations between outdoor air pollutants and non-viral asthma exacerbations and airway inflammatory responses in children and adolescents living in urban areas in the USA: a ret...

por Altman, Matthew C, Kattan, Meyer, O’Connor, George T, Murphy, Ryan C, Whalen, Elizabeth, LeBeau, Petra, Calatroni, Agustin, Gill, Michelle A, Gruchalla, Rebecca S, Liu, Andrew H, Lovinsky-Desir, Stephanie, Pongracic, Jacqueline A, Kercsmar, Carolyn M, Khurana, Gurjit K Hershey, Zoratti, Edward M, Teach, Stephen J, Bacharier, Leonard B, Wheatley, Lisa M, Sigelman, Steve M, Gergen, Peter J, Togias, Alkis, Busse, William W, Gern, James E, Jackson, Daniel J
Publicado 2023

Multi-omic association study identifies DNA methylation-mediated genotype and smoking exposure effects on lung function in children living in urban settings

por Dapas, Matthew, Thompson, Emma E., Wentworth-Sheilds, William, Clay, Selene, Visness, Cynthia M., Calatroni, Agustin, Sordillo, Joanne E., Gold, Diane R., Wood, Robert A., Makhija, Melanie, Khurana Hershey, Gurjit K., Sherenian, Michael G., Gruchalla, Rebecca S., Gill, Michelle A., Liu, Andrew H., Kim, Haejin, Kattan, Meyer, Bacharier, Leonard B., Rastogi, Deepa, Altman, Matthew C., Busse, William W., Becker, Patrice M., Nicolae, Dan, O’Connor, George T., Gern, James E., Jackson, Daniel J., Ober, Carole
Publicado 2023

Development of a fixed module repertoire for the analysis and interpretation of blood transcriptome data

por Altman, Matthew C., Rinchai, Darawan, Baldwin, Nicole, Toufiq, Mohammed, Whalen, Elizabeth, Garand, Mathieu, Syed Ahamed Kabeer, Basirudeen, Alfaki, Mohamed, Presnell, Scott R., Khaenam, Prasong, Ayllón-Benítez, Aaron, Mougin, Fleur, Thébault, Patricia, Chiche, Laurent, Jourde-Chiche, Noemie, Phillips, J. Theodore, Klintmalm, Goran, O’Garra, Anne, Berry, Matthew, Bloom, Chloe, Wilkinson, Robert J., Graham, Christine M., Lipman, Marc, Lertmemongkolchai, Ganjana, Bedognetti, Davide, Thiebaut, Rodolphe, Kheradmand, Farrah, Mejias, Asuncion, Ramilo, Octavio, Palucka, Karolina, Pascual, Virginia, Banchereau, Jacques, Chaussabel, Damien
Publicado 2021

Immunophenotyping assessment in a COVID-19 cohort (IMPACC): A prospective longitudinal study

por Rouphael, Nadine, Maecker, Holden, Montgomery, Ruth R., Diray-Arce, Joann, Kleinstein, Steven H., Altman, Matthew C., Bosinger, Steven E., Eckalbar, Walter, Guan, Leying, Hough, Catherine L., Krammer, Florian, Langelier, Charles, Levy, Ofer, McEnaney, Kerry, Peters, Bjoern, Rahman, Adeeb, Rajan, Jayant V., Sigelman, Steven, Steen, Hanno, van Bakel, Harm, Ward, Alyssa, Wilson, Michael R., Woodruff, Prescott, Zamecnik, Colin R., Augustine, Alison D., Ozonoff, Al, Reed, Elaine F., Becker, Patrice M., Higuita, Nelson Agudelo, Altman, Matthew C., Atkinson, Mark A., Baden, Lindsey R., Becker, Patrice M., Bime, Christian, Brakenridge, Scott C., Calfee, Carolyn S., Cairns, Charles B., Corry, David, Davis, Mark M., Augustine, Alison D., Ehrlich, Lauren I. R., Haddad, Elias K., Erle, David J., Fernandez-Sesma, Ana, Hafler, David A., Hough, Catherine L., Kheradmand, Farrah, Kleinstein, Steven H., Kraft, Monica, Levy, Ofer, McComsey, Grace A., Melamed, Esther, Messer, William, Metcalf, Jordan, Montgomery, Ruth R., Nadeau, Kari C., Ozonoff, Al, Peters, Bjoern, Pulendran, Bali, Reed, Elaine F., Rouphael, Nadine, Sarwal, Minnie, Schaenman, Joanna, Sekaly, Rafick, Shaw, Albert C., Simon, Viviana
Publicado 2021

Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: Results from the IMPACC study

por Ozonoff, Al, Schaenman, Joanna, Jayavelu, Naresh Doni, Milliren, Carly E., Calfee, Carolyn S., Cairns, Charles B., Kraft, Monica, Baden, Lindsey R., Shaw, Albert C., Krammer, Florian, van Bakel, Harm, Esserman, Denise A., Liu, Shanshan, Sesma, Ana Fernandez, Simon, Viviana, Hafler, David A., Montgomery, Ruth R., Kleinstein, Steven H., Levy, Ofer, Bime, Christian, Haddad, Elias K., Erle, David J., Pulendran, Bali, Nadeau, Kari C., Davis, Mark M., Hough, Catherine L., Messer, William B., Higuita, Nelson I. Agudelo, Metcalf, Jordan P., Atkinson, Mark A., Brakenridge, Scott C., Corry, David, Kheradmand, Farrah, Ehrlich, Lauren I.R., Melamed, Esther, McComsey, Grace A., Sekaly, Rafick, Diray-Arce, Joann, Peters, Bjoern, Augustine, Alison D., Reed, Elaine F., Altman, Matthew C., Becker, Patrice M., Rouphael, Nadine
Publicado 2022

African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans

por Washington, Charles, Dapas, Matthew, Biddanda, Arjun, Magnaye, Kevin M., Aneas, Ivy, Helling, Britney A., Szczesny, Brooke, Boorgula, Meher Preethi, Taub, Margaret A., Kenny, Eimear, Mathias, Rasika A., Barnes, Kathleen C., Khurana Hershey, Gurjit K., Kercsmar, Carolyn M., Gereige, Jessica D., Makhija, Melanie, Gruchalla, Rebecca S., Gill, Michelle A., Liu, Andrew H., Rastogi, Deepa, Busse, William, Gergen, Peter J., Visness, Cynthia M., Gold, Diane R., Hartert, Tina, Johnson, Christine C., Lemanske, Robert F., Martinez, Fernando D., Miller, Rachel L., Ownby, Dennis, Seroogy, Christine M., Wright, Anne L., Zoratti, Edward M., Bacharier, Leonard B., Kattan, Meyer, O’Connor, George T., Wood, Robert A., Nobrega, Marcelo A., Altman, Matthew C., Jackson, Daniel J., Gern, James E., McKennan, Christopher G., Ober, Carole
Publicado 2022

Multi-omic longitudinal study reveals immune correlates of clinical course among hospitalized COVID-19 patients

por Diray-Arce, Joann, Fourati, Slim, Doni Jayavelu, Naresh, Patel, Ravi, Maguire, Cole, Chang, Ana C., Dandekar, Ravi, Qi, Jingjing, Lee, Brian H., van Zalm, Patrick, Schroeder, Andrew, Chen, Ernie, Konstorum, Anna, Brito, Anderson, Gygi, Jeremy P., Kho, Alvin, Chen, Jing, Pawar, Shrikant, Gonzalez-Reiche, Ana Silvia, Hoch, Annmarie, Milliren, Carly E., Overton, James A., Westendorf, Kerstin, Cairns, Charles B., Rouphael, Nadine, Bosinger, Steven E., Kim-Schulze, Seunghee, Krammer, Florian, Rosen, Lindsey, Grubaugh, Nathan D., van Bakel, Harm, Wilson, Michael, Rajan, Jayant, Steen, Hanno, Eckalbar, Walter, Cotsapas, Chris, Langelier, Charles R., Levy, Ofer, Altman, Matthew C., Maecker, Holden, Montgomery, Ruth R., Haddad, Elias K., Sekaly, Rafick P., Esserman, Denise, Ozonoff, Al, Becker, Patrice M., Augustine, Alison D., Guan, Leying, Peters, Bjoern, Kleinstein, Steven H.
Publicado 2023