Dr. Ashish Kumar did his Ph.D. at the National Institute of Immunology, New Delhi, India, in the laboratory of Dr. Dinakar M. Salunke, determining the structural function role of medicinally important plants. Later, he moved to the National Institute of Health, Bethesda, US, for his postdoctoral training under the direction of Dr. Joseph Marcotrigiano, and he determined the first structure of the hepatitis C virus surface glycoprotein E2 with its cognate human receptor, CD81, as a complex (Nature Journal, 2021). Dr. Ashish Kumar published numerous papers in the area of structural virology. From 2022, he became a research associate scientist (RF-FTE). He received the prestigious Salzman Award for the year 2022 from the Foundation of the National Institute of Health and, most recently, was a finalist in the prestigious trans-NIH Earl Stadtman Early Independent Faculty Career Award.

• Ph.D. in Life Science (2008-2014) National Institute of Immunology, Jawaharlal Nehru University, New Delhi, India
• MS in Biotechnology (2006-2008) University of Jammu, Jammu & Kashmir, India
• B.Sc in Life Sciences (Zoology, Botany and Chemistry) (2003-2005) University of Lucknow, Uttar Pradesh, India

Publications

• Sara M Maloney, Teressa M Shaw, Kylie M Nennig, Malorie S Larsen, Aadit Shah, Ashish Kumar, Joseph Marcotrigiano, Joe Grove, Eric J Snijder, Robert N Kirchdoerfer, Adam L Bailey. CD81 is a receptor for equine arteritis virus (family: Arteriviridae). mBio 16:e00623-25. https://doi.org/10.1128/mbio.00623-25
• Mart Reimund, Altaira D. Dearborn, Giorgio Graziano, Haotian Lei, Anthony M. Ciancone, Francis J. O’Reilly, Ashish Kumar, Ronald Holewinski, Edward B. Neufeld, Alan T. Remaley†, Joseph Marcotrigiano†. Structure of apolipoprotein b100 bound to low-density lipoprotein receptor. Nature (August 2024, In press)
• Wei Bu, Ashish Kumar, Nathan L Board, JungHyun Kim, Kennichi Dowdell, Shu Zhang, Yona Lei, Anna Hostal, Tammy Krogmann, Yanmei Wang, Stefania Pittaluga, Joseph Marcotrigiano, Jeffrey I Cohen. Epstein-Barr virus gp42 antibodies reveal sites of vulnerability for receptor binding and fusion to B cells. Immunity, 57(3), 559–573.e6 (2024). https://doi.org/10.1016/j.immuni.2024.02.008
• Jennifer Casiano Matos, Kaneemozhe Harichandran, Jingrong Tang, Denis O Sviri-dov, Giacomo Sidoti Migliore, Motoshi Suzuki, Lisa R Olano, Alvaro Hobbs, Ashish Kumar, Myeisha U Paskel, Mattia Bonsignori, Altaira D Dearborn, Alan T Remaley, Joseph Marcotrigiano. Hepatitis C virus E1 recruits high-density lipoprotein to support infectivity and evade antibody recognition. Journal of Virology 98(1):e0084923 (2024). http://doi:10.1128/jvi.00849-23
• Ashish Kumar, Tiana Rohe, Elizabeth J. Elrod, Abdul G. Khan, Altaira D. Dearborn, Ryan Kissinger, Arash Grakoui, Joseph Marcotrigiano. “Regions of hepatitis C virus E2 required for membrane association. Nature Communications 14, 433 (2023). https://doi.org/10.1038/s41467-023-36183-y
• Ashish Kumar, Reafa A. Hossain, Samantha A. Yost, Wei Bu, Yuanyuan Wang, Altaira D. Dearborn, Arash Grakoui, Jeffrey I. Cohen, and Joseph Marcotrigiano. “Structural insights into hepatitis C virus receptor binding and entry.” Nature 598, 521–525 (2021). https://doi.org/10.1038/s41586-021-03913-5
• Abha Jain, Amit Kumar, Meha Shikhi, Ashish Kumar, Deepak. T. Nair, and Dinakar M. Salunke. “The structure of MP-4 from Mucuna pruriens at 2.22 Å resolution.” Acta Crystallographica Section F: Structural Biology Communications 76, no. 2 (2020): 47-57. https://doi.org/10.1107/S2053230X20000199
• Sarita Chandan Sharma, Ashish Kumar, Sharad Vashisht, and Dinakar M. Salunke. “High resolution structural and functional analysis of a hemopexin motif protein from Dolichos.” Scientific reports 9, no. 1 (2019): 1-13. https://doi.org/10.1038/s41598-019-56257-6
• Ashish Kumar, Harmeet Kaur, Abha Jain, Deepak T. Nair, and Dinakar M. Salunke. “Docking, thermodynamics and molecular dynamics (MD) studies of a non-canonical protease inhibitor, MP-4, from Mucuna pruriens.” Scientific reports 8, no. 1 (2018): 1-12. https://doi.org/10.1038/s41598-017-18733-9
• Pidathala RV Shabareesh, Ashish Kumar, Dinakar M. Salunke, and Kanwal J. Kaur. “Structural and functional studies of differentially O‐glycosylated analogs of a thrombin inhibitory peptide–variegin.” Journal of Peptide Science 23, no. 12 (2017): 880-888. https://doi.org/10.1002/psc.3052
• Ashish Kumar, Chitra Gupta, Deepak T. Nair, and Dinakar M. Salunke. “MP-4 contributes to snake venom neutralization by Mucuna pruriens seeds through an indirect antibody-mediated mechanism.” Journal of Biological Chemistry 291, no. 21 (2016): 11373-11384. https://doi.org/10.1074/jbc.M115.699173
• Abha Jain, Ashish Kumar, and Dinakar M. Salunke. “Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets.” Scientific reports 6, no. 1 (2016): 1-11. https://doi.org/10.1038/srep23600
• Sharad Vashisht, Ashish Kumar, Kanwal J. Kaur, and Dinakar M. Salunke. “Antibodies can exploit molecular crowding to bind new antigens at noncanonical paratope positions.” ChemistrySelect 1, no. 19 (2016): 6287-6292. https://doi.org/10.1002/slct.201600945
• For complete list of publications: https://scholar.google.com/citationshl=en&user=htNcKOEAAAAJ&view_op=list_works&sortby=pubdate

• Research Associate Scientist (RF-FTE) (February 2022- present) National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Health (NIH), Bethesda, Maryland 20892 US
• Visiting Post-Doctoral Fellow (February 2018- January 2022) National Institute of Allergy and Infectious Diseases (NIAID), National Institute of Health (NIH), Bethesda, Maryland 20892 US
• Post-Doctoral Research Fellow (December 2016- January 2018) The Pennsylvania State University, Eberly College of Science, University Park, PA-16802
• Post-Doctoral Research Fellow and Senior Technology Office (December 2014- December 2016) National Institute of Immunology, Jawaharlal Nehru University, New Delhi, India, and Regional Centre for Biotechnology (RCB), Faridabad, Haryana (NCR Delhi), India

• The goal of my research is to perform translational research based on knowledge being acquired through in vitro and in vivo and structural information on RNA viruses, particularly newly emerging and mutating viruses. One of the RNA virus families is flavivirus; it is an old family; however, many members still need attention to develop effective therapeutics. Flaviviruses have been identified as the causative agents of a number of human diseases. It consists of more than 70 small, positive-sense, single-stranded RNA viruses transmitted by arthropods, primarily ticks and mosquitoes. Since the global incidence of flavivirus infections is increasing due to climate change, globalization, and urbanization, there is an increased emphasis on understanding the molecular mechanisms underlying flavivirus infections and pathogenesis. Vaccines continue to be the most effective method for preventing viral infections. However, existing flavivirus vaccines can induce severe adverse effects and have certain limitations. Therefore, systematic and novel approaches to vaccine and drug discovery are required in the field of flavivirus. Mostly flaviviruses enter host cells via receptor-mediated endocytosis; however, flaviviruses utilize diverse receptors and attachment factors in various tissues of their natural hosts. Understanding the molecular mechanism by which flaviviruses use host cell receptors and factors for entry could facilitate the development of novel therapeutics. And, understanding the pathways that are being utilized by these viruses for the pathogenesis could be potential checkpoints for the development of an effective vaccine or drug. We will utilize cutting age techniques such as Cryo-electron microscopy (Cryo-EM), X-ray crystallography, and other biophysical techniques as a basic tool to address the questions in RNA virology.
• Major Areas of Research-
  • Assembly and entry of RNA viruses
  • Understanding the molecular mechanisms of membrane fusion used by RNA viruses
  • Humoral immunity to RNA viruses
  • The development of therapeutics based on structural knowledge using either viral proteins or the whole virus

Manish obtained his Ph.D. in Biotechnology from Calcutta University/Bose Institute, Kolkata in 2019. During his doctoral research in the laboratory of Prof. Basu, he studied the role of host microRNAs and transcription factors mediated regulation of Mycobacterium tuberculosis infection. Subsequently, he joined Dr. Altan-Bonnet’ lab at National Heart, Lung, and Blood Institute, National Institutes of Health, USA from 2019-2021, as a postdoctoral fellow to study Host-Virus dynamics and role of extracellular vesicles in virus transmission. He then moved to Dr. Vidigal’s lab at National Cancer Institute, National Institutes of Health, USA from 2022-2025 to explore the role of RNAi in disease and development. He joined Centre for Life Sciences as an Assistant Professor in 2025.

• Ph.D. in Biotechnology from Calcutta University/Bose Institute, Kolkata (2011-2019).
• M.Sc. in Biotechnology from Babasaheb Bhimrao Ambedkar University, Lucknow (2008-2010).
• B.Sc. in Applied Science from University of Allahabad, Allahabad (2005-2008).

Publications

• Google scholar link: https://scholar.google.com/citations?user=G4a_gCUAAAAJ&hl=en

• Manish Kumar, Andrea G. Maria, Mahendra Prajapat & Joana A. Vidigal. AGO2 slicing of a domesticated retrotransposon is necessary for normal vasculature development. bioRxiv, 2025.04. 02.646793. PMID: 40235999

• Manish Kumar & Joana A. Vidigal. AGO2 localizes to the nucleus in quiescence and represses transposon expression. Nature Structural & Molecular Biology. 2023, 30:1838-1839.
• Laura Sala*, Manish Kumar* (equal contribution), Mahendra Prajapat*, Srividya Chandrasekhar, Rachel L. Cosby, Gaspare La Rocca, Todd S. Macfarlan, Parirokh Awasthi, Raj Chari, Michael Kruhlak, and Joana A. Vidigal. AGO2 silences mobile transposons in the nucleus of quiescent cells. Nature Structural & Molecular Biology. 2023, 30:1985-1995.
• Pankaj Birari, Soumya Mal, Debayan Majumder, Arun K Sharma, Manish Kumar, Troyee Das, Zhumur Ghosh, Kuladip Jana, Umesh D Gupta, Manikuntala Kundu, Joyoti Basu, Nur77 influences immunometabolism to regulate the release of proinflammatory cytokines and the formation of lipid bodies during Mycobacterium tuberculosis infection of macrophages. Pathogens and Disease. 2023, 81: ftad033.
• Lepcha, Thurbu, Manish Kumar, Arun Kumar Sharma, Soumya Mal, Debayan Majumder, Kuladip Jana, Joyoti Basu, and Manikuntala Kundu. Uncovering the role of microRNA671-5p/CDCA7L/monoamine oxidase-A signaling in Helicobacter pylori mediated apoptosis in gastric epithelial cells. Pathogens and Disease. 2023, 81: ftad006.

• Abhishek Pandeya, Raj Kumar Khalko, Sukhveer Singh, Manish Kumar, and Sunil Babu Gosipatala. Hcmv-miR-UL148D regulates the staurosporine-induced apoptosis by targeting the Endoplasmic Reticulum to nucleus signaling (ERN1). PLOS One. 2022, 17(9): e0275072.
• Sourish Ghosh, Manish Kumar, Marianita Santiana, Ashish Mishra, Mengyang Zhang, ChiblyA.M., Hakashi Nakamura, Tsutomu Tanaka, John Chiorini, Matthew Hoffman, and Nihal Altan-Bonnet. Enteric viruses replicate in salivary glands and bypass the fecal-oral route of transmission. Nature. 2022, 607(7918): 345-350.

• Manish Kumar and Nihal Altan-Bonnet. Viral pores are everywhere. Molecular Cell. 2021,81(10): 2061-2063.
• Mengyang Zhang, Sourish Ghosh, Manish Kumar, Marianita Santiana, Christopher K. E. Bleck, Natthawan Chaimongkol, Nihal Altan-Bonnet, and Danmeng Shuai. Emerging Pathogenic Unit of Vesicle-Cloaked Murine Norovirus Clusters is Resistant to Environmental Stresses and UV254 Disinfection. Environmental Science & Technology. 2021, 55(9):6197-6205.

• Manish Kumar, Debayan Majumdar, Soumya Mal, Sohini Chakraborty, Pushpa Gupta, Kuladip Jana, Umesh D. Gupta, Zhumur Ghosh, Manikuntala Kundu and Joyoti Basu. Activating transcription factor 3 modulates the macrophage immune response to Mycobacterium tuberculosis infection via reciprocal regulation of inflammatory genes and lipid body formation. Cell. Microbiol. 2020, 22(3): e13142.
• Arijita Subuddhi, Manish Kumar, Debayan Majumder, Arijita Sarkar, Zhumur Ghosh, Madavan Vasudevan, Manikuntala Kundu and Joyoti Basu. Unraveling the role of H3K4 trimethylation lncRNA HOTAIR in SATB1 and DUSP4-dependent survival of virulent Mycobacterium tuberculosis in macrophages. Tuberculosis. 2020, 120:101897.

• Srijon Kaushik Banerjee, Suruchi Lata, Arun Kumar Sharma, Shreya Bagchi, Manish Kumar, Sanjaya Kumar Sahu, Pushpa Gupta, Kuladip Jana, Umesh D. Gupta, Ramandeep Singh, Sudipto Saha, Joyoti Basu and ManikuntalaKundu. The sensor kinase MtrB of Mycobacterium tuberculosis regulates hypoxic survival and establishment of infection. J. Biol. Chem. 2019, 294(52):19852- 19876.

• Chandreyee Datta, Arijita Subuddhi*, Manish Kumar* (equal contribution), Thurbu Lepcha, Sohini Chakraborty, Zhumur Ghosh, Asish kumar Mukhopadhyay, Joyoti Basu, and Manikuntala Kundu. Genome-wide mRNA- miRNA profiling uncovers a role of the microRNAmiR-29b-1-5p/PHLPP1 signaling pathway in Helicobacter pylori-driven matrix metalloproteinase production in gastric epithelial cells. Cell Microbiol. 2018, 11: e12859.
• Ayan Chatterjee, Arun Kumar Sharma, Amar Chandra Mahatha, Srijon Kaushik Banerjee, Manish Kumar, Sudipto Saha, Joyoti Basu and Manikuntala Kundu. Global mapping of MtrA-binding sites links MtrA to the regulation of its targets in Mycobacterium tuberculosis. Microbiology. 2018, 164:99-110.

• Sanjaya Kumar Sahu*, Manish Kumar* (equal contribution), Sohini Chakraborty, Srijon Kaushik Banerjee, Ranjeet Kumar, Pushpa Gupta, Kuladip Jana, Umesh D. Gupta, Zhumur Ghosh, Manikuntala Kundu, and Joyoti Basu. miR-26a/KLF4 and CREB-C/EBP-β regulate innate immune signaling, the polarization of macrophages, and the trafficking of Mycobacterium tuberculosis to lysosomes during infection. PLOS Pathogens. 2017, 13(5): e1006410.

• Srijon Kaushik Banerjee, Manish Kumar, Reshma Alokam, Arun Kumar Sharma, Ayan Chatterjee, Ranjeet Kumar, Sanjaya Kumar Sahu, Kuladip Jana, Ramandeep Singh, Perumal Yogeeswari, Dharmarajan Sriram, Joyoti Basu and Manikuntala Kundu. Targeting multiple response regulators of Mycobacterium tuberculosis augments the host immune response to infection. Sci. Reports. 2016, 6: 25851.
• Ranjeet Kumar, Sanjaya Kumar Sahu, Manish Kumar, Kuladip Jana, Pushpa Gupta, Umesh D. Gupta, Manikuntala Kundu and Joyoti Basu. MicroRNA-17-5p regulates autophagy in Mycobacterium tuberculosis-infected macrophages by targeting Mcl-1 and Stat3. Cell. Microbiol. 2016, 18(5): 679-691.

• Manish Kumar*, Sanjaya Kumar Sahu*, Ranjeet Kumar* (equal contribution), Arijita Subuddhi, Ranjan Kumar Maji, Kuladip Jana, Pushpa Gupta, Johanna Raffetseder, Maria Lerm, Zhumur Ghosh, Geert Van Loo, Rudi Beyaert, Umesh D. Gupta, Manikuntala Kundu and Joyoti Basu. MicroRNA let-7 modulates the immune response to Mycobacterium tuberculosis infection via control of A20, an inhibitor of the NF-κB pathway. Cell Host & Microbe. 2015, 17(3): 345-356.

• Ranjeet Kumar, Priyanka Halder, Sanjaya Kumar Sahu, Manish Kumar, Mandavi Kumari,Kuladip Jana, Zhumur Ghosh, Pawan Sharma, Manikuntala Kundu and Joyoti Basu. Identification of the novel role of ESAT-6-dependent miR-155 induction during infection of macrophages with Mycobacterium tuberculosis. Cell. Microbiol. 2012, 14(10): 1620-1631.
• Nisha Singh, Manish Kumar, and Rakesh Kumar Singh. Leishmaniasis: Current status of available drugs and new potential drug targets. Asian Pac. J. Trop. Med. 2012, 5(6): 485-497.

Book Chapter

• Manish Kumar, Manikuntala Kundu and Joyoti Basu. The role of microRNAs in bacterial infections. AGO-Driven Non-Coding RNAs. 2019, pages 57-71. Published by Academic Press.

• 2025- Present- Assistant Professor, Centre for Life Sciences, Mahindra University
• 2022-2025- Postdoctoral Fellow, National Cancer Institute, NIH, USA.
• 2019-2021- Postdoctoral Fellow, National Heart, Lung, and Blood Institute, NIH, USA.

• Research concept
• Welcome to our research laboratory dedicated to Innate Immunity & Extracellular Vesicles (EVs), where we explore the host’s defense mechanisms in the context of infectious diseases. The ability of innate immune system to sense pathogenic organisms and respond appropriately to control infection is paramount for our survival. To achieve this, innate immune system identify invading pathogens and respond by initiating inflammation. Macrophages, vital components of innate immunity are found in various tissue and play a crucial role in coordinating inflammatory responses and eliminating invading microorganisms. Macrophage derived extracellular vesicles also play crucial role in immune surveillance, inflammation, and intercellular communication, in addition to its direct microbes killing ability. Our primary goal is to combat specific pathogens by harnessing the body’s natural defense mechanism, rather than relying on antibiotics that bacteria can quickly develop resistance to.
• Research projects 
• Exploring macrophage biology in the context of pathogenic infections
  Our goal is to develop a nuanced understanding of epigenetic, transcriptional, and post-transcription regulation of innate immune cell signaling pathways in order to identify therapeutic targets that are mediated by the host.
• Exploring the role of EVs in modulating immune responses
  We are exploring the contents of EVs derived from macrophages and other immune cells, focusing on their role in cellular communication and their impact on the establishment or resolution of infection.
• Development of EVs- based diagnostics and therapeutics for infectious diseases
  We are identifying membrane-displayed antigens on EVs during infection and utilizing these antigens to develop, optimize, and evaluate detection assays. Additionally, we are engineering EVs for the targeted delivery of RNAi therapeutics.
• Research approaches
•           We are using multidisciplinary approaches to validate our hypothesis like:
• Molecular biology & Immunology techniques
• Cellular biology & advanced imaging techniques
• High-throughput omics
• EV engineering using CRISPR and advanced EV isolation
• In vitro and in vivo immune models
• We are seeking enthusiastic Ph.D. candidates in accordance with Mahindra University guidelines. Master students interested in pursuing dissertations are also welcome to apply.
• Postdoctoral candidates with their own research grants, such as NPDF, ICMR, DBT etc are encouraged to apply. We are also open to discussing project proposals to help secure these fellowships.
• If our research excites you, feel free to write manish.kumar@mahindrauniversity.edu.in or visit our lab by contacting us in advance.

Sarat Chandra Togarcheti is an Assistant Professor in Centre for Life Sciences at Mahindra University. He was awarded PhD from Indian Institute of Technology Bombay in 2018. He has received “Best Ph.D. Thesis award” for the year 2018 from IIT Bombay.

He is an experienced fermentation scientist with transferable skills from industry and academia. He has 10 years of experience in bioprocess development, scaling up of microbial fermentation processes for food/ bio-actives production, Life Cycle and Sustainability Analysis. He has experience in developing bioproducts and flavors via bacterial and fungal fermentations from bench scale to demonstration at pilot scale. He has practical knowledge in yeast manufacturing and in-depth understanding of yeast biomass processing, applications of yeast derivatives in consumer foods & cell nutrition.

• Ph.D. (2013 to 2018), Centre for Environmental Science and Engineering, Indian Institute of Technology Bombay, India
• M.Tech. in Industrial Biotechnology (2010- 2012), National Institute of Technology Suratkal, Karnataka
• B.Tech. in Biotechnology (2006- 2010), Gandhi Institute of Technology and Management, Andhra University, India

• Sarat Chandra, T*., Ramesh Babu, P., 2020. Comparative life cycle assessment of EPA and DHA production from microalgae and farmed fish. Clean Technologies, 3(4), 699-710.

• K. Madhubalaji, T Sarat Chandra, V. S. Chauhan, R. Sarada, S. N. Mudliar, 2019. Chlorella vulgaris cultivation in airlift photobioreactor with transparent draft tube: effect of hydrodynamics, light and carbon dioxide on biochemical profile particularly ω-6/ω-3 fatty acid ratio. Journal of Food Science and Technology, 1-11.

• T. Sarat Chandra, M. Maneesh Kumar, S. Mukherji, V. S. Chauhan, R. Sarada, S. N. Mudliar, 2018. Comparative life cycle assessment of microalgae-mediated CO2 capture in open raceway pond and airlift photobioreactor system. Clean Technology Environmental Policy, 20(10), 2357-2364.
• Shahabazuddin, T. Sarat Chandra, S. Meena, R. Sukumaran, S. N. Mudliar, 2018. Thermal assisted alkali pre-treatment of rice husk for enhanced biomass deconstruction and enzymatic saccharification: Physico-chemical and structural characterization. Bioresource Technology, 263, 199-206.
• M. Maneesh Kumar, K. Prasad, T. Sarat Chandra, S. Debnath, 2018. Evaluation of physical properties and hydration kinetics of red lentil (Lens Culinaris) at different processed levels and soaking temperatures. Journal of Saudi Society of Agricultural Sciences, 17(3), 330-338.

• Sarat Chandra, M. Maneesh Kumar, V. S. Chauhan, S. Mukherji, R. Sarada, S. N. Mudliar, 2017. Lifecycle assessment of biodiesel production coupled to biogas production from Scenedesmus dimorphus cultivated in outdoor open raceway pond. Resource Recycling and Conservation, 122, 286- 294.
• T. Sarat Chandra, S. Aditi, M. Maneesh Kumar, S. Mukherji, J. Modak, V. S. Chauhan, R. Sarada, S. N. Mudliar, 2017. Growth and biochemical characteristics of indigenous fresh water microalga, Scenedesmus obtusus cultivated in closed air lift photobioreactor: Effect of reactor hydrodynamics, light intensity and photoperiod. Bioprocess and Biosystems Engineering. 40 (7), 1057-1068

• Sarat Chandra, R. S. Deepak, M. Maneesh Kumar, S. Aditi, V. S. Chauhan, S. Mukherji, R. Sarada, S. N. Mudliar, 2016. Evaluation of indigenous fresh water microalga Scenedesmus obtusus for feed and fuel applications: Effect of CO₂, culture conditions on growth and biochemical characteristics. Bioresource Technology, 207, 430-439
• M. T. Usha, T. Sarat Chandra, R. Sarada, V. S. Chauhan, 2016. Removal of nutrients and organic pollution load from pulp and paper mill effluent by microalgae in outdoor open pond. Bioresource Technology, 214, 856-860

• T. Sarat Chandra, S. N. Mudliar, S. Mukherji, S. Vidyashankar, R. Sarada, K. Krishnamurthy, V. S. Chauhan, 2015. Defatted algal biomass as a non- conventional low- cost adsorbent: Surface characterization and its adsorption characteristics by methylene blue based adsorption. Bioresource Technology, 184, 395-404
• G. Suvidha, T. Sarat Chandra, S. N. Malik, Abhinav Sharma, Satish. K. Lokhande, S. N. Mudliar, 2015. Ozone induced biodegradability enhancement and color reduction of a complex pharmaceutical effluent. Ozone Science and Engineering, 37(6), 538-545.
• G. Suvidha, A. Sharma, T. Sarat Chandra, S. N. Malik, V. Waindeskar, S. N. Mudliar, 2015. Effect of ozone pretreatment on biodegradability enhancement and biogas generation potential from bio-methanated distillery effluent. Ozone Science and Engineering, 37(5), 411-419

• Sarat Chandra, G. Suvidha, S. Mukherji, V. S. Chauhan, S. Vidyashankar, K. Krishnamurthy, R. Sarada, S. N. Mudliar, 2014. Statistical optimization of thermal pretreatment conditions for enhanced biomethane production from defatted algal biomass. Bioresource Technology, 162, 157-165
• Sarat Chandra, S. N. Malik, G. Suvidha, M. L. Padmere, P. Shanmugam, S. N. Mudliar, 2014. Wet air oxidation pretreatment of bio-methanated distillery effluent: Mapping pretreatment efficiency in terms color, toxicity reduction and biogas generation. Bioresource Technology, 158, 135-140
• S. N. Malik, T. Sarat Chandra, P. D. Tembhekar, K. V. Padoley, S. L. Mudliar, S. N. Mudliar, 2014. Wet air oxidation induced enhanced biodegradability of distillery effluent. Journal of environmental management, 136, 132-138

• K.V. Padoley, P.D. Tembhekar, T. Sarat Chandra, A.B. Pandit, R. A. Pandey, S. N. Mudliar, 2012. Wet Air oxidation as a Pretreatment Option for Selective Biodegradability Enhancement and Biogas Generation Potential from Complex Effluent. Bioresource Technology, 120, 157-164

Google Scholar Profile: https://scholar.google.com/citations?user=481ydlQAAAAJ&hl=en

• May 2018 to May 2019 -Postdoctoral Research Fellow, School of Physics, Trinity College Dublin.
• June 2019 to October 2021: Marie Sklodowska Curie Fellow, School of Chemistry, Trinity College Dublin
• November 2021 to July 2024: Senior Fermentation Scientist, Global Technology and Innovation Centre, Kerry Group, Naas, Ireland
• June 2016 to December 2016: Newton Bhabha Fellow, European Bioenergy Research Institute, Aston University, United Kingdom
• June 2011 to June 2013: CSIR- GATE- JRF, CSIR- National Environmental Engineering Research Institute, Nagpur
• July 2013 to June 2016: CSIR- GATE- SRF, CSIR- Central Food Technological Research Institute, Mysuru

• Bioprocess Design and Scale-Up
• Fermentation for High-Value Products
• Food Processing and Nutrition
• Life Cycle and Sustainability Analysis

Sudhanshu Shanker has expertise in structural bioinformatics, with a focus on developing theoretical models to address critical biological challenges. His research spans multiple domains, emphasizing the creation of innovative computational solutions.

He completed his Ph.D. at Jawaharlal Nehru University, where he developed Monte Carlo-based methods for biomolecular structure optimization and a density clustering method for analyzing hydration networks around non-Watson-Crick base pairs in RNA.

As a postdoctoral fellow at Kyoto University, Japan, he worked on a JSPS sponsored project on supramolecular polymerization and self-assembly systems. He later moved to Johns Hopkins University as a postdoctoral researcher in a Rosetta developer lab, where he focused on protein-carbohydrate interactions and developed CAPSIF, the first 3D-UNet and EGNN-based carbohydrate interaction site predictor. Subsequently, at The Scripps Research Institute, he led the development of AutoDock CrankPep V1.1, a state-of-the-art peptide docking method.

His current research interests lie in computational glycosciences, with a focus on developing new methods to study glycan-protein interactions and exploring the role of glycosylation in cancer and autoimmune diseases.

• Ph.D. (2010-2016) in Computational Biology and Bioinformatics; Jawaharlal Nehru University, New Delhi.
• M.Sc. (2005-2008) in Bioinformatics; University of Allahabad, Allahabad, Uttar Pradesh.
• B.Sc. (2000-2004) in Botany & Chemistry; University of Allahabad, Allahabad, Uttar Pradesh

Publications

• Canner S.W., Shanker S., Gray J.J., “Structure-Based Neural Network Protein-Carbohydrate Interaction Predictions at the Residue Level”, Front. Bioinform. 3, 2023. https://doi.org/10.3389/fbinf.2023.1186531
• Shanker S., Sanner M., “Predicting Protein–Peptide Interactions: Benchmarking Deep Learning Techniques and a Comparison with Focused Docking”, J. Chem. Inf. Model. 63 (10), 2023. https://doi.org/10.1021/acs.jcim.3c00602

• Li M., Zheng X., Shanker S., Jaroentomeechai T., Kocer I., Byrne J., Cox E.C., Fu Q., Zhang S., Labonte J.W., Gray J.J., DeLisa M.P., “Fine-mapping the consequences of site-specific glycan installation by shotgun scanning glycomutagenesis”, PNAS 118(39) e2107440118, 2021. https://doi.org/10.1073/pnas.2107440118

• Yamamoto T., Arefi H.H., Shanker S., Sato H., and Hiraoka S., “Self-Assembly of Nanocubic Molecular Capsules via Solvent-Guided Formation of Rectangular Blocks”, J. Phys. Chem. Lett. 9(20): 6082-6088, 2018. https://doi.org/10.1021/acs.jpclett.8b02624

• Shanker S., Bandyopadhyay P., “How Mg2+ ion and water network affect the stability and structure of non-Watson-Crick base pairs in E coli Loop E RNA: A Molecular Dynamics and Reference Interaction Site Model (RISM) study”, Journal of Biomolecular Structure and Dynamics 35 (10): 2103-2122, 2017. https://doi.org/10.1080/07391102.2016.1213186

• Shrivastava R., Rakshit A., Shanker S., Vig L., Bandyopadhyay P., “A combination of Monte Carlo Temperature Basin Paving and graph theory: water cluster low energy structures and completeness of search”, Journal of Chemical Sciences: 1-10, 2016. https://doi.org/10.1007/s12039-016-1135-8

• Shanker S., Bandyopadhyay P., “Determination of low energy structures of a small RNA hairpin using Monte Carlo based techniques”, J. Biosciences 37(3): 533-538., 2012. https://doi.org/10.1007/s12038-012-9209-3
• Furtado J.P., Rahalkar A.P., Shanker S., Bandyopadhyay P., Gadre S.R., “Facilitating Minima Search for Large Water Clusters at MP2 level via Molecular Tailoring”, J. Phys. Chem. Lett. 3, 2253-2258, 2012. https://doi.org/10.1021/jz300663u

• Shanker S., Bandyopadhyay P., “Monte Carlo Temperature Basin Paving with Effective Fragment Potential: An Efficient and Fast Method for Finding Low Energy Structures of Water Clusters (H2O)20 and (H2O)25”, J. Phys. Chem. A, 115 (42): 11866-11875., 2011. https://doi.org/10.1021/jp2073864
• Chaturvedi N., Shanker S., Singh V.K., Sinha D., Pandey P.N., “Hidden Markov model for the prediction of transmembrane proteins using MATLAB”, Bioinformation 7(8): 418-421, 2011. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280443/

Non-Peer Reviewed

• Shanker S., Li M., Zheng X., Labonte J.W., DeLisa M.P., Gray J.J, “Geometric and energy calculations to predict protein stability and activity changes due to site-specific glycosylation”, Glycobiology 30(12): 1110-1110, 2020 : Conference Abstract.

• Shanker S., Bandyopadhyay P., “Interplay of Water molecules and Mg2+ ions in stability of non-Watson-Crick base pairs”, Journal of Biomolecular Structure and Dynamics 33: 57-58, 2015 : Conference Abstract. https://doi.org/10.1080/07391102.2015.1032705

• Postdoc Associate | Scripps Research Institute, La Jolla, USA
  Supervisor: Prof. Michel F. Sanner | 8/2022-11/2023
• Postdoc Researcher | Johns Hopkins University, Baltimore, USA
  Supervisor: Prof. Jeffrey J. Gray | 11/2018-7/2022
• Postdoc Researcher | Kyoto University, Kyoto, Japan
  Supervisor: Prof. Hirofumi Sato, Dr. Takeshi Yamamoto | 10/2016-10/2018

• Developing hybrid methods that integrate deep learning and physics-based approaches for biomolecular interaction analysis.
• Designing and advancing tools for the modeling and study of protein-carbohydrate interactions.
• Exploring the development of carbohydrate-based therapeutics.
• Investigating the role of aberrant glycosylation in autoimmune diseases and cancer.

Dr. Balan Ramesh is a computational biologist with a research focus on comparative genomics. With numerous publications in prestigious journals, he has made significant contributions to understanding complex non-model systems. His work spans various inter disciplinary fields, including sex chromosome and genome evolution, sexual selection, venom regulation and toxin synthesis, emphasizing the integration of computational tools with experimental research. Dr. Ramesh is dedicated to fostering innovation in the field and mentoring emerging scientists.

• Dr. Balan Ramesh has a Ph.D. with specialization in Quantitative Biology from University of Texas, Arlington

Publications

• Robben M;Ramesh B;Pau S;Meletis D;Luber J;Demuth J; (n.d.). ScRNA-seq reveals novel genetic pathways and sex chromosome regulation in Tribolium spermatogenesis. Genome biology and evolution. https://pubmed.ncbi.nlm.nih.gov/38513111/
• Ramesh, B., Small, C., Bassham, S., Johnson, B., Barker, E., Rose, E., Currey, M., Healey, H., Myers, M., Ahnesjö, I., Lotta Kvarnemo, Monteiro, N., Cresko, W. and Jones, A. (2024b). Chromosome-scale genome assemblies for 10 syngnathiform fishes produced using a standardized sequencing and annotation workflow. Authorea (Authorea). [online] doi:https://doi.org/10.22541/au.172467565.57384610/v1.

• Ramesh, B., Small, C.M., Healey, H., Johnson, B., Barker, E., Currey, M., Bassham, S., Myers, M., Cresko, W.A. and Adam Gregory Jones (2023). Improvements to the Gulf pipefish Syngnathus scovelli genome. Gigabyte, [online] 2023, pp.1–11. doi: https://doi.org/10.46471/gigabyte.76.

• Firneno, T.J., Ramesh, B., Maldonado, J.A., Hernandez-Briones, A.I., Emery, A.H., Roelke, C.E. and Fujita, M.K. (2022). Transcriptomic analysis reveals potential candidate pathways and genes involved in toxin biosynthesis in true toads. Journal of Heredity. doi:https://doi.org/10.1093/jhered/esac015.

• Ramesh, B., Firneno, T.J. and Demuth, J.P. (2021b). Divergence time estimation of genus Tribolium by extensive sampling of highly conserved orthologs. Molecular Phylogenetics and Evolution, [online] 159, p.107084. doi: https://doi.org/10.1016/j.ympev.2021.107084.

• Ramesh, B. and Demuth, J. (2020). Using Ancestral Reconstruction of Chromosome Expression States (ARChES) to Understand the Evolution of Dosage Compensation. [online] Utexas.edu. Available at: https://repositories.lib.utexas.edu/items/2b4aba04-7fd3-45e8-94c8-dd05b15e81be.

• Schield, D.R., Card, D.C., Hales, N.R., Perry, B.W., Pasquesi, G.M., Blackmon, H., Adams, R.H., Corbin, A.B., Smith, C.F., Ramesh, B., Demuth, J.P., Betrán, E., Tollis, M., Meik, J.M., Mackessy, S.P. and Castoe, T.A. (2019). The origins and evolution of chromosomes, dosage compensation, and mechanisms underlying venom regulation in snakes. Genome Research, 29(4), pp.590–601. doi: https://doi.org/10.1101/gr.240952.118.

• Muthukumaran P, J. Aravind, A. Thirumurugan, Sridhar, S., Balan, R. and P. Indumathi (2017). Screening, Isolation and Development of Fungal Consortia with Textile Reactive Dyes Decolorizing Capability. Environmental science and engineering, pp.295–303. doi: https://doi.org/10.1007/978-3-319-48439-6_22.

• Kanmani, P., Kumaresan, K., Aravind, J., Karthikeyan, S. and Balan, R. (2016). Enzymatic degradation of polyhydroxyalkanoate using lipase from Bacillus subtilis. International Journal of Environmental Science and Technology, 13(6), pp.1541–1552. doi: https://doi.org/10.1007/s13762-016-0992-5.
• Aravind, Paulraj Kanmani, G.T. Sudha and Balan, R. (2016). Optimization of chromium(VI) biosorption using gooseberry seeds by response surface methodology. Global Journal of Environmental Science and Management, 2(1), pp.61–68. doi: https://doi.org/10.7508/gjesm.2016.01.007.
• Muthukumaran, P., Saraswathy, N., Yuvapriya, S., Balan, R., Gokhul, V. and Indumathi, P. (2016). In vitro phytochemical screening and antibacterial activity of Amorphophallus paeonifolius (Dennst. Nicolson) against some human pathogens. Available online www.jocpr.com Journal of Chemical and Pharmaceutical Research, [online] 8(2), pp.388–392. Available at: https://www.jocpr.com/articles/in-vitro-phytochemical-screening-and-antibacterial-activity-of-amorphophallus-paeonifolius-dennst-nicolson-against-some.pdf.
• Peraman Muthukumaran, Nachimuthu Saraswathy, Vijayasekar Aswitha, Balan, R., Venkatesh Babu Gokhul, Palanikumar Indumathi and Sivasubramani Yuvapriya (2016b). Assessment of Total Phenolic, Flavonoid, Tannin Content and Phytochemical Screening of Leaf and Flower Extracts from Peltophorum pterocarpum (DC.) Backer ex K.Heyne: a comparative study. Pharmacognosy Journal, [online] 8(2). Available at: https://www.phcogj.com/article/129 .
• Kumaresan, K., Balan, R., Sridhar, A., Aravind, J. and Kanmani, P. (2016). An integrated approach of composting methodologies for solid waste management. Global Journal of Environmental Science and Management, [online] 2(2), pp.157–162. doi: https://doi.org/10.7508/gjesm.2016.02.006.

• Balan Ramesh is currently working as an Assistant Professor at Mahindra University.
• He has done Post-Doctoral Fellow with specialization in Comparative Genomics and Transcriptomics from University of Idaho

• Members of a species (males and females) share the same genetic material (DNA), yet there are remarkable morphological and functional differences between the sexes. These differences primarily arise due to the sex chromosomes (traditionally X and Y chromosomes), which determine the sex of a species. However, across the animal kingdom, there is a wide variety of sex-determination systems. This variety is especially true for fishes, which shed light on the early stages of sex chromosome evolution, which in turn helps us understand the genes and gene network responsible for the differences between the sexes. With sequencing technologies, comparative framework, and cluster computers, I am excited to answer questions broadly under the umbrella of Why there is a difference in lifespans between the sexes. What factors accelerate or decelerate aging? How does the accumulation of mobile genetic elements (Transposons) on sex-limited chromosomes affect aging? Do sexually dimorphic species live longer than monomorphic species? Tackling these questions would provide sex-specific genes responsible for rapid growth and fast aging that control cell cycle, gene transcriptions, and translations. To summarize, I am a computational biologist interested in studying the role of sexual selection in the evolution of sex chromosomes and sex determination mechanisms and its effects on aging and lifespan.

Biopharmaceutical Technology is a highly translational area that brings together molecular biologists, biochemists, analytical chemists and chemical and biomedical engineers to develop novel therapeutic solutions. Within this, Dr. Srishti Joshi is active in the structural characterization space. Because of the inherent structure to function relationship, biopharmaceuticals need to be characterized throughout their life cycle from early stages of cell culture till approval of Drug Product and after. Dr. Joshi’s research expertise includes developing comprehensive analytical platforms using biophysical techniques and validated methods for characterization of protein-based biopharmaceuticals including biosimilars.

Dr. Joshi has a diverse global educational background. She obtained her bachelors from University of Delhi, India, Masters at University of Nottingham, UK, PhD (molecular biology and biochemistry) from Massey University, NZ and gained post-doctoral experience at Massey University, NZ; Korea University, South Korea and the DBT Centre of Excellence for Biopharmaceutical Technology (DBT-COE-CBT), IIT Delhi.

In addition to research, she also holds significant administrative experience. She served as the Coordinator for Analytical Characterization Division within DBT-COE-CBT from 2018-2023, Coordinator for Bioprocessing Society of India (BPI) from 2021-23. She has a keen interested in Internationalization of Higher Education and has served as the Coordinator of International Programs at IITD from 2023-24. She joined Mahindra University as an Assistant Professor at the Centre for Life Sciences in Sept 2024.

• Ph.D. – Molecular Biology and Biochemistry – Massey University (NZ) – 2010- 2015
• M.Sc – Crop Biotechnology and Entrepreneurship – University of Nottingham (UK) – 2008- 2009
• B.Sc – Botany (Hons) – Delhi University – 2005-2008

• Joshi, Srishti¹; Dubey, Ankita¹; Rathore, Anurag S., Protocol for simultaneous quantification of 20 amino acids in cell culture for biopharmaceutical development, BioTechniques (2023)
• Rachayita Nag, Joshi, Srishti, Anurag Rathore, Subhabrata Majumdar, Profiling enzyme activity of L asparaginase II by NMR based methyl fingerprinting at natural abundance, Journal of the American Chemical Society, (2023) 145, 19, 10826–10838
• Joshi, Srishti¹; Bhattacharya, Sanghati¹; Rathore, Anurag;  A native multi-dimensional MAM workflow for at-line characterization of mAb titer, size, charge, and glycoform heterogeneities in cell culture supernatant, Journal of Chromatography A (2023), 1696, 463983

• Joshi, Srishti; Nupur, Neh;  Nikita; Saxena,  Bhattacharya;  Sanghati,  Roy;  Souhardya, Taking the individual bias out of examining comparability of biosimilars: A case study on monoclonal antibody therapeutics,  International Journal of Biological Macromolecules (2022), 227, 124-133
• Rathore, Anurag S., Srishti Joshi, Ahluwalia, Akshdeep; Auclair, Jared, On replication in biopharmaceutical analysis, LCGC North America, (2022), 40, 11, 536-542
• Joshi, Srishti; Upadhyay, Kratika; Rathore, Anurag S., Fluorescence detection as a sensitive, orthogonal alternative to UV detection for charge variant analysis of monoclonal antibodies: Trastuzumab as a case study, Journal of Chromatography B, (2022), 123511
• Joshi, Srishti; Khatri, Lakshya Raj; Kumar, Ashutosh; Rathore, Anurag S., NMR based quality evaluation of mAb therapeutics: A proof of concept higher order structure biosimilarity assessment of trastuzumab biosimilars, Journal of Pharmaceutical and Biomedical Analysis, (2022), 114710
• Bhojane, Purva. P; Joshi, Srishti; Sahoo Jagriti, Sushree; Rathore, Anurag S, Unexplored excipients in biotherapeutic formulations: Natural osmolytes as potential stabilizers against thermally induced aggregation of IgG1 biotherapeutics, PharmSciTech, (2022), 23

• Joshi, Srishti; Maharana, Chinmoyee; Rathore, Anurag S. An application of Nano Differential Scanning Fluorimetry for Higher Order Structure assessment between mAb originator and biosimilars: Trastuzumab and Rituximab as case studies, Journal of Pharmaceutical and Biomedical Analysis, (2021), 113270
• Joshi, Srishti; Khatri, Lakshya Raj; Kumar, Ashutosh; Rathore, Anurag S., Monitoring size and oligomeric-state distribution of therapeutic mAbs by NMR and DLS: Trastuzumab as a case study, Journal of Pharmaceutical and Biomedical Analysis, (2021) 195, 113841
• Srishti Joshi, Sudha Kumari, Anurag S. Rathore, Identification and characterization of carbonylation sites in trastuzumab biosimilars, International Journal of Biological Macromolecules (2021), 169, 95-102

• Joshi, Srishti; Rathore, Anurag. S, Assessment of Structural and Functional Comparability of Biosimilar Products: Trastuzumab as a Case Study, BioDrugs,(2020), 34, 209-223
• Mishra, Avinash; Bansal, Rohit; Sreenivasan, Shravan; Dash, Rozaleen; Joshi, Srishti; Singh, Richa; Rathore, Anurag S; Goel, Gaurav; Structure-based Design of Small Peptide Ligands to Inhibit Early-Stage Protein Aggregation Nucleation, Journal of Chemical Information and Modeling, (2020), 60 (6), 3304-3314

• Khosa, Jiffinvir; Lee, Robyn; Joshi, Srishti; Shaw, Martin; McCallum, John; Macknight, Richard, A Guide for the Cultivation of Onion under Controlled Environment Conditions, HortScience, (2018), 53, 12, 1746-1749

• McKenzie, Marian J; Chen, Ronan KY; Leung, Susanna; Joshi, Srishti; Rippon, Paula E; Joyce, Nigel I; McManus, Michael T, Selenium treatment differentially affects sulfur metabolism in high and low glucosinolate producing cultivars of broccoli (Brassica oleracea L.), Plant physiology and biochemistry, (2017), 121, 176-186

• McManus, Michael T; Joshi, Srishti; Searle, Bruce; Pither-Joyce, Meeghan; Shaw, Martin; Leung, Susanna; Albert, Nick; Shigyo, Masayoshi; Jakse, Jernej; Havey, Michael J; Genotypic variation in sulfur assimilation and metabolism of onion (Allium cepa L.) III. Characterization of sulfite reductase, Phytochemistry, (2012), 83, 34-42

Reviews/Major Reference Works/Book Chapters/Articles

• Joshi, Srishti; Gomes James, Affordability and Financial Challenges in the Internationalisation of Higher Education, International Seminar on Internationalisation of Higher Education, 2024

• Rathore, Anurag S; Guttman, Andras; Shrivastava, Anuj; Joshi, Srishti, Recent progress in high-throughput and automated characterization of N-glycans in biopharmaceuticals, Trends in Analytical Chemistry TrAC (2023), 117397
• Sarin, Deepika; Joshi, Srishti; Rathore, Anurag S, Hydrophobic Interaction Chromatography, Liquid Chromatography: Fundamentals and Instrumentation, Third Edition, edited by Drs. Salvatore Fanali, Bezhan Chankvetadze, Paul R. Haddad, Colin Poole, and Marja-Liisa Riekkola. Elsevier, 2023 (book in production)

• Rathore, Anurag S.; Joshi, Srishti; Establishing Analytical and Functional Comparability for Biosimilars, Recent advances in Biopharmaceutical Analysis, LCGC North America, (2022), July.
• Shrivastava, Anuj; Joshi, Srishti; Guttman, Andras; Rathore, Anurag S; N-Glycosylation of monoclonal antibody therapeutics: A comprehensive review on significance and characterization, Analytica Chimica Acta, (2022), 339828
• Joshi, Srishti; Nupur, Neh; Gulliarme, David; Rathore, Anurag S; Analytical similarity assessment of biosimilars: Global regulatory landscape, recent studies and major advancements in orthogonal platforms, Frontiers in Bioengineering and Biotechnology, (2022), 36

• Rathore, Anurag S.; Joshi, Srishti; Dash, Rozaleen; Nupur, Neh; Sreenivasan, Shravan; Emergence of India as a Global Manufacturing Hub for Biosimilars, BioPharm International, (2021) 34; 11, (pp.42-44)

• Rathore, Anurag S.; Joshi, Srishti; Liquid Chromatography| Historical Development, 2019, Encyclopedia of Analytical Science (pp.86-92)
• Rathore, Anurag S.; Krull, Ira; Srishti Joshi, Analytical Characterization of Biotherapeutic Products, Part I: Quality Attributes, LCGC North America, (2018) 36: 376-384.
• Rathore, Anurag S, Krull, Ira; Srishti Joshi, Analytical Characterization of Biotherapeutic Products, Part II: The Analytical ToolBox, LCGC North America (2018) (In-print Nov Issue).
• Rathore, Anurag S; Joshi, Srishti; Bhargava, Ankita; Nupur, Neh, Development and Commercialization of Biosimilars in India: Current Regulatory and Clinical Experience, Biosimilars, 2018, Springer, 653-674

• Joshi, Srishti; Leung, Susanna CS; McCallum, John A; McManus, Michael T, Comparison of Nitrite Reductase (AcNiR1) with Sulfite Reductase (AcSiR1) in Allium cepa (L.), Molecular Physiology and Ecophysiology of Sulfur, 2015, 93-97

Thesis

• Joshi, Srishti; Interaction between sulfur (S) and nitrogen (N) assimilation pathways in response to S and N supply in onion (Allium cepa L, 2014 Massey University

Google Scholar Profile: https://scholar.google.com/citations?user=daAvJ7QAAAAJ&hl=en

• Assistant Professor Center for Life Sciences Mahindra University. (2024 – Present)
• Program Coordinator – International Relations – Indian Institute of Technology Delhi (2023-2024)
• Coordinator (Analytical Characterization Division) – DBT Centre of Excellence for Biopharamceutical Technology, IIT Delhi (2018-2023)
• Post Doctorate Fellow – Indian Institute of Technology, Delhi (2017-2023)
• Post Doctorate Fellow- Korea University, South Korea (2015-2016)
• Research Associate – Massey University (2014-2015)

• The Biologics Analysis and Research Lab – Our research focuses on addressing contemporary and emerging physicochemical characterization needs of the biopharmaceutical industry through structural analysis. This includes:
• Designing efficient, High-Throughput, multi-attribute analytical workflows for physicochemical characterization of biologics including biosimilars and emerging modalities.
• Understanding impact of stress on Critical Quality Attributes and its fingerprint on product quality and stability.
• Current specific interests include – analytical Quality by Design (aQbD) in biopharma, multi-attribute monitoring methods and quantitative biosimilarity scoring.

Having a background in Bioinformatics, Swarit Jasial did his Masters in Life Science Informatics and PhD in Computational Life Sciences from University of Bonn, Germany. During his studies, Swarit was involved in several projects concerning data mining and machine learning. He worked in the research area of computer aided drug design or Chemoinformatics. His PhD work focused on analysis of multitarget activities and assay interference characteristics of pharmaceutically relevant compounds. He studied promiscuity of compounds present in publicly available databases and his data analysis revealed interesting results for state-of-the-art PAINS filters, which are generally used to flag assay interference compounds. The machine learning models built in this project further extended the capacity of PAINS filters as they also took structural context into account. He published his studies in several journals mostly belonging to American Chemical Society (ACS).

Swarit Jasial did his post doctoral studies (2019-2024) in Data-Driven Chemistry lab, Data Science Center, Nara Institute of Science and Technology, Japan where he also worked as a specially appointed assistant professor. He worked on projects such as predicting antiviral activity of odorants with Kao corporation and monomer concentration prediction of polymerization reactions from infra-red spectra in collaboration with JSR corporation. He also supervised students in their research focusing on Chemoinformatics.

• Ph.D. in Computational Life Sciences, Bonn-Aachen International Center for Information Technology (B-IT), Rheinische Friedrich-Wilhelms-Universität Bonn, Germany (2015-2019)
• M.Sc. in Life Science Informatics, Bonn-Aachen International Center for Information Technology (B-IT), Rheinische Friedrich-Wilhelms-Universität Bonn, Germany (2012-2014)
• B.Tech. in Bioinformatics, Jaypee University of Information Technology, Waknaghat, India (2007-2011)

• Riadhi Syahdhi, R.; Jasial, S.; Maeda, I.; Miyao, T. Bridging Structure-and Ligand-Based Virtual Screening through Fragmented Interaction Fingerprint. ACS Omega 2024, 9, 38957-38969.
• Wakiuchi, A.; Jasial, S.; Asano, S.; Hashizume, R.; Hatanaka, M.; Ohnishi, Y.; Matsubara, T.; Ajiro, H.; Sugawara, T.; Fujii, M.; Miyao, T. Multiple comonomer concentrations prediction from FTIR spectra with quantum chemistry-based interpretation. MRS Comm 2024, 14, 439-444.
• Wakiuchi, A.; Jasial, S.; Asano, S.; Hashizume, R.; Hatanaka, M.; Ohnishi, Y.; Matsubara, T.; Ajiro, H.; Sugawara, T.; Fujii, M.; Miyao, T. Chemometrics Approach Based on Wavelet Transforms for the Estimation of Monomer Concentrations from FTIR Spectra. ACS Omega 2023, 8, 19781-19788.

• Jasial, S.; Hu, J.; Miyao, T.; Hirama, Y.; Onishi, S.; Matsui, R.; Osaki, K.; Funatsu, K. Screening and Validation of Odorants against Influenza A Virus Using Interpretable Regression Models. ACS Pharmacol. Transl. Sci. 2022, 6, 139-150.

• Tamura, S.; Jasial, S.; Miyao, T.; Funatsu, K. Interpretation of Ligand-Based Activity Cliff Prediction Models Using the Matched Molecular Pair Kernel. Molecules 2021, 39, 2000103.

• Miyao, T.; Jasial, S.; Bajorath, J.; Funatsu, K. Evaluation of Different Virtual Screening Strategies on the Basis of Compound Sets with Characteristic Core Distributions and Dissimilarity Relationships. J. Comput. Aided Mol. Des. 2019, 33, 729-743.

• Jasial, S.; Gilberg, E.; Blaschke, T.; Bajorath, J. Machine Learning Distinguishes with High Accuracy between Pan-Assay Interference Compounds That Are Promiscuous or Represent Dark Chemical Matter. J. Med. Chem. 2018, 61, 10255-10264.
• Vogt, M.; Jasial, S.; Bajorath, J. Extracting Compound Profiling Matrices from Screening Data. ACS Omega 2018, 3, 4706-4712.

• Jasial, S.; Bajorath, J. Dark Chemical Matter in Public Screening Assays and Derivation of Target Hypotheses. Med. Chem. Commun. 2017, 8, 2100–2104.
• Jasial, S.; Hu, Y.; Bajorath, J. How Frequently Are Pan-Assay Interference Compounds Active? Large-Scale Analysis of Screening Data Reveals Diverse Activity Profiles, Low Global Hit Frequency, and Many Consistently Inactive Compounds. J. Med. Chem. 2017, 60, 3879-3886.

• Jasial, S.; Hu, Y.; Vogt, M.; Bajorath, J. Activity-Relevant Similarity Values for Fingerprints and Implications for Similarity Searching. F1000Research 2016, 5 (Chem. Inf. Sci.): 591.
• Jasial, S.; Hu, Y.; Bajorath, J. Determining the Degree of Promiscuity of Extensively Assayed Compounds. PLoS One 2016, 11, e0153873.
• Jasial, S.; Hu, Y.; Bajorath, J. Assessing the Growth of Bioactive Compounds and Scaffolds over Time: Implications for Lead Discovery and Scaffold Hopping. J. Chem. Inf. Model. 2016, 56, 300-307.
• Jasial, S.; Balfer, J.; Vogt, M.; Bajorath, J. Determination of Meta-Parameters for Support Vector Machine Linear Combinations. Mol. Inf. 2015, 34, 127-133.

Google Scholar Profile: https://scholar.google.com/citations?user=EM_ZtG6p8LYC&hl=en_

• 2024 – Present Assistant Professor Center for Life Sciences Mahindra University.
• Specially Appointed Assistant Professor, Data-Driven Chemistry Laboratory,Data Science Center, Division of Materials Science, Nara Institute of Science and Technology (NAIST), Nara, Japan (2019-2024)

• The main theme of Swarit Jasial’s research is Computer-Aided Drug Design and Chemoinformatics. His work focuses on the application of informatics in chemistry, where data related to chemical compounds and approved drugs is utilized to study diseases and identify potential therapeutic candidates. He aims to develop computational techniques and predictive models that can analyze the activity of compounds against different biological targets, thereby assisting drug discovery programs through the identification of promising drug candidates for further validation.
• His research primarily involves data mining and machine learning using biological and chemical datasets. By applying machine learning algorithms, he studies how computers can recognize hidden structural patterns and molecular features responsible for the biological activity of compounds. He is particularly interested in understanding how algorithms learn from complex data and how machine learning models can be tailored to solve specific scientific problems. Therefore, his work emphasizes both the developmental aspects of computational models and their interpretability.
• His current research interests include the integration of knowledge from multiple domains for improved prediction and rationalization, the use of generative AI for de novo molecular design, and the identification of targets and pathways associated with natural products.

Bhaskar Paidimuddala obtained his M.Sc. in Biochemistry (Gold medalist) from Sri Venkateswara University, Tirupati. He qualified in various national level exams: ICMR-JRF, CSIR-UGC NET and GATE. With the support of ICMR fellowship, he did his Ph.D. in the Department of Biotechnology, Indian Institute of Technology Madras, Chennai. His Ph.D. work was focused on the Biochemical and Structural characterization of Xylose Reductase from a novel yeast, Debaryomyces nepalensis in the scope of development of enzyme-based bioprocess for the production of xylitol, a natural sugar substitute for the diabetic patients.

He did his first post doc (2018–2019) specialized in structural biology at Boston Children’s Hospital/ Harvard Medical School, Boston, USA, where he was well trained in negative electron microscopy and novel protein structure determination procedures. His second postdoc (2019–2023) specialized in Immunology was carried out at Oregon Health & Science University, Portland, USA. His research work on NAIP-NLRC4 Inflammasome that confers immunity against pathogenic bacterial infections revealed the unprecedented molecular mechanisms of inflammasome activation and bacterial flagellin induced immune response. During his postdoc, he acquired the skills in mammalian cell-based protein expression and purification, inflammasome related functional assays and cryo-electron microscopy.

He joined the Centre for Life Sciences at Mahindra University as an Assistant Professor in March 2024. His current research focuses on the elucidation of human inflammasome signalling pathways and functional roles of NLR family proteins using cellular, biochemical and structural approaches for the development of effective therapeutics to treat the inflammasome associated immune diseases and cancers.

• Ph.D. Biotechnology (Specialized in Biochemistry & Structural Biology), Indian Institute of Technology Madras, Chennai, India. (2012–2018)
• M.Sc. Biochemistry, Sri Venkateswara University, Tirupati, Andhra Pradesh, India. (2010–2012)
• B.Sc. Biotechnology, Sri Venkateswara University, Tirupati, Andhra Pradesh, India. (2007–2010)

• Paidimuddala, B., Cao, J. and Zhang, L. (2023) Structural basis for flagellin-induced NAIP5 activation. Science Advances, 9: eadi8539.
• Paidimuddala, B*., Cao, J*., Nash, G., Xie, Q., Wu, H. and Zhang, L. (2023) Mechanism of NAIP-NLRC4 inflammasome activation revealed by cryo-EM structure of unliganded NAIP5. Nature Structural & Molecular Biology, 30: 159–166. (*equal contribution)Nash, G., 
• Paidimuddala, B. and Zhang, L. (2022) Structural aspects of MHC expression control system. Biophysical Chemistry, 284: 106781.
• Paidimuddala, B., Mohapatra, S.B., Gummadi, S.N., and Manoj, N. (2018) Crystal structure of yeast xylose reductase in complex with a novel NADP-DTT adduct provides insights into substrate recognition and catalysis. The FEBS Journal, 285: 4445–4464.
• Paidimuddala, B., Aradhyam, G.K., and Gummadi, S.N. (2017) A halotolerant aldose reductase from Debaryomyces nepalensis: gene isolation, overexpression and biochemical characterization. RSC Advances, 7: 20384–20393.
• Paidimuddala, B., Rathod, A., and Gummadi, S.N. (2017) Inhibition of Debaryomyces nepalensis xylose reductase by lignocellulose derived by-products. Biochemical Engineering Journal, 121: 73–82.

• 2024- Present Assistant Professor Center for Life Sciences Mahindra University.
• Postdoctoral Scholar, Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, USA.
• Postdoctoral Research Fellow, Department of Biological Chemistry and Molecular Pharmacology, Program in Cellular and Molecular Medicine, Boston Children’s Hospital/ Harvard Medical School, Boston, MA, USA.

• Human immune system fights against infections and pathological conditions. It comprises a complex network of immune cells and proteins that specifically recognize pathogen associated and damage associated molecular patterns, and execute the immune responses. Among the immune proteins, the Nucleotide-binding domain and Leucine rich Repeat containing (NLR) family proteins are specialized in responding to microbial infections and metabolic distress, and establishing the innate immunity (a first line of defense) by forming inflammasomes (the large multiprotein complexes that mediate inflammation) as well as the T-cell mediated adaptive immunity by activating the expression of major histocompatibility (MHC) molecules. Thus, NLR proteins are crucial for conferring immunity and implicated in various autoimmune, genetic, gastrointestinal, neurodegenerative diseases and cancers. Our research aims at the following,
• Understanding the functional and regulatory mechanisms of NLR family proteins in conferring immunity.
• Developing the effective therapeutics for inflammasome associated diseases and cancers

Dr. Jayato Nayak, is a prominent researcher with more than 9 years of experience in the field of novel design and applications embracing the theme of process intensification. He completed his M.Tech & PhD from NIT Durgapur on “Process Intensification in Acetic acid manufacture from waste material” and collaborated his research with CSIR-CMERI. His core expertise includes Process Intensification, Bioprocess Engineering, water and wastewater treatment, graphene integrated photocatalyst development and bio-synthesis of value-added products. Currently, along with the national collaboration with IITs, NITs and CSIR Labs, he has extended research collaborations with research professionals in Poland, Brazil, Malaysia, Vietnam etc. Till August 2022, he has published 25 international SCI/SCOPUS indexed peer reviewed journal papers, more than 10 book chapters and filed 3 patents. As of now, with more than 400 Citations, he is having h-index of 10 and i10- index of 11. He is providing his expertise as Resource person for several Webinars and FDPs; and also as Senior Editor, Review Editor, Guest Editor, Editorial board member and recognized reviewer of more than 15 international journals. He has received 2 best research awards and 5 distinguished awards from various National and International organizations.

Vision of research is the propagation of advanced thoughts to make a better future. Involvement of students in academic and research activities will nurture their developing minds. Indulgence of aspiring minds in novel research, journal publications and patenting can foster the desire of students.

For teaching the vision is to offer a student-friendly interactive atmosphere through the conduction of mutual understanding which will prosper the growth of knowledge from scientific and engineering perspectives. With a vision of incandescent knowledge with proper technical interaction, enrichment of brain could be fostered. Building of a strong learned character will be always encouraged.

• Total citations: 401, h-index:10, i10 index: 11 (as on 08.08.2022); Cumulative Impact Factor: ~111;
• Google scholar: https://scholar.google.co.in/citations?user=EunZG5AAAAAJ&hl=en ;
• ORCID ID: https://orcid.org/0000-0001-7678-2019
• International Journal Paper Publications(SCI/SCIE/SCOPUS/WOSindexed):

Authored Text/Reference Books :

• Concise Perspectives of Intellectual Property Rights, 2020, LAP-Lambert Publication, Mauritius , ISBN: 978-620-0-58914-9
• Versatility in the world of Chemical Engineers: Principles of Chemical Engineering, 2020, LAP-Lambert Publication, Mauritius , ISBN: 978-620-2-51797-3
• An insight to Cracking and Refining of Petroleum: Petroleum refining and Petrochemicals, 2020, LAP-Lambert Publication, Mauritius , ISBN: 978-620-2-51974-8
• Climate change and its Impact. 2020, Krishna-Hitech Publishers, Chennai, India, ISBN: 978-93-89878-14-1

Authored Book Chapters :

• Application of Electrospun Polymeric Nanofibrous Membranes for Water Treatment, In: Industrial Wastewater Treatment Emerging Technologies for Sustainability, 2022, Elsevier, ISSN 1872-4663 (electronic) Water Science and Technology Library ISBN 978-3-030-98201-0 ISBN 978-3-030-98202-7 (eBook) https://doi.org/10.1007/978-3-030-98202-7
• Photo (Catalytic) Oxidation Processes for the Removal of Dye: Focusing on TiO2 Performance, In: Advanced Oxidation Processes in Dye-Containing Wastewater. Sustainable Textiles: Production, Processing, Manufacturing & Chemistry , May-2022, Springer, Singapore. ISBN: 978-981-19-0986-3

• Aerobic synthesis of value-added organic acid: Routes towards sustainable industrialization, in: Green Innovation, Sustainable Development, and Circular Economy, 1stEdition, 2020, CRC Press, Taylor & Francis, Florida, United States, ISBN 9780367441746
• Green Synthesis of Food Flavouring Agents, in: Green Innovation, Sustainable Development, and Circular Economy, 1stEdition, 2020, CRC Press, Taylor & Francis, Florida, United States, ISBN 9780367441746
• Metabolic products of mixed culture fermentation, PP: 75-92, in: Engineering of Microbial Biosynthetic Pathways. 1stEdition, 2020, Springer, New York, United States, Online ISBN 978-981-15-2604-6
• Bacterial Production of Organic Acids and Subsequent Metabolism, PP 153-173,in: Engineering of Microbial Biosynthetic Pathways. 1st Edition, 2020, Springer, New York, United States, Online ISBN 978-981-15-2604-6
• Nanomaterials for photocatalytic reduction of carbon dioxide, in: nanomaterials for CO2capture, storage, conversion and utilization, 1st Edition, 2020, Elsevier, New York, United States , ISBN: 9780128228944
• Clean Water Reclamation from Tannery Industry Wastewater in Membrane Integrated Green Approach, in: Integrated and Hybrid Process Technology for Water and Wastewater Treatment, 1stEdition, 2020, Elsevier, New York, United States , ISBN: 595806.
• Prediction of NOX Concentration in the Vicinity of Cement Industry Employing AERMOD Dispersion Modeling, pp 473-487, in: Clean Water Advances in Computational and Bio-Engineering, CBE 2019, 1stEdition, 2020, Volume 2, Springer, ISBN: 978-3-030-46942-9
• Recent trends of mixed biopolymers in food and its diverse applications, In: Recent Advances in Food Biotechnology, 1stEdition, 2020, Volume 1, SpringerNature, Malaysia.

International/National Conference Papers/Proceedings :

Online full paper publication in Conference Proceeding :

• A Green Process for Acetic Acid Production, ISBN 978-93-84468-30-9, 47-51, URL: org/images/extraimages/615045.pdf

• Existence of Cohesive Force Explains All Phenomena that are in Material Which Holds Strong Bond of All Forces of Attraction: A Case Study with Carbon Material, AIP Conference Proceedings 2087, 020015 (2019); https://doi.org/10.1063/1.5095231
• Development of integrated photo-catalyst adsorbent (IPCA) for simultaneous capture and conversion of CO2 tomethanol, AIP Conference Proceedings 2105, 020006 (2019); https://doi.org/10.1063/1.5100691

• (2022 – Present) Assistant Professor Center for Life Sciences Mahindra University

• Currently possessing several years of experience in Bioprocess Engineering, biofuel generation, photocatalysis, graphene based nanomaterial development, water and wastewater treatment by Membrane Technology, valuable product generation and polishing by Membrane Technology, performing different types of bio-sample analyses, development of novel membrane based process technologies, Membrane characterization, Sample Characterization, different types of membrane synthesis methods, development of mathematical models, Cost analysis, Statistical error analysis tools, Sustainability and process intensification analysis etc. Experienced in handling high end analytical and chromatographic instruments, pilot scale set-up, computer simulation languages and design and optimization softwares.
• For Further research, the vision leads towards the propagation of advanced thoughts to make a better world for the better future. The vision may include production of bio-based products from wastes, waste water reclamation, environmentally benign process and technologies, development of novel schemes and bench-scale set-up, waste-to-wealth transformation, development and usage of low temperature and low energy consuming processes, finding of sustainable solution out-performing the classical technologies and analysis of process intensification. Development of Research Laboratories (membrane technology and Photocatalyst) with GOI funds and further commercialization of the developed technologies will be main focus of R& D strategy.
• Collaborative research: National/International universities and research centres: Polish Academy of Sciences (Poland), University Kebangsaan Malaysia, Laboratory of Processes (Brazil), Institute for Tropical Technology (Vietnam Academy of Science and Technology), Hanyang University (Republic of Korea), Wroclaw University of Science and Technology (Poland), CSIR – NIIST, IIPE Vizag, IIT Khargpur, NIT Durgapur, CSIR-CMERI, Jadavpur University, Burdwan University, KIITs Bhubaneswar, Kalasalingam Academy of Research and Education etc.

Current research is getting continued on the following areas:

• Production of Bio-Methanol and its derivatives from CO2
• Production of Biodiesel
• Production of Bio molecules (food additives) from biomass
• Production of bio surfactants
• Treatment of wastewater/ Degradation of Pollutants (PAH/PAC)
• Development of Novel Membranes and modules