Group members - The Systems Virology Lab

Learn more about the members of The Systems Virology Lab.

Research Group Leader

Photo of Ujjwal Neogi, Department of Laboratory Medicine

Ujjwal Neogi, Senior Researcher

I obtained my doctoral degree from Department of Medicine Huddinge, Karolinska Institutet (KI) in 2013. My research expertise is in virology, molecular biology, high-throughput sequencing and translational research. My research focuses on bedside to bench and back approach using well defined clinical material and ex vivo immunological assays amalgamating the translational research to understand the host and viral factors associated with disease progression and control in HIV-1. I intend to use high-throughput multi-omics integrated trans-omics approach to find out the mechanism of natural immune control of HIV-1 replication followed by deep insight in the individual pathways. My research interest also includes evaluation of the gut-microbiome metabolome axis and it’s role in disease progression and treatment efficacy.

Group photo of The Systems Virology Lab at the Department of Laboratory Medicine.
The Systems Virology Lab at the Department of Laboratory Medicine. Photo: Rui Benfeitas

Group members

Soham Gupta

Assistant Professor

I completed my Ph.D. studies on translational genomics of HIV-1 subtypes circulating in India (HIV-1CIN) at St. John’s Medical College, Rajiv Gandhi University of Health Sciences, India, in 2014. Post Ph.D. in 2015 I joined Prof. Maria Masucci’s group at Department of Cell and Molecular Biology, Karolinska Institutet as a postdoctoral researcher studying the role of herpesvirus encoded cysteine protease on evasion of host innate immune response. In 2019 I was appointed Assistant Professor at Neogi Group, Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet. My research is aimed at understanding the mechanism of immune regulation during chronic viral infections. The focus of my research is on latent viruses like HIV-1 and herpesviruses and expand our understanding of the interplay between these viruses and host immune system using an integrative approach combining multi-omics with immunology, molecular, cell-biological and biochemical assays.

Maike Sperk

PhD student

I completed my master degree in Molecular Medicine from Tuebingen University, Germany (January 2018). In my master thesis, I focused on proteomics as well as cell biology and I will pursue these fields in a deeper way during my Ph.D. In particular, in my doctoral studies, I aim to perform immuno-proteomics research to map the intracellular pathways that are significantly modulated in HIV-1 immune control in Elite Controllers. I use high throughput techniques such as mass spectrometry, proximity extension assay, FACS, confocal microscopy, etc. My primary interests are death receptor signaling and stimulatory immune checkpoint molecules, and their roles in HIV-1 disease progression.

Anoop T Ambikan

PhD student

I got my Master’s Degree in Bioinformatics from Amrita School of Biotechnology, India in 2012 and had more than two years experience as Bioinformatics Programmer, at SciGenome Pvt Ltd. My doctoral studies aim at dealing with bioinformatics analysis of various kinds of "omics data" like transcriptome, proteome, microbiome and metabolome data related to HIV research. I am working to develop a simplified and efficient pipeline to integrate multi-omics data to draw a clinically relevant inference with reduced manual effort.

Sara Svensson Akusjärvi

PhD student

After completing my master's degree in Molecular Medicine from Uppsala University (2016) I continued validating the findings from my master thesis as a research assistant at MTC, Karolinska Institutet. In this work, I utilized cell biology and molecular techniques to identify the mechanism of action of a small molecule targeting cancer cells. Since 2017 I have been a Ph.D. student at Karolinska Institutet. My doctoral studies aim to understand mechanism controlling HIV-1 persistence. I use molecular, immunological and cell biology approaches to study signaling pathways that control and maintain HIV in a latent stage and how these correlate to the immunometabolism of cells.

Xi Chen

PhD student

I finished my master degree in immunology, Sun Yat-sen University, China (July 2018). During my master study, my research direction was towards finding an effective latency reversing agent (LRA) and cytotoxic T-lymphocytes’ (CTLs’) influence on the establishment and maintenance of HIV-1 latent reservoir. In my doctoral study, I aim to understand the role of mammalian target of rapamycin, also known as the mechanistic target of rapamycin (mTOR) pathway in HIV-1 latency and inflamm-aging in people living with HIV (PLHIV) using proteomics, metabolomics, and immunological studies. I am the recipient of China Govt China Scholarship Council (CSC) funding.

Flora Mikaeloff

PhD student

I have completed a double master’s degree in Genetics and Bioinformatics at Paris Diderot University in France. I joined Neogi Group as a Ph.D. student in August 2019. My Ph.D. project is about developing multi-omics pipelines in HIV-associated immune-aging.  I am working mostly on transcriptomics, proteomics, and metabolomics data obtained from cells and plasma from HIV-infected patients following antiretroviral therapy. My research aims to find biomarkers and pathways related to immune-aging in HIV context using single-cell, multi-omics, system biology, and machine learning approaches.

Shuba Krishnan

Postdoc

The crux of many human diseases involves abnormal metabolic states that affect normal physiological functions. Comprehensive understanding of how alterations in cellular functions contribute to human diseases and use the knowledge to derive drug development and therapeutic targets has been my long term research interests. I obtained my PhD from Department of Laboratory medicine, Karolinska Institutet in 2016 in Prof. Anna Karlsson’s group. During my PhD I studied the role of mitochondrial DNA in human inherited diseases and used the knowledge to derive therapeutic targets. Post PhD I joined Laboratory of Molecular and Vascular Medicine, NTU, Singapore as a postdoctoral researcher in 2017. My project focused on functional elucidation of biomarkers for cerebrovascular disorders such as stroke and patient-specific approach for improved prognosis and diagnosis. I joined as a postdoc in Ujjwal Neogi’s group, Dept. of Laboratory Medicine, KI, in Sept 2019. My research is aimed at unravelling intracellular metabolic pathways for accelerated ageing in people living with HIV-1 on ART treatment using high-throughput omics platforms and experimental models.

Alejandra Escos Lopez

Postdoc

The signaling pathway of mitogen-activated kinases (MAPK) is one of the regulatory mechanisms most widely spread. The receptors that are implicated in the immune response activate these signaling pathways and coordinate the immune response. During my Ph.D. until 2019 under Ana Cuenda’s supervision in the CNB (Madrid, Spain), I studied the role of p38g and p38d MAPK in both LPS septic shock and C.albicans infection mouse model. In these models, macrophages are the key cells involve in the resolution of the infection by being the main secreters of cytokines.

One of the key groups to modulate gene expression in the immune response is RNA binding proteins (RBPs). Post-transductional modifications of the RBPs, regulate ribonucleoprotein complexes induced by kinases controlling transportation, localization, translation, and mRNA degradation which modulate gene expression. During my Ph.D., my research took me to study how p38g and p38d MAPK affected mRNA-specific translation through the modification of RBPs; I stayed four months in 2018 in Nahum Sonenberg’s laboratory at Mcgill University (Montreal, Canada). Afterward, I did a short postdoc at Encarna Martinez-Salas’s laboratory at CBMSO (Madrid, Spain) working in dsRNA stimulation to elucidate possible kinases phosphorylating the RBP Gemin5 protein. Finally, I arrived 2021 as a postdoc to Ujjwal Neogi’s laboratory to study signaling pathways in HIV infection and ART-treated patients to elucidate possible therapeutical targets.

Mbanyamsig Mispa Yivala

Master Thesis Student

I have a master in biochemistry from the university of Yaoundé 1, Cameroon, (2018). My previous master’s work was based on HIV-drug resistance specifically analysing the genes of HIV-1 integrase sequences from treatment naive individuals in Yaoundé- Cameroon at the Division of Medical Virology Stellenbosch University, South Africa in 2017. Currently am doing a master in system biology (molecular biotechnology) at the University of Skovde. In the Systems Biology Lab, I will do my master thesis project focusing on understanding the immune-aging in HIV-infected individuals on therapy from Cameroon using multi-omics technologies.

Samvrit Rao

High School Internship, Thomas Jefferson High School, US

I am a 9th grader at the Thomas Jefferson High School (TJ) for Science and Technology (Ranked No.1 high school in the United states according to US News Rankings) At TJ, my core interests are Experimental Biology, Statistics, and Computer Science. In 2020, I was recognized as one of the top 10 Young Scientists in the United States by 3M, and in the same year I was awarded the US Army sponsored STEM grant to pursue his scientific interests.  In 2021, I founded a STEM non-profit (STEMForU) with the goal of helping elementary school kids from underrepresented minority  communities gain STEM problem solving and science communication skills. In next one year, I shall perform system biology study to understand the the disease pathogenesis of SARS-CoV-2 using multi-omics technology in this group.

Associated

Siddappa Byrareddy

Professor & Vice Chair of Research | Department of Pharmacology and Experimental Neuroscience | Nebraska Center for Substance Abuse Research | Durham Research Center, 8052

Ziad El-Khatib

Past Members

  1. Beatriz Sá Vinhas, 2020-2021, University of Porto, Portugal, Master thesis.
  2. Duncan T Njenda, PhD  Student (2016-2020)
  3. Wang Zhang, PhD Student (2015 –2019)
  4. Dr. Haleh Ganjian, PostDoc, (2019)
  5. Dr. Ashokkumar Manikam, PostDoc, (2018 – 2019)
  6. Abu Bakar Siddik, 2016. Skovde University, Sweden, Master thesis.
  7. Mohammed Monzur Morshed, 2016, Uppsala University, Sweden. Master thesis.
  8. Mira Akber, 2017, Uppsala University, Sweden, Master thesis.
  9. Evelyn Halitzki, 2019. Furtwangen University, Germany, Bachelor Thesis.
  10. Philip Kalus, 2017, Vrije Universiteit Brussel, Belgium, Bachelor Thesis.
  11. Md.Shanawazur Rahman, 2016, Södertörn University, Sweden, Internship.
  12. Grossmann Sebastian, 2014. Heidelberg University, Internship.
  13. Isabelle Wemar, Summer Research School for High School Students, 2015 and Degree Project in Medicine 2020
  14. Risha Ghosh, Summer Research School for High School Students, 2018
  15. Homayon Vaghef, Summer Research School for High School Students, 2018