A5103163072- Advanced biosensing and bioanalysis techniques
- DNA and Nucleic Acid Chemistry
- RNA Interference and Gene Delivery
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Click Chemistry and Applications
- T-cell and B-cell Immunology
- Genetics, Bioinformatics, and Biomedical Research
- Cancer Genomics and Diagnostics
- Genomics and Phylogenetic Studies
- Metabolomics and Mass Spectrometry Studies
- Cell Image Analysis Techniques
- Immune Cell Function and Interaction
- Plant Virus Research Studies
- Gene expression and cancer classification
- Advanced Proteomics Techniques and Applications
- Diabetes and associated disorders
- Hemoglobin structure and function
- Machine Learning in Bioinformatics
- vaccines and immunoinformatics approaches
- Plant Molecular Biology Research
- Advanced Control Systems Design
- Cytokine Signaling Pathways and Interactions
Broad Institute
2022-2025
University of Oslo
2022-2024
Aarhus University
2016-2023
Binghamton University
2020-2023
Indian Institute of Technology Bombay
2017-2021
RIKEN Center for Biosystems Dynamics Research
2019-2020
Danish National Research Foundation
2016
Indian Institute of Technology Madras
2013-2014
National Research Foundation
2014
University of California, Los Angeles
1991-2001
JASPAR (https://jaspar.elixir.no/) is a widely-used open-access database presenting manually curated high-quality and non-redundant DNA-binding profiles for transcription factors (TFs) across taxa. In this 10th release 20th-anniversary update, the CORE collection has expanded with 329 new profiles. We updated three existing provided orthogonal support 72 from previous release's UNVALIDATED collection. Altogether, 2024 update provides 20% increase in release. A trimming algorithm enhanced by...
Abstract Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding how complex tissues are constructed 1–6 . However, missing from these measurements is ability to routinely easily spatially localize profiled cells. We developed a strategy, Slide-tags, in which single nuclei an intact tissue section tagged with spatial barcode oligonucleotides derived DNA-barcoded beads...
Blood plasma is one of the most widely used samples for cancer biomarker discovery research as well clinical investigations diagnostic and therapeutic purposes. However, proteome extremely complex due to its wide dynamic range protein concentrations presence high-abundance proteins. Here we have described an optimized integrated quantitative proteomics pipeline combining label-free multiplexed-labeling-based (Isobaric tags relative absolute quantitation) profiling methods discovery, followed...
Abstract Recent technological innovations have enabled the high-throughput quantification of gene expression and epigenetic regulation within individual cells, transforming our understanding how complex tissues are constructed. Missing from these measurements, however, is ability to routinely easily spatially localise profiled cells. We developed a strategy, Slide-tags, in which single nuclei an intact tissue section ‘tagged’ with spatial barcode oligonucleotides derived DNA-barcoded beads...
Tubulin is an essential protein involved in microtubule dynamics that regulate mitotic cell division normal cells. Specifically, the colchicine-binding site of tubulin serves as a therapeutic target to disrupt dynamics, inducing arrest and leading death. In current study, we synthesized methoxy fluorine substituted novel chalcones (4a-o) chalcone compounds showed promising anticancer activity by vitro viability using MTT assay lung cancer (A549) breast (MCF-7) lines silico docking...
RNA folding is driven by the formation of double-helical segments interspaced loops unpaired nucleotides. Among latter, bulges formed one or several nucleotides are most common structural motifs that play an important role in stabilizing RNA–RNA, RNA–protein, and RNA–small molecule interactions. Single-nucleotide can fold alternative structures where nucleobase either looped-out (flexible) a solvent stacked-in (intercalated) between base pairs. In present study, we discovered triplex-forming...
A novel nucleic acid analogue called acyclic (S)-butyl (BuNA) composed of an backbone containing a phosphodiester linkage and bearing natural nucleobases was synthesized. Next, (S)-BuNA nucleotides were incorporated in DNA strands their effect on duplex stability changes structural conformation investigated. Circular dichroism (CD), UV-melting non-denatured gel electrophoresis (native PAGE) studies revealed that is capable making duplexes with its complementary integration into does not...
Abstract DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, computational tool for fast, stochastic modeling of molecular contacts from capable simulating realistic contact patterns wide in few minutes. MoDLE accurately simulates maps concordance with existing dynamics approaches Micro-C data does so orders magnitude faster than approaches. runs efficiently on machines ranging laptops to high performance computing clusters opens up...
DNA vaccination has been used to generate effective cellular as well humoral immunity against target antigens. Here we have investigated the induction and involvement of regulatory T cell (Treg) responses in mediating prevention experimental autoimmune encephalomyelitis (EAE), following with plasmid encoding TCR Vβ8.2 chain predominantly displayed on disease-causing lymphocytes. Vaccination wild-type results priming type 1 CD4 Treg skewing global response myelin basic protein a Th2...
Recent experiments have shown that during the course of chronic experimental allergic encephalomyelitis, there is a shift in determinant hierarchy away from dominant to other subdominant and cryptic self determinants. It was therefore interest define pattern dominance for mouse myelin basic protein three commonly used encephalomyelitis model strains mice, i.e., B10.PL, SJL/J, (SJL x B10.PL)F1. Our studies indicate many determinants are demonstrable, which only activate T cells on injection...
Novel G-quadruplex structures are constructed by acyclic (<sc>l</sc>)-threninol nucleic acid and their synthesis biophysical properties described.
Abstract Oligonucleotides are increasingly being used as a programmable connection material to assemble molecules and proteins in well‐defined structures. For the application of such assemblies for vivo diagnostics or therapeutics it is crucial that oligonucleotides form highly stable, non‐toxic, non‐immunogenic Only few oligonucleotide derivatives fulfil all these requirements. Here we report on acyclic l ‐threoninol nucleic acid (aTNA) four‐way junction (4WJ) stable enables facile assembly...
Acyclic (L)-threoninol nucleic acid (aTNA) containing thymine, cytosine and adenine nucleobases were synthesized shown to form surprisingly stable triplexes with complementary single stranded homopurine DNA or RNA targets. The triplex structures consist of two (L)-aTNA strands one RNA, these are significantly stronger than the corresponding duplexes as in competition experiments. As a unique property (L)-aTNAs exclusively no duplex observed by gel electrophoresis. results compared known...
Abstract Peptide nucleic acid (PNA) forms a triple helix with double‐stranded RNA (dsRNA) stabilized by hydrogen‐bonding zipper formed PNA's backbone amides (N−H) interacting phosphate oxygens. This pattern is enabled the matching ∼5.7 Å spacing (typical for A‐form dsRNA) between and We hypothesized that extending one −CH 2 − group might bring distance PNA amide groups closer to 7 Å, which favourable hydrogen bonding B‐form dsDNA Extension of was expected selectively stabilize PNA‐DNA...
Abstract Triplex forming oligonucleotides are used as a tool for gene regulation and in DNA nanotechnology. By incorporating artificial nucleic acids, target affinity biological stability superior to that of natural may be obtained. This work demonstrates how chimeric clamp consisting acyclic (L)‐threoninol acid (aTNA) can bind RNA by the formation highly stable triplex structure. The (L)‐aTNA is released from again addition releasing strand displacement type reaction. It shown efficiently...
SUMMARY The cardinal interneuron classes are a useful simplification of cortical diversity, but such broad subgroupings glosses over the molecular, morphological, and circuit specificity subtypes, most notably among somatostatin class. organizing principles by which connectivity these subtypes is specified unknown. To address this knowledge gap, we designed series genetic strategies to target breadth subtypes. Using three that span entire column, examined their afferent efferent...
Abstract Tissue organization arises from the coordinated molecular programs of cells. Spatial genomics maps cells and their within spatial context tissues. However, current methods measure information through imaging or direct registration, which often require specialized equipment are limited in scale. Here, we developed an imaging-free transcriptomics method that uses diffusion patterns to computationally reconstruct data. To do so, utilize a simple experimental protocol on two dimensional...
Abstract Summary Since high-throughput techniques became a staple in biological science laboratories, computational algorithms, and scientific software have boomed. However, the development of bioinformatics usually lacks quality standards. The resulting code is hard to test, reuse, maintain. We believe that root inefficiency implementing best practices academic settings individualistic approach, which has traditionally been norm for recognizing achievements and, by extension, developing...
2,4-Difluorotoluene is a nonpolar isostere of thymidine that has been used as powerful mechanistic probe to study the role hydrogen bonding in nucleic acid recognition and interactions with polymerases. In present study, we evaluated five fluorinated benzenes nucleobase analogues peptide acids designed for triple helical double RNA. We found having para ortho fluorine substitution patterns (as 2,4-difluorotoluene) selectively stabilized Hoogsteen triplets U-A base pairs. The results were...
Acyclic (<sc>l</sc>)-threoninol nucleic acids ((<sc>l</sc>)-aTNA) containing poly-cytosines are prepared and investigated at various pH values, revealing the formation of a highly stable structure lower that have characteristics an i-motif.
Abstract DNA nanostructures have considerable biomedical potential as intracellular delivery vehicles they are highly homogeneous and can be functionalized with high spatial resolution. However, challenges like instability under physiological conditions, limited cellular uptake, lysosomal degradation limit their use. This paper presents a bio‐reducible, cationic polymer poly(cystaminebisacrylamide‐1,6‐diaminohexane) (PCD) reversible origami protector. PCD displays stronger affinity than...