A5070935191- Cancer Genomics and Diagnostics
- Molecular Biology Techniques and Applications
- Antifungal resistance and susceptibility
- Cancer Cells and Metastasis
- Single-cell and spatial transcriptomics
- Microbial Natural Products and Biosynthesis
- Mycotoxins in Agriculture and Food
- Genomics and Phylogenetic Studies
- Genetics, Bioinformatics, and Biomedical Research
- Lung Cancer Treatments and Mutations
- Fungal Biology and Applications
- Infectious Diseases and Mycology
- Cancer-related molecular mechanisms research
- Gene expression and cancer classification
- Cancer Treatment and Pharmacology
- Chromosomal and Genetic Variations
- Gut microbiota and health
- Genetic factors in colorectal cancer
- Fungal Infections and Studies
- Plant Pathogens and Fungal Diseases
- Sirtuins and Resveratrol in Medicine
- Lung Cancer Diagnosis and Treatment
- IL-33, ST2, and ILC Pathways
- Fungal and yeast genetics research
- Child Nutrition and Feeding Issues
Harvard University
2020-2025
AstraZeneca (United States)
2024-2025
Boston Children's Hospital
2020-2022
Prince of Songkla University
2021
University of Utah
2016-2020
Harvard Stem Cell Institute
2020
Office of Infectious Diseases
2017
Indian Agricultural Research Institute
2009-2016
Jamia Millia Islamia
2009-2014
Northern Illinois University
2014
Abstract Background When interpreting sequencing data from multiple spatial or longitudinal biopsies, detecting sample mix-ups is essential, yet more difficult than in studies of germline variation. In most genomic tumors, genetic variation detected through pairwise comparisons the tumor and a matched normal tissue donor. many cases, only somatic variants are reported, which hinders use existing tools that detect swaps solely based on genotypes inherited variants. To address this problem, we...
8005 Background: Osimertinib (osi) is a third-generation, central nervous system-active EGFR-TKI, that potently and selectively inhibits EGFR-TKI sensitizing EGFR T790M resistance mutations. Adj osi (3 years [yrs]) recommended for resected EGFRm stage IB–IIIA NSCLC, based on significant improvements in disease-free survival (DFS) overall (OS) the Phase III ADAURA study (NCT02511106). A trend towards an increased DFS event rate beyond 3 yrs suggests some pts may benefit from longer adj...
Circulating tumor-derived cell-free DNA (ctDNA) enables non-invasive diagnosis, monitoring, and treatment susceptibility testing in human cancers. However, accurate detection of variant alleles, particularly during untargeted searches, remains a principal obstacle to widespread application clinical oncology. In this study, isolation short fragments is shown enrich for tumor variants improve correction PCR- sequencing-associated errors. Subfractions the mononucleosome circulating (ccfDNA)...
Abstract Background In FLAURA2, 1L osi with addition of platinum-pemetrexed chemotherapy (osi + CTx) significantly improved PFS vs alone in pts EGFRm advanced NSCLC. Prior FLAURA analyses showed detected BL plasma to be prognostic and early clearance correlated outcomes. We explored correlation detection, its clearance, FLAURA2 determine potential identify who derive particular benefit from CTx. Methods Treatment-naïve (Ex19del or L858R) NSCLC were randomized CTx 80 mg once daily [QD]...
Vertebrate embryogenesis requires the precisely timed specification of 3 germ cell layers- ectoderm, mesoderm, and endoderm- which give rise to tissues organs in developing organism. The tumor suppressor gene NF2, moesin-ezrin-radixin like (MERLIN) (Nf2) is expressed all layers during mouse development its homozygous deletion causes embryonic lethality. People with heterozygous NF2 mutations typically develop Schwann tumors, especially vestibular schwannoma, but specific role human unclear....
Abstract Cancers display cellular, genetic and epigenetic heterogeneity, complicating disease modeling. Multiple cell states defined by gene expression have been described in lung adenocarcinoma (LUAD). However, the functional contributions of state regulatory programs that control chromatin early stages tumor initiation are not well understood. Using single-cell RNA ATAC sequencing Kras/p53-driven organoids, we identified two major cellular states: one more closely resembling alveolar type...
Osimertinib—a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor—is recommended as adjuvant therapy for resected stage IB–IIIA receptor-mutated non-small-cell lung cancer, based on significant disease-free survival (DFS) and overall improvement shown in the previously reported phase 3 ADAURA trial. A trend toward an increased DFS event rate after completion of years treatment suggests that some patients may benefit from longer osimertinib treatment. We therefore...
Perivascular fibrosis, characterized by increased amount of connective tissue around vessels, is a hallmark for vascular disease. Ang II (angiotensin II) contributes to disease and end-organ damage via promoting T-cell activation. Despite recent data suggesting the role T cells in progression perivascular underlying mechanisms are poorly understood.
Coriandrum sativum (Coriander) or Chinese parsley is a culinary herb with multiple medicinal effects, which widely used in cooking and traditional medicine. It enriched essential oils anti-oxidant compounds unknown significance. To explore the untapped reservoir of Coriander, we studied transcriptome metabolic profiles from three developmental stages. Here, identified 10 tyrosine pathway-related genes (TMPRGs), six porphyrins chlorophyll (PCMPRGs), five Vitamin E (VEMPRGs). These were...
Abstract Multiple sclerosis (MS) is an autoimmune disease characterized by multiple lesions in the brain and spinal cord. We used RNA sequencing to identify microbial sequences characterize human gene expression patterns 30 biopsy specimens. RNAs which aligned known taxa, were significantly enriched 10 of 12 primary demyelination specimens compared a group 15 epilepsy controls, leading list 29 MS candidate genera from 11 different phyla. Most microbes are anaerobic bacteria. While there some...
Polyketide synthases (PKSs) of Aspergillus species are multidomain and multifunctional megaenzymes that play an important role in the synthesis diverse polyketide compounds. Putative PKS protein sequences from representing medically, agriculturally, industrially were chosen screened for silico studies. Six candidate species, fumigatus Af293, flavus NRRL3357, niger CBS 513.88, terreus NIH2624, oryzae RIB40, clavatus NRRL1, selected to study phylogeny. Full-length proteins only ketosynthase...
It has been suggested that Human endogenous retroviruses (HERVs) are associated with multiple sclerosis (MS) pathogenesis. The objective of this study was to broadly evaluate the expression HERV core (GAG) and envelope (ENV) genes in diseased brain white matter samples from MS patients compared normal controls.
Challenges with distinguishing circulating tumor DNA (ctDNA) from next-generation sequencing (NGS) artifacts limits variant searches to established solid mutations. Here we show early and random PCR errors are a principal source of NGS noise that persist despite duplex molecular barcoding, removal due clonal hematopoiesis indeterminate potential, suppression patterned errors. We also demonstrate sample duplicates necessary eliminate the stochastic associated NGS. Integration into analytics...
Our group has used deep sequencing to identify viral RNA signatures in human brain specimens. We have previously this method detect HSV1, GBV-C, and measles virus sequence tissue from deceased donors. Deep was performed on specimens a cohort of patients who died with progressive forms MS, revealing evidence increased expression some endogenous retrovirus (HERV) domains.Identify sequences new antigens involved the pathogenesis MS.Deep extracted 12 2 neuromyelitis optica (MS/NMO =...
Alveolar type 2 (AT2) cells, the epithelial progenitor cells of distal lung, are known to be prominent cell origin for lung adenocarcinoma. The regulatory programs that control chromatin and gene expression in AT2 during early stages tumor initiation not well understood. Here, we dissected response Kras activation p53 loss (KP) using combined single RNA ATAC sequencing an established organoid system. Multi-omic analysis showed KP exhibit two major cellular states: one more closely resembling...