Publications by authors named "Waleed Iqbal"

6 Publications

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Computational methods for single-cell DNA methylomes.

Genomics Proteomics Bioinformatics 2022 Jun 16. Epub 2022 Jun 16.

Center for Computational and Genomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, United States; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, United States. Electronic address:

Dissecting intercellular epigenetic differences is key to understanding tissue heterogeneity. Recent advances in single-cell DNA methylome profiling have presented opportunities to resolve this heterogeneity at the maximum resolution. While these advances enable us to explore frontiers of chromatin biology and better understand cell lineage relationships, they pose new challenges in data processing and interpretation. This review surveys the current state of computational tools developed for single-cell DNA methylome data. We discuss critical components of single-cell DNA methylome data analysis, including data preprocessing, quality control, imputation, dimensionality reduction, cell clustering, supervised cell annotation, cell lineage reconstruction, gene activity scoring, and integration with transcriptomics data. We will highlight unique aspects of single-cell DNA methylome data analysis and how techniques common to other single-cell omics data analyses can be adapted to analyzing DNA methylomes. Finally, we discuss existing challenges and opportunities for future development.
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http://dx.doi.org/10.1016/j.gpb.2022.05.007DOI Listing
June 2022

A deep dive into COVID-19-related messages on WhatsApp in Pakistan.

Soc Netw Anal Min 2022 15;12(1). Epub 2021 Nov 15.

MIT, Cambridge, USA.

The spread of COVID-19 and the lockdowns that followed led to an increase in activity on online social networks. This has resulted in users sharing unfiltered and unreliable information on social networks like WhatsApp, Twitter, Facebook, etc. In this work, we give an extended overview of how Pakistan's population used public WhatsApp groups for sharing information related to the pandemic. Our work is based on a major effort to annotate thousands of text and image-based messages. We explore how information propagates across WhatsApp and the user behavior around it. Specifically, we look at political polarization and its impact on how users from different political parties shared COVID-19-related content. We also try to understand information dissemination across different social networks-Twitter and WhatsApp-in Pakistan and find that there is no significant bot involvement in spreading misinformation about the pandemic.
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http://dx.doi.org/10.1007/s13278-021-00833-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8590927PMC
November 2021

RRM2B Is Frequently Amplified Across Multiple Tumor Types: Implications for DNA Repair, Cellular Survival, and Cancer Therapy.

Front Genet 2021 12;12:628758. Epub 2021 Mar 12.

Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, PA, United States.

plays a crucial role in DNA replication, repair and oxidative stress. While germline mutations have been implicated in mitochondrial disorders, its relevance to cancer has not been established. Here, using TCGA studies, we investigated alterations in cancer. We found that is highly amplified in multiple tumor types, particularly in -amplified tumors, and is associated with increased mRNA expression. We also observed that the chromosomal region 8q22.3-8q24, is amplified in multiple tumors, and includes , along with several other cancer-associated genes. An analysis of genes within this 8q-amplicon showed that cancers that have both -amplified along with have a distinct pattern of amplification compared to cancers that are unaltered or those that have amplifications in or only. Investigation of curated biological interactions revealed that gene products of the amplified 8q22.3-8q24 region have important roles in DNA repair, DNA damage response, oxygen sensing, and apoptosis pathways and interact functionally. Notably, -amplified cancers are characterized by mutation signatures of defective DNA repair and oxidative stress, and at least -amplified breast cancers are associated with poor clinical outcome. These data suggest alterations in RR2MB and possibly the interacting 8q-proteins could have a profound effect on regulatory pathways such as DNA repair and cellular survival, highlighting therapeutic opportunities in these cancers.
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http://dx.doi.org/10.3389/fgene.2021.628758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8045241PMC
March 2021

Securing Machine Learning in the Cloud: A Systematic Review of Cloud Machine Learning Security.

Front Big Data 2020 12;3:587139. Epub 2020 Nov 12.

Hamad Bin Khalifa University (HBKU), Doha, Qatar.

With the advances in machine learning (ML) and deep learning (DL) techniques, and the potency of cloud computing in offering services efficiently and cost-effectively, Machine Learning as a Service (MLaaS) cloud platforms have become popular. In addition, there is increasing adoption of third-party cloud services for outsourcing training of DL models, which requires substantial costly computational resources (e.g., high-performance graphics processing units (GPUs)). Such widespread usage of cloud-hosted ML/DL services opens a wide range of attack surfaces for adversaries to exploit the ML/DL system to achieve malicious goals. In this article, we conduct a systematic evaluation of literature of cloud-hosted ML/DL models along both the important dimensions- and -related to their security. Our systematic review identified a total of 31 related articles out of which 19 focused on attack, six focused on defense, and six focused on both attack and defense. Our evaluation reveals that there is an increasing interest from the research community on the perspective of attacking and defending different attacks on Machine Learning as a Service platforms. In addition, we identify the limitations and pitfalls of the analyzed articles and highlight open research issues that require further investigation.
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http://dx.doi.org/10.3389/fdata.2020.587139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7931962PMC
November 2020

Interaction of germline variants in a family with a history of early-onset clear cell renal cell carcinoma.

Mol Genet Genomic Med 2019 03 24;7(3):e556. Epub 2019 Jan 24.

Cancer Prevention and Control Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania.

Background: Identification of genetic factors causing predisposition to renal cell carcinoma has helped improve screening, early detection, and patient survival.

Methods: We report the characterization of a proband with renal and thyroid cancers and a family history of renal and other cancers by whole-exome sequencing (WES), coupled with WES analysis of germline DNA from additional affected and unaffected family members.

Results: This work identified multiple predicted protein-damaging variants relevant to the pattern of inherited cancer risk. Among these, the proband and an affected brother each had a heterozygous Ala45Thr variant in SDHA, a component of the succinate dehydrogenase (SDH) complex. SDH defects are associated with mitochondrial disorders and risk for various cancers; immunochemical analysis indicated loss of SDHB protein expression in the patient's tumor, compatible with SDH deficiency. Integrated analysis of public databases and structural predictions indicated that the two affected individuals also had additional variants in genes including TGFB2, TRAP1, PARP1, and EGF, each potentially relevant to cancer risk alone or in conjunction with the SDHA variant. In addition, allelic imbalances of PARP1 and TGFB2 were detected in the tumor of the proband.

Conclusion: Together, these data suggest the possibility of risk associated with interaction of two or more variants.
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http://dx.doi.org/10.1002/mgg3.556DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6418363PMC
March 2019

FTIR spectroscopic study of poly(ethylene glycol)-nifedipine dispersion stability in different relative humidities.

J Pharm Sci 2015 Jan 19;104(1):280-4. Epub 2014 Nov 19.

Institute of Pharmaceutical Science, King's College London, London, SE1 9NH, UK.

Solid dispersion has shown to be a promising formulation strategy to enhance dissolution for hydrophobic drugs. However, solid dispersions are often thermodynamically unstable, there is a continuous interest in studying their stabilities. In this study, attenuated total reflectance Fourier transform infrared (ATR-FTIR) was used to compare the amount of crystalline nifedipine formed in different formula of poly(ethylene glycol) (PEG)-nifedipine solid dispersions when exposed at various relative humidities (RHs) for 2 h at 40°C. The ratio of the crystalline nifedipine band and an internal reference band in the out of plane δ(C-H) region has been used to indicate the relative degree of drug crystallisation in a sample. A band ratio of ∼0.05 and 0.5 was respectively indicative of a fully amorphous or crystallised drug in the formula. Results show that increasing the RH generally increases the amount of crystalline nifedipine. Formulations with low (5%, w/w) nifedipine concentration in higher molecular weight PEG were found to be better at resisting crystallisation. Deliquescence of the 10% nifedipine in PEG 4000 was observed at 77% and 100% RH with a reduction in crystalline nifedipine. All 5% (w/w) nifedipine samples were stable at RH below 77%. Crystallisation of nifedipine occurred at all RH when drug loading was increased to 10% (w/w).
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http://dx.doi.org/10.1002/jps.24261DOI Listing
January 2015
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