Nasal and blood transcriptomic pathways underpinning the clinical response to grass pollen immunotherapy

Authors: Altman, Matthew C., Segnitz, R. Max, Larson, David, Jayavelu, Naresh Doni, Smith, Malisa T., Patel, Sana, Scadding, Guy W., Qin, Tielin, Sanda, Srinath, Steveling, Esther, Eifan, Aarif O., Penagos, Martin, Jacobson, Mikila R., Parkin, Rebecca V., Shamji, Mohamed H., Togias, Alkis, Durham, Stephen R.

Source: In The Journal of Allergy and Clinical Immunology November 2023 152(5):1247-1260

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

Authors: 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, Chris, 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., McEnaney, Kerry, Barton, Brenda, Lentucci, Claudia, Saluvan, Mehmet, Chang, Ana C., Hoch, Annmarie, Albert, Marisa, Shaheen, Tanzia, Kho, Alvin T., Thomas, Sanya, Chen, Jing, Murphy, Maimouna D., Cooney, Mitchell, Presnell, Scott, Fragiadakis, Gabriela K., Patel, Ravi, Guan, Leying, Gygi, Jeremy, Pawar, Shrikant, Brito, Anderson, Khalil, Zain, Maguire, Cole, Fourati, Slim, Overton, James A., Vita, Randi, Westendorf, Kerstin, Salehi-Rad, Ramin, Leligdowicz, Aleksandra, Matthay, Michael A., Singer, Jonathan P., Kangelaris, Kirsten N., Hendrickson, Carolyn M., Krummel, Matthew F., Langelier, Charles R., Woodruff, Prescott G., Powell, Debra L., Kim, James N., Simmons, Brent, Goonewardene, I. Michael, Smith, Cecilia M., Martens, Mark, Mosier, Jarrod, Kimura, Hiroki, Sherman, Amy C., Walsh, Stephen R., Issa, Nicolas C., Dela Cruz, Charles, Farhadian, Shelli, Iwasaki, Akiko, Ko, Albert I., Chinthrajah, Sharon, Ahuja, Neera, Rogers, Angela J., Artandi, Maja, Siegel, Sarah A.R., Lu, Zhengchun, Drevets, Douglas A., Brown, Brent R., Anderson, Matthew L., Guirgis, Faheem W., Thyagarajan, Rama V., Rousseau, Justin F., Wylie, Dennis, Busch, Johanna, Gandhi, Saurin, Triplett, Todd A., Yendewa, George, Giddings, Olivia, Anderson, Evan J., Mehta, Aneesh K., Sevransky, Jonathan E., Khor, Bernard, Rahman, Adeeb, Stadlbauer, Daniel, Dutta, Jayeeta, Xie, Hui, Kim-Schulze, Seunghee, Gonzalez-Reiche, Ana Silvia, van de Guchte, Adriana, Farrugia, Keith, Khan, Zenab, Maecker, Holden T., Elashoff, David, Brook, Jenny, Ramires-Sanchez, Estefania, Llamas, Megan, Rivera, Adreanne, Perdomo, Claudia, Ward, Dawn C., Magyar, Clara E., Fulcher, Jennifer A., Abe-Jones, Yumiko, Asthana, Saurabh, Beagle, Alexander, Bhide, Sharvari, Carrillo, Sidney A., Chak, Suzanna, Ghale, Rajani, Gonzalez, Ana, Jauregui, Alejandra, Jones, Norman, Lea, Tasha, Lee, Deanna, Lota, Raphael, Milush, Jeff, Nguyen, Viet, Pierce, Logan, Prasad, Priya A., Rao, Arjun, Samad, Bushra, Shaw, Cole, Sigman, Austin, Sinha, Pratik, Ward, Alyssa, Willmore, Andrew, Zhan, Jenny, Rashid, Sadeed, Rodriguez, Nicklaus, Tang, Kevin, Altamirano, Luz Torres, Betancourt, Legna, Curiel, Cindy, Sutter, Nicole, Paz, Maria Tercero, Tietje-Ulrich, Gayelan, Leroux, Carolyn, Connors, Jennifer, Bernui, Mariana, Kutzler, Michel A., Edwards, Carolyn, Lee, Edward, Lin, Edward, Croen, Brett, Semenza, Nicholas C., Rogowski, Brandon, Melnyk, Nataliya, Woloszczuk, Kyra, Cusimano, Gina, Bell, Mathew R., Furukawa, Sara, McLin, Renee, Marrero, Pamela, Sheidy, Julie, Tegos, George P., Nagle, Crystal, Mege, Nathan, Ulring, Kristen, Seyfert-Margolis, Vicki, Conway, Michelle, Francisco, Dave, Molzahn, Allyson, Erickson, Heidi, Wilson, Connie Cathleen, Schunk, Ron, Sierra, Bianca, Hughes, Trina, Smolen, Kinga, Desjardins, Michael, van Haren, Simon, Mitre, Xhoi, Cauley, Jessica, Li, Xiaofang, Tong, Alexandra, Evans, Bethany, Montesano, Christina, Licona, Jose Humberto, Krauss, Jonathan, Chang, Jun Bai Park, Izaguirre, Natalie, Chaudhary, Omkar, Coppi, Andreas, Fournier, John, Mohanty, Subhasis, Muenker, M. Catherine, Nelson, Allison, Raddassi, Khadir, Rainone, Michael, Ruff, William E., Salahuddin, Syim, Schulz, Wade L., Vijayakumar, Pavithra, Wang, Haowei, Wunder Jr., Elsio, Young, H. Patrick, Zhao, Yujiao, Saksena, Miti, Altman, Deena, Kojic, Erna, Srivastava, Komal, Eaker, Lily Q., Bermúdez-González, Maria C., Beach, Katherine F., Sominsky, Levy A., Azad, Arman R., Carreño, Juan Manuel, Singh, Gagandeep, Raskin, Ariel, Tcheou, Johnstone, Bielak, Dominika, Kawabata, Hisaaki, Mulder, Lubbertus CF, Kleiner, Giulio, Lee, Alexandra S., Do, Evan Do, Fernandes, Andrea, Manohar, Monali, Hagan, Thomas, Blish, Catherine A., Din, Hena Naz, Roque, Jonasel, Yang, Samuel, Brunton, Amanda, Sullivan, Peter E., Strnad, Matthew, Lyski, Zoe L., Coulter, Felicity J., Booth, J. Leland, Sinko, Lauren A., Moldawer, Lyle L., Borresen, Brittany, Roth-Manning, Brittney, Song, Li-Zhen, Nelson, Ebony, Lewis-Smith, Megan, Smith, Jacob, Tipan, Pablo Guaman, Siles, Nadia, Bazzi, Sam, Geltman, Janelle, Hurley, Kerin, Gabriele, Gio, Sieg, Scott, Vaysman, Tatyana, Bristow, Laurel, Hussaini, Laila, Hellmeister, Kieffer, Samaha, Hady, Cheng, Andrew, Spainhour, Christine, Scherer, Erin M., Johnson, Brandi, Bechnak, Amer, Ciric, Caroline R., Hewitt, Lauren, Carter, Erin, Mcnair, Nina, Panganiban, Bernadine, Huerta, Christopher, Usher, Jacob, Ribeiro, Susan Pereira, Altman, Matthew C., Becker, Patrice M., Rouphael, Nadine, Bime, Christian, Davis, Mark M.

Source: In eBioMedicine September 2022 83

ISNCA: A new iterative approach for constrained matrix factorization methods

Authors: Jayavelu, Naresh Doni, Bar, Nadav

Source: In Journal of Process Control December 2017 60:24-33

Identification of functional enhancer variants associated with type I diabetes in CD4+ T cells.

Authors: Mishra, Arpit, Jajodia, Ajay, Weston, Eryn, Jayavelu, Naresh Doni, Garcia, Mariana, Hossack, Daniel, Hawkins, R. David

Source: Frontiers in Immunology; 2024, p1-9, 9p

Subject Terms: TYPE 1 diabetes, GENE enhancers, T cells, PANCREATIC beta cells, CD4 antigen, GENOME-wide association studies

Host-microbe multiomic profiling reveals age-dependent immune dysregulation associated with COVID-19 immunopathology.

Authors: Phan, Hoang Van, Tsitsiklis, Alexandra, Maguire, Cole P., Haddad, Elias K., Becker, Patrice M., Kim-Schulze, Seunghee, Lee, Brian, Chen, Jing, Hoch, Annmarie, Pickering, Harry, van Zalm, Patrick, Altman, Matthew C., Augustine, Alison D., Calfee, Carolyn S., Bosinger, Steve, Cairns, Charles B., Eckalbar, Walter, Guan, Leying, Jayavelu, Naresh Doni, Kleinstein, Steven H.

Source: Science Translational Medicine; 4/17/2024, Vol. 16 Issue 743, p1-16, 16p

Corrigendum to “Phenotypes of disease severity in a cohort of hospitalized COVID-19 patients: results from the IMPACC study” [eBioMedicine 83 (2022) 104208]

Authors: 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, Chris, Haddad, Elias K., Erle, David J., Pulendran, Bali, Nadeau, Kari C., Davis, Mark M., Hough, Catherine L., Messer, William B., Agudelo Higuita, Nelson I., 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

Source: In eBioMedicine December 2023 98

Features of acute COVID-19 associated with post-acute sequelae of SARS-CoV-2 phenotypes: results from the IMPACC study.

Authors: Ozonoff, Al, Jayavelu, Naresh Doni, Liu, Shanshan, Melamed, Esther, Milliren, Carly E., Qi, Jingjing, Geng, Linda N., McComsey, Grace A., Cairns, Charles B., Baden, Lindsey R., Schaenman, Joanna, Shaw, Albert C., Samaha, Hady, Seyfert-Margolis, Vicki, Krammer, Florian, Rosen, Lindsey B., Steen, Hanno, Syphurs, Caitlin, Dandekar, Ravi, Shannon, Casey P.

Source: Nature Communications; 1/3/2024, Vol. 15 Issue 1, p1-17, 17p

Subject Terms: FIBROBLAST growth factors, SARS-CoV-2, PATIENT reported outcome measures, COVID-19, ANTIBODY titer, B cells

Constrained Fourier estimation of short-term time-series gene expression data reduces noise and improves clustering and gene regulatory network predictions.

Authors: Bar, Nadav, Nikparvar, Bahareh, Jayavelu, Naresh Doni, Roessler, Fabienne Krystin

Source: BMC Bioinformatics; 8/9/2022, Vol. 23 Issue 1, p1-21, 21p

Subject Terms: GENE regulatory networks, GENE expression, GENE clusters, NOISE control, SIGNAL-to-noise ratio, NOISE

Reconstruction of temporal activity of microRNAs from gene expression data in breast cancer cell line.

Authors: Jayavelu, Naresh Doni¹ (AUTHOR) nareshd@chemeng.nnu.no, Bar, Nadav¹ (AUTHOR) nadi.bar@chemeng.ntnu.no

Source: BMC Genomics. 12/18/2015, Vol. 16, p1-15. 15p. 2 Diagrams, 4 Charts, 4 Graphs.

Iterative sub-network component analysis enables reconstruction of large scale genetic networks.

Authors: Jayavelu, Naresh Doni¹, Aasgaard, Lasse S.¹, Bar, Nadav¹ nadi.bar@ntnu.no

Source: BMC Bioinformatics. 11/4/2015, Vol. 16, p1-13. 13p. 1 Diagram, 5 Charts, 4 Graphs.

Subject Terms: *GENETIC algorithms, *GENETIC programming, *GENE expression, *GENETIC transcription, *BIOINFORMATICS, *PHYSIOLOGY

Genome-scale cold stress response regulatory networks in ten Arabidopsis thaliana ecotypes.

Authors: Barah, Pankaj¹ pankaj.barah@bio.ntnu.no, Jayavelu, Naresh Doni² naresh.jayavelu@chemeng.ntnu.no, Rasmussen, Simon³ simon@cbs.dtu.dk, Nielsen, Henrik Bjørn³ hbjorn@cbs.dtu.dk, Mundy, John⁴ mundy@bio.ku.dk, Bones, Atle M.¹ atle.bones@bio.ntnu.no

Source: BMC Genomics. 2013, Vol. 14 Issue 1, p1-34. 34p.

Subject Terms: *ARABIDOPSIS thaliana, *CROP losses, *GENETIC polymorphisms, *REGULONS, *AMINO acids, *PHYSIOLOGICAL effects of cold temperatures

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Transcriptional regulatory networks in Arabidopsis thalianaduring single and combined stresses.

Authors: Barah, Pankaj, B. N., Mahantesha Naika, Jayavelu, Naresh Doni, Sowdhamini, Ramanathan, Shameer, Khader, Bones, Atle M.

Source: Nucleic Acids Research; 4/20/2016, Vol. 44 Issue 7, p3147-3164, 18p

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Integrated longitudinal multiomics study identifies immune programs associated with acute COVID-19 severity and mortality.

Authors: Gygi, Jeremy P., Maguire, Cole, Patel, Ravi K., Shinde, Pramod, Konstorum, Anna, Shannon, Casey P., Leqi Xu, Hoch, Annmarie, Jayavelu, Naresh Doni, Haddad, Elias K., Reed, Elaine F., Kraft, Monica, McComsey, Grace A., Metcalf, Jordan P., Ozonoff, Al, Esserman, Denise, Cairns, Charles B., Rouphael, Nadine, Bosinger, Steven E., Seunghee Kim-Schulze

Source: Journal of Clinical Investigation. 5/1/2024, Issue 9, p1-17. 17p.

Subjects: COVID-19, MORTALITY, B cells, LONGITUDINAL method, T cells, BLOOD coagulation