Sharmili Roy

All Publications

• Single-cell multi-gene identification of somatic mutations and gene rearrangements in cancer. NAR cancer Grimes, S. M., Kim, H. S., Roy, S., Sathe, A., Ayala, C. I., Bai, X., Almeda-Notestine, A. F., Haebe, S., Shree, T., Levy, R., Lau, B. T., Ji, H. P. 2023; 5 (3): zcad034

  Abstract

  In this proof-of-concept study, we developed a single-cell method that provides genotypes of somatic alterations found in coding regions of messenger RNAs and integrates these transcript-based variants with their matching cell transcriptomes. We used nanopore adaptive sampling on single-cell complementary DNA libraries to validate coding variants in target gene transcripts, and short-read sequencing to characterize cell types harboring the mutations. CRISPR edits for 16 targets were identified using a cancer cell line, and known variants in the cell line were validated using a 352-gene panel. Variants in primary cancer samples were validated using target gene panels ranging from 161 to 529 genes. A gene rearrangement was also identified in one patient, with the rearrangement occurring in two distinct tumor sites.

  View details for DOI 10.1093/narcan/zcad034

  View details for PubMedID 37435532

  View details for PubMedCentralID PMC10331933

• Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing. Scientific reports Lau, B., Chandak, S., Roy, S., Tatwawadi, K., Wootters, M., Weissman, T., Ji, H. P. 2023; 13 (1): 8514

  Abstract

  The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, basecalling errors, and limitations with scaling up read operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. By conjugating synthesized DNA to magnetic agarose beads, we enabled repeated data readouts while preserving the original DNA analyte and maintaining data readout quality. MDRAM utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.

  View details for DOI 10.1038/s41598-023-29575-z

  View details for PubMedID 37231057

• A critical review on prospects of bio-refinery products from second and third generation biomasses CHEMICAL ENGINEERING JOURNAL Goswami, L., Kayalvizhi, R., Dikshit, P., Sherpa, K., Roy, S., Kushwaha, A., Kim, B., Banerjee, R., Jacob, S., Rajak, R. 2022; 448

  View details for DOI 10.1016/j.cej.2022.137677

  View details for Web of Science ID 000830813800001

• Novel coronavirus (COVID-19) in environmental engineering perspective. Environmental science and pollution research international Dehghani, M. H., Roy, S., Karri, R. R. 1800

  View details for DOI 10.1007/s11356-022-18572-w

  View details for PubMedID 35022982

• Recent nanobiotechnological advancements in lignocellulosic biomass valorization: A review. Journal of environmental management Roy, S., Dikshit, P. K., Sherpa, K. C., Singh, A., Jacob, S., Chandra Rajak, R. 2021; 297: 113422

  Abstract

  Increase in human population, rapid industrialization, excessive utilization of fossil fuel utilization and anthropogenic activities have caused serious threats to the environment in terms of greenhouse gas emissions (GHGs), global warming, air pollution, acid rain, etc. This destruction in sustainability can be averted by a paradigm shift in the fuel production from fossil resources to bioenergy. Amongst different forms of bioenergy, lignocellulosic biomass can be utilized as an attractive substrate for the production of several high-value products owing to its renewability, easy availability, and abundance. Additionally, utilization of these waste biomasses reduces the environmental hazards associated with its disposal. Impedance of lignin and crystalline nature of cellulose pose major bottlenecks in biomass based energy. Though, several physio-chemicals processes are recommended as mitigation route but none of them seems to be promising for large scale application. In recent years, a right fusion of biological treatment combined with nanotechnology for efficient pretreatment and subsequent hydrolysis of biomass by ubiquitous enzymes seems to be promising alternative. In addition, to overcome these difficulties, nanotechnology-based methods have been recently adopted in catalytic valorization of lignocellulosic biomass. The present review has critically discussed the application of nano-biotechnology in lignocellulosic biomass valorization in terms of pretreatment and hydrolysis. A detailed discussion on the application of various nanoparticles in these processes, enzyme immobilization and end-production utilization is presented in this review. Finally, the review emphasizes the major challenges of this process along with different routes and recommendations to address the issues.

  View details for DOI 10.1016/j.jenvman.2021.113422

  View details for PubMedID 34351298

• COVID-19 transmission, vulnerability, persistence and nanotherapy: a review. Environmental chemistry letters Khan, A. H., Tirth, V., Fawzy, M., Mahmoud, A. E., Khan, N. A., Ahmed, S., Ali, S. S., Akram, M., Hameed, L., Islam, S., Das, G., Roy, S., Dehghani, M. H. 2021: 1–15

  Abstract

  End 2019,the zoonotic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), named COVID-19 for coronavirus disease 2019, is the third adaptation of a contagious virus following the severe acute respiratory syndrome coronavirus in 2002, SARS-CoV, and the Middle East respiratory syndrome virus in 2012, MERS-CoV. COVID-19 is highly infectious and virulent compared to previous outbreaks. We review sources, contagious routes, preventive measures, pandemic, outbreak, epidemiology of SARS-CoV, MERS-CoV and SARS-CoV-2 from 2002 to 2020 using a Medline search. We discuss the chronology of the three coronaviruses, the vulnerability of healthcare workers, coronaviruses on surface and in wastewater, diagnostics and cures, and measures to prevent spreading.

  View details for DOI 10.1007/s10311-021-01229-4

  View details for PubMedID 33846683

• Immunotherapeutics for Covid-19 and post vaccination surveillance. 3 Biotech Sampath Kumar, N. S., Chintagunta, A. D., Jeevan Kumar, S. P., Roy, S., Kumar, M. 2020; 10 (12): 527

  Abstract

  Severe acute respiratory syndrome coronavirus (SARS-CoV-2) has emerged as a pandemic and named as novel coronavirus disease (nCOVID-19). SARS-CoV-2 is different from other known viruses due to multiple mutations on the sites of nonstructural proteins (NSP) 2 and 3, and the varying nature of virulence between different persons. Immunotherapies such as vaccines and monoclonal antibodies have a protective effect on the patients bringing them to the front of the line of potential treatments. The present review intends to cover the development of 20 different vaccine candidates categorized under live attenuated vaccines, inactivated vaccines, subunit vaccines, viral vector-based vaccines, and nucleic acid vaccines. Formulation of these vaccine candidates by various companies in collaboration with global organizations and their status of clinical trials were addressed. On the other hand, various approaches for post-vaccination surveillance using nucleic acid and protein biomarkers imbued on suitable platforms were also highlighted to sum up the immune therapeutics for Covid-19.

  View details for DOI 10.1007/s13205-020-02522-9

  View details for PubMedID 33200061

• Diverse Molecular Techniques for Early Diagnosis of COVID-19 and Other Coronaviruses Diagnostic Strategies for COVID-19 and other Coronaviruses Roy, S., et al Springer . 2020: 135–159

  View details for DOI https://doi.org/10.1007/978-981-15-6006-4_7

• Diagnostic Strategies for COVID-19 and other Coronaviruses Medical Virology: From Pathogenesis to Disease Control edited by Roy, S., et al Springer . 2020

  View details for DOI 10.1007/978-981-15-6006-4

• Insights into Novel Coronavirus and COVID-19 Outbreak Diagnostic Strategies for COVID-19 and other Coronaviruses Roy, S. Springer . 2020: 1–17

  View details for DOI https://doi.org/10.1007/978-981-15-6006-4_1