Anoop Tholamplackil Ambikan

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About me

I am currently working as post-doctoral researcher in The Systems Virology
Lab at Department of Laboratory Medicine. I hold Ph.D. degree in Medical
Science (specialization in systems biology applications in infectious disease
research) received from Karolinska Institutet under the supervision of Dr.
Ujjwal Neogi. My areas of interest are, systems biology, network analysis,
contextualization of networks and multi-omics analysis.
Feb 2018 - April 2023
Ph.D. in Medical Science, Karolinska Institutet, Sweden
June 2010 - July 2012
MSc in Bioinformatics, Amrita School of Biotechnology, India

Research

My work is focused on various applications of network based systems biology
methodologies to solve problems in infectious disease research. I develop
networks representing association/co-expression among various molecular
features to identify communities of coordinated response. Contextualization
of metabolic and signalling networks specific cell/tissue is another major
area of attention. I also perform other omics data analysis such as,
TMT-lablled LC-MS/MS proteomics, quantitative metabolomics and metageomics
data.

Articles

Article: ISCIENCE. 2024;27(4):109346
Inflammatory, metabolic, and sex-dependent gene-regulatory dynamics of microglia and macrophages in neonatal hippocampus after hypoxia-ischemia
Di Martino E; Ambikan A; Ramskold D; Umekawa T; Giatrellis S; Vacondio D; Romero AL; Galan MG; Sandberg R; Aden U; Lauschke VM; Neogi U; Blomgren K; Kele J
Article: NATURE COMMUNICATIONS. 2024;15(1):2532
Parechovirus infection in human brain organoids: host innate inflammatory response and not neuro-infectivity correlates to neurologic disease
Capendale PE; Garcia-Rodriguez I; Ambikan AT; Mulder LA; Depla JA; Freeze E; Koen G; Calitz C; Sood V; de Sa RV; Neogi U; Pajkrt D; Sridhar A; Wolthers KC
Article: VIRUS RESEARCH. 2024;341:199306
Temporal cytokine storm dynamics in dengue infection predicts severity
Bhatt P; Varma M; Sood V; Ambikan A; Jayaram A; Babu N; Gupta S; Mukhopadhyay C; Neogi U
Article: ALLERGY. EUROPEAN JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. 2024;79(1):65-79
Rural and urban exposures shape early life immune development in South African children with atopic dermatitis and nonallergic children
Lunjani N; Ambikan AT; Hlela C; Levin M; Mankahla A; Heldstab-Kast JI; Boonpiyathad T; Tan G; Altunbulakli C; Gray C; Nadeau KC; Neogi U; Akdis CA; O'Mahony L
Article: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2023;120(37):e2304722120
Systems-level temporal immune- metabolic profile in Crimean-Congo hemorrhagic fever virus infection
Ambikan AT; Elaldi N; Akusjaervi SS; Bagci B; Pektas AN; Hewson R; Bagci G; Arasli M; Appelberg S; Mardinoglu A; Sood V; Vegvari A; Benfeitas R; Gupta S; Cetin I; Mirazimi A; Neogi U
Article: AIDS. 2023;37(7):1023-1033
Role of myeloid cells in system-level immunometabolic dysregulation during prolonged successful HIV-1 treatment
Svensson Akusjarvi S; Krishnan S; Ambikan AT; Mikaeloff F; Munusamy Ponnan S; Vesterbacka J; Lourda M; Nowak P; Sonnerborg A; Neogi U
Article: LIFE SCIENCE ALLIANCE. 2022;5(9):e202201405
Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection
Ambikan AT; Svensson-Akusjarvi S; Krishnan S; Sperk M; Nowak P; Vesterbacka J; Sonnerborg A; Benfeitas R; Neogi U
Article: CELL SYSTEMS. 2022;13(8):665-681.e4
Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity
Ambikan AT; Yang H; Krishnan S; Akusjarvi SS; Gupta S; Lourda M; Sperk M; Arif M; Zhang C; Nordqvist H; Ponnan SM; Sonnerborg A; Treutiger CJ; O'Mahony L; Mardinoglu A; Benfeitas R; Neogi U
Article: ELIFE. 2022;11:e76071
Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target
Neogi U; Elaldi N; Appelberg S; Ambikan A; Kennedy E; Dowall S; Bagci BK; Gupta S; Rodriguez JE; Svensson-Akusjarvi S; Monteil V; Vegvari A; Benfeitas R; Banerjea A; Weber F; Hewson R; Mirazimi A
Article: COMMUNICATIONS BIOLOGY. 2022;5(1):357
Peripheral blood CD4⁺CCR6⁺ compartment differentiates HIV-1 infected or seropositive elite controllers from long-term successfully treated individuals
Svensson Akusjarvi S; Krishnan S; Jutte BB; Ambikan AT; Gupta S; Rodriguez JE; Vegvari A; Sperk M; Nowak P; Vesterbacka J; Svensson JP; Sonnerborg A; Neogi U
Article: ISCIENCE. 2022;25(1):103607
Integrative proteo-transcriptomic and immunophenotyping signatures of HIV-1 elite control phenotype: A cross-talk between glycolysis and HIF signaling
Akusjarvi SS; Ambikan AT; Krishnan S; Gupta S; Sperk M; Vegvari A; Mikaeloff F; Healy K; Vesterbacka J; Nowak P; Sonnerborg A; Neogi U
Article: HRB OPEN RESEARCH. 2022;5:31
Impact of Long COVID on health and quality of life.
O' Mahony L; Buwalda T; Blair M; Forde B; Lunjani N; Ambikan A; Neogi U; Barrett P; Geary E; O'Connor N; Dineen J; Clarke G; Kelleher E; Horgan M; Jackson A; Sadlier C
Article: MICROBIOLOGY SPECTRUM. 2021;9(2):e0047021-e00421
Deciphering the Role of Mucosal Immune Responses and the Cervicovaginal Microbiome in Resistance to HIV Infection in HIV-Exposed Seronegative (HESN) Women
Ponnan SM; Thiruvengadam K; Tellapragada C; Ambikan AT; Narayanan A; Kathirvel S; Mathayan M; Shankar J; Rajaraman A; Amanulla MA; Dinesha TR; Poongulali S; Saravanan S; Murugavel KG; Swaminathan S; Velu V; Shacklett B; Neogi U; Hanna LE
Article: JOURNAL OF VIROLOGY. 2021;95(18):e0047921-10.1128/jvi.00421
Fecal Metabolome Signature in the HIV-1 Elite Control Phenotype: Enrichment of Dipeptides Acts as an HIV-1 Antagonist but a Prevotella Agonist
Sperk M; Ambikan AT; Ray S; Singh K; Mikaeloff F; Diez RC; Narayanan A; Vesterbacka J; Nowak P; Sonnerborg A; Neogi U
Article: BMC INFECTIOUS DISEASES. 2021;21(1):214
Increased acquired protease inhibitor drug resistance mutations in minor HIV-1 quasispecies from infected patients suspected of failing on national second-line therapy in South Africa
Obasa AE; Ambikan AT; Gupta S; Neogi U; Jacobs GB
Article: ISCIENCE. 2021;24(2):102111
Distinct lipid profile, low-level inflammation, and increased antioxidant defense signature in HIV-1 elite control status
Sperk M; Mikaeloff F; Svensson-Akusjarvi S; Krishnan S; Ponnan SM; Ambikan AT; Nowak P; Sonnerborg A; Neogi U
Article: AIDS. 2021;35(2):227-234
High-throughput sequencing reveals a high prevalence of pretreatment HIV-1 drug resistance in Sweden
Andersson E; Ambikan A; Brannstrom J; Aralaguppe SG; Yilmaz A; Albert J; Neogi U; Sonnerborg A
Article: MOLECULAR & CELLULAR PROTEOMICS. 2021;20:100159
Metabolic Perturbation Associated With COVID-19 Disease Severity and SARS-CoV-2 Replication
Krishnan S; Nordqvist H; Ambikan AT; Gupta S; Sperk M; Svensson-Akusjarvi S; Mikaeloff F; Benfeitas R; Saccon E; Ponnan SM; Rodriguez JE; Nikouyan N; Odeh A; Ahlen G; Asghar M; Sallberg M; Vesterbacka J; Nowak P; Vegvari A; Sonnerborg A; Treutiger CJ; Neogi U
Article: FRONTIERS IN MICROBIOLOGY. 2021;12:627861
Genomic Insights Into Clinical Shiga Toxin-Producing Escherichia coli Strains: A 15-Year Period Survey in Jonkoping, Sweden
Bai X; Zhang J; Hua Y; Jernberg C; Xiong Y; French N; Lofgren S; Hedenstrom I; Ambikan A; Mernelius S; Matussek A
Article: EMERGING MICROBES AND INFECTIONS. 2020;9(1):1748-1760
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells
Appelberg S; Gupta S; Svensson Akusjarvi S; Ambikan AT; Mikaeloff F; Saccon E; Vegvari A; Benfeitas R; Sperk M; Stahlberg M; Krishnan S; Singh K; Penninger JM; Mirazimi A; Neogi U
Article: PATHOGENS. 2020;9(5):E320-320
Feasibility of Known RNA Polymerase Inhibitors as Anti-SARS-CoV-2 Drugs
Neogi U; Hill KJ; Ambikan AT; Heng X; Quinn TP; Byrareddy SN; Soennerborg A; Sarafianos SG; Singh K
Article: METABOLITES. 2019;9(10):E210-210
Plasma Metabolic Signature and Abnormalities in HIV-Infected Individuals on Long-Term Successful Antiretroviral Therapy
Babu H; Sperk M; Ambikan AT; Rachel G; Viswanathan VK; Tripathy SP; Nowak P; Hanna LE; Neogi U
Article: VIRUSES. 2019;11(9):E806-806
MiDRMpol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors
Aralaguppe SG; Ambikan AT; Ashokkumar M; Kumar MM; Hanna LE; Amogne W; Sonnerborg A; Neogi U
Article: SCIENTIFIC REPORTS. 2019;9(1):5619
Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden
Bai X; Zhang J; Ambikan A; Jernberg C; Ehricht R; Scheutz F; Xiong Y; Matussek A
Article: FRONTIERS IN IMMUNOLOGY. 2019;10:1965
Systemic Inflammation and the Increased Risk of Inflamm-Aging and Age-Associated Diseases in People Living With HIV on Long Term Suppressive Antiretroviral Therapy
Babu H; Ambikan AT; Gabriel EE; Akusjarvi SS; Palaniappan AN; Sundaraj V; Mupanni NR; Sperk M; Cheedarla N; Sridhar R; Tripathy SP; Nowak P; Hanna LE; Neogi U
Article: FRONTIERS IN MICROBIOLOGY. 2019;10:2632
Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions
Al-Farsi HM; Al-Adwani S; Ahmed S; Vogt C; Ambikan AT; Leber A; Al-Jardani A; Al-Azri S; Al-Muharmi Z; Toprak MS; Giske CG; Bergman P
Article: EBIOMEDICINE. 2018;27:40-50
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; Russom A; Sonnerborg A; Neogi U
Article: JOURNAL OF VIROLOGICAL METHODS. 2016;236:98-104
Multiplexed next-generation sequencing and de novo assembly to obtain near full-length HIV-1 genome from plasma virus
Aralaguppe SG; Siddik AB; Manickam A; Ambikan AT; Kumar MM; Fernandes SJ; Amogne W; Bangaruswamy DK; Hanna LE; Sonnerborg A; Neogi U
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All other publications

Preprint: RES SQ. 2023;RES SQ
Proteomic landscape of astrocytes and pericytes infected with HIV/SARS-CoV-2 mono/co-infection, impacting on neurological complications.
Acharya A; Ambikan AT; Thurman M; Malik MR; Dyavar SR; Végvári Á; Neogi U; Byrareddy SN
Thesis / dissertation: 2023
Multi-dimensional omics approaches to dissect natural immune control mechanisms associated with RNA virus infections
Ambikan, Anoop Tholamplackil

Employments

Postdoctoral Researcher, Department of Laboratory Medicine, Karolinska Institutet, 2023-2025

Degrees and Education

Degree Of Doctor Of Philosophy, Department of Laboratory Medicine, Karolinska Institutet, 2023

About me

Research

Articles

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Degrees and Education

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