Ramneek Gupta
A5040730315- Acute Lymphoblastic Leukemia research
- Testicular diseases and treatments
- Cancer Genomics and Diagnostics
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Glycosylation and Glycoproteins Research
- Genomics and Phylogenetic Studies
- Diet and metabolism studies
- Metabolomics and Mass Spectrometry Studies
- Cancer Treatment and Pharmacology
- Childhood Cancer Survivors' Quality of Life
- Genetic Associations and Epidemiology
- Gut microbiota and health
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Liver Disease Diagnosis and Treatment
- Forensic and Genetic Research
- Pancreatitis Pathology and Treatment
- Colorectal Cancer Treatments and Studies
- RNA modifications and cancer
- Genomics and Rare Diseases
- Artificial Intelligence in Healthcare
- Machine Learning in Healthcare
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Cancer-related molecular mechanisms research
Novo Nordisk (United Kingdom)
2021-2025
Novo Nordisk (Finland)
2023-2024
Theodore Roosevelt High School
2024
University of Ulster
2024
Technical University of Denmark
2014-2023
University of Copenhagen
2015-2023
Novo Nordisk Foundation
2023
Madurai Kamaraj University
2020
Danmarks Nationalbank
2020
Epidemic Intelligence Service
2019
O-GalNAc-glycosylation is one of the main types glycosylation in mammalian cells. No consensus recognition sequence for O-glycosyltransferases known, making prediction methods necessary to bridge gap between large number known protein sequences and small proteins experimentally investigated with regard status. From O-GLYCBASE a total 86 vivo O-GalNAc sites were extracted. Mammalian homolog comparisons showed that glycosylated serine or threonine less likely be precisely conserved than...
We report here the genome sequence of an ancient human. Obtained from ∼4,000-year-old permafrost-preserved hair, represents a male individual first known culture to settle in Greenland. Sequenced average depth 20×, we recover 79% diploid genome, amount close practical limit current sequencing technologies. identify 353,151 high-confidence single-nucleotide polymorphisms (SNPs), which 6.8% have not been reported previously. estimate raw read contamination be no higher than 0.8%. use...
We present a thorough analysis of nuclear export signals and prediction server, which we have made publicly available. The machine learning method is significant improvement over the generally used consensus patterns. Nuclear (NESs) are extremely important regulators subcellular location proteins. This regulation has an impact on transcription other processes, fundamental to viability cell. NESs studied in relation cancer, cell cycle, differentiation aspects molecular biology. Our conclusion...
Whole-genome data indicate that early modern humans expanded into Australia 62,000 to 75,000 years ago.
Objective To investigate whether a whole grain diet alters the gut microbiome and insulin sensitivity, as well biomarkers of metabolic health functionality. Design 60 Danish adults at risk developing syndrome were included in randomised cross-over trial with two 8-week dietary intervention periods comprising refined diet, separated by washout period ≥6 weeks. The response to interventions on composition sensitivity measures glucose lipid metabolism, functionality, inflammatory markers,...
In recent years, studies on the human intestinal microbiota have attracted tremendous attention. Application of next generation sequencing for mapping bacterial phylogeny and function has opened new doors to this field research. However, little attention been given effects choice methodology output resulting from such studies. study we conducted a systematic comparison DNA extraction methods used by two major collaborative efforts: The European MetaHIT American Human Microbiome Project...
Abstract Building a population-specific catalogue of single nucleotide variants (SNVs), indels and structural (SVs) with frequencies, termed national pan-genome, is critical for further advancing clinical public health genetics in large cohorts. Here we report Danish pan-genome obtained from sequencing 10 trios to high depth (50 × ). We 536k novel SNVs 283k short mapping approaches develop population-wide de novo assembly approach identify 132k larger than nucleotides low false discovery...
Abstract Osteoarthritis (OA) is increasing in prevalence and has a severe impact on patients’ lives. However, our understanding of biomarkers driving OA risk remains limited. We developed model predicting the five-year diagnosis, integrating retrospective clinical, lifestyle biomarker data from UK Biobank (19,120 patients with OA, ROC-AUC: 0.72, 95%CI (0.71–0.73)). Higher age, BMI prescription non-steroidal anti-inflammatory drugs contributed most to increased prediction ahead diagnosis....
Abstract The biological process of RNA translation is fundamental to cellular life and has wide-ranging implications for human disease. Accurate delineation variation represents a significant challenge due the complexity technical limitations. Here, we introduce RiboTIE, transformer model-based approach designed enhance analysis ribosome profiling data. Unlike existing methods, RiboTIE leverages raw counts directly robustly detect translated open reading frames (ORFs) with high precision...
O-GLYCBASE is a database of glycoproteins with O-linked glycosylation sites. Entries at least one experimentally verified O-glycosylation site have been compiled from protein sequence databases and literature. Each entry contains information about the glycan involved, species, sequence, literature reference http-linked cross-references to other databases. Version 4.0 179 entries, an approximate 15% increase over last version. Sequence logos representing acceptor specificity patterns for...
The human genome project has led to the discovery of many protein coding genes which were previously unknown. As a large fraction these are functionally uncharacterized, it is interest develop methods for predicting their molecular function from sequence.We have developed method prediction subset classes Gene Ontology classification scheme. This includes several pharmaceutically interesting categories-transcription factors, receptors, ion channels, stress and immune response proteins,...
Hundreds of thousands human genomes are now being sequenced to characterize genetic variation and use this information augment association mapping studies complex disorders other phenotypic traits. Genetic is identified mainly by short reads the reference genome or performing local assembly. However, these approaches biased against discovery structural variants in more parts genome. Hence, large-scale de novo assembly needed. Here we show that it possible construct excellent assemblies from...
Adherence to a low-gluten diet has become increasingly common in parts of the general population. However, effects reducing gluten-rich food items including wheat, barley and rye cereals healthy adults are unclear. Here, we undertook randomised, controlled, cross-over trial involving 60 middle-aged Danish without known disorders with two 8-week interventions comparing (2 g gluten per day) high-gluten (18 day), separated by washout period at least six weeks habitual (12 day). We find that,...
Summary Root‐knot nematodes (RKNs, Meloidogyne incognita ) are economically important endoparasites with a wide host range. We used comprehensive transcriptomic approach to investigate the expression of both tomato and RKN genes in roots at five infection time intervals from susceptible plants two resistant plants, grown under soil conditions. Differentially expressed during (1827, tomato; 462, RKN) resistance (25, 160, interactions were identified. In responses, involved cell wall...
We applied digital gene expression profiling to determine the transcriptome of brown and white adipose tissues (BAT WAT, respectively) during cold exposure. Male C57BL/6J mice were exposed for 2 or 4 days. A notable induction genes related glucose uptake, glycolysis, glycogen metabolism, pentose phosphate pathway was observed in BAT from cold-exposed animals. In addition, glycerol-3-phosphate dehydrogenase 1 induced cold-challenged mice, suggesting increased synthesis glycerol glucose....