Shadma Fatima

Shadma Fatima
Monash University (Australia) · Department of Biochemistry and Molecular Biology

Doctor of Philosophy in Biochemistry, Master of Veterinary Science (Animal genetics and Breeding)

About

43
Publications
19,688
Reads
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233
Citations
Additional affiliations
September 2018 - present
Children cancer research institute, Australia
Position
  • Research Officer
January 2018 - September 2018
UNSW Sydney
Position
  • Project Manager
Description
  • RNA seq Data Analysis and ScRNA seq analysis using R, Galaxy and Python
January 2009 - December 2017
Monash University (Australia)
Position
  • RESEARCH

Publications

Publications (43)
Article
Liquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and the potential for novel biomarker discovery. However, the low concentration of relevant blood-based biosources and the heterogeneity of samples (i.e. the variability of relative abundance of molecules identified), pose major challenges to biomarker discove...
Article
Full-text available
Immunotherapy (IO), involving the use of immune checkpoint inhibition, achieves improved response-rates and significant disease-free survival for some cancer patients. Despite these beneficial effects, there is poor predictability of response and substantial rates of innate or acquired resistance, resulting in heterogeneous responses among patients...
Preprint
Long non-coding RNAs (lncRNAs) are emerging as key regulators in many biological processes. The dysregulation of lncRNA expression has been associated with many diseases, including cancer. Mounting evidence suggests that lncRNAs are involved in cancer initiation, progression, and metastasis. Thus, understanding the functional implications of lncRNA...
Preprint
Liquid biopsy has shown promise for cancer diagnosis due to its minimally invasive nature and the potential for novel biomarker discovery. However, the low concentration of relevant blood-based biosources and the heterogeneity of samples (i.e. the variability of relative abundance of molecules identified), pose major challenges to biomarker discove...
Article
Full-text available
The ongoing pandemic of coronavirus disease 2019 (COVID-19) has made a serious public health and economic crisis worldwide which united global efforts to develop rapid, precise, and cost-efficient diagnostics, vaccines, and therapeutics. Numerous multi-disciplinary studies and techniques have been designed to investigate and develop various approac...
Article
Full-text available
Phospholipase A2 (PLA2) enzymes were first recognized as an enzyme activity class in 1961. The secreted (sPLA2) enzymes were the first of the five major classes of human PLA2s to be identified and now number nine catalytically-active structurally homologous proteins. The best-studied of these, group IIA sPLA2, has a clear role in the physiological...
Preprint
Full-text available
An effective monotherapy to target the complex and multifactorial pathology of SARS-CoV-2 infection poses a challenge to drug repositioning, which can be improved by combination therapy. We developed an online network pharmacology-based drug repositioning platform, COVID-CDR (http://vafaeelab.com/COVID19repositioning.html), that enables a visual an...
Preprint
An effective monotherapy to target the complex and multifactorial pathology of SARS-CoV-2 infection poses a challenge to drug repositioning, which can be improved by combination therapy. We developed an online network pharmacology-based drug repositioning platform, COVID-CDR (http://vafaeelab.com/COVID19repositioning.html), that enables a visual an...
Article
Full-text available
An effective monotherapy to target the complex and multifactorial pathology of SARS-CoV-2 infection poses a challenge to drug repositioning, which can be improved by combination therapy. We developed an online network pharmacology-based drug repositioning platform, COVID-CDR (http://vafaeelab.com/COVID19repositioning.html), that enables a visual an...
Preprint
The ongoing pandemic of coronavirus disease 2019 (COVID-19) has made serious public health and economic crisis worldwide which united global efforts to develop rapid, precise, and cost-efficient diagnostics, vaccines, and therapeutics. Numerous multi-disciplinary studies and techniques have been designed to investigate and develop various approache...
Article
Nuclear transporter Importin (Imp, Ipo) 13 is known to transport various mammalian cargoes into/out of the nucleus, but its role in directing cell-fate is unclear. Here we examine the role of Imp13 in the maintenance of pluripotency and differentiation of embryonic stem cells (ESCs) for the first time, using an embryonic body (EB)-based model. When...
Preprint
p>Repurposing of the existing medications has become the mainstream focus of anti-COVID-19 drug discovery as it offers rapid and cost-effective solutions for therapeutic development. However, there is still a great deal to enhance efficacy of repurposing therapeutic options through combination therapy, in which promising drugs with varying mechanis...
Article
Full-text available
Although selective BRAF inhibitors and novel immunotherapies have improved short-term treatment responses in metastatic melanoma patients, acquired resistance to these therapeutics still represent a major challenge in clinical practice. In this study, we evaluated the efficacy of Withaferin A (WFA), derived from the medicinal plant Withania Somnife...
Article
Objective: To determine the prevalence of vitamin D deficiency in women with breast carcinoma and to determine the association of vitamin D levels with histopathological tumor characteristics. Study Design: Observational Study. Place and Duration of Study: This study was conducted at the Oncology Department, Nishtar Medical College / Hospital Multa...
Article
Aim: To report acute transfusion reactions occurring in patients receiving transfusion of whole blood/components in a tertiary care hospital. Methods: A total number of 250 patients who received transfusion of blood components from April 2016 to Dec 2016 were selected for analysis. All transfusion reactions were diagnosed clinically as well as by l...
Article
Importin 13 (Imp13) is a bidirectional nuclear transporter of proteins involved in a range of important cellular processes, with an N-terminally truncated inhibitory isoform (tImp13) specifically expressed in testis. To gain insight into tImp13 function, we performed a yeast-2-hybrid screen from a human testis cDNA library, identifying for the firs...
Article
Full-text available
There are two families, six genera and eight species of freshwater turtles found in Pakistan, and the same species have also been recorded in Sindh province, six of which are threatened, and all species are listed in CITES Appendices I / II. Family Geoemydidae consists of Hard shelled turtles viz Spotted Pond turtle (Geoclemys hamiltonii), Crowned...
Article
Full-text available
Although the negative regulator of nuclear import (NRNI) BRCA1 binding protein 2 (BRAP2) is highly expressed in testis, its role is largely unknown. Here we address this question by documenting the BRAP2 interactome from human testis, using the yeast 2-hybrid system to identify BRAP2-interacting proteins with roles in diverse cellular processes, in...
Data
The Indian riverine buffaloes are more susceptible to variations in the environment. These variations affect seminal plasma proteins, which in turn affect fertility. This study was conducted to evaluate variations in the Indian Bubalus bubalis seminal plasma protein profile using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) during w...
Article
Objective: To observe the histological changes in gallbladder mucosa due to Cholelithiasis. Study Design: Observational study Place and Duration of Study: This study was carried out at Department of Surgery, Anatomy and Pathology of Isra University Hospital and Institute of Biochemistry Sindh University Jamshoro. Materials and Methods: Sixty nine c...
Article
The Indian riverine buffaloes are more susceptible to variations in the environment. These variations affect seminal plasma proteins, which in turn affect fertility. This study was conducted to evaluate variations in the Indian Bubalus bubalis seminal plasma protein profile using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) during w...
Article
objectives: This study was carried out to evaluate homocysteine as a risk factor for ischemic stroke. design: Descriptive study setting: Isra University & Liaquat university of Medical and health sciences Jamshoro (lumhs). study design: Twenty five diagnosed cases of ischemic stroke were selected from different wards of two hospitals. Twenty five h...
Article
Congenital nephrogenic diabetes insipidus is a rare disorder in which the kidney is insensitive to antidiuretic hormone. It is mostly because of mutation in vasopressin type 2 receptor gene. Few cases have been reported with incidence of 3 in 100,000. We report here a case of an 11 month old infant who presented in emergency with dehydration, exces...
Article
Full-text available
This study describes for the first time the ability of the novel BRCA1-binding protein 2 (BRAP2) to inhibit the nuclear import of specific viral proteins dependent on phosphorylation. Ectopic expression of BRAP2 in transfected African green monkey kidney COS-7 cells was found to significantly reduce nuclear localization signal (NLS)-dependent nucle...
Article
Full-text available
The Indian riverine buffaloes are more susceptible to variations in environment. These variations affect seminal plasma proteins which in turn, affect fertility. This study was conducted to evaluate variations in the Indian Bubalus bubalis seminal plasma protein profile using two-dimensional polyacrylamide gel electrophoresis (2DPAGE) during winter...
Article
Full-text available
One hundred forty-five individuals from two cattle breeds, Kenkatha and Gaolao, in India were studied using 25 fluorescently-labelled microsatellite markers. Genetic diversities within and between populations were studied. A total of 197 and 239 distinct alleles were identified across 25 microsatellite loci in Kenkatha and Gaolao cattle, respective...
Article
Full-text available
The IGF plays an important role in lactation. Polymorphs of IGF gene are reported to be significantly associated with milk production and constituent traits. This study was undertaken to detect polymorphism at the genetic level and to explore allelic variability at this locus. A total of 150 animals, belonging to three breeds of riverine buffalo, v...
Article
Full-text available
Se estudiaron 145 individuos de dos razas de cebús en la India, Kenkatha y Gaolao, utilizando 25 microsatélites marcados por fluorescencia. Se estudiaron las diversidades genéticas dentro y entre poblaciones. Se identificaron un total de 197 y 239 alelos distintos de entre 25 loci de microsatélites en los cebús Kenkatha y Gaolao, respectivamente. S...
Article
Full-text available
Indian goat breeds are recognized as an invaluable component of the world’s goat genetic resources. Microsatellite pairs were chosen from the list suggested by International Society for Animal Genetics (ISAG) and amplified in two multiplexes (Set-I: 7 microsatellites and Set-II: 11 microsatellites) for automated fluorescence genotyping to assess bo...
Article
Full-text available
Molecular genetic selection on individual genes is a promising method to genetically improve economically important traits in chickens. The chicken growth hormone gene (cGH) was amplified from 36 Bantam, 53 Bantamised White Leghorn and 43 White Leghorn birds. The PCR amplification yielded approximately 1200 bp fragment against an expected fragment...
Data
Full-text available
Indian goat breeds are recognized as an invaluable component of the world's goat genetic resources. Microsatellite pairs were chosen from the list suggested by International Society for Animal Genetics (ISAG) and amplified in two multiplexes (Set-I: 7 microsatellites and Set-II: 11 microsatellites) for automated fluorescence genotyping to assess bo...
Article
Full-text available
Escherichia coli (E. coli) continues to result in significant morbidity and mortality in domestic poultry causing a variety of diseases either alone or as an adjunct to other pathogens. The methods of definitive diagnosis and identification of bacteria, which are time consuming, are based on cultural, biochemical and serological characters. To addr...
Data
Full-text available
Escherichia coli (E. coli) continues to result in significant morbidity and mortality in domestic poultry causing a variety of diseases either alone or as an adjunct to other pathogens. The methods of definitive diagnosis and identification of bacteria, which are time consuming, are based on cultural, biochemical and serological characters. To addr...
Data
Full-text available
Escherichia coli (E. coli) continues to result in significant morbidity and mortality in domestic poultry causing a variety of diseases either alone or as an adjunct to other pathogens. The methods of definitive diagnosis and identification of bacteria, which are time consuming, are based on cultural, biochemical and serological characters. To addr...
Article
The present study was undertaken for population genetic analysis of microsatellite variation in three indigenous goat breeds viz: Gohilwadi, Surti and Zalawadi using 19 microsatellite markers selected from the list suggested by International Society for Animal Genetics (ISAG). Out of 19 microsatellites, 18 microsatellites were amplified and observe...

Questions

Question (1)
Question
Can someone help me how to desgin a workable matrix file from Raw RNAseq data. I am very new to R , Please help?

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Cited By

Projects

Projects (5)
Project
Using High throughput WGS/WES and ScRNA sequencing to determine differentially factors and genes involved in developing cancer in kids. Furthermore using deep sequencing to determine inherent germline and acquired somatic mutations in children with cancers.
Project
Molecular characterization of Kenkatha breed of cattle using 25 microsatellite markers