A5064121346- Microbial Metabolic Engineering and Bioproduction
- Fungal and yeast genetics research
- Adipose Tissue and Metabolism
- Biochemical and biochemical processes
- Bioinformatics and Genomic Networks
- Biofuel production and bioconversion
- Enzyme-mediated dye degradation
- Endoplasmic Reticulum Stress and Disease
- Gene expression and cancer classification
- Fermentation and Sensory Analysis
- Control Systems and Identification
- Cardiovascular Disease and Adiposity
- Neural Networks and Applications
- CRISPR and Genetic Engineering
- Viral Infectious Diseases and Gene Expression in Insects
- Medicinal Plants and Neuroprotection
- Machine Learning and ELM
- Evolutionary Algorithms and Applications
- Advanced Proteomics Techniques and Applications
- RNA Research and Splicing
- Lipid metabolism and biosynthesis
- Immune responses and vaccinations
- Machine Learning in Bioinformatics
- Wind Turbine Control Systems
- Neonatal Respiratory Health Research
University of Kurdistan
2024
Chalmers University of Technology
2013-2022
University of Shahrood
2018-2022
Novo Nordisk (United Kingdom)
2019-2020
University of Oxford
2020
Novo Nordisk (Denmark)
2019
Novo Nordisk (Finland)
2018
Novo Nordisk Foundation
2015
Novozymes (Denmark)
2015
Technical University of Denmark
2015
Ethanol production for use as a biofuel is mainly achieved through simultaneous saccharification and fermentation by yeast. Operating at ≥40°C would be beneficial in terms of increasing efficiency the process reducing costs, but yeast does not grow efficiently those temperatures. We used adaptive laboratory evolution to select strains with improved growth ethanol ≥40°C. Sequencing whole genome, genome-wide gene expression, metabolic-flux analyses revealed change sterol composition, from...
Copper (Cu) is essential for living organisms, and acts as a cofactor in many metabolic enzymes. To avoid the toxicity of free Cu, organisms have specific transport systems that 'chaperone' metal to targets. Cancer progression associated with increased cellular Cu concentrations, whereby proliferative immortality, angiogenesis metastasis are cancer hallmarks defined requirements Cu. The aim this study gather all known Cu-binding proteins reveal their putative involvement cancers using...
Abstract In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on secretion different proteins. Unraveling diverse is particularly important for biopharmaceutical production. Here we delineate core functions and integrate them with genome-scale metabolic reconstructions human, mouse, Chinese hamster ovary cells. resulting enable computation energetic costs machinery demands each secreted protein....
Increasing the amounts of functionally competent brown adipose tissue (BAT) in adult humans has potential to restore dysfunctional metabolism and counteract obesity. In this study, we aimed characterize human perirenal fat depot, hypothesized that there would be regional, within-depot differences signature depending on local sympathetic activity. We characterized specimens from four different regions kidney donors, through a combination qPCR mapping, immunohistochemical staining,...
Abstract Eukaryotic cells are used as cell factories to produce and secrete multitudes of recombinant pharmaceutical proteins, including several the current top-selling drugs. Due essential role complexity secretory pathway, improvement for protein production through metabolic engineering has traditionally been relatively ad-hoc; a more systematic approach is required generate novel design principles. Here, we present proteome-constrained genome-scale model yeast Saccharomyces cerevisiae...
The protein secretory machinery in Eukarya is involved post-translational modification (PTMs) and sorting of the many transmembrane proteins. While has been well-studied using classic reductionist approaches, a holistic view its complex nature lacking. Here, we present first genome-scale model for yeast which captures knowledge generated through more than 50 years research. based on concept Protein Specific Information Matrix (PSIM: characterized by seven PTMs features). An algorithm was...
Protein secretory pathway in eukaryal cells is responsible for delivering functional proteins. The dysfunction of this causes a range important human diseases from congenital disorders to cancer. Despite the piled-up knowledge on molecular biology and biochemistry level, tissue-specific expression genes has not been analyzed transcriptome level. Based recent RNA-sequencing studies, largest fraction encodes secretome (secretory proteins). Here, question arises that if levels have tuning. In...
Purpose. Autophagy plays a key role in host defence responses against microbial infections by promoting degradation of pathogens and participating acquired immunity. The interaction between autophagy viruses is complex, this pathway hijacked several viruses. Influenza virus (IV) interferes with through its replication increases the accumulation autophagosomes blocking lysosome fusion. Thus, could be an effective area for antiviral research. Methodology. In study, we evaluated effect on IV...
The koji mold, Aspergillus oryzae is widely used for the production of industrial enzymes due to its particularly high protein secretion capacity and ability perform post-translational modifications. However, systemic analysis system lacking, generally poorly annotated proteome. Here we defined a functional secretory component list A. using previously reported model S. cerevisiae as scaffold. Additional components were obtained by blast search with in other closely related fungal species...
Biology is increasingly dependent on large-scale analysis, such as proteomics, creating a requirement for efficient bioinformatics. Bioinformatic predictions of biological functions rely upon correctly annotated database sequences, and the presence inaccurately or otherwise poorly described sequences introduces noise bias to analyses. Accurate annotations are, example, pivotal correct identification polypeptide fragments. However, standards how sequence databases are organized presented...
Abstract Background The impact of exposure to air pollutants, such as fine particulate matter (PM), on the immune system and its consequences pediatric asthma, are not well understood. We investigated whether ambient levels PM with aerodynamic diameter ≤2.5 microns (PM 2.5 ) associated alterations in circulating monocytes children or without asthma. Methods Monocyte phenotyping was performed by cytometry time‐of‐flight (CyTOF). Cytokines were measured using cytometric bead array Luminex...
The human cancer secretome database (HCSD) is a comprehensive for data. describes proteins secreted by cells and structuring information about the will enable further analysis of how this related with tumor biology. from are believed to play deterministic role in progression therefore may be key find novel therapeutic targets biomarkers many cancers. Consequently, huge data on have been generated recent years lack coherent limiting ability query increasing community knowledge. We developed...
The product yield and titers of biological processes involving the conversion biomass to desirable chemicals can be limited by environmental stresses encountered microbial hosts used for bioconversion. One these main is growth inhibition due exposure low pH conditions. In order circumvent this problem, understanding mechanisms involved in acid stress response tolerance essential. Characterisation wild yeasts that have a natural ability resist such harsh conditions will pave way understand...
Cancer cells can have a broad scope of proliferation rates. Here we aim to identify the molecular mechanisms that allow some cancer cell lines grow up 4 times faster than other lines. The correlation gene expression profiles with growth rate in 60 different has been analyzed using several genome-scale biological networks and new algorithms. New possible regulatory feedback loops suggested known roles cycle related transcription factors confirmed. Over 100 growth-correlated metabolic...
Support vector machine (SVM) is a supervised machine-learning method which can be used for both classification and regression models. In this paper, we introduce new model of SVM any training samples containing inputs outputs are considered the random variables with known probability functions. The first converted into equivalent quadratic programming (QP) formulations in linear nonlinear cases. An artificial neural network learning then proposed. presented framework guarantees to obtain...
Abstract In mammalian cells, >25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on secretion different proteins. Unraveling diverse is particularly important for biopharmaceutical production. Here we delineate core functions and integrate them with genome-scale metabolic reconstructions human, mouse, Chinese hamster cells. resulting enable computation energetic costs machinery demands each secreted protein. By...
Reverse engineering of gene regulatory networks (GRNs) is the process estimating genetic interactions a cellular system from expression data. In this paper, we propose novel hybrid systematic algorithm based on neurofuzzy network for reconstructing GRNs observational data when only medium-small number measurements are available. The approach uses fuzzy logic to transform values into qualitative descriptors that can be evaluated by using set defined rules. model genes effects other followed...
Clustering of genes using their expression data has been a major topic in recent years. A large amount gene even time series are obtained by microarray technology. Finding clusters with similar functions and interconnecting networks an important role mining biological functional analysis. In this paper, Two Phase Functional presented as new approach clustering. The proposed is based on finding patterns Fuzzy C-Means (FCM) K-means methods. function similarities over number experimental...