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Article ; Online: Unearthing Insights into Metabolic Syndrome by Linking Drugs, Targets, and Gene Expressions Using Similarity Measures and Graph Theory.

Zafar, Alwaz / Wajid, Bilal / Shabbir, Ans / Gohar, Fahim / Ahsan, Momina / Ahmad, Sarfraz / Wajid, Imran / Anwar, Faria / Mazhar, Fazeelat

Current computer-aided drug design

2023

Abstract: Aims and objectives: Metabolic syndrome (MetS) is a group of metabolic disorders that includes obesity in combination with at least any two of the following conditions, i.e., insulin resistance, high blood pressure, low HDL cholesterol, and high ... ...

Abstract	Aims and objectives: Metabolic syndrome (MetS) is a group of metabolic disorders that includes obesity in combination with at least any two of the following conditions, i.e., insulin resistance, high blood pressure, low HDL cholesterol, and high triglycerides level. Treatment of this syndrome is challenging because of the multiple interlinked factors that lead to increased risks of type-2 diabetes and cardiovascular diseases. This study aims to conduct extensive insilico analysis to (i) find central genes that play a pivotal role in MetS and (ii) propose suitable drugs for therapy. Our objective is to first create a drug-disease network and then identify novel genes in the drug-disease network with strong associations to drug targets, which can help in increasing the therapeutical effects of different drugs. In the future, these novel genes can be used to calculate drug synergy and propose new drugs for the effective treatment of MetS. Methods: For this purpose, we (a) investigated associated drugs and pathways for MetS, (b) employed eight different similarity measures to construct eight gene regulatory networks, (c) chose an optimal network, where a maximum number of drug targets were central, (d) determined central genes exhibiting strong associations with these drug targets and associated disease-causing pathways, and lastly (e) employed these candidate genes to propose suitable drugs. Results: Our results indicated (i) a novel drug-disease network complex, with (ii) novel genes associated with MetS. Conclusion: Our developed drug-disease network complex closely represents MetS with associated novel findings and markers for an improved understanding of the disease and suggested therapy.
Language	English
Publishing date	2023-08-17
Publishing country	United Arab Emirates
Document type	Journal Article
ISSN	1875-6697
ISSN (online)	1875-6697
DOI	10.2174/1573409920666230817101913
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Article ; Online: A novel missense compound heterozygous variant in TLR1 gene is associated with susceptibility to rheumatoid arthritis - structural perspective and functional annotations.

Pasha, Usman / Hanif, Kiran / Nisar, Haseeb / Abid, Rizwan / Mirza, Muhammad Usman / Wajid, Bilal / Sadaf, Saima

Clinical rheumatology

2023 Volume 42, Issue 11, Page(s) 3097–3111

Abstract: Introduction: Besides human leukocyte antigen (HLA-DRB1) locus, more than 100 loci across the genome have been identified and linked with the onset, expression and/or progression of rheumatoid arthritis (RA). However, there are still grey areas in our ... ...

Abstract	Introduction: Besides human leukocyte antigen (HLA-DRB1) locus, more than 100 loci across the genome have been identified and linked with the onset, expression and/or progression of rheumatoid arthritis (RA). However, there are still grey areas in our understanding of the key genetic contributors of the disease, particularly in familial cases. Methods: In the present study, we have performed the whole exome sequencing (WES) of RA patients from two consanguineous families of Pakistan in a quest to identify novel, high-impact, RA-susceptibility genetic variants. Results: Through stepwise filtering, around 17,000 variants (common in the affected members) were recognized, out of which 2651 were predicted to be deleterious. Of these, 196 had direct relevance to RA. When selected for homozygous recessive mode of inheritance, two novel pathogenic variants (c.1324T>C, p.Cys Conclusion: The results, validated through case-control study subjects, suggested that the variants identified through WES and confirmed through Sanger sequencing and MDS are the novel disease variants and are likely to confer RA-susceptibility, independently and/or in a family-specific context. Key Points • Exploration of population based/ethno-specific big data is imperative to identify novel causal variants of RA. • Two new deleterious missense mutations in mutational hotspot exon 4 of TLR1 gene have been identified in Pakistani RA patients. • MD simulation data provides evidence for domain's rigidification, conferring stability to mutant TLR1-TIR/TIRAP-TIR complex, with concomitant increase in production of pro-inflammatory cytokines, thus adding to the onset/erosive outcome of RA.
MeSH term(s)	Humans ; Arthritis, Rheumatoid/genetics ; Case-Control Studies ; Cytokines ; Genetic Predisposition to Disease ; Mutation, Missense ; Toll-Like Receptor 1/genetics
Chemical Substances	Cytokines ; Toll-Like Receptor 1 ; TLR1 protein, human
Language	English
Publishing date	2023-07-21
Publishing country	Germany
Document type	Journal Article
ZDB-ID	604755-5
ISSN	1434-9949 ; 0770-3198
ISSN (online)	1434-9949
ISSN	0770-3198
DOI	10.1007/s10067-023-06702-9
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Article ; Online: Do it yourself guide to genome assembly.

Wajid, Bilal / Serpedin, Erchin

Briefings in functional genomics

2016 Volume 15, Issue 1, Page(s) 1–9

Abstract: Bioinformatics skills required for genome sequencing often represent a significant hurdle for many researchers working in computational biology. This humble effort highlights the significance of genome assembly as a research area, focuses on its need to ... ...

Abstract	Bioinformatics skills required for genome sequencing often represent a significant hurdle for many researchers working in computational biology. This humble effort highlights the significance of genome assembly as a research area, focuses on its need to remain accurate, provides details about the characteristics of the raw data, examines some key metrics, emphasizes some tools and draws attention to a generic tutorial with example data that outlines the whole pipeline for next-generation sequencing. The article concludes by pointing out some major future research problems.
MeSH term(s)	Algorithms ; Computational Biology/methods ; Genome, Human ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Sequence Analysis, DNA/methods
Language	English
Publishing date	2016-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2540916-5
ISSN	2041-2657 ; 2041-2649 ; 2041-2647
ISSN (online)	2041-2657
ISSN	2041-2649 ; 2041-2647
DOI	10.1093/bfgp/elu042
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Article: Music of metagenomics—a review of its applications, analysis pipeline, and associated tools [Erratum: February 2022, v.22(1); p.137]

Wajid, Bilal / Anwar, Faria / Wajid, Imran / Nisar, Haseeb / Meraj, Sharoze / Zafar, Ali / Al-Shawaqfeh, Mustafa Kamal / Ekti, Ali Riza / Khatoon, Asia / Suchodolski, Jan S.

Functional & integrative genomics. 2022 Feb., v. 22, no. 1

2022

Abstract: This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of ... ...

Abstract	This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the “metagenome.”
Keywords	ecosystems ; genome ; metagenomics ; music ; taxonomy
Language	English
Dates of publication	2022-02
Size	p. 3-26.
Publishing place	Springer Berlin Heidelberg
Document type	Article
Note	Review
ZDB-ID	2014670-X
ISSN	1438-7948 ; 1438-793X
ISSN (online)	1438-7948
ISSN	1438-793X
DOI	10.1007/s10142-021-00810-y
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Article ; Online: MetumpX-a metabolomics support package for untargeted mass spectrometry.

Wajid, Bilal / Iqbal, Hasan / Jamil, Momina / Rafique, Hafsa / Anwar, Faria

Bioinformatics (Oxford, England)

2019 Volume 36, Issue 5, Page(s) 1647–1648

Abstract: Motivation: Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and ... ...

Abstract	Motivation: Metabolomics is a data analysis and interpretation field aiming to study functions of small molecules within the organism. Consequently Metabolomics requires researchers in life sciences to be comfortable in downloading, installing and scripting of software that are mostly not user friendly and lack basic GUIs. As the researchers struggle with these skills, there is a dire need to develop software packages that can automatically install software pipelines truly speeding up the learning curve to build software workstations. Therefore, this paper aims to provide MetumpX, a software package that eases in the installation of 103 software by automatically resolving their individual dependencies and also allowing the users to choose which software works best for them. Results: MetumpX is a Ubuntu-based software package that facilitate easy download and installation of 103 tools spread across the standard metabolomics pipeline. As far as the authors know MetumpX is the only solution of its kind where the focus lies on automating development of software workstations. Availability and implementation: https://github.com/hasaniqbal777/MetumpX-bin. Supplementary information: Supplementary data are available at Bioinformatics online.
MeSH term(s)	Data Analysis ; Mass Spectrometry ; Metabolomics ; Software
Language	English
Publishing date	2019-10-09
Publishing country	England
Document type	Journal Article
ZDB-ID	1422668-6
ISSN	1367-4811 ; 1367-4803
ISSN (online)	1367-4811
ISSN	1367-4803
DOI	10.1093/bioinformatics/btz765
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Article ; Online: Bioinformatics and systems biology analysis revealed PMID26394986-Compound-10 as potential repurposable drug against covid-19.

Nisar, Haseeb / Wajid, Bilal / Anwar, Faria / Ahmad, Ashfaq / Javaid, Anum / Attique, Syed Awais / Nisar, Wardah / Saeed, Amir / Shahid, Samiah / Sadaf, Saima

Journal of biomolecular structure & dynamics

2023 , Page(s) 1–14

Abstract: The global health pandemic known as COVID-19, which stems from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a significant concern worldwide. Several treatment methods exist for COVID-19; however, there is an urgent demand ... ...

Abstract	The global health pandemic known as COVID-19, which stems from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has become a significant concern worldwide. Several treatment methods exist for COVID-19; however, there is an urgent demand for previously established drugs and vaccines to effectively combat the disease. Since, discovering new drugs poses a significant challenge, making the repurposing of existing drugs can potentially reduce time and costs compared to developing entirely new drugs from scratch. The objective of this study is to identify hub genes and associated repurposed drugs targeting them. We analyzed differentially expressed genes (DEGs) by analyzing RNA-seq transcriptomic datasets and integrated with genes associated with COVID-19 present in different databases. We detected 173 Covid-19 associated genes for the construction of a protein-protein interaction (PPI) network which resulted in the identification of the top 10 hub genes/proteins (STAT1, IRF7, MX1, IRF9, ISG15, OAS3, OAS2, OAS1, IRF3, and IRF1). Hub genes were subjected to GO functional and KEGG pathway enrichment analyses, which indicated some key roles and signaling pathways that were strongly related to SARS-CoV-2 infections. We conducted drug repurposing analysis using CMap, TTD, and DrugBank databases with these 10 hub genes, leading to the identification of Piceatannol, CKD-712, and PMID26394986-Compound-10 as top-ranked candidate drugs. Finally, drug-gene interactions analysis through molecular docking and validated
Language	English
Publishing date	2023-08-03
Publishing country	England
Document type	Journal Article
ZDB-ID	49157-3
ISSN	1538-0254 ; 0739-1102
ISSN (online)	1538-0254
ISSN	0739-1102
DOI	10.1080/07391102.2023.2242500
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Article ; Online: Whole-genome sequencing as a first-tier diagnostic framework for rare genetic diseases.

Nisar, Haseeb / Wajid, Bilal / Shahid, Samiah / Anwar, Faria / Wajid, Imran / Khatoon, Asia / Sattar, Mian Usman / Sadaf, Saima

Experimental biology and medicine (Maywood, N.J.)

2021 Volume 246, Issue 24, Page(s) 2610–2617

Abstract: Rare diseases affect nearly 300 million people globally with most patients aged five or less. Traditional diagnostic approaches have provided much of the diagnosis; however, there are limitations. For instance, simply inadequate and untimely diagnosis ... ...

Abstract	Rare diseases affect nearly 300 million people globally with most patients aged five or less. Traditional diagnostic approaches have provided much of the diagnosis; however, there are limitations. For instance, simply inadequate and untimely diagnosis adversely affects both the patient and their families. This review advocates the use of whole genome sequencing in clinical settings for diagnosis of rare genetic diseases by showcasing five case studies. These examples specifically describe the utilization of whole genome sequencing, which helped in providing relief to patients via correct diagnosis followed by use of precision medicine.
MeSH term(s)	Humans ; Rare Diseases/diagnosis ; Rare Diseases/genetics ; Whole Genome Sequencing/methods
Language	English
Publishing date	2021-09-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	4015-0
ISSN	1535-3699 ; 1525-1373 ; 0037-9727
ISSN (online)	1535-3699 ; 1525-1373
ISSN	0037-9727
DOI	10.1177/15353702211040046
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Article ; Online: Review of general algorithmic features for genome assemblers for next generation sequencers.

Wajid, Bilal / Serpedin, Erchin

Genomics, proteomics & bioinformatics

2012 Volume 10, Issue 2, Page(s) 58–73

Abstract: In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly ... ...

Abstract	In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.
MeSH term(s)	Algorithms ; Computational Biology ; Contig Mapping ; Genome ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2012-06-09
Publishing country	China
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2012.05.006
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Article: Review of General Algorithmic Features for Genome Assemblers for Next Generation Sequencers

Wajid, Bilal / Serpedin, Erchin

Genomics, proteomics & bioinformatics. 2012 Apr., v. 10, no. 2

2012

Abstract	In the realm of bioinformatics and computational biology, the most rudimentary data upon which all the analysis is built is the sequence data of genes, proteins and RNA. The sequence data of the entire genome is the solution to the genome assembly problem. The scope of this contribution is to provide an overview on the art of problem-solving applied within the domain of genome assembly in the next-generation sequencing (NGS) platforms. This article discusses the major genome assemblers that were proposed in the literature during the past decade by outlining their basic working principles. It is intended to act as a qualitative, not a quantitative, tutorial to all working on genome assemblers pertaining to the next generation of sequencers. We discuss the theoretical aspects of various genome assemblers, identifying their working schemes. We also discuss briefly the direction in which the area is headed towards along with discussing core issues on software simplicity.
Keywords	RNA ; algorithms ; bioinformatics ; computer software ; genes ; genome assembly ; high-throughput nucleotide sequencing ; problem solving ; proteins
Language	English
Dates of publication	2012-04
Size	p. 58-73.
Publishing place	Elsevier Ltd
Document type	Article
ZDB-ID	2240213-5
ISSN	2210-3244 ; 1672-0229
ISSN (online)	2210-3244
ISSN	1672-0229
DOI	10.1016/j.gpb.2012.05.006
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Article ; Online: The A, C, G, and T of Genome Assembly.

Wajid, Bilal / Sohail, Muhammad U / Ekti, Ali R / Serpedin, Erchin

BioMed research international

2016 Volume 2016, Page(s) 6329217

Abstract: Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in ... ...

Abstract	Genome assembly in its two decades of history has produced significant research, in terms of both biotechnology and computational biology. This contribution delineates sequencing platforms and their characteristics, examines key steps involved in filtering and processing raw data, explains assembly frameworks, and discusses quality statistics for the assessment of the assembled sequence. Furthermore, the paper explores recent Ubuntu-based software environments oriented towards genome assembly as well as some avenues for future research.
MeSH term(s)	Genome, Human/genetics ; Humans ; Sequence Analysis, DNA/methods ; Software
Language	English
Publishing date	2016
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	2698540-8
ISSN	2314-6141 ; 2314-6133
ISSN (online)	2314-6141
ISSN	2314-6133
DOI	10.1155/2016/6329217
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