Sidra Ilyas

Dr. Sidra Ilyas

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Research Focus & Metrics

Academic Career Length

15Years (2012-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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12 November 2014 in Environmental Monitoring and Assessment
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Journal Article
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SISidra Ilyas
Sidra Ilyas
ARAbdul Rehman
Abdul Rehman

21 January 2013 in Iranian Journal of Environmental Health Science and Engineering
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Journal Article
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SISidra Ilyas
Sidra Ilyas
ARAbdul Rehman
Abdul Rehman
In the present investigation the fungi, Aspergillus niger and Nigrospora sp. were employed for decolorization of Synozol red HF-6BN. Decolorization study showed that Aspergillus niger and Nigrospora sp. were able to decolorize 88% and 96% Synozol red 6BN, respectively, in 24 days. It was also studied that 86% and 90% Synozol red containing of dye effluent was decolorized by Aspergillus niger and Nigrospora sp. after 28 days of incubation at room temperature. A fungal-based protein with relative molecular mass of 70 kDa was partially purified and examined for enzymatic characteristics. The enzyme exhibited highest activity at temperature ranging from 40-50°C and at pH=6.0. The enzyme activity was enhanced in the presence of metal cations. High performance liquid chromatography analysis confirmed that these fungal strains are capable to degrade Synozol red dye into metabolites. No zones of inhibition on agar plates and growth of Vigna radiata in the presence of dye extracted sample, indicated that the fungal degraded dye metabolites are nontoxic to beneficial micro-flora and plant growth. Aspergillus niger and Nigrospora sp. have promising potential in color removal from textile wastewater-containing azo dyes.

5 June 2018 in eLife
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Journal Article
Open access
MRMeytal Radzinski
Meytal Radzinski
RFRosi Fassler
Rosi Fassler
OYOhad Yogev
Ohad Yogev
WBWilliam Breuer
William Breuer
NSNadav Shai
Nadav Shai
DRDana Reichmann
Dana Reichmann
Cellular redox status affects diverse cellular functions, including proliferation, protein homeostasis, and aging. Thus, individual differences in redox status can give rise to distinct sub-populations even among cells with identical genetic backgrounds. Here, we have created a novel methodology to track redox status at single cell resolution using the redox-sensitive probe Grx1-roGFP2. Our method allows identification and sorting of sub-populations with different oxidation levels in either the cytosol, mitochondria or peroxisomes. Using this approach, we defined a redox-dependent heterogeneity of yeast cells and characterized growth, as well as proteomic and transcriptomic profiles of distinctive redox subpopulations. We report that, starting in late logarithmic growth, cells of the same age have a bi-modal distribution of oxidation status. A comparative proteomic analysis between these populations identified three key proteins, Hsp30, Dhh1, and Pnc1, which affect basal oxidation levels and may serve as first line of defense proteins in redox homeostasis.

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AMAbdul Manan
Abdul Manan
EBEunhye Baek
Eunhye Baek
SISidra Ilyas
Sidra Ilyas
Donghun LeeDonghun Lee
Donghun Lee
This review provides a comprehensive analysis of the transformative impact of artificial intelligence (AI) and machine learning (ML) on modern drug design, specifically focusing on how these advanced computational techniques address the inherent limitations of traditional small-molecule drug design methodologies. It begins by outlining the historical challenges of the drug discovery pipeline, including protracted timelines, exorbitant costs, and high clinical failure rates. Subsequently, it examines the core principles of structure-based virtual screening (SBVS) and ligand-based virtual screening (LBVS), establishing the critical bottlenecks that have historically impeded efficient drug development. The central sections elucidate how cutting-edge ML and deep learning (DL) paradigms, such as generative models and reinforcement learning, are revolutionizing chemical space exploration, enhancing binding affinity prediction, improving protein flexibility modeling, and automating critical design tasks. Illustrative real-world case studies demonstrating quantifiable accelerations in discovery timelines and improved success probabilities are presented. Finally, the review critically examines prevailing challenges, including data quality, model interpretability, ethical considerations, and evolving regulatory landscapes, while offering forward-looking critical perspectives on the future trajectory of AI-driven pharmaceutical innovation.

25 July 2014 in PLOS ONE
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Journal Article
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SISidra Ilyas
Sidra Ilyas
ARAbdul Rehman
Abdul Rehman
AVAna Coelho Varela
Ana Coelho Varela
DSDavid Sheehan
David Sheehan
Trichosporon asahii is a yeast pathogen implicated in opportunistic infections. Cultures of an isolate collected from industrial wastewater were exposed for 2 days to 100 mg/L sodium arsenite (NaAsO2) and cadmium (CdCl2). Both metals reduced glutathione transferase (GST) activity but had no effect on superoxide dismutase or catalase. NaAsO2 exposure increased glutathione reductase activity while CdCl2 had no effect. Protein thiols were labeled with 5-iodoacetamido fluorescein followed by one dimensional electrophoresis which revealed extensive protein thiol oxidation in response to CdCl2 treatment but thiol reduction in response to NaAsO2. Two dimensional electrophoresis analyses showed that the intensity of some protein spots was enhanced on treatment as judged by SameSpots image analysis software. In addition, some spots showed decreased IAF fluorescence suggesting thiol oxidation. Selected spots were excised and tryptic digested for identification by MALDI-TOF/TOF MS. Twenty unique T. asahii proteins were identified of which the following proteins were up-regulated in response to NaAsO2: 3-isopropylmalate dehydrogenase, phospholipase B, alanine-glyoxylate aminotransferase, ATP synthase alpha chain, 20S proteasome beta-type subunit Pre3p and the hypothetical proteins A1Q1_08001, A1Q2_03020, A1Q1_06950, A1Q1_06913. In addition, the following showed decreased thiol-associated fluorescence consistent with thiol oxidation; aconitase; aldehyde reductase I; phosphoglycerate kinase; translation elongation factor 2; heat shock protein 70 and hypothetical protein A1Q2_04745. Some proteins showed both increase in abundance coupled with decrease in IAF fluorescence; 3-hydroxyisobutyryl- CoA hydrolase; homoserine dehydrogenase Hom6 and hypothetical proteins A1Q2_03020 and A1Q1_00754. Targets implicated in redox response included 10 unique metabolic enzymes, heat shock proteins, a component of the 20S proteasome and translation elongation factor 2. These data suggest extensive proteomic alterations in response to metal-induced oxidative stress in T. asahii. Amino acid metabolism, protein folding and degradation are principally affected.