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Hire Dr. Raja K.

India

USD 20 /hr

Veterinarian | Postdoctoral Researcher | RNA Biology | Data Analysis | Bioinformatics | Scientific Editing & Visualizati

Profile Summary

Dr. Raja Khan was a postdoctoral researcher in Dr. Eric Greer’s laboratory at Washington University in St. Louis, where he led independent projects focused on RNA modifications and gene regulation in C. elegans and mouse models. His research career integrates molecular biology, biochemistry, genetics, and computational genomics to understand how RNA methylation influences aging, neuronal function, and disease. Dr. Khan’s scientific journey has been shaped by progressive training through his Master’s, Ph.D., and postdoctoral research, each stage strengthening his foundation in RNA biology, epigenetics, and functional genomics. His early training at GB Pant University under Dr. Mumtesh Saxena established a strong base in molecular cloning, gene expression, and protein purification through the mapping of the Salmonella outer membrane protein F (ompF). This formative experience, coupled with his natural curiosity and strong analytical aptitude, earned him a prestigious fellowship from India’s Department of Biotechnology to pursue a Ph.D. at the Indian Veterinary Research Institute (IVRI), where he investigated the interplay between host mRNA methylation and viral pathogenesis in Peste des petits ruminants virus (PPRV) infection. At IVRI, Dr. Khan employed a multi-omics approach combining m⁶A-seq, proteomics, and small RNA-seq to delineate the post-transcriptional regulatory landscape during infection. His doctoral work revealed that PPRV-induced reprogramming of host RNA methylation impacts immune responses and viral persistence, highlighting epitranscriptomic control as a key host–pathogen interface. After completing his Ph.D., Dr. Khan pursued postdoctoral research at Rutgers University, where he studied m⁶A RNA methylation in stem cell differentiation and neuroblastoma, examining how RNA modifications regulate DDX RNA-binding protein interactions. This experience broadened his understanding of RNA epigenetics in developmental and cancer contexts. Building on this foundation, he joined Boston Children’s Hospital and later Washington University in St. Louis to explore the roles of RNA modifications in aging and cognition. His first major postdoctoral project focused on ribosome heterogeneity and aging in C. elegans, where he confirmed the causal role of these methylation marks in lifespan regulation, thus revealing a novel RNA-based mechanism underlying aging. His second project at Washington University investigates the role of PCIF1, an m⁶Am RNA cap methyltransferase, in cognitive function and splicing regulation in mice. Dr. Khan’s findings uncover a novel regulatory axis where epitranscriptomic modifications shape neuronal gene expression and behavior, and he is currently co–first authoring a manuscript on this work. Dr. Khan’s technical expertise spans a broad range of molecular and computational methods. He is highly proficient in molecular cloning, RNA and protein purification, RNA immunoprecipitation, in vitro transcription and splicing assays, EMSA, qPCR, and flow cytometry. His extensive cell culture experience includes HeLa, Kelly neuroblastoma, and mouse embryonic stem cells, as well as primary PBMC cultures. In animal research, he manages multiple genetically engineered mouse models—maintaining knockout, conditional knockout, and floxed lines—and oversees all aspects of colony management including genotyping, breeding, and regulatory compliance. During a major laboratory relocation from Boston to St. Louis, he played a key role in reestablishing lab operations, managing IACUC and IBC protocols, procurement, and compliance documentation, showcasing strong leadership and organizational skills. On the computational front, Dr. Khan is an accomplished bioinformatician experienced in large-scale transcriptomic and epitranscriptomic analysis. He routinely employs tools such as HISAT2, STAR, featureCounts, DESeq2, and rMATS for differential gene expression and splicing analyses, complemented by visualization using ggplot2 in R. His work with MeRIP-seq and 2′-O-Me mapping pipelines involves tools like exomePeak, MACS2, and HOMER to identify and annotate methylated RNA regions. He is proficient in R, Python, and Bash, leveraging high-performance computing (HPC) clusters for workflow automation, data integration, and reproducibility. His analyses extend to public databases such as TCGA, GEO, and cBioPortal, and he frequently customizes open-source scripts for multi-omics integration. His code repositories are available on Google Drive, reflecting transparency and collaboration in scientific computing. Beyond his bench and computational work, Dr. Khan is an accomplished scientific writer and communicator. He has authored and co-authored multiple peer-reviewed publications, including first and corresponding author works on RNA methylation in cancer (PMID: 34118382), SARS-CoV-2’s impact on the male reproductive system (Hum Reprod, 2020), and tumor-specific apoptin strategies (PMID: 32671070). These publications demonstrate his ability to synthesize complex molecular mechanisms into clear, compelling scientific narratives. His scientific writing reflects intellectual independence, critical thinking, and the ability to connect fundamental discoveries to translational implications. Dr. Khan’s career vision is to establish himself as an independent academic researcher focused on elucidating the molecular mechanisms linking physiological and pathological transitions, with an emphasis on RNA modifications and gene regulation. He aims to integrate functional genomics, molecular biology, and bioinformatics approaches to explore how dynamic RNA methylation controls gene expression during aging, infection, and neurological function. His long-term goal is to contribute to translational science by uncovering RNA-based regulatory mechanisms that can inform therapeutic interventions for neurodegenerative and infectious diseases. His interdisciplinary training—from viral pathogenesis to RNA epigenetics and mammalian neurobiology—positions him uniquely to bridge molecular mechanisms with complex biological phenotypes. In summary, Dr. Raja Khan brings over a decade of multidisciplinary research experience encompassing RNA biology, epigenomics, molecular physiology, and computational analysis. His combination of rigorous experimental training, advanced data analytics, and leadership in collaborative research environments makes him exceptionally suited for roles in academic or translational research. His contributions have expanded our understanding of RNA modifications as dynamic regulators of cellular and behavioral processes, underscoring his potential to drive innovative research at the interface of molecular biology and systems genomics.

Subject Matter Expertise

• ☆ Animal Science
• ☆ Animal Biotechnology
• ☆ Molecular Biology
• ☆ Epigenetics
• ☆ RNA Sequencing
• ☆ Biotechnology & Bioengineering
• ☆ Animal Husbandry

Services

• Writing
• Data & AI

Writing Clinical Trial Documentation, Medical Writing, Non-Medical Regulatory Writing, Technical Writing

Data & AI Image Analysis, Data Visualization, Big Data Analytics, Text Mining & Analytics

Work Experience

PostdoctoralResearcher

Greer Lab, Washington University in St. Louis, USA

January 2023 - August 2025

PostdoctoralResearcher

Pirouz Lab, Rutgers University, New Jersey, USA

October 2021 - September 2023

PostdoctoralResearcher

Greer Lab, Boston Children’s Hospital, Harvard University, USA

September 2022 - January 2023

Education

PhD Animal Biotechnology (Division of Veterinary Biotechnology )

Indian Veterinary Research Institute

August 2016 - March 2021

Masters in Molecular Biology & Biotechnology (College of Basic Sciences And Humanities)

Govind Ballabh Pant University of Agriculture & Technology

July 2014 - August 2016

Bachelors in Veterinary Science & Animal Husbandry (Faculty of Veterinary Science & Animal Husbandry)

Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir

June 2009 - June 2014

Certifications

• NA

  NA

  January 2025 - January 2025

Publications

JOURNAL ARTICLE

Praharaj, M.R., Budamgunta, H., Ambati, T., Khan, R.I.N., Dey, B., Gandham, R.K., Sharma, G.T., Majumdar, S.S.(2024). Proteome modulation triggers potent antiviral response in Japanese Encephalitis Virus infected human macrophages . Archives of Microbiology. 206. (12).

Verma, H., Rawat, M., Verma, R., Gandham, R., Tiwari, A.K., Khan, R.I.N., Praharaj, M.R., Smith, E.(2023). First report of whole genome sequence of septicemic Pasteurella multocida serovar B:2 ‘Soron’ strain isolated from swine . Brazilian Journal of Microbiology. 54. (3). p. 2445-2460.

Khan, Raja Ishaq Nabi and Praharaj, Manas Ranjan and Malla, Waseem Akram and Hosamani, Neelima and Saxena, Shikha and Mishra, Bina and Rajak, Kaushal Kishor and Dhanavelu, Muthuchelvan and Mishra, BP and Sajjanar, Basavaraj and others(2022). Changes in m6A RNA methylation of goat lung following PPRV infection. bioRxiv. Cold Spring Harbor Laboratory

Pandey, Aruna and Malla, Waseem Akram and Sahu, Amit Ranjan and Wani, Sajad Ahmad and Khan, Raja Ishaq Nabi and Saxena, Shikha and Ramteke, PW and Praharaj, Manas Ranjan and Kumar, Amit and Rajak, Kaushal Kishor and others(2022). Differential expression of long non-coding RNAs under Peste des petits ruminants virus (PPRV) infection in goats. Virulence. 13. (1). p. 310--322. Taylor \& Francis

Pandey, A., Malla, W.A., Sahu, A.R., Wani, S.A., Khan, R.I.N., Saxena, S., Ramteke, P.W., Praharaj, M.R., Kumar, A., Rajak, K.K., et al.(2022). Differential expression of long non-coding RNAs under Peste des petits ruminants virus (PPRV) infection in goats . Virulence. 13. (1). p. 310-322.

Praharaj, MR and Garg, P and Kesarwani, V and Topno, NA and Khan, RIN and Sharma, S and Panigrahi, M and Mishra, BP and Mishra, B and Kumar, GS and others(2022). SARS-CoV-2 Spike Glycoprotein and ACE2 Interaction Reveals Modulation of Viral Entry in Wild and Domestic Animals. Front. Med. 8: 775572. doi: 10.3389/fmed.

Praharaj, M.R., Garg, P., Kesarwani, V., Topno, N.A., Khan, R.I.N., Sharma, S., Panigrahi, M., Mishra, B.P., Mishra, B., Kumar, G.S., et al.(2022). SARS-CoV-2 Spike Glycoprotein and ACE2 Interaction Reveals Modulation of Viral Entry in Wild and Domestic Animals . Frontiers in Medicine. 8.

Sonowal, J., Patel, C.L., Gandham, R.K., Khan, R.I.N., Praharaj, M.R., Malla, W.A., Dev, K., Barkathullah, N., Bharali, K., Dubey, A., et al.(2022). Temporal dysregulation of genes in lamb testis cell during sheeppox virus infection . Letters in Applied Microbiology. 75. (6). p. 1628-1638.

Sonowal, Joyshikh and Patel, Chhabi Lal and Gandham, Ravi Kumar and Sajjanar, Basavaraj and Khan, Raja Ishaq Nabi and Praharaj, Manas Ranjan and Malla, Waseem Akram and Kumar, Deepak and Dev, Kapil and Barkathullah, N and others(2021). Genome-wide expression analysis reveal host genes involved in immediate-early infections of different sheeppox virus strains. Gene. 801. p. 145850. Elsevier

Wani, Sajad Ahmad and Sahu, Amit Ranjan and Khan, Raja Ishaq Nabi and Praharaj, Manas Ranjan and Saxena, Shikha and Rajak, Kaushal Kishor and Muthuchelvan, Dhanavelu and Sahoo, Aditya and Mishra, Bina and Singh, RK and others(2021). Proteome Modulation in Peripheral Blood Mononuclear Cells of Peste des Petits Ruminants Vaccinated Goats and Sheep. Frontiers in veterinary science. 8. Frontiers Media SA

Wani, S.A., Sahu, A.R., Khan, R.I.N., Praharaj, M.R., Saxena, S., Rajak, K.K., Muthuchelvan, D., Sahoo, A., Mishra, B., Singh, R.K., et al.(2021). Proteome Modulation in Peripheral Blood Mononuclear Cells of Peste des Petits Ruminants Vaccinated Goats and Sheep . Frontiers in Veterinary Science. 8.

Wani, Sajad Ahmad and Praharaj, Manas Ranjan and Sahu, Amit R and Khan, Raja Ishaq Nabi and Saxena, Shikha and Rajak, Kaushal Kishor and Muthuchelvan, Dhanavelu and Sahoo, Aditya and Mishra, Bina and Singh, Raj Kumar and others(2021). Systems Biology behind immunoprotection of both Sheep and Goats after Sungri/96 PPRV vaccination. Msystems. 6. (2). p. e00820--20. American Society for Microbiology 1752 N St., NW, Washington, DC

Khan, Raja Ishaq Nabi and Sahu, Amit Ranjan and Malla, Waseem Akram and Praharaj, Manas Ranjan and Hosamani, Neelima and Kumar, Shakti and Gupta, Smita and Sharma, Shweta and Saxena, Archana and Varshney, Anshul and others(2021). Systems Biology under heat stress in Indian Cattle. Gene. 805. p. 145908. Elsevier

Wani, S.A., Praharaj, M.R., Sahu, A.R., Khan, R.I.N., Saxena, S., Rajak, K.K., Muthuchelvan, D., Sahoo, A., Mishra, B., Singh, R.K., et al.(2021). Systems biology behind immunoprotection of both sheep and goats after Sungri/96 PPRV Vaccination . Msystems. 6. (2).

Khan, R.I.N., Sahu, A.R., Malla, W.A., Praharaj, M.R., Hosamani, N., Kumar, S., Gupta, S., Sharma, S., Saxena, A., Varshney, A., et al.(2021). Systems biology under heat stress in Indian cattle . Gene. 805.

Khan, Raja Ishaq Nabi and Malla, Waseem Akram(2021). m6A modification of RNA and its role in cancer, with a special focus on lung cancer. Genomics. 113. (4). p. 2860--2869. Academic Press

Khan, R.I.N., Malla, W.A.(2021). m6A modification of RNA and its role in cancer, with a special focus on lung cancer . Genomics. 113. (4). p. 2860-2869.

Raja Khan, Sameera Farah, Ashwin Atkulwar, Manas Ranjan Praharaj, Ravikumar Gandham, Mumtaz Baig (2020). Phylogenomics and Phylodynamics of SARS-CoV-2 Genomes Retrieved From India . Future Virology.

Irshad Ahmad Para, Parvez Ahmad Dar, Bilal Ahmad Malla, Meeti Punetha, Ankita Rautela, Ishfaq Maqbool, Aquil Mohd, Mudasir Ahmad Shah, Zahoor Ahmad War, Raja Ishaaq, et al.(2020). Impact of heat stress on the reproduction of farm animals and strategies to ameliorate it . Biological Rhythm Research. p. 1--17. Informa {UK} Limited

Malla, W.A., Arora, R., Khan, R.I.N., Mahajan, S., Tiwari, A.K.(2020). Apoptin as a Tumor-Specific Therapeutic Agent: Current Perspective on Mechanism of Action and Delivery Systems . Frontiers in Cell and Developmental Biology. 8.

Malla, Waseem Akram and Arora, Richa and Khan, Raja Ishaq Nabi and Mahajan, Sonalika and Tiwari, Ashok Kumar(2020). Apoptin as a tumor-specific therapeutic agent: current perspective on mechanism of action and delivery systems. Frontiers in cell and developmental biology. 8. p. 524. Frontiers

Khan, Raja Ishaq Nabi and Malla, Waseem Akram(2020). Does SARS-CoV-2 have influence on male reproductive system?. Human Reproduction. 35. (11). p. 2626--2627. Oxford University Press

Khan, R.I.N., Malla, W.A.(2020). Does SARS-CoV-2 have influence on male reproductive system? . Human Reproduction. 35. (11). p. 2626-2627.

Pandey, A., Saxena, S., Khan, R.I., Gandham, R.K., Ramteke, P.W.(2020). Expression profiling of host long non-coding RNAs under ORF virus infection . Indian Journal of Animal Sciences. 90. (3). p. 13-17.

Ahmad Para, Irshad and Ahmad Dar, Parvez and Ahmad Malla, Bilal and Punetha, Meeti and Rautela, Ankita and Maqbool, Ishfaq and Mohd, Aquil and Ahmad Shah, Mudasir and Ahmad War, Zahoor and Ishaaq, Raja and others(2020). Impact of heat stress on the reproduction of farm animals and strategies to ameliorate it. Biological Rhythm Research. 51. (4). p. 616--632. Taylor \& Francis

Farah, Sameera and Atkulwar, Ashwin and Praharaj, Manas Ranjan and Khan, Raja and Gandham, Ravikumar and Baig, Mumtaz(2020). Phylogenomics and phylodynamics of SARS-CoV-2 genomes retrieved from India. Future Virology. 15. (11). p. 747--753. Future Medicine Ltd London, UK

Pandey, Aruna and Saxena, Shikha and Khan, Raja Ishaq Nabi and Ramteke, Pramod W(2019). Computational pipeline for the annotation of long non-coding RNAs in a newly assembled genome.

Wani, Sajad Ahmad and Sahu, Amit Ranjan and Khan, Raja Ishaq Nabi and Pandey, Aruna and Saxena, Shikha and Hosamani, Neelima and Malla, Waseem Akram and Chaudhary, Dheeraj and Kanchan, Sonam and Sah, Vaishali and others(2019). Contrasting gene expression profiles of monocytes and lymphocytes from peste-des-petits-ruminants virus infected goats. Frontiers in immunology. p. 1463. Frontiers

Wani, S.A., Sahu, A.R., Khan, R.I.N., Pandey, A., Saxena, S., Hosamani, N., Malla, W.A., Chaudhary, D., Kanchan, S., Sah, V., et al.(2019). Contrasting gene expression profiles of monocytes and lymphocytes from peste-des-petits-ruminants virus infected goats . Frontiers in Immunology. 10. (JULY).

Khanduri, Alok and Sahu, Amit Ranjan and Wani, Sajad Ahmad and Khan, Raja Ishaq Nabi and Pandey, Aruna and Saxena, Shikha and Malla, Waseem Akram and Mondal, Piyali and Rajak, Kaushal Kishor and Muthuchelvan, D and others(2018). Dysregulated miRNAome and proteome of PPRV infected goat PBMCs reveal a coordinated immune response. Frontiers in immunology. p. 2631. Frontiers

Khanduri, A., Sahu, A.R., Wani, S.A., Khan, R.I.N., Pandey, A., Saxena, S., Malla, W.A., Mondal, P., Rajak, K.K., Muthuchelvan, D., et al.(2018). Dysregulated miRNAome and proteome of PPRV infected goat PBMCs reveal a coordinated immune response . Frontiers in Immunology. 9. (NOV).

Ganaie, MY and Qureshi, S and Kashoo, Z and Wani, SA and Hussain, MI and Kumar, R and Maqbool, R and Sikander, P and Banday, MS and Malla, WA and others(2018). Isolation and characterization of two lytic bacteriophages against Staphylococcus aureus from India: newer therapeutic agents against Bovine mastitis. Veterinary research communications. 42. (4). p. 289--295. Springer Netherlands

Ganaie, M.Y., Qureshi, S., Kashoo, Z., Wani, S.A., Hussain, M.I., Kumar, R., Maqbool, R., Sikander, P., Banday, M.S., Malla, W.A., et al.(2018). Isolation and characterization of two lytic bacteriophages against Staphylococcus aureus from India: newer therapeutic agents against Bovine mastitis . Veterinary Research Communications. 42. (4). p. 289-295.

Sahu, Amit Ranjan and Wani, Sajad Ahmad and Saxena, Shikha and Rajak, Kaushal Kishor and Chaudhary, Dheeraj and Sahoo, Aditya Prasad and Khanduri, Alok and Pandey, Aruna and Mondal, Piyali and Malla, Waseem Akram and others(2018). Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection. Scientific reports. 8. (1). p. 1--11. Nature Publishing Group

Sahu, A.R., Wani, S.A., Saxena, S., Rajak, K.K., Chaudhary, D., Sahoo, A.P., Khanduri, A., Pandey, A., Mondal, P., Malla, W.A., et al.(2018). Selection and validation of suitable reference genes for qPCR gene expression analysis in goats and sheep under Peste des petits ruminants virus (PPRV), lineage IV infection . Scientific Reports. 8. (1).

OTHER

Khan, R.I.N., Praharaj, M.R., Malla, W.A., Hosamani, N., Saxena, S., Rajak, K.K., Dhanavelu, M., Tiwari, A.K., Mishra, B.P., Sajjanar, B., et al.(2022). Changes in m6A RNA methylation of goat lung following PPRV infection . Biorxiv.

Wani, S.A., Praharaj, M.R., Sahu, A.R., Khan, R.I.N., Rajak, K.K., Muthuchelvan, D., Sahoo, A., Mishra, B., Singh, R.K., Mishra, B.P., et al.(2020). Systems biology behind immunoprotection of both sheep and goats after sungri/96 PPRV vaccination . Biorxiv.

Khan, R.I.N., Sahu, A.R., Malla, W.A., Praharaj, M.R., Hosamani, N., Kumar, S., Gupta, S., Sharma, S., Saxena, A., Varshney, A., et al.(2020). Transcriptome profiling in Indian Cattle revealed novel insights into response to heat stress . Biorxiv.