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62
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Introduction
Safee Ullah Chaudhary received his B.S. in computer systems engineering from the Ghulam Ishaq Khan Institute of Engineering Sciences and Technology, Topi, Pakistan in 2002. He spent the next four years at Ultimus Inc (HQ NC) serving in the software development group. Later, he proceeded for graduate studies and obtained a Ph.D. in Bio & Brain Engineering in 2013 from KAIST, South Korea.
In 2014, he joined the Department of Biology at LUMS where he established the Biomedical Informatics Research Laboratory (BIRL) which is now involved in the development of cutting-edge techniques, software and data analysis pipelines for applications in proteogenomics and systems biology towards "scientific wellness".
Skills and Expertise
Education
August 2008 - February 2013
Publications
Publications (62)
Febrile neutropenia (FN) in cancer patients undergoing chemotherapy can result in life-threatening outcomes. Hence, an evaluation of associated risk factors can enable clinical surveillance as well as inform prophylactic measures. In this retrospective cohort study, we report a mortality prognostication model for chemotherapy-treated cancer patient...
Schizophrenia (SZ) is a debilitating disorder in which patients exhibit psychotic behavior due to aberrant connectivity between different regions of the brain. Advances in neuroimaging have now enabled the diagnosis and analysis of SZ in order to elucidate the whole brain functional connectivity networks. In the present study, we have used resting-...
The emergence of drug-resistance-inducing mutations in Hepatitis C virus (HCV) coupled with genotypic heterogeneity has made targeting NS3/4A serine protease difficult. In this work, we investigated the mutagenic variations in the binding pocket of Genotype 3 (G3) HCV NS3/4A and evaluated ligands for efficacious inhibition. We report mutations at 1...
The emergence of drug resistance inducing mutations in Hepatitis C virus (HCV) coupled with genotypic heterogeneity has made targeting NS3/4A serine protease difficult. In this work, we investigated the mutagenic variations in the binding pocket of Genotype 3 (G3) HCV NS3/4A and evaluated ligands for efficacious inhibition. We report mutations at 1...
Hyperglycemia is an outcome of dysregulated glucose homeostasis in the human body and may induce chronic elevation of blood glucose levels. Lifestyle factors such as overnutrition, physical inactivity, and psychosocials coupled with systemic low-grade inflammation have a strong negative impact on glucose homeostasis, in particular, insulin sensitiv...
Hyperglycemia is an outcome of dysregulated glucose homeostasis in the human body and may induce chronic elevation of blood glucose levels. Lifestyle factors such as overnutrition, physical inactivity, and psychosocials coupled with systemic low-grade inflammation have a strong negative impact on glucose homeostasis, in particular, insulin sensitiv...
Cotton (Gossypium hirsutum) is an economically important crop and is widely cultivated around the globe. However, the major problem of cotton is its high vulnerability to biotic and abiotic stresses. It has been around three decades since the cotton plant was genetically engineered with genes encoding insecticidal proteins (mainly Cry proteins) wit...
The Escherichia coli CheY protein belongs to a large bacterial response regulator superfamily. X-ray hydroxy radical foot-printing with mass spectroscopy (XFMS) has shown that allosteric activation of CheY by its motor target triggers a concerted internalization of aromatic sidechains. We reanalyzed the XFMS data to compare polar versus non-polar C...
Computational modeling and analysis of biomolecular network models annotated with cancer patient-specific multi-omics data can enable the development of personalized therapies. Current endeavors aimed at employing in silico models towards personalized cancer therapeutics remain to be fully translated. In this work, we present 'CanSee' a novel multi...
Mosquitoes act as vectors for the transmission of various infectious pathogens. The associated diseases are prevalent in tropical and subtropical regions of the world and can be prevented by effective vector control and management. Natural compounds have become a potential alternative to synthetic repellents that are unsafe and harmful to the envir...
Background
While antimicrobial resistance (AMR) continues to be a major public health problem in Pakistan, data regarding trends of resistance among pathogenic bacteria remain scarce, with few studies presenting long-term trends in AMR. This study was therefore designed to analyse long-term AMR trends at a national level in Pakistan.
Methods
We re...
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of scale-specific biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built using this data have the potential to provide specific insights into complex multi...
Meat is a rich source of energy that provides high-value animal protein, fats, vitamins, minerals and trace amounts of carbohydrates. Globally, different types of meats are consumed to fulfill nutritional requirements. However, the increasing burden on the livestock industry has triggered the mixing of high-price meat species with low-quality/-pric...
Background:
Photosynthesis is a key process in plants that is compromised by the oxygenase activity of Rubisco, which leads to the production of toxic compound phosphoglycolate that is catabolized by photorespiratory pathway. Transformation of plants with photorespiratory bypasses have been shown to reduce photorespiration and enhance plant biomas...
In silico models of biomolecular regulation in cancer, annotated with patient-specific gene expression data, can aid in the development of novel personalized cancer therapeutic strategies. Drosophila melanogaster is a well-established animal model that is increasingly being employed to evaluate such preclinical personalized cancer therapies. Here,...
Rapid advancements in high-throughput omics technologies and experimental protocols have led to the generation of vast amounts of biomolecular data on cancer that now populates several online databases and resources. Cancer systems biology models built on top of this data have the potential to provide specific insights into complex multifactorial a...
Multi-scale models integrating biomolecular data from genetic, transcriptional, and translational levels, coupled with extracellular microenvironments can assist in decoding the complex mechanisms underlying system-level diseases such as cancer. To investigate the emergent properties and clinical translation of such cancer models, we present Theatr...
While antimicrobial resistance (AMR) continues to be a major public health problem in Pakistan, data regarding trends of resistance among pathogenic bacteria remains scarce, with few studies presenting long-term trends in AMR. This study was therefore designed to analyze long-term AMR trends at a national level in Pakistan. We report here results o...
PERCEPTRON is a next-generation freely available web-based proteoform identification and characterization platform for top-down proteomics (TDP). PERCEPTRON search pipeline brings together algorithms for (i) intact protein mass tuning, (ii) de novo sequence tags-based filtering, (iii) characterization of terminal as well as post-translational modif...
Hepatitis C is an inflammatory liver disease caused by the single-stranded RNA
(ssRNA) hepatitis C virus (HCV). The genetic diversity of the virus and quasispecies
produced during replication have resulted in viral resistance to direct-acting antivirals
(DAAs) as well as impediments in vaccine development. The recent adaptation of
CRISPR-Cas as an...
Purpose
The aim of this study was to explore the utility of inflammatory biomarkers in the peripheral blood to predict response to treatment in extrapulmonary tuberculosis (EPTB).
Methods
A Luminex xMAP-based multiplex immunoassay was used to measure 40 inflammatory biomarkers in un-stimulated plasma of 91 EPTB patients (48 lymphadenitis, and 43 p...
Sedentary life styles coupled with high-calorie diets and unhealthy social habits such as smoking, have put an ever-increasing number of people at risk of cardiovascular disorders (CVD), worldwide. A concomitant increase in the prevalence of type 2-diabetes (hyperglycemia), a risk factor for CVD, has further contributed towards escalating CVD-relat...
Plants employ photosynthesis to produce sugars for supporting their growth. During photosynthesis, an enzyme Ribulose 1,5 bisphosphate carboxylase/oxygenase (Rubisco) combines its substrate Ribulose 1,5 bisphosphate (RuBP) with CO2 to produce phosphoglycerate (PGA). Alongside, Rubisco also takes up O2 and produce 2-phosphoglycolate (2-PG), a toxic...
Schizophrenia is a psychotic brain disorder in which patients exhibit aberrant connectivity between different regions of the brain. Neuroimaging is a state-of-the-art technique that is now increasingly been employed in clinical investigation of Schizophrenia. In the present study, we have used resting-state functional magnetic resonance neuroimagin...
In silico models of biomolecular regulation in cancer, annotated with patient-specific gene expression data can aid in the development of novel personalized cancer therapeutics strategies. Drosophila melanogaster is a well-established animal model that is increasingly being employed to evaluate preclinical personalized cancer therapies. Here, we re...
Background: Only a few studies have presented long-term trends in antimicrobial resistance (AMR) at a nationwide level in Pakistan. This study presents a comprehensive situational analysis of AMR trends among pathogens isolated from blood and cerebrospinal fluid (CSF) cultures, between 2011 and 2015, in Pakistan.
Methods: A retrospective analysis o...
Background: Only a few studies have presented long-term trends in antimicrobial resistance (AMR) at a nationwide level in Pakistan. This study presents a comprehensive situational analysis of AMR trends among pathogens isolated from blood and cerebrospinal fluid (CSF) cultures, between 2011 and 2015, in Pakistan.
Methods: A retrospective analysis o...
Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhan...
Background
Hepatitis C virus (HCV) infections are amongst the leading public health concerns in Pakistan with a high disease burden. Despite the availability of effective antiviral treatments in the country the disease burden in general population has not lowered. This could be attributed to the asymptomatic nature of this infection that results in...
Seroprevalence of anti-HCV antibodies in 32 districts of the Punjab province (Table A). Anti-HCV antibody seroprevalence in different age groups of the total tested samples (Table B). Anti-HCV antibody seroprevalence in different genders (Table C).
(DOCX)
Anti-HCV antibody seroprevalence in different occupational groups while controlling the age as confounder.
Anti-HCV antibody positive population is shown in percent of the total population in every group.
(PDF)
Hepatitis C compromises the quality of life of more than 350 million individuals worldwide. Over the last decade, therapeutic regimens for treating hepatitis C virus (HCV) infections have undergone rapid advancements. Initially, structure‐based drug design was used to develop molecules that inhibit viral enzymes. Subsequently, establishment of cell...
Increased industrial processes have introduced emerging toxic pollutants into the environment. Phytoremediation is considered to be a very useful, economical and ecofriendly way of controlling these pollutants, however, certain pollutants can potentially travel through the food chain and accumulate at hazardous levels. Four isomers of dinitrotoluen...
Boolean modelling of biological networks is a well-established technique for abstracting dynamical biomolecular regulation in cells. Specifically, decoding linkages between salient regulatory network states and corresponding cell fate outcomes can help uncover pathological foundations of diseases such as cancer. Attractor landscape analysis is one...
Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhan...
Purpose: Human beings frequently experience fear, phobia, migraine and hallucinations, however, the cerebral mechanisms underpinning these conditions remain poorly understood. Towards this goal, in this work, we aim to correlate the human ocular perceptions with visual hallucinations, and map them to their cerebral origins.
Methods: An fMRI study...
The Cucumber mosaic virus (CMV) suppressor 2b co-localizes with AGO4 in cytoplasmic and nuclear fractions of Arabidopsis thaliana Biochemical fractionation of A. thaliana cellular extracts revealed that 2b and AGO4 coexist in multiple size exclusions. 2b transgenic A. thaliana exhibited an enhanced accumulation of 24nt siRNAs from FWA and other het...
This study explores the patterns of activation in brain regions toward classifying decision making voxels from among four major Brodmann areas (BAs) upon stimulus of visual tasks. Toward this goal, a well-known clustering analysis has been performed on real-time data of the human brain obtained using functional magnetic resonance imaging (fMRI). Th...
The provision of Antenatal Care (ANC) for pregnant women plays a vital role in ensuring infant and maternal health. Limited access to antenatal care in Low and Middle Income Countries (LMIC) results in high Infant and Maternal Mortality Rate (IMR and MMR, respectively). In this work, we propose a cloud-based clinical Decision Support System (DSS) i...
Drosophila melanogaster larvae are classified as herbivores and known to feed on non-carnivorous diet under normal conditions. However, when nutritionally challenged these larvae exhibit cannibalistic behaviour by consuming a diet composed of larger conspecifics. Herein, we report that cannibalism in Drosophila larvae is confined not only to scaven...
We introduce a novel slice-wise latent structure regression (LSR) method for the analysis of functional magnetic resonance imaging (fMRI) data instead of the conventional voxel-wise generalized least squares (GLS) method. LSR method is designed for application to data sets from slices where fMRI responses (voxels Y* of a slice) are highly correlate...
Motivation:
Computational multiscale models help cancer biologists to study the spatiotemporal dynamics of complex biological systems and to reveal the underlying mechanism of emergent properties.
Results:
To facilitate the construction of such models, we have developed a next generation modelling platform for cancer systems biology, termed 'ELE...
There is a renewed interest in tumorigenesis provoked by glycolysis and prosurvival autophagy following the mitochondrial permeability transition during cell death. To investigate such mitochondrial dysfunction, we have developed a multiscale model by integrating the dynamic behaviors of essential oncogenic proteins, cells, and their microenvironme...
In this paper, computational strategies are defined for protein quantisation by considering the shapes of the protein spots. The technique uses the clustering techniques like K-mean and fuzzy C-mean to distinguish between different types of protein spots and unwanted artifacts. The resulting technique is used in 2D electrophoresis gel image process...
Questions
Question (1)
Dear Colleagues,
Any recommendation on a good quality 2D gel system with a low running cost?
Thank you.
-Safee