Selected publications
Selected publications for The Systems Virology Lab.
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
Ambikan AT, Yang H, Krishnan S, Svensson Akusjärvi S, Gupta S, Lourda M, Sperk M, Arif M, Zhang C, Nordqvist H, Ponnan SM, Sönnerborg A, Treutiger CJ, O'Mahony L, Mardinoglu A, Benfeitas R, Neogi U
Cell Syst 2022 Aug;13(8):665-681.e4
Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection.
Mikaeloff F, Gelpi M, Benfeitas R, Knudsen AD, Vestad B, Høgh J, Hov JR, Benfield T, Murray D, Giske CG, Mardinoglu A, Trøseid M, Nielsen SD, Neogi U
Elife 2023 Feb;12():
Functional SARS-CoV-2 cross-reactive CD4+ T cells established in early childhood decline with age.
Humbert M, Olofsson A, Wullimann D, Niessl J, Hodcroft EB, Cai C, Gao Y, Sohlberg E, Dyrdak R, Mikaeloff F, Neogi U, Albert J, Malmberg KJ, Lund-Johansen F, Aleman S, Björkhem-Bergman L, Jenmalm MC, Ljunggren HG, Buggert M, Karlsson AC
Proc Natl Acad Sci U S A 2023 Mar;120(12):e2220320120
A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2.
Albrich WC, Ghosh TS, Ahearn-Ford S, Mikaeloff F, Lunjani N, Forde B, Suh N, Kleger GR, Pietsch U, Frischknecht M, Garzoni C, Forlenza R, Horgan M, Sadlier C, Negro TR, Pugin J, Wozniak H, Cerny A, Neogi U, O'Toole PW, O'Mahony L
Gut Microbes 2022 ;14(1):2073131
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.
Appelberg S, Gupta S, Svensson Akusjärvi S, Ambikan AT, Mikaeloff F, Saccon E, Végvári Á, Benfeitas R, Sperk M, Ståhlberg M, Krishnan S, Singh K, Penninger JM, Mirazimi A, Neogi U
Emerg Microbes Infect 2020 Dec;9(1):1748-1760
Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs.
Neogi U, Hill KJ, Ambikan AT, Heng X, Quinn TP, Byrareddy SN, et al
Pathogens 2020 Apr;9(5):
Unique Phenotypic Characteristics of Recently Transmitted HIV-1 Subtype C Envelope Glycoprotein gp120: Use of CXCR6 Coreceptor by Transmitted Founder Viruses.
Ashokkumar M, Aralaguppe SG, Tripathy SP, Hanna LE, Neogi U
J. Virol. 2018 05;92(9):
Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.
Zhang W, Ambikan AT, Sperk M, van Domselaar R, Nowak P, Noyan K, et al
EBioMedicine 2018 Jan;27():40-50
Phenotypic co-receptor tropism and Maraviroc sensitivity in HIV-1 subtype C from East Africa.
Siddik AB, Haas A, Rahman MS, Aralaguppe SG, Amogne W, Bader J, et al
Sci Rep 2018 02;8(1):2363
Plasma soluble factor following two decades prolonged suppressive antiretroviral therapy in HIV-1-positive males: A cross-sectional study.
Sperk M, Zhang W, Nowak P, Neogi U
Medicine (Baltimore) 2018 Feb;97(5):e9759
Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden.
Häggblom A, Svedhem V, Singh K, Sönnerborg A, Neogi U
Lancet HIV 2016 Apr;3(4):e166-74