Safee Ullah Chaudhary

Safee Ullah Chaudhary
Lahore University of Management Sciences | LUMS · Biomedical Informatics & Engineering Research Laboratory (BIRL)

Ph.D.

About

62
Publications
15,760
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383
Citations
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".
Education
August 2008 - February 2013
Korea Advanced Institute of Science and Technology
Field of study
  • Bio & Brain Engineering

Publications

Publications (62)
Preprint
Full-text available
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...
Preprint
Full-text available
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-...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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,...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Preprint
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Data
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)
Data
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)
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Poster
Full-text available
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...
Article
Full-text available
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...
Article
Full-text available
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...
Article
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...
Conference Paper
Full-text available
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...
Article
Full-text available
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...
Article
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...
Article
Full-text available
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...
Article
Full-text available
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...
Conference Paper
Full-text available
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)
Question
Dear Colleagues,
Any recommendation on a good quality 2D gel system with a low running cost?
Thank you.
-Safee

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