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About me

I obtained my doctoral degree from Department of Medicine Huddinge, Karolinska Institutet (KI) in 2013. Following my two year postdoc  I joined the  Department of Laboratory Medicine as Assistant Professor in 2015, where my research focuses  on multi-omics system biology approach to understand the disease control mechanism in a group of HIV-1 positive individuals who control viral replication without any therapy called Elite Controller.

Education

March 2014- May 2015

Post-Doctoral Fellow, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden 

June 2013-March 2014

Post-Doctoral Reserach Scientist, St. John's Research Institute, Bangalore, India

2009 – 2013

Ph.D. in Medical Sciences, Karolinska Institutet, Stockholm, Sweden 

Thesis title: Translational genomics of HIV-1 subtype C in India: Molecular phylogeny and drug resistance

2005-2007                    

M.Sc Microbiology, Bangalore University Bangalore, India                                                        

Research description

Theme I: A multi-omics system biology approach to identify disease control mechanisms in HIV-1 Elite Controller

The purpose of this research program is through translational research integrating the multi-omics techniques and the clinical data to understand the disease control mechanism in a group of HIV-1 positive individuals, who control viral replication and restrained progression to AIDS, without any antiretroviral therapy for a longer duration of time (Elite controller). In a systemic approach, we apply the molecular data-first approach (using Genomics, transcriptomics and proteomics) classifies persistent genetic variants or expression patterns in order to reduce host influenced heterogeneity followed by the phenotypic profiling, virological and immunological characterizations of the disease control mechanism. This understanding of the unique gene expression and immunological characteristics of EC will predict a frame of reference for what may be required in clinical intervention strategies to induce immune control of HIV-1 and the future development of functional HIV-cure.

Selected Publications:

  • Zhang W, Morshed MM, Noyan K, Russom A, Sönnerborg A, Neogi U† (2017) Quantitative humoral profiling of the HIV-1 proteome in elite controllers and patients with very long-term efficient antiretroviral therapy. Sci Rep ;7(1):666. doi: 10.1038/s41598-017-00759-8. [PMID: 28386076]
  • Nowak P*, Trøseid M*, Avershina E, Barqasho B, Neogi U, Holm K, Hov J, Noyan K, Vesterbacka J, Svärd J, Rudi MK, Sönnerborg (2015) Gut microbiota diversity predicts immune status in HIV-1 infection. AIDS 29(18):2409-18. [PMID: 26355675]

Funding: Harald and Greta Jeansson Foundation, Jonas Söderquist’s Stipendium for Experimental Virology and Immunology Research, Karolinska Institutet

Techniques: High through-put sequencing (Exome sequencing, RNAseq, amplicon sequencing), protein microarray, viral metagenomics, RNAflow, RNAscope, western blots, FACS etc.

Theme II: Mechanisms of drug resistance dynamics and efficacy of newly emerging long acting antiretroviral compounds in diverse HIV-1 subtypes

The prime research question in this program is to achieve the maximum efficacy of the newly emerging antiretroviral compounds (reverse transcriptase inhibitors, integrase inhibitor and protease inhibitor) understanding the viral suppression potentials, mechanisms of resistance and viral persistence across diverse subtypes. The consequent optimization of the use of these drugs could potentially lead to that they will become the drug-of-choice in globally including the low- and middle- income countries. The studies run as a part of large multi-disciplinary expert project in the field of molecular biology, virology, structural protein modelling and biochemistry, high throughput genomics, evolutionary dynamics and clinical science.

Selected publications:

  • Häggblom A, Svedhem V, Singh K, Sönnerborg A, Neogi U†(2016) Virological failure in patients with HIV-1 subtype C receiving antiretroviral therapy: an analysis of a prospective national cohort in Sweden. Lancet HIV 3(4):e166-74 [http://dx.doi.org/10.1016/S2352-3018(16)00023-0. [PMID: 27036992]
  • Neogi U†, Häggblom A, Singh K, Rogers L, Rao SD, Amogne W, Schülter E, Zazzi M, Arnold E, Sarafianos S, Sonnerborg A (2015) Factors influencing the efficacy of rilpivirine on HIV-1 subtype C in low- and middle-income countries. J Antimicrob Chemother, 71(2):367-71.  [PMID: 26518047]
  • Neogi U†, Rao SD, Bontell I, Verheyen J, Rao VR, Gore SC, Soni N, Shet A, Schülter E, Ekstrand ML, Wondwossen A, Kaiser R, Madhusudhan MS, Prasad VR, Sonnerborg A (2014) Novel tetra-peptide insertion in Gag p6 ALIX-binding motif in HIV-1 subtype C associated with protease inhibitor failure in Indian patients. AIDS; 28(15): 2319-22.  [PMID: 25102091]

Funding: US National Institute of Health (R01 GM118012-01), Karolinska Institutet, Stockholm County Council, Swedish Physicians against AIDS Foundation

Teaching portfolio

Teaching assignments under the Biomedical Laboratory Science program

Academic honors, awards and prizes

SUPERVISION

Doctoral Study

1.1. Main Supervisor

1.2. Co-supervisor

Master Thesis

  • Ms. Maike Sperk, Master in Molecular MedicineTübingen University, 03/2017-
  • Ms. Mira Akber, Master Thesis (30 Credits), Uppsala Graduate School in Biomedical Research (UGSBR), Uppsala University, 08/2016 - 08/2017
  • Md. Monzur Morshed, Master Thesis (30 Credits), Cell and Molecular Biology Uppsala University, (04/2016-10/2016)
  • Mr. Abu Bakar Siddik, Master Thesis (60 Credits), Molecular Biotechnology, University of Skövde (06/2015- 08/2016).
  • Md Shanawazur Rahman, Master Thesis (15 Credits), Infectious Disease Control, Sodertorns Hogskola, Sweden (04/2016 – 08/2016)

Research Internship

  • Mr Philipp Kalus, Vrije Universiteit Brussel Bachelor’s Program Biomedical Science (02/2017-04/2017)

FELLOWSHIPS

2016

Jonas Söderquist’s Stipendium for Experimental Virology and Immunology Research-2016 for research in development of high-throughput techniques to quantify HIV-1 latent reservoir.

2012

AIDS International Training and Research Program (AITRP) fellowship, sponsored by National Institute of Health (NIH), US for training at Albert Einstein College of Medical Science, NY.

GRANTS

1.1. Ongoing                                  

2017-2021 Karolinska Institutet Doctoral Student Funding (KID2016-0022)

Characterization of HIV-1 persistence and dynamics in the latent viral reservoir

Role: Co-Investigator

11/2016-10/2018 Harald and Greta Jeansson Foundation (JS2016-0185)

Mechanisms of HIV-1 persistence and latency: Implications for a cure

Role: Principal Investigator

01/2017-12/2019 Stockholm County Council, ALF-Project Funding Medicine (Ref#20160074)

Clinical and translational studies of virus-host interactions for optimization of HIV treatment and possible cure of HIV

Role: Co-Investigator

07/2016-06/2020  US National Institute of Health (R01 GM118012-01)

Reverse transcriptase multi-class drug resistance and rilpivirine susceptibility in diverse HIV-1 Subtypes

Role: Co-PI

http://grantome.com/grant/NIH/R01-GM118012-01A1

03/2016-02/2020 Karolinska Institutet Doctoral Student Funding (KID2015-154)

High throughput system biology approach to identify resistance mechanisms against protease inhibitors in South African HIV-1C

Role: Principal Investigator

01/2016-07/2017  Swedish Physicians Against AIDS Foundation (Fob2015-009)

Viral genome wide association study to understand the mechanism of protease inhibitor failure

Role: Principal Investigator

01/2016-12/2018 Swedish Research Council  (2015-05914) 

Development of a molecular surveillance phylogeographic tool to track HIV transmission networks in Bangladesh

Role: Co-Investigator

Amount: SEK 1,140, 000

06/2015-05/2019 Karolinska Institutet Doctoral Student Funding (KID2014-114)

Role of viral evolution for HIV-1 subtype C fitness, host-reactivity and therapeutic response

Role: Co-Investigator

1.2. Completed

01/2015-12/2016 Karolinska Institutet Research Foundation Grants (2014fobi41250)

Genome Wide Association Study in HIV-1: Molecular adaptation following therapy failure affecting viral fitness

(Special grant for Young Scientist)

Role: Principal Investigator

Amount: SEK 248,000

03/2015-02/2019 (Declined)  Wellcome Trust/ DBT India Alliance Early Career Fellowship (IA/E/13/1/501245)

A multi-approach translational research for better therapeutic management: Viral genomic adaptation in HIV-1 subtype C affecting viral fitness following drug resistance

Role: Principal Investigator

10/2010-06/2013     European Commission

Erasmus Mundus External Co-operation Window 13 (India) fellowship

Translational genomics of HIV-1 subtype C in India: Molecular phylogeny and drug resistance

Role: Principal Investigator

01/2011-06/2012 Swedish Physicians against AIDS Research Foundation (FOa2011-0014)

Human APOBEC mediated hypermutations induced drug resistance

Role: Main Applicant

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