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1. Sepsis endotypes identified by host gene expression across global cohorts

Author

Chenoweth, Josh G., Brandsma, Joost, Striegel, Deborah A., Genzor, Pavol, Chiyka, Elizabeth, Blair, Paul W., Krishnan, Subramaniam, Dogbe, Elliot, Boakye, Isaac, Fogel, Gary B., Tsalik, Ephraim L., Woods, Christopher W., Owusu-Ofori, Alex, Oppong, Chris, Oduro, George, Vantha, Te, Letizia, Andrew G., Beckett, Charmagne G., Schully, Kevin L., and Clark, Danielle V.

Published
2024
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2. List of contributors

Author

Aizawa, Shin-Ichi, primary, Alberdi, Pilar, additional, Alexander, David C., additional, Alía, Alberto, additional, Allison, D.G., additional, Amyes, Sebastian G.B., additional, An, Haoran, additional, Andrade, María J., additional, Antelmann, Haike, additional, Arias, Cesar A., additional, Asensio, Miguel A., additional, Axell-House, Dierdre B., additional, Bae, Hee-Won, additional, Baena, Laura Muñoz, additional, Baig, Abdul Mannan, additional, Bailey, Spenser O., additional, Baize, Sylvain, additional, Baldi, Pablo C., additional, Barbosa, Angela Silva, additional, Barbuddhe, Sukhadeo B., additional, Bard, Emilie, additional, Barry, Eileen M., additional, Basarab, Gregory S., additional, Beloborodova, N.V, additional, Bermúdez, Elena, additional, Bidmos, Fadil A., additional, Bisgaard, Magne, additional, Blakely, Garry W., additional, Bloch, Evan, additional, Boesen, Thias Oberg, additional, Bose, Dipayan, additional, Botero, Javier Enrique, additional, Bouabe, Hicham, additional, Bouchard, Michael J., additional, Bozue, Joel A., additional, Bradbury, Richard S., additional, Brett Moreau, G., additional, Cabezas-Cruz, Alejandro, additional, Cai, Rong-Jun, additional, Calderón, Enrique J., additional, Cao, Boyang, additional, Carmena, David, additional, Carvalho, Eneas, additional, Caulfield, Amanda D., additional, Cen, Shan, additional, Chai, Jong-Yil, additional, Chamberland, Robin R., additional, Champredon, David, additional, Chan, Edward D., additional, Charbon, Godefroid, additional, Chato, Connor, additional, Chelomina, G.N., additional, Chen, Jingyu, additional, Chen, Min, additional, Chen, Shuyu, additional, Chen, Suilin, additional, Chen, Yanfei, additional, Chen, Zhaoyuan, additional, Cheng, Aimin, additional, Cheng, Keding, additional, Chiu, Charles Y., additional, Cho, You-Hee, additional, Christensen, Henrik, additional, Chrtdernevskaya, E.A., additional, Contreras, Adolfo, additional, Contreras, Marinela, additional, Córdoba, Juan J., additional, Córdoba, María G., additional, Costa, Rita, additional, Cote, Christopher K., additional, Cui, Xiangling, additional, Cui, Yujun, additional, Dacal, Elena, additional, Dammann, Allison N., additional, Das, Shubhagata, additional, Dashti, Alejandro, additional, de la Fuente, José, additional, de la Garza, Mireya, additional, Delgado, Josué, additional, Delgado-Cuesta, Juan, additional, Deng, Haiteng, additional, Deng, Li, additional, Dey, Debajit, additional, Dhama, Kuldeep, additional, Diego, Juan García-Bernalt, additional, Ding, Hao, additional, Doern, Christopher D., additional, Dorman, Charles J., additional, Du, Zongmin, additional, Dunbar, Sherry A., additional, Duthie, Malcolm, additional, Dybvig, Kevin F., additional, Eakin, Ann E., additional, Eallonardo, Samuel J., additional, Eberly, Allison R., additional, Echeverry, Adriana Jaramillo, additional, Egland, Paul G., additional, El Zowalaty, Mohamed E., additional, Endsley, Janice Jones, additional, Eom, Keeseon S., additional, Evans, Benjamin A., additional, Falkinham, Joseph O., additional, Feng, Siwei, additional, Feng, Yaoyu, additional, Feng, Zongdi, additional, Fernández-Soto, Pedro, additional, Ferreira, Roux-Cil, additional, Flores-Huerta, Nadia, additional, Foster, Timothy J., additional, Fox-Moon, Sandra M., additional, Fraga, Tatiana Rodrigues, additional, Fredricks, David N., additional, Freitag, Nancy E., additional, Frimodt-Møller, Jakob, additional, Fuller, Risa, additional, Ganesh, Balasubramanian, additional, Gao, Ning, additional, García-Carnero, Laura C., additional, Garzetti, Debora, additional, Geoghegan, Joan A., additional, Ghenim, Raed, additional, Giambartolomei, Guillermo H., additional, Gilbert, Nicole M., additional, Gillis, Thomas Phillip, additional, Gladstone, Camilla A., additional, Gómez-Gaviria, Manuela, additional, Gómez-Marín, Jorge E., additional, Gong, Tengfang, additional, González, Ramón A., additional, Gray-Owen, Scott D., additional, Gu, Bing, additional, Guzmán-Téllez, Paula, additional, Hajal, Caroline, additional, Han, Yanping, additional, Hao, Yi, additional, Harrington, Amanda T., additional, Harris, Jason B., additional, Harvill, Eric T., additional, Hasan, S. Saif, additional, He, Guang-Jun, additional, He, Yongqun, additional, Heffron, Jared D., additional, Hidalgo, Paloma, additional, Hindiyeh, Musa Y., additional, Hreha, Teri N., additional, Hu, Xiaoyu, additional, Huang, Guanghua, additional, Huang, Jiangqing, additional, Huang, Liang, additional, Huang, Shifeng, additional, Huang, Xingxu, additional, Huang, Xueting, additional, Huang, Yilun, additional, Huffman, Anthony, additional, Humphreys, Tricia L., additional, Hunstad, David A., additional, Inglis, Timothy J.J., additional, Isaac, Lourdes, additional, Jacobs, Samantha E., additional, Janowicz, Diane M., additional, Jeon, Hyeong-Kyu, additional, Ji, Quanjiang, additional, Jia, Qi, additional, Jia, Wei, additional, Jin, Shouguang, additional, Jneidi, Lama, additional, Jose, Shinsmon, additional, Jung, Bong-Kwang, additional, Kattan, Randa, additional, Kaushik, Rahul, additional, Khare, Reeti, additional, Kim, Eun Sook, additional, Kirn, Thomas J., additional, Koo, Hyun, additional, Köster, Pamela C., additional, Krause, Peter J., additional, Kumar, Sanjai, additional, Kupz, Andreas, additional, Lambert, P.A., additional, Lamont, Richard J., additional, Langford, Paul R., additional, Lebeaux, David, additional, Legname, Giuseppe, additional, Li, Bin, additional, Li, Chunhao, additional, Li, Fen, additional, Li, Jun, additional, Li, Lanjuan, additional, Li, Ruofan, additional, Li, Ruoyu, additional, Li, Ting, additional, Li, Yang-Yang, additional, Li, Yanhua, additional, Li, Zhuorong, additional, Liang, Xiaomeng, additional, Liao, Guojian, additional, Lin, Ping, additional, Ling, Yun, additional, Liu, Bo, additional, Liu, Dongyou, additional, Liu, Guohua, additional, Liu, Huidi, additional, Liu, Jiafeng, additional, Liu, Jintao, additional, Liu, Qi, additional, Liu, Shu-Lin, additional, Liu, Taiping, additional, Liu, Tongbao, additional, Liu, Wei, additional, Liu, Yan, additional, Liu, Yanni, additional, Liu, Yisong, additional, Liu, Yuan, additional, Løbner-Olesen, Anders, additional, Loeffelholz, Michael, additional, Lu, Hongzhou, additional, Luna, Brian, additional, Ma, Bingting, additional, Ma, Chengying, additional, Ma, Shuang, additional, Ma, TianLi, additional, Madan, Rajat, additional, Mahle, Rachael E., additional, Mahlen, Steven D., additional, Malik, Satya Veer Singh, additional, Malik, Yashpal Singh, additional, Malvy, Denis, additional, Mann, Barbara J., additional, Marasini, Daya, additional, Maris, Alexander S., additional, Marjomäki, Varpu, additional, Marjuki, Henju, additional, Martín, Alberto, additional, Martín, Irene, additional, Martínez-Castillo, Moisés, additional, Martínez-Pabón, María Cecilia, additional, Mathison, Blaine A., additional, Ma’ayeh, Showgy, additional, McDowell, Andrew, additional, McLaughlin, Stephanie E., additional, McSheffrey, Gordon G., additional, Medrano, Francisco J., additional, Meehan, Conor J., additional, Mehta, Dhwani, additional, Mejía-Oquendo, Manuela, additional, Melo-Cristino, José, additional, Mendoza-Barberá, Elena, additional, Meng, Xinan, additional, Merino, Susana, additional, Merritt, Adam J., additional, Miller, Steve, additional, Miller, William R., additional, Minamino, Tohru, additional, Mirzaei, Mohammadali Khan, additional, Mora-Montes, Héctor M., additional, Mortensen, Joel, additional, Mostafa, Heba H., additional, Muhsen, Khitam, additional, Mujahed, Ahlam, additional, Muro, Antonio, additional, Murphy, Olwen C., additional, Newton, Hayley J., additional, Nguyen, April H., additional, Nichols, Wright W., additional, Niu, Siqiang, additional, Núñez, Félix, additional, Obregon, Dasiel, additional, Okamoto, Akira, additional, Okutani, Akiko, additional, Olabode, Abayomi, additional, Omar, Muna, additional, Ong, Edison, additional, Ouyang, Zhiming, additional, Pacak, Christina A., additional, Pacheco-Yépez, Judith, additional, Palmer, John, additional, Pang, Xiaoli, additional, Paredes-Sabja, Daniel, additional, Peng, Zhong, additional, Peng, Zonggen, additional, Pérez-Nevado, Francisco, additional, Poon, Art, additional, Pospíšilová, Petra, additional, Potts, Caelin C., additional, Pu, Qinqin, additional, Pujic, Petar, additional, Qi, Rui, additional, Qian, Chenyun, additional, Qian, Liu, additional, Qin, Aiping, additional, Qu, Fen, additional, Rakin, Alexander, additional, Ramesh, Ashwin, additional, Ramirez, Mario, additional, Rao, Yu, additional, Ratner, Adam J., additional, Rawool, Deepak B., additional, Rehman, Asma, additional, Ren, Jie, additional, Ren, Ping, additional, Retchless, Adam C., additional, Robertson, Erle S., additional, Rodríguez, Alicia, additional, Rodriguez, Azucena, additional, Rodríguez-Medina, Carolina, additional, Rodriguez-Nava, Veronica, additional, Rohde, Manfred, additional, Romero-Rodríguez, Alba, additional, Rosales-Morgan, Gabriela, additional, Rosenkranz, Andrea L., additional, Ruiz-Moyano, Santiago, additional, Ruokolainen, Visa, additional, Sabateen, Ali, additional, Sahu, Radhakrishna, additional, Sails, Andrew, additional, Sang, Yu, additional, Santana, Clarissa H., additional, Santos, Jesus A., additional, Santos, Renato L., additional, Schmitz, Jonathan E., additional, Serrano-Luna, Jesús, additional, Shen, Jianzhong, additional, Shen, Zhangqi, additional, Shibayama, Mineko, additional, Shirtliff, Mark E., additional, Silva-Costa, Catarina, additional, Silva-Olivares, Angélica, additional, Singh, Niraj Kumar, additional, Šmajs, David, additional, Smith, Robert P., additional, Smith, Sophie, additional, Snyder, Lori A.S., additional, Song, Yinggai, additional, Soro, Aurea Simon, additional, Spearman, Paul, additional, Spellberg, Brad, additional, Sprague, Lisa D., additional, Stratton, Charles W., additional, Strenk, Susan M., additional, Strugnell, Richard A., additional, Sun, Keer, additional, Suo, Xun, additional, Suzuki-Hatano, Silveli, additional, Svärd, Staffan, additional, Talbot, Elizabeth A., additional, Tamez-Castrellón, Alma K., additional, Tan, Nie, additional, Tang, Cynthia Y., additional, Tang, Yi-Wei, additional, Tao, Jia, additional, Tao, Lili, additional, Terrero-Salcedo, David, additional, Tharmalingam, Jayaraman, additional, Thwe, Phyu M., additional, Tiamani, Kawtar, additional, Tomás, Juan M., additional, Topaz, Nadav, additional, Tsai, Ang-Chen, additional, Tsalik, Ephraim L., additional, Tuomanen, Elaine I., additional, Turenne, Christine Y., additional, Tyagi, Anuj, additional, Uprety, Priyanka, additional, Valour, Florent, additional, van Hensbergen, Vincent P., additional, Venkatesan, Arun, additional, Vergis, Jess, additional, Villar, Margarita, additional, Vollmer, Waldemar, additional, Waites, Ken B., additional, Wan, Xiu-Feng, additional, Wang, Guiqing, additional, Wang, Lijun, additional, Wang, Lin, additional, Wang, Linqi, additional, Wang, Xiangru, additional, Wang, Xin, additional, Wang, Xinjie, additional, Wang, Ya-Ting, additional, Wang, Yang, additional, Wang, Yating, additional, Weil, Ana A., additional, Welkos, Susan L., additional, Wengenack, Nancy L., additional, Westblade, Lars F., additional, Whitfield, Chris, additional, Wu, Hui, additional, Wu, Lijuan, additional, Wu, Min, additional, Wu, Yarong, additional, Wu, Zhaowei, additional, Xiang, Ye, additional, Xiao, Di, additional, Xiao, Li, additional, Xiao, Lihua, additional, Xu, Tao, additional, Xu, Wenyue, additional, Xu, Xinping, additional, Xue, Jinling, additional, Yadav, Jay Prakash, additional, Yan, Junxiang, additional, Yan, Yixin, additional, Yang, Changmei, additional, Yang, Ruifu, additional, Yang, Ying, additional, Yao, Kaihu, additional, Yao, Yu-Feng, additional, Yeakle, Kyle C., additional, Yu, Demin, additional, Yu, Hao, additional, Yu, Xue-Jie, additional, Yuan, Zhenghong, additional, Zai, Wenjing, additional, Zhang, Jianzhong, additional, Zhang, Jing-Ren, additional, Zhang, Lanyue, additional, Zhang, Lijie, additional, Zhang, Qiwei, additional, Zhang, Wenbao, additional, Zhang, Wenhong, additional, Zhang, Xinxin, additional, Zhao, Youbao, additional, Zhou, Chuanmin, additional, Zhu, Feng, additional, Zhu, Jingting, additional, and Zhu, Yongqun, additional

Published
2024
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4. Envisioning Future Urinary Tract Infection Diagnostics.

Author

Patel, Robin, Polage, Christopher R, Dien Bard, Jennifer, May, Larissa, Lee, Francesca M, Fabre, Valeria, Hayden, Mary K, Doernberg, Sarah DB, Haake, David A, Trautner, Barbara W, Grigoryan, Larissa, Tsalik, Ephraim L, and Hanson, Kimberly E

Subjects
Biodefense, Prevention, Antimicrobial Resistance, Vaccine Related, Urologic Diseases, Emerging Infectious Diseases, Infectious Diseases, Development of treatments and therapeutic interventions, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Anti-Bacterial Agents, Drug Resistance, Bacterial, Humans, United States, Urinary Tract Infections, urinary tract infection, UTI, laboratory diagnosis, diagnostics, Biological Sciences, Medical and Health Sciences, Microbiology
Abstract

Urinary tract infections (UTIs) are among the most common bacterial infections in the United States and are a major driver of antibiotic use, both appropriate and inappropriate, across healthcare settings. Novel UTI diagnostics are a strategy that might enable better UTI treatment. Members of the Antibacterial Resistance Leadership Group Laboratory Center and the Infectious Diseases Society of America Diagnostics Committee convened to envision ideal future UTI diagnostics, with a view towards improving delivery of healthcare, patient outcomes and experiences, and antibiotic use, addressing which types of UTI diagnostics are needed and how companies might approach development of novel UTI diagnostics.

Published
2022

5. Host-response transcriptional biomarkers accurately discriminate bacterial and viral infections of global relevance

Author

Ko, Emily R., Reller, Megan E., Tillekeratne, L. Gayani, Bodinayake, Champica K., Miller, Cameron, Burke, Thomas W., Henao, Ricardo, McClain, Micah T., Suchindran, Sunil, Nicholson, Bradly, Blatt, Adam, Petzold, Elizabeth, Tsalik, Ephraim L., Nagahawatte, Ajith, Devasiri, Vasantha, Rubach, Matthew P., Maro, Venance P., Lwezaula, Bingileki F., Kodikara-Arachichi, Wasantha, Kurukulasooriya, Ruvini, De Silva, Aruna D., Clark, Danielle V., Schully, Kevin L., Madut, Deng, Dumler, J. Stephen, Kato, Cecilia, Galloway, Renee, Crump, John A., Ginsburg, Geoffrey S., Minogue, Timothy D., and Woods, Christopher W.

Published
2023
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6. Author Correction: Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion

Author

Giroux, Nicholas S., Ding, Shengli, McClain, Micah T., Burke, Thomas W., Petzold, Elizabeth, Chung, Hong A., Rivera, Grecia O., Wang, Ergang, Xi, Rui, Bose, Shree, Rotstein, Tomer, Nicholson, Bradly P., Chen, Tianyi, Henao, Ricardo, Sempowski, Gregory D., Denny, Thomas N., De Ussel, Maria Iglesias, Satterwhite, Lisa L., Ko, Emily R., Ginsburg, Geoffrey S., Kraft, Bryan D., Tsalik, Ephraim L., Shen, Xiling, and Woods, Christopher W.

Published
2023
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8. Analytical Evaluation of the Abbott RealTime CT/NG Assay for Detection of Chlamydia trachomatis and Neisseria gonorrhoeae in Rectal and Pharyngeal Swabs

Author

Adamson, Paul C, Pandori, Mark W, Doernberg, Sarah B, Komarow, Lauren, Sund, Zoe, Tran, Thuy Tien T, Jensen, David, Tsalik, Ephraim L, Deal, Carolyn D, Chambers, Henry F, Fowler, Vance G, Evans, Scott R, Patel, Robin, Klausner, Jeffrey D, and Group, Antibacterial Resistance Leadership

Subjects
Medical Microbiology, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Urologic Diseases, Sexually Transmitted Infections, 2.2 Factors relating to the physical environment, Infection, Good Health and Well Being, Chlamydia Infections, Chlamydia trachomatis, Data Accuracy, Female, Gonorrhea, Humans, Limit of Detection, Male, Neisseria gonorrhoeae, Pharynx, Real-Time Polymerase Chain Reaction, Rectum, Sensitivity and Specificity, Antibacterial Resistance Leadership Group, Pathology, Clinical sciences, Oncology and carcinogenesis
Abstract

Chlamydia trachomatis and Neisseria gonorrhoeae infections in the rectum and pharynx are important extragenital reservoirs of infection. Few assays approved by the US Food and Drug Administration are commercially available to diagnose pharyngeal or rectal infections. The current study reports on the analytical performance of the Abbott RealTime CT/NG assay, including the limit of detection, inclusivity, and analytical specificity for C. trachomatis and N. gonorrhoeae in rectal and pharyngeal specimens. The limit of detection was performed using known concentrations of organisms, elementary bodies per milliliter (EB/mL) for C. trachomatis and colony-forming units per milliliter (CFU/mL) for N. gonorrhoeae, in clinical rectal and pharyngeal swab matrices. Inclusivity was performed against 12 serovars of C. trachomatis and seven strains of N. gonorrhoeae. The analytical specificity was performed using 28 different bacteria and viruses. The limit of detection for C. trachomatis was 2.56 EB/mL in pharyngeal specimens and 12.8 EB/mL in rectal specimens. The limit of detection for N. gonorrhoeae was 0.0256 CFU/mL for both pharyngeal and rectal specimens. The inclusivity and analytical specificity were 100% for both rectal and pharyngeal specimens. These analytical performance data demonstrate that the Abbott CT/NG RealTime assay is an accurate, sensitive, and specific assay in rectal and pharyngeal specimens, supporting the potential of the assay for detection of rectal and pharyngeal C. trachomatis and N. gonorrhoeae infections.

Published
2020

10. Pathogen class-specific transcriptional responses derived from PBMCs accurately discriminate between fungal, bacterial, and viral infections.

Author

Steinbrink, Julie M., Liu, Yiling, Henao, Ricardo, Tsalik, Ephraim L., Ginsburg, Geoffrey S., Ramsburg, Elizabeth, Woods, Christopher W., and McClain, Micah T.

Subjects
LEUCOCYTES, INVASIVE candidiasis, BACTERIAL diseases, COMMUNICABLE diseases, CRYPTOCOCCUS neoformans, VIRUS diseases
Abstract

Immune responses during acute infection often contain canonical elements which are shared across the responses to an array of agents within a given pathogen class (i.e., respiratory viral infection). Identification of these shared, canonical elements across similar infections offers the potential for impacting development of novel diagnostics and therapeutics. In this way, analysis of host gene expression patterns ('signatures') in white blood cells has been shown to be useful for determining the etiology of some acute viral and bacterial infections. In order to study conserved immune elements shared across the host response to related pathogens, we performed in vitro human PBMC challenges with common fungal pathogens (Candida albicans, Cryptococcus neoformans and gattii); four strains of influenza virus (Influenza A/Puerto Rico/08/34 [H1N1, PR8], A/Brisbane/59/2007 [H1N1], A/Solomon Islands/3/2006 [H1N1], and A/Wisconsin/67/2005 [H3N2]); and gram-negative (Escherichia coli) and gram-positive (Streptococcus pneumoniae) bacteria. Exposed human cells were then analyzed for differential gene expression utilizing Affymetrix microarrays. Analysis of pathogen exposure of PBMCs revealed strong, conserved gene expression patterns representing these canonical immune response elements to each broad pathogen class. A 41-gene multinomial signature was developed which correctly classified fungal, viral, or bacterial exposure with 94–98% accuracy. Furthermore, a 21-gene signature consisting of a subset of the discriminatory PBMC-derived genes was capable of accurately differentiating human patients with invasive candidiasis, acute viral infection, or bacterial infection (AUC 0.94, 0.83, and 0.96 respectively). These data reinforce the conserved nature of the genomic responses in human peripheral blood cells upon exposure to infectious agents and highlight the potential for in vitro models to augment our ability to develop novel diagnostic classifiers for acute infectious diseases, particularly devastating fungal infections. [ABSTRACT FROM AUTHOR]

Published
2024
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12. Differential chromatin accessibility in peripheral blood mononuclear cells underlies COVID-19 disease severity prior to seroconversion

Author

Giroux, Nicholas S., Ding, Shengli, McClain, Micah T., Burke, Thomas W., Petzold, Elizabeth, Chung, Hong A., Rivera, Grecia O., Wang, Ergang, Xi, Rui, Bose, Shree, Rotstein, Tomer, Nicholson, Bradly P., Chen, Tianyi, Henao, Ricardo, Sempowski, Gregory D., Denny, Thomas N., De Ussel, Maria Iglesias, Satterwhite, Lisa L., Ko, Emily R., Ginsburg, Geoffrey S., Kraft, Bryan D., Tsalik, Ephraim L., Shen, Xiling, and Woods, Christopher W.

Published
2022
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14. Mucosal-associated invariant T cell responses differ by sex in COVID-19

Author

Yu, Chen, Littleton, Sejiro, Giroux, Nicholas S., Mathew, Rose, Ding, Shengli, Kalnitsky, Joan, Yang, Yuchen, Petzold, Elizabeth, Chung, Hong A., Rivera, Grecia O., Rotstein, Tomer, Xi, Rui, Ko, Emily R., Tsalik, Ephraim L., Sempowski, Gregory D., Denny, Thomas N., Burke, Thomas W., McClain, Micah T., Woods, Christopher W., Shen, Xiling, and Saban, Daniel R.

Published
2021
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16. Non-Gaussian Discriminative Factor Models via the Max-Margin Rank-Likelihood

Author

Yuan, Xin, Henao, Ricardo, Tsalik, Ephraim L., Langley, Raymond J., and Carin, Lawrence

Subjects
Statistics - Machine Learning
Abstract

We consider the problem of discriminative factor analysis for data that are in general non-Gaussian. A Bayesian model based on the ranks of the data is proposed. We first introduce a new {\em max-margin} version of the rank-likelihood. A discriminative factor model is then developed, integrating the max-margin rank-likelihood and (linear) Bayesian support vector machines, which are also built on the max-margin principle. The discriminative factor model is further extended to the {\em nonlinear} case through mixtures of local linear classifiers, via Dirichlet processes. Fully local conjugacy of the model yields efficient inference with both Markov Chain Monte Carlo and variational Bayes approaches. Extensive experiments on benchmark and real data demonstrate superior performance of the proposed model and its potential for applications in computational biology., Comment: 14 pages, 7 figures, ICML 2015

Published
2015

17. Viewing both sides of the coin for infectious disease diagnosis

Author

Strouts, Fiona R., McAllister, Linda B., and Tsalik, Ephraim L.

Subjects
Medical tests -- Evaluation, Respiratory tract infections -- Diagnosis, Health care industry
Abstract

Optimal management of lower respiratory tract infection relies on distinguishing infectious from noninfectious etiologies and identifying the microbiologic cause if applicable. This process is complicated by overlapping clinical symptoms and the colonizing lung microbiota. In a recent issue of the JCI, Mick, Tsitsiklis, and colleagues apply RNA-Seq to tracheal aspirates from critically ill children and demonstrate how integration of the host response with microbial identification results in a harmonious and accurate diagnostic classifier. Though promising, there are numerous barriers to realizing a combined host and pathogen diagnostic., A multipronged approach Defining the presence of a lower respiratory tract infection (LRTI) in children is challenging due in part to low rates of pathogen detection by conventional microbiologic testing [...]

Published
2023
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18. Host response to influenza infections in human blood: association of influenza severity with host genetics and transcriptomic response.

Author

Schughart, Klaus, Smith, Amber M., Tsalik, Ephraim L., Threlkeld, Stephen C., Sellers, Subhashini, Fischer II, William A., Schreiber, Jens, Lücke, Eva, Cornberg, Markus, Debarry, Jennifer, Woods, Christopher W., McClain, Micah T., and Heise, Mark

Subjects
GENE expression, MOLECULAR genetics, VIRUS diseases, GENETIC variation, INFLUENZA viruses
Abstract

Introduction: Influenza virus infections are a major global health problem. Influenza can result in mild/moderate disease or progress to more severe disease, leading to high morbidity and mortality. Severity is thought to be primarily driven by immunopathology, but predicting which individuals are at a higher risk of being hospitalized warrants investigation into host genetics and the molecular signatures of the host response during influenza infections. Methods: Here, we performed transcriptome and genotype analysis in healthy controls and patients exhibiting mild/moderate or severe influenza (ICU patients). A unique aspect of our study was the genotyping of all participants, which allowed us to assign ethnicities based on genetic variation and assess whether the variation was correlated with expression levels. Results: We identified 169 differentially expressed genes and relatedmolecular pathways between patients in the ICU and those who were not in the ICU. The transcriptome/ genotype association analysis identified 871 genes associated to a genetic variant and 39 genes distinct between African-Americans and Caucasians. We also investigated the effects of age and sex and found only a few discernible gene effects in our cohort. Discussion: Together, our results highlight select risk factors that may contribute to an increased risk of ICU admission for influenza-infected patients. This should help to develop better diagnostic tools based on molecular signatures, in addition to a better understanding of the biological processes in the host response to influenza. [ABSTRACT FROM AUTHOR]

Published
2024
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19. Implementation of a Prospective Index-Cluster Sampling Strategy for the Detection of Presymptomatic Viral Respiratory Infection in Undergraduate Students

Author

Uthappa, Diya M, primary, McClain, Micah T, additional, Nicholson, Bradly P, additional, Park, Lawrence P, additional, Zhbannikov, Ilya, additional, Suchindran, Sunil, additional, Jimenez, Monica, additional, Constantine, Florica J, additional, Nichols, Marshall, additional, Jones, Daphne C, additional, Hudson, Lori L, additional, Jaggers, L Brett, additional, Veldman, Timothy, additional, Burke, Thomas W, additional, Tsalik, Ephraim L, additional, Ginsburg, Geoffrey S, additional, and Woods, Christopher W, additional

Published
2024
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22. Dysregulated transcriptional responses to SARS-CoV-2 in the periphery

Author

McClain, Micah T., Constantine, Florica J., Henao, Ricardo, Liu, Yiling, Tsalik, Ephraim L., Burke, Thomas W., Steinbrink, Julie M., Petzold, Elizabeth, Nicholson, Bradly P., Rolfe, Robert, Kraft, Bryan D., Kelly, Matthew S., Saban, Daniel R., Yu, Chen, Shen, Xiling, Ko, Emily M., Sempowski, Gregory D., Denny, Thomas N., Ginsburg, Geoffrey S., and Woods, Christopher W.

Published
2021
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23. Validation of a host response test to distinguish bacterial and viral respiratory infection

Author

Lydon, Emily C., Henao, Ricardo, Burke, Thomas W., Aydin, Mert, Nicholson, Bradly P., Glickman, Seth W., Fowler, Vance G., Quackenbush, Eugenia B., Cairns, Charles B., Kingsmore, Stephen F., Jaehne, Anja K., Rivers, Emanuel P., Langley, Raymond J., Petzold, Elizabeth, Ko, Emily R., McClain, Micah T., Ginsburg, Geoffrey S., Woods, Christopher W., and Tsalik, Ephraim L.

Published
2019
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26. Epigenetic and transcriptional responses in circulating leukocytes are associated with future decompensation during SARS-CoV-2 infection

Author

McClain, Micah T., primary, Zhbannikov, Ilya, additional, Satterwhite, Lisa L., additional, Henao, Ricardo, additional, Giroux, Nicholas S., additional, Ding, Shengli, additional, Burke, Thomas W., additional, Tsalik, Ephraim L., additional, Nix, Christina, additional, Balcazar, Jorge Prado, additional, Petzold, Elizabeth A., additional, Shen, Xiling, additional, and Woods, Christopher W., additional

Published
2023
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31. Plasma Microbial Cell-Free DNA Sequencing in Immunocompromised Patients with Pneumonia: A Prospective Observational Study

Author

Bergin, Stephen P, primary, Chemaly, Roy F, additional, Dadwal, Sanjeet S, additional, Hill, Joshua A, additional, Lee, Yeon Joo, additional, Haidar, Ghady, additional, Luk, Alfred, additional, Drelick, Alexander, additional, Chin-Hong, Peter V, additional, Benamu, Esther, additional, Khawaja, Fareed, additional, Nanayakkara, Deepa, additional, Papanicolaou, Genovefa A, additional, Small, Catherine Butkus, additional, Fung, Monica, additional, Barron, Michelle A, additional, Davis, Thomas, additional, McClain, Micah T, additional, Maziarz, Eileen K, additional, Madut, Deng B, additional, Bedoya, Armando D, additional, Gilstrap, Daniel L, additional, Todd, Jamie L, additional, Barkauskas, Christina E, additional, Bigelow, Robert, additional, Leimberger, Jeffrey D, additional, Tsalik, Ephraim L, additional, Wolf, Olivia, additional, Mughar, Mona, additional, Hollemon, Desiree, additional, Duttagupta, Radha, additional, Lupu, Daniel S, additional, Bercovici, Sivan, additional, Perkins, Bradley A, additional, Blauwkamp, Timothy A, additional, Fowler, Vance G, additional, and Holland, Thomas L, additional

Published
2023
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32. Access to COVID-19 testing by individuals with housing insecurity during the early days of the COVID-19 pandemic in the United States: a scoping review

Author

Johannesson, Jon M., primary, Glover, William A., additional, Petti, Cathy A., additional, Veldman, Timothy H., additional, Tsalik, Ephraim L., additional, Taylor, Donald H., additional, Hendren, Stephanie, additional, Neighbors, Coralei E., additional, Tillekeratne, L. Gayani, additional, Kennedy, Scott W., additional, Harper, Barrie, additional, Kibbe, Warren A., additional, Corbie, Giselle, additional, Cohen-Wolkowiez, Michael, additional, Woods, Christopher W., additional, and Lee, Mark J., additional

Published
2023
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33. Nasopharyngeal Protein Biomarkers of Acute Respiratory Virus Infection

Author

Burke, Thomas W., Henao, Ricardo, Soderblom, Erik, Tsalik, Ephraim L., Thompson, J. Will, McClain, Micah T., Nichols, Marshall, Nicholson, Bradly P., Veldman, Timothy, Lucas, Joseph E., Moseley, M. Arthur, Turner, Ronald B., Lambkin-Williams, Robert, Hero, Alfred O., III, Woods, Christopher W., and Ginsburg, Geoffrey S.

Published
2017
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34. RADx-UP Testing Core: Access to COVID-19 Diagnostics in Community-Engaged Research with Underserved Populations

Author

Narayanasamy, Shanti, primary, Veldman, Timothy H., additional, Lee, Mark J., additional, Glover, William A., additional, Tillekeratne, L. Gayani, additional, Neighbors, Coralei E., additional, Harper, Barrie, additional, Raghavan, Vidya, additional, Kennedy, Scott W., additional, Carper, Miranda, additional, Denny, Thomas, additional, Tsalik, Ephraim L., additional, Reller, Megan E., additional, Kibbe, Warren A., additional, Corbie, Giselle, additional, Cohen-Wolkowiez, Michael, additional, Woods, Christopher W., additional, and Petti, Cathy A., additional

Published
2023
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37. Contributors

Author

Athuluri-Divakar, Sai Krishna, primary, Barnes, Peter J., additional, Blazes, David L., additional, Chambers, Eileen Tsai, additional, Clark, Danielle V., additional, Colón-López, Daisy D., additional, DeLeo, Frank R., additional, Doroudchi, Ali, additional, Dowell, Scott F., additional, Falsey, Ann Regina, additional, Filkins, Laura, additional, Hoshida, Yujin, additional, Hsueh, Ming-Feng, additional, Jones, Letitia D., additional, Khatri, Purvesh, additional, Kobayashi, Scott D., additional, Koehler, Jeffrey W., additional, Kraus, Virginia Byers, additional, Lambova, Sevdalina, additional, Langley, Raymond J., additional, Le Roch, Karine G., additional, Limou, Sophie, additional, Modena, Brian D., additional, Moody, M. Anthony, additional, Müller-Ladner, Ulf, additional, Patel, Keyur, additional, Patel, Parth, additional, Patsopoulos, Nikolaos A., additional, Ploumakis, Athanasios, additional, Robert, Schlaberg, additional, Sathish, Varshini, additional, Schully, Kevin L., additional, Shackel, Nicholas A, additional, Shaw, Brian I., additional, Stefan, Christopher P., additional, Surana, Neeraj K., additional, Sweeney, Timothy E., additional, Tan, Yong B., additional, Thompson, Amelia B., additional, Tsalik, Ephraim L., additional, Weiner, Howard L., additional, Wester, C. William, additional, Willard, Huntington F., additional, Williams, Desiree, additional, Winkler, Cheryl A., additional, Wong, Hector R., additional, and Woods, Christopher W., additional

Published
2019
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40. Multi-layer gene bundling: A new approach to gene clustering

Author

Fazli, Mehran, primary, Oppong, Chris, additional, Som, Tin, additional, Ko, Emily R., additional, Tsalik, Ephraim L., additional, Chenoweth, Josh, additional, Brandsma, Joost, additional, Woods, Chris, additional, Letizia, Andrew, additional, Fox, Anne, additional, Faix, Dennis, additional, Vantha, Te, additional, Oduro, George, additional, Schully, Kevin L., additional, Bertram, Richard, additional, Clark, Danielle V., additional, and Striegel, Deborah A., additional

Published
2023
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41. Insight into septic subpopulations from proteomic trajectory clusters

Author

Junior, Francis Baffour-Awuah, primary, Oppong, Chris, additional, Som, Tin, additional, Ko, Emily R., additional, Tsalik, Ephraim L., additional, Chenoweth, Josh, additional, Woods, Chris, additional, Letizia, Andrew, additional, Fox, Anne, additional, Schully, Kevin L., additional, Faix, Dennis, additional, Vantha, Te, additional, Oduro, George, additional, Cogan, Nick G., additional, Clark, Danielle V., additional, and Striegel, Deborah A., additional

Published
2023
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42. Blood RNA alternative splicing events as diagnostic biomarkers for infectious disease

Author

Zhang, Zijun, primary, Sauerwald, Natalie, additional, Cappuccio, Antonio, additional, Ramos, Irene, additional, Nair, Venugopalan D., additional, Nudelman, German, additional, Zaslavsky, Elena, additional, Ge, Yongchao, additional, Gaitas, Angelo, additional, Ren, Hui, additional, Brockman, Joel, additional, Geis, Jennifer, additional, Ramalingam, Naveen, additional, King, David, additional, McClain, Micah T., additional, Woods, Christopher W., additional, Henao, Ricardo, additional, Burke, Thomas W., additional, Tsalik, Ephraim L., additional, Goforth, Carl W., additional, Lizewski, Rhonda A., additional, Lizewski, Stephen E., additional, Weir, Dawn L., additional, Letizia, Andrew G., additional, Sealfon, Stuart C., additional, and Troyanskaya, Olga G., additional

Published
2023
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43. Screening tools for predicting mortality of adults with suspected sepsis: an international sepsis cohort validation study

Author

Blair, Paul W, primary, Mehta, Rittal, additional, Oppong, Chris Kwaku, additional, Tin, Som, additional, Ko, Emily, additional, Tsalik, Ephraim L, additional, Chenoweth, Josh, additional, Rozo, Michelle, additional, Adams, Nehkonti, additional, Beckett, Charmagne, additional, Woods, Christopher W, additional, Striegel, Deborah A, additional, Salvador, Mark G, additional, Brandsma, Joost, additional, McKean, Lauren, additional, Mahle, Rachael E, additional, Hulsey, William R, additional, Krishnan, Subramaniam, additional, Prouty, Michael, additional, Letizia, Andrew, additional, Fox, Anne, additional, Faix, Dennis, additional, Lawler, James V, additional, Duplessis, Chris, additional, Gregory, Michael G, additional, Vantha, Te, additional, Owusu-Ofori, Alex Kwame, additional, Ansong, Daniel, additional, Oduro, George, additional, Schully, Kevin L, additional, and Clark, Danielle V, additional

Published
2023
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44. Renal systems biology of patients with systemic inflammatory response syndrome

Author

Tsalik, Ephraim L., Willig, Laurel K., Rice, Brandon J., van Velkinburgh, Jennifer C., Mohney, Robert P., McDunn, Jonathan E., Dinwiddie, Darrell L., Miller, Neil A., Mayer, Eric S., Glickman, Seth W., Jaehne, Anja K., Glew, Robert H., Sopori, Mohan L., Otero, Ronny M., Harrod, Kevin S., Cairns, Charles B., Fowler, Vance G., Rivers, Emanuel P., Woods, Christopher W., Kingsmore, Stephen F., and Langley, Raymond J.

Published
2015
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46. Host-response Transcriptional Biomarkers Accurately Discriminate Bacterial and Viral Infections of Global Relevance

Author

Ko, Emily R., primary, Reller, Megan E., additional, Tillekeratne, L. Gayani, additional, Bodinayake, Champica K., additional, Miller, Cameron, additional, Burke, Thomas W., additional, Henao, Ricardo, additional, McClain, Micah T., additional, Suchindran, Sunil, additional, Nicholson, Bradly, additional, Blatt, Adam, additional, Petzold, Elizabeth, additional, Tsalik, Ephraim L., additional, Nagahawatte, Ajith, additional, Devasiri, Vasantha, additional, Rubach, Matthew P., additional, Maro, Venance P., additional, Lwezuala, Bingileki F., additional, Kodikara-Arachichi, Wasantha, additional, Kurukulasooriya, Ruvini, additional, Silva, Aruna D., additional, Clark, Danielle V., additional, Schully, Kevin L., additional, Madut, Deng, additional, Dumler, J. Stephen, additional, Kato, Cecilia, additional, Galloway, Renee, additional, Crump, John A., additional, Ginsburg, Geoffrey S., additional, Minogue, Timothy D., additional, and Woods, Christopher W., additional

Published
2023
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47. Efficacy and safety of azithromycin versus placebo to treat lower respiratory tract infections associated with low procalcitonin: a randomised, placebo-controlled, double-blind, non-inferiority trial

Author

Tsalik, Ephraim L, primary, Rouphael, Nadine G, additional, Sadikot, Ruxana T, additional, Rodriguez-Barradas, Maria C, additional, McClain, Micah T, additional, Wilkins, Dana M, additional, Woods, Christopher W, additional, Swamy, Geeta K, additional, Walter, Emmanuel B, additional, El Sahly, Hana M, additional, Keitel, Wendy A, additional, Mulligan, Mark J, additional, Tuyishimire, Bonifride, additional, Serti, Elisavet, additional, Hamasaki, Toshimitsu, additional, Evans, Scott R, additional, Ghazaryan, Varduhi, additional, Lee, Marina S, additional, Lautenbach, Ebbing, additional, Alaaeddine, Ghina, additional, Zreloff, Jennifer J., additional, McNair, Nina, additional, Kraft, Colleen S., additional, Roberts, David L., additional, Bergquist, Sharon H., additional, Beydoun, Nour, additional, Waggoner, Jesse J., additional, Kalangara, Merin E., additional, Collins, Matthew H., additional, Dretler, Alexandra W., additional, Bechnak, Amer R., additional, Oh, Laura, additional, Yuan, Zhihong, additional, Burrows, Brian J., additional, Ko, Emily R., additional, Dai, Weixiao, additional, and Zeng, Lijuan, additional

Published
2022
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48. 1169. Derivation And Validation of an International Clinical Prognostication Model for 28-day Sepsis Mortality.

Author

Blair, Paul W, primary, Mehta, Rittal, additional, Som, Tin, additional, Okello, Stephen, additional, Tsalik, Ephraim L, additional, Wailagala, Abdullah, additional, Woods, Christopher W, additional, Prouty, Michael, additional, Chenoweth, Josh, additional, Letizia, Andrew, additional, Faix, Dennis, additional, Adams, Nehkonti, additional, Ko, Emily R, additional, Duplessis, Chris, additional, Lamorde, Mohammed, additional, Owusu-Ofori, Alex, additional, Naluyima, Prossy, additional, Kayiira, Mubaraka, additional, Oppong, Chris, additional, Rozo, Michelle, additional, Fox, Ann, additional, Lawler, James, additional, Waitt, Peter, additional, Prouty, Angela, additional, Vantha, Te, additional, Beckett, Charmagne, additional, Kibuuka, Hannah, additional, Oduro, George, additional, Schully, Kevin, additional, and Clark, Danielle, additional

Published
2022
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50. Unsupervised Analysis of Transcriptomics in Bacterial Sepsis Across Multiple Datasets Reveals Three Robust Clusters

Author

Sweeney, Timothy E., Azad, Tej D., Donato, Michele, Haynes, Winston A., Perumal, Thanneer M., Henao, Ricardo, Bermejo-Martin, Jesús F., Almansa, Raquel, Tamayo, Eduardo, Howrylak, Judith A., Choi, Augustine, Parnell, Grant P., Tang, Benjamin, Nichols, Marshall, Woods, Christopher W., Ginsburg, Geoffrey S., Kingsmore, Stephen F., Omberg, Larsson, Mangravite, Lara M., Wong, Hector R., Tsalik, Ephraim L., Langley, Raymond J., and Khatri, Purvesh

Published
2018
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