A5030550883- Gene Regulatory Network Analysis
- CRISPR and Genetic Engineering
- Advanced biosensing and bioanalysis techniques
- Cell Image Analysis Techniques
- Biosensors and Analytical Detection
- Viral Infectious Diseases and Gene Expression in Insects
- Bioinformatics and Genomic Networks
- Circadian rhythm and melatonin
- Microbial Metabolic Engineering and Bioproduction
- Mathematical Biology Tumor Growth
- Single-cell and spatial transcriptomics
- Light effects on plants
- CAR-T cell therapy research
- Bacterial Genetics and Biotechnology
- Photoreceptor and optogenetics research
- RNA Research and Splicing
- Evolution and Genetic Dynamics
- RNA and protein synthesis mechanisms
- Advanced Biosensing Techniques and Applications
- Platelet Disorders and Treatments
- Computational Drug Discovery Methods
- 3D Printing in Biomedical Research
- DNA and Nucleic Acid Chemistry
- Neurobiology and Insect Physiology Research
- RNA Interference and Gene Delivery
Iran University of Medical Sciences
2025
Northwestern University
2015-2024
University of Rome Tor Vergata
2019-2024
University of Washington
2019-2024
Allen Institute for Cell Science
2022-2024
University of California, San Diego
2024
Dr. Daneshbod Labratory
2010-2022
Isfahan University of Technology
2018-2021
University of Mazandaran
2021
Sheikh Bahaei University
2017
Little is known about the relative importance of monocyte and tissue-resident macrophages in development lung fibrosis. We show that specific genetic deletion monocyte-derived alveolar after their recruitment to ameliorated fibrosis, whereas did not contribute Using transcriptomic profiling flow-sorted cells, we found macrophage differentiation unfolds continuously over course fibrosis its resolution. During fibrotic phase, differ significantly from expression profibrotic genes. A population...
A new, energy-based descriptor for porous materials is highly predictive hydrogen adsorption using an interpretable regression model.
Abstract The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field nucleic acid-based detection. Here, we report on enhancement trans-cleavage Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate due to its improved affinity (Km) for structures, provide mechanistic insights our findings through Molecular Dynamics simulations. Using probes significantly enhance signal transduction...
The precision and versatility of CRISPR-based techniques, combined with the advantages nucleic acid-based nanotechnology, hold great promise in transforming landscape molecular diagnostics. While significant progress has been made, current platforms primarly focus on acid detection. To expand applicability fully leverage offered by diagnostics, ongoing efforts explore strategies to develop CRISPR sensors capable detecting a diverse range analytes beyond acids. In addition, challenges still...
The growth of (bio)sensors in analytical chemistry is mainly attributable to the development affordable, effective, portable, and user-friendly tools. In field sensors, paper-based devices are gaining a relevant position for their outstanding features including foldability, ease use, instrument-free microfluidics. Herein, multifarious use filter paper detect copper ions bodily fluids reported by exploiting this eco-friendly material (i) synthesize AuNPs without reductants and/or external...
Abstract Engineering mammalian cells to carry out sophisticated and customizable genetic programs requires a toolkit of multiple orthogonal well-characterized transcription factors (TFs). To address this need, we develop the COmposable Mammalian Elements Transcription (COMET)—an ensemble TFs promoters that enable design tuning gene expression an extent not, best our knowledge, previously possible. COMET currently comprises 44 activating 12 inhibitory zinc-finger 83 cognate promoters,...
Abstract The RNA‐programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio‐engineering strategies are required to achieve control over activity. Here, we show that Toehold Switch DNA hairpins, presenting rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used response inputs. Reconfiguring from hairpin duplex conformation through strand displacement reaction provides an effective...
Significance Discovery of gene regulatory networks (GRNs) is crucial for gaining insights into biological processes involved in development or disease. Although time-resolved, high-throughput data are increasingly available, many algorithms do not account temporal delays underlying systems—such as protein synthesis and posttranslational modifications—leading to inaccurate network inference. To overcome this challenge, we introduce Sliding Window Inference Network Generation (SWING), which...
Abstract The RNA‐programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio‐engineering strategies are required to achieve control over activity. Here, we show that Toehold Switch DNA hairpins, presenting rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used response inputs. Reconfiguring from hairpin duplex conformation through strand displacement reaction provides an effective...
Major depressive disorder (MDD) is a critical cause of morbidity and disability with an economic cost hundreds billions dollars each year, necessitating more effective treatment strategies novel approaches to translational research. A notable barrier in addressing this public health threat involves reliable identification the disorder, as many affected individuals remain undiagnosed or misdiagnosed. An objective blood-based diagnostic test using transcript levels panel markers would provide...
Computational models are most impactful when they explain and characterize biological phenomena that non-intuitive, unexpected, or difficult to study experimentally. Countless equation-based have been built for these purposes, but we yet realize the extent which rules-based offer an intuitive framework encourages computational experimental collaboration. We develop ARCADE, a multi-scale agent-based model interrogate emergent behavior of heterogeneous cell agents within dynamic...
The identification of informative elements the host response to infection may improve diagnosis and management bacterial pneumonia.
Circadian entrainment is necessary for rhythmic physiological functions to be appropriately timed over the 24-hour day. Disruption of circadian rhythms has been associated with sleep and neuro-behavioral impairments as well cancer. To date, light widely accepted most powerful synchronizer, motivating its use a key control input phase resetting. Through sensitivity analysis, we identify additional targets whose individual simultaneous manipulation (via model predictive algorithm) out-perform...
Oncolytic adenoviruses, such as ONYX-015, have been tested in clinical trials for currently untreatable tumors, but yet to demonstrate adequate therapeutic efficacy. The extent which viruses infect targeted cells determines the efficacy of this approach many tumors down-regulate Coxsackievirus and Adenovirus Receptor (CAR), rendering them less susceptible infection. Disrupting MAPK pathway signaling by pharmacological inhibition MEK up-regulates CAR expression, offering possible enhanced...
A suite of genetic components and computational models enables the predictive design mammalian cellular functions.
Chimeric antigen receptor (CAR) T-cell therapy shows promise for treating liquid cancers and increasingly solid tumors as well. While potential design strategies exist to address translational challenges, including the lack of unique tumor antigens presence an immunosuppressive microenvironment, testing all possible choices in vitro vivo is prohibitively expensive, time consuming, laborious. To this gap, we extended modeling framework ARCADE (Agent-based Representation Cells And Dynamic...
BACKGROUND: Competency-based approach is the dominant in curriculum planning. Despite use of competency other fields related to healthcare system various countries and also some Iran, undergraduate Anesthesia Technology Iran predominantly presented traditionally (goal-oriented). Since obtaining for Technologists important, this study aimed determine required educational competencies them. MATERIALS AND METHODS: This quantitative developmental was conducted 2022–2023 three general stages:...
Abstract Motivation: Sensitivity analysis provides key measures that aid in unraveling the design principles responsible for robust performance of biological networks. Such metrics allow researchers to investigate comprehensively model performance, develop more realistic models, and informative experiments. However, sensitivity oscillatory systems focuses on period amplitude characteristics, while biologically relevant effects phase are neglected. Results: Here, we introduce a novel set...
Abstract A nonlinear model predictive control algorithm is developed to investigate the phase‐resetting properties of robust biological oscillators; in particular, those circadian rhythm. This pacemaker an autonomous biochemical oscillator with a free‐running period close 24 h. Research chronobiology indicates that light stimuli may delay or advance phase oscillator, allowing it synchronize physiological processes and entrain environment. In this paper, closed‐loop optimal tracking applied...