| HIV integration sites in latently infected cell lines: evidence of ongoing replication J Symons, A Chopra, E Malatinkova, W De Spiegelaere, S Leary, ... Retrovirology 14, 1-11, 2017 | 79 | 2017 |
| Generation of a novel SARS-CoV-2 sub-genomic RNA due to the R203K/G204R variant in nucleocapsid: homologous recombination has potential to change SARS-CoV-2 at both protein and … S Leary, S Gaudieri, MD Parker, A Chopra, I James, S Pakala, E Alves, ... Pathogens and Immunity 6 (2), 27, 2021 | 58 | 2021 |
| Subgenomic RNA identification in SARS-CoV-2 genomic sequencing data MD Parker, BB Lindsey, S Leary, S Gaudieri, A Chopra, M Wyles, ... Genome research 31 (4), 645-658, 2021 | 48 | 2021 |
| Strong spontaneous tumor neoantigen responses induced by a natural human carcinogen J Creaney, S Ma, SA Sneddon, MR Tourigny, IM Dick, JS Leon, A Khong, ... Oncoimmunology 4 (7), e1011492, 2015 | 32 | 2015 |
| Pan-genomic analyses identify key Helicobacter pylori pathogenic loci modified by carcinogenic host microenvironments JM Noto, A Chopra, JT Loh, J Romero-Gallo, MB Piazuelo, M Watson, ... Gut 67 (10), 1793-1804, 2018 | 31 | 2018 |
| Altered subgenomic RNA expression in SARS-CoV-2 B. 1.1. 7 infections MD Parker, BB Lindsey, DR Shah, S Hsu, AJ Keeley, DG Partridge, ... bioRxiv, 2021.03. 02.433156, 2021 | 22 | 2021 |
| New genetic predictors for abacavir tolerance in HLA-B* 57: 01 positive individuals R Pavlos, P Deshpande, A Chopra, S Leary, K Strautins, D Nolan, ... Human immunology 81 (6), 300-304, 2020 | 22 | 2020 |
| Identifying patient-specific Epstein-Barr nuclear antigen-1 genetic variation and potential autoreactive targets relevant to multiple sclerosis pathogenesis M Tschochner, S Leary, D Cooper, K Strautins, A Chopra, H Clark, L Choo, ... PloS one 11 (2), e0147567, 2016 | 22 | 2016 |
| Single-cell analysis shows that adipose tissue of persons with both HIV and diabetes is enriched for clonal, cytotoxic, and CMV-specific CD4+ T cells CN Wanjalla, WJ McDonnell, R Ram, A Chopra, R Gangula, S Leary, ... Cell Reports Medicine 2 (2), 2021 | 20 | 2021 |
| Single-cell transcriptomics reveal polyclonal memory T-cell responses in skin with positive abacavir patch test results AJ Redwood, F Rwandamuriye, A Chopra, S Leary, R Ram, W McDonnell, ... Journal of Allergy and Clinical Immunology 144 (5), 1413-1416. e7, 2019 | 20 | 2019 |
| Three adjacent nucleotide changes spanning two residues in SARS-CoV-2 nucleoprotein: possible homologous recombination from the transcription-regulating sequence S Leary, S Gaudieri, A Chopra, S Pakala, E Alves, M John, S Das, ... bioRxiv 10 (2020.04), 10.029454, 2020 | 18 | 2020 |
| Visual genomics analysis studio as a tool to analyze multiomic data RJ Hertzman, P Deshpande, S Leary, Y Li, R Ram, A Chopra, D Cooper, ... Frontiers in genetics 12, 642012, 2021 | 17 | 2021 |
| Deep sequence analysis of HIV adaptation following vertical transmission reveals the impact of immune pressure on the evolution of HIV J Currenti, A Chopra, M John, S Leary, E McKinnon, E Alves, M Pilkinton, ... PLoS Pathogens 15 (12), e1008177, 2019 | 17 | 2019 |
| Identification of a CD8+ T-cell response to a predicted neoantigen in malignant mesothelioma S Sneddon, CM Rive, S Ma, IM Dick, RJN Allcock, SD Brown, RA Holt, ... Oncoimmunology 9 (1), 1684713, 2020 | 15 | 2020 |
| Altered subgenomic RNA abundance provides unique insight into SARS-CoV-2 B. 1.1. 7/Alpha variant infections MD Parker, H Stewart, OM Shehata, BB Lindsey, DR Shah, S Hsu, ... Communications biology 5 (1), 666, 2022 | 14 | 2022 |
| Sequence-based HLA-a, b, c, DP, DQ, and DR typing of 339 adults from Managua, Nicaragua D Weiskopf, A Grifoni, CSL Arlehamn, M Angelo, S Leary, J Sidney, ... Human immunology 79 (1), 1-2, 2018 | 14 | 2018 |
| Helicobacter pylori genetic diversification in the Mongolian gerbil model AC Beckett, JT Loh, A Chopra, S Leary, AS Lin, WJ McDonnell, ... PeerJ 6, e4803, 2018 | 13 | 2018 |
| Sequence-based HLA-A, B, C, DP, DQ, and DR typing of 100 Luo infants from the Boro area of Nyanza Province, Kenya CSL Arlehamn, R Copin, S Leary, SJ Mack, E Phillips, S Mallal, A Sette, ... Human immunology 78 (4), 325-326, 2017 | 11 | 2017 |
| Sequence-based HLA-a, b, c, DP, DQ, and DR typing of 496 adults from San Diego, California, USA E Moore, A Grifoni, D Weiskopf, V Schulten, CSL Arlehamn, M Angelo, ... Human immunology 79 (12), 821-822, 2018 | 10 | 2018 |
| State A MD Parker, BB Lindsey, DR Shah, S Hsu, AJ Keeley, DG Partridge, ... Johnson K, Ali N, Raghei R, Heffer J, Smith N, Zhang P, Gallis M, Louka SF …, 2021 | 7 | 2021 |
