Search Results - "KHATRI, Purvesh"

Host-response-based gene signatures for tuberculosis diagnosis: A systematic comparison of 16 signatures by Warsinske, Hayley, Vashisht, Rohit, Khatri, Purvesh

“…The World Health Organization (WHO) and Foundation for Innovative New Diagnostics (FIND) have published target product profiles (TPPs) calling for…”
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Mechanisms of innate and adaptive immunity to the Pfizer-BioNTech BNT162b2 vaccine by Li, Chunfeng, Lee, Audrey, Grigoryan, Lilit, Arunachalam, Prabhu S., Scott, Madeleine K. D., Trisal, Meera, Wimmers, Florian, Sanyal, Mrinmoy, Weidenbacher, Payton A., Feng, Yupeng, Adamska, Julia Z., Valore, Erika, Wang, Yanli, Verma, Rohit, Reis, Noah, Dunham, Diane, O’Hara, Ruth, Park, Helen, Luo, Wei, Gitlin, Alexander D., Kim, Peter, Khatri, Purvesh, Nadeau, Kari C., Pulendran, Bali

“…Despite the success of the BNT162b2 mRNA vaccine, the immunological mechanisms that underlie its efficacy are poorly understood. Here we analyzed the innate…”
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A clinically meaningful metric of immune age derived from high-dimensional longitudinal monitoring by Alpert, Ayelet, Pickman, Yishai, Leipold, Michael, Rosenberg-Hasson, Yael, Ji, Xuhuai, Gaujoux, Renaud, Rabani, Hadas, Starosvetsky, Elina, Kveler, Ksenya, Schaffert, Steven, Furman, David, Caspi, Oren, Rosenschein, Uri, Khatri, Purvesh, Dekker, Cornelia L., Maecker, Holden T., Davis, Mark M., Shen-Orr, Shai S.

“…Immune responses generally decline with age. However, the dynamics of this process at the individual level have not been characterized, hindering…”
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Ten years of pathway analysis: current approaches and outstanding challenges by Khatri, Purvesh, Sirota, Marina, Butte, Atul J

“…Pathway analysis has become the first choice for gaining insight into the underlying biology of differentially expressed genes and proteins, as it reduces…”
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A comprehensive time-course-based multicohort analysis of sepsis and sterile inflammation reveals a robust diagnostic gene set by Sweeney, Timothy E, Shidham, Aaditya, Wong, Hector R, Khatri, Purvesh

“…Although several dozen studies of gene expression in sepsis have been published, distinguishing sepsis from a sterile systemic inflammatory response syndrome…”
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A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections by Mayhew, Michael B., Buturovic, Ljubomir, Luethy, Roland, Midic, Uros, Moore, Andrew R., Roque, Jonasel A., Shaller, Brian D., Asuni, Tola, Rawling, David, Remmel, Melissa, Choi, Kirindi, Wacker, James, Khatri, Purvesh, Rogers, Angela J., Sweeney, Timothy E.

“…Improved identification of bacterial and viral infections would reduce morbidity from sepsis, reduce antibiotic overuse, and lower healthcare costs. Here, we…”
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Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis by Sweeney, Timothy E, MD, Braviak, Lindsay, Tato, Cristina M, PhD, Khatri, Purvesh, Dr

“…Summary Background Active pulmonary tuberculosis is difficult to diagnose and treatment response is difficult to effectively monitor. A WHO consensus statement…”
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A molecular atlas of innate immunity to adjuvanted and live attenuated vaccines, in mice by Lee, Audrey, Scott, Madeleine K. D., Wimmers, Florian, Arunachalam, Prabhu S., Luo, Wei, Fox, Christopher B., Tomai, Mark, Khatri, Purvesh, Pulendran, Bali

“…Adjuvants hold great potential in enhancing vaccine efficacy, making the understanding and improving of adjuvants critical goals in vaccinology. The TLR7/8…”
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The single-cell epigenomic and transcriptional landscape of immunity to influenza vaccination by Wimmers, Florian, Donato, Michele, Kuo, Alex, Ashuach, Tal, Gupta, Shakti, Li, Chunfeng, Dvorak, Mai, Foecke, Mariko Hinton, Chang, Sarah E., Hagan, Thomas, De Jong, Sanne E., Maecker, Holden T., van der Most, Robbert, Cheung, Peggie, Cortese, Mario, Bosinger, Steven E., Davis, Mark, Rouphael, Nadine, Subramaniam, Shankar, Yosef, Nir, Utz, Paul J., Khatri, Purvesh, Pulendran, Bali

“…Emerging evidence indicates a fundamental role for the epigenome in immunity. Here, we mapped the epigenomic and transcriptional landscape of immunity to…”
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Ontological analysis of gene expression data: current tools, limitations, and open problems by Khatri, Purvesh, Drăghici, Sorin

“…Independent of the platform and the analysis methods used, the result of a microarray experiment is, in most cases, a list of differentially expressed genes…”
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Increasing reproducibility, robustness, and generalizability of biomarker selection from meta-analysis using Bayesian methodology by Kalesinskas, Laurynas, Gupta, Sanjana, Khatri, Purvesh

“…A major limitation of gene expression biomarker studies is that they are not reproducible as they simply do not generalize to larger, real-world, heterogeneous…”
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A robust gene expression signature for NASH in liver expression data by Hasin-Brumshtein, Yehudit, Sakaram, Suraj, Khatri, Purvesh, He, Yudong D., Sweeney, Timothy E.

“…Non-Alcoholic Fatty Liver Disease (NAFLD) is a progressive liver disease that affects up to 30% of worldwide population, of which up to 25% progress to…”
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The immunoregulatory landscape of human tuberculosis granulomas by McCaffrey, Erin F., Donato, Michele, Keren, Leeat, Chen, Zhenghao, Delmastro, Alea, Fitzpatrick, Megan B., Gupta, Sanjana, Greenwald, Noah F., Baranski, Alex, Graf, William, Kumar, Rashmi, Bosse, Marc, Fullaway, Christine Camacho, Ramdial, Pratista K., Forgó, Erna, Jojic, Vladimir, Van Valen, David, Mehra, Smriti, Khader, Shabaana A., Bendall, Sean C., van de Rijn, Matt, Kalman, Daniel, Kaushal, Deepak, Hunter, Robert L., Banaei, Niaz, Steyn, Adrie J. C., Khatri, Purvesh, Angelo, Michael

“…Tuberculosis (TB) in humans is characterized by formation of immune-rich granulomas in infected tissues, the architecture and composition of which are thought…”
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Leveraging heterogeneity across multiple datasets increases cell-mixture deconvolution accuracy and reduces biological and technical biases by Vallania, Francesco, Tam, Andrew, Lofgren, Shane, Schaffert, Steven, Azad, Tej D., Bongen, Erika, Haynes, Winston, Alsup, Meia, Alonso, Michael, Davis, Mark, Engleman, Edgar, Khatri, Purvesh

“…In silico quantification of cell proportions from mixed-cell transcriptomics data (deconvolution) requires a reference expression matrix, called basis matrix…”
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Discovery of Distinct Immune Phenotypes Using Machine Learning in Pulmonary Arterial Hypertension by Sweatt, Andrew J, Hedlin, Haley K, Balasubramanian, Vidhya, Hsi, Andrew, Blum, Lisa K, Robinson, William H, Haddad, Francois, Hickey, Peter M, Condliffe, Robin, Lawrie, Allan, Nicolls, Mark R, Rabinovitch, Marlene, Khatri, Purvesh, Zamanian, Roham T

“…RATIONALE:Accumulating evidence implicates inflammation in pulmonary arterial hypertension (PAH) and therapies targeting immunity are under investigation,…”
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Single-cell technologies — studying rheumatic diseases one cell at a time by Cheung, Peggie, Khatri, Purvesh, Utz, Paul J., Kuo, Alex J.

“…Cells, the basic units of life, have striking differences at transcriptomic, proteomic and epigenomic levels across tissues, organs, organ systems and…”
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T cell-inducing vaccine durably prevents mucosal SHIV infection even with lower neutralizing antibody titers by Arunachalam, Prabhu S., Charles, Tysheena P., Joag, Vineet, Bollimpelli, Venkata S., Scott, Madeleine K. D., Wimmers, Florian, Burton, Samantha L., Labranche, Celia C., Petitdemange, Caroline, Gangadhara, Sailaja, Styles, Tiffany M., Quarnstrom, Clare F., Walter, Korey A., Ketas, Thomas J., Legere, Traci, Jagadeesh Reddy, Pradeep Babu, Kasturi, Sudhir Pai, Tsai, Anthony, Yeung, Bertrand Z., Gupta, Shakti, Tomai, Mark, Vasilakos, John, Shaw, George M., Kang, Chil-Yong, Moore, John P., Subramaniam, Shankar, Khatri, Purvesh, Montefiori, David, Kozlowski, Pamela A., Derdeyn, Cynthia A., Hunter, Eric, Masopust, David, Amara, Rama R., Pulendran, Bali

“…Recent efforts toward an HIV vaccine focus on inducing broadly neutralizing antibodies, but eliciting both neutralizing antibodies (nAbs) and cellular…”
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A novel signaling pathway impact analysis by Tarca, Adi Laurentiu, Draghici, Sorin, Khatri, Purvesh, Hassan, Sonia S., Mittal, Pooja, Kim, Jung-sun, Kim, Chong Jai, Kusanovic, Juan Pedro, Romero, Roberto

“…Motivation: Gene expression class comparison studies may identify hundreds or thousands of genes as differentially expressed (DE) between sample groups…”
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Single-cell RNA-seq methods to interrogate virus-host interactions by Ratnasiri, Kalani, Wilk, Aaron J., Lee, Madeline J., Khatri, Purvesh, Blish, Catherine A.

“…The twenty-first century has seen the emergence of many epidemic and pandemic viruses, with the most recent being the SARS-CoV-2-driven COVID-19 pandemic. As…”
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A community approach to mortality prediction in sepsis via gene expression analysis by Sweeney, Timothy E., Perumal, Thanneer M., Henao, Ricardo, Nichols, Marshall, Howrylak, Judith A., Choi, Augustine M., Bermejo-Martin, Jesús F., Almansa, Raquel, Tamayo, Eduardo, Davenport, Emma E., Burnham, Katie L., Hinds, Charles J., Knight, Julian C., Woods, Christopher W., Kingsmore, Stephen F., Ginsburg, Geoffrey S., Wong, Hector R., Parnell, Grant P., Tang, Benjamin, Moldawer, Lyle L., Moore, Frederick E., Omberg, Larsson, Khatri, Purvesh, Tsalik, Ephraim L., Mangravite, Lara M., Langley, Raymond J.

“…Improved risk stratification and prognosis prediction in sepsis is a critical unmet need. Clinical severity scores and available assays such as blood lactate…”
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