| Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults C Langelier, KL Kalantar, F Moazed, MR Wilson, ED Crawford, T Deiss, ... Proceedings of the National Academy of Sciences 115 (52), E12353-E12362, 2018 | 329 | 2018 |
| IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring KL Kalantar, T Carvalho, CFA de Bourcy, B Dimitrov, G Dingle, R Egger, ... Gigascience 9 (10), giaa111, 2020 | 217 | 2020 |
| Metagenomic sequencing detects respiratory pathogens in hematopoietic cellular transplant patients C Langelier, MS Zinter, K Kalantar, GA Yanik, S Christenson, ... American journal of respiratory and critical care medicine 197 (4), 524-528, 2018 | 190 | 2018 |
| Pulmonary metagenomic sequencing suggests missed infections in immunocompromised children MS Zinter, CC Dvorak, MY Mayday, K Iwanaga, NP Ly, ME McGarry, ... Clinical Infectious Diseases 68 (11), 1847-1855, 2019 | 135 | 2019 |
| Metagenomic next-generation sequencing of samples from pediatric febrile illness in Tororo, Uganda A Ramesh, S Nakielny, J Hsu, M Kyohere, O Byaruhanga, C de Bourcy, ... PloS one 14 (6), e0218318, 2019 | 85 | 2019 |
| Unbiased metagenomic sequencing for pediatric meningitis in Bangladesh reveals neuroinvasive chikungunya virus outbreak and other unrealized pathogens S Saha, A Ramesh, K Kalantar, R Malaker, M Hasanuzzaman, LM Khan, ... MBio 10 (6), 10.1128/mbio. 02877-19, 2019 | 74 | 2019 |
| Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults KL Kalantar, L Neyton, M Abdelghany, E Mick, A Jauregui, S Caldera, ... Nature microbiology 7 (11), 1805-1816, 2022 | 54 | 2022 |
| Co-occurrence of Campylobacter Species in Children From Eastern Ethiopia, and Their Association With Environmental Enteric Dysfunction, Diarrhea, and Host … Y Terefe, L Deblais, M Ghanem, YA Helmy, B Mummed, D Chen, N Singh, ... Frontiers in public health 8, 99, 2020 | 50 | 2020 |
| Metagenomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota KL Kalantar, F Moazed, SC Christenson, J Wilson, T Deiss, A Belzer, ... American Journal of Physiology-Lung Cellular and Molecular Physiology 316 (3 …, 2019 | 42 | 2019 |
| Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections PH Serpa, X Deng, M Abdelghany, E Crawford, K Malcolm, S Caldera, ... Genome medicine 14 (1), 74, 2022 | 39 | 2022 |
| Discovering disease-causing pathogens in resource-scarce Southeast Asia using a global metagenomic pathogen monitoring system JA Bohl, S Lay, S Chea, V Ahyong, DM Parker, S Gallagher, J Fintzi, ... Proceedings of the National Academy of Sciences 119 (11), e2115285119, 2022 | 37 | 2022 |
| Microbiome and antimicrobial resistance gene dynamics in international travelers C Langelier, M Graves, K Kalantar, S Caldera, R Durrant, M Fisher, ... Emerging infectious diseases 25 (7), 1380, 2019 | 37 | 2019 |
| Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics A Tsitsiklis, CM Osborne, J Kamm, K Williamson, K Kalantar, G Dudas, ... The Lancet Microbe 3 (4), e284-e293, 2022 | 33 | 2022 |
| Rapid metagenomic characterization of a case of imported COVID-19 in Cambodia JE Manning, JA Bohl, S Lay, S Chea, L Sovann, Y Sengdoeurn, S Heng, ... BioRxiv, 2020 | 27 | 2020 |
| IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring. Gigascience 2020; 9 KL Kalantar, T Carvalho, CFA De Bourcy, B Dimitrov, G Dingle, R Egger, ... Epub 2020/10/16. doi: 10.1093/gigascience/giaa111. PubMed PMID: 33057676, 0 | 24 | |
| Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children E Mick, A Tsitsiklis, J Kamm, KL Kalantar, S Caldera, A Lyden, M Tan, ... The Journal of Clinical Investigation 133 (7), 2023 | 16 | 2023 |
| Etiology of fever in Ugandan children: identification of microbial pathogens using metagenomic next-generation sequencing and IDseq, a platform for unbiased metagenomic analysis A Ramesh, S Nakielny, J Hsu, M Kyohere, O Byaruhanga, C Bourcy, ... Biorxiv, 385005, 2018 | 10 | 2018 |
| Pneumonia surveillance with culture-independent metatranscriptomics in HIV-positive adults in Uganda: a cross-sectional study N Spottiswoode, JD Bloomstein, S Caldera, A Sessolo, K McCauley, ... The Lancet Microbe 3 (5), e357-e365, 2022 | 9 | 2022 |
| Hyperinflammatory ARDS is characterized by interferon-stimulated gene expression, T-cell activation, and an altered metatranscriptome in tracheal aspirates A Sarma, SA Christenson, BS Zha, A Oliveira, LPA Neyton, E Mick, ... medRxiv, 2022 | 9 | 2022 |
| Host and microbe blood metagenomics reveals key pathways characterizing critical illness phenotypes LPA Neyton, P Sinha, A Sarma, E Mick, K Kalantar, S Chen, N Wu, ... American journal of respiratory and critical care medicine 209 (7), 805-815, 2024 | 8 | 2024 |
