Article
Biology
Lu Yang, Yan Er Ng, Haipeng Sun, Ying Li, Lucas C. S. Chini, Nathan K. Lebrasseur, Jun Chen, Xu Zhang
Summary: In this study, a single-cell annotation tool called scMayoMap was developed, which can provide fast and accurate cell type annotation by integrating with a comprehensive cell marker database named scMayoMapDatabase. The effectiveness of scMayoMap was demonstrated in multiple independent scRNA-seq datasets, and it has the potential to assist researchers in analyzing and annotating cell types in a user-friendly manner.
Article
Biochemical Research Methods
Shangru Jia, Artem Lysenko, Keith A. Boroevich, Alok Sharma, Tatsuhiko Tsunoda
Summary: Cell-type annotation is a critical step in analyzing scRNA-seq data. Most current methods use unsupervised clustering algorithms, resulting in rough classification. To address this issue, we propose scDeepInsight, a supervised annotation method that performs manifold assignments, data integration, supervised training, outlier detection, and cell-type annotation. It can also identify active genes related to cell-types.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Isar Nassiri, Benjamin Fairfax, Angela Lee, Yanxia Wu, David Buck, Paolo Piazza
Summary: This study presents an R package, scQCEA, for quality control and enrichment analysis of single-cell RNA sequencing data. It can generate reports and visualize quality scores for comparison and evaluation. It also provides automated cell type annotation and reference gene sets. The tool allows examination of biases and outliers and objective selection of optimal cluster numbers before downstream analysis. Rating: 8/10.
Article
Genetics & Heredity
Roger P. Alexander, Robert R. Kitchen, Juan Pablo Tosar, Matthew Roth, Pieter Mestdagh, Klaas E. A. Max, Joel Rozowsky, Karolina Elzbieta Kaczor-Urbanowicz, Justin Chang, Leonora Balaj, Bojan Losic, Eric L. Van Nostrand, Emily LaPlante, Bogdan Mateescu, Brian S. White, Rongshan Yu, Aleksander Milosavljevic, Gustavo Stolovitzky, Ryan M. Spengler
Summary: We now understand the importance of extracellular RNA (exRNA) in intercellular signaling, disease biomarkers, and new strategies for disease treatment. The online workshop hosted by the Extracellular RNA Communication Consortium (ERCC) aimed to address the challenges of exRNA data analysis and discuss best practices and open problems in the field. The workshop targeted three main audiences - experimentalists, computational and data scientists, and newcomers to the field.
FRONTIERS IN GENETICS
(2022)
Article
Chemistry, Analytical
Youngchun Kwon, Hyukju Kwon, Jongmin Han, Myeonginn Kang, Ji-Yeong Kim, Dongyeeb Shin, Youn-Suk Choi, Seokho Kang
Summary: This study presents an improved transfer learning method using a pretrained graph neural network (GNN) to better predict the retention time (RT) of molecules for a target chromatographic system. The proposed method achieves superior predictive performance on various chromatographic systems, particularly when only a small training data set is available.
ANALYTICAL CHEMISTRY
(2023)
Review
Biochemistry & Molecular Biology
Mattia Furlan, Anna Delgado-Tejedor, Logan Mulroney, Mattia Pelizzola, Eva Maria Novoa, Tommaso Leonardi
Summary: The covalent modification of RNA molecules plays fundamental roles in cellular processes, and nanopore direct RNA sequencing technology offers a way to detect modifications at a single-molecule resolution. However, analyzing the data for RNA modification detection remains a complex task with many challenges. Various approaches have been proposed to address this issue, resulting in a diverse range of tools available.
Article
Biochemical Research Methods
Anna-Maria Liebhoff, Kevin Menden, Alena Laschtowitz, Andre Franke, Christoph Schramm, Stefan Bonn
Summary: Pathonoia is an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall, and provides an easy-to-use analysis framework to highlight potential microbe-host interactions.
BMC BIOINFORMATICS
(2023)
Review
Biochemical Research Methods
Zilong Zhang, Feifei Cui, Chen Lin, Lingling Zhao, Chunyu Wang, Quan Zou
Summary: This review summarizes the most widely used methods in single-cell RNA sequencing data analysis, covering clustering, trajectory inference, cell-type annotation, and dataset integration. Advantages and limitations of these methods are comprehensively discussed, providing suggestions for selecting appropriate methods in different situations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Alex Hildebrandt, Benedikt Kirchner, Esther N. M. Nolte-'t Hoen, Michael W. Pfaffl
Summary: Extracellular vesicles (EVs) are nanometer-sized, membrane-enclosed vesicles released by cells for intercellular communication. miRNAs in EVs are of interest as diagnostic biomarkers in liquid biopsies. miREV is a database that assists researchers in finding suitable reference miRNAs for their experimental setups, facilitating validation experiments without the need for complex transcriptome analyses beforehand.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Computer Science, Software Engineering
Bogdan Ruszczak, Krzysztof Kotowski, Jacek Andrzejewski, Christoph Haskamp, Jakub Nalepa
Summary: Satellite telemetry data presents challenges in terms of volume, sampling rates, redundancy, and interconnections. Existing tools do not efficiently handle satellite telemetry and lack a user-friendly interface. To address this gap, we propose the web-based OXI tool, optimized for handling real satellite telemetry data, with improved data loading, visualization, and annotation capabilities. The tool was designed and evaluated in collaboration with domain experts from Airbus and ESA.
Review
Plant Sciences
Vahid Jalali Javaran, Peter Moffett, Pierre Lemoyne, Dong Xu, Charith Raj Adkar-Purushothama, Mamadou Lamine Fall
Summary: Grapevine is one of the most cultivated fruit plants in the world and has a significant impact on economies through wine and fruit production. The grape and wine industry has been facing outbreaks of viral diseases and nanopore sequencing technology, as a third-generation sequencing platform, shows potential in understanding grapevine viruses. Nanopore sequencing allows for direct sequencing of RNA and DNA, is faster and more cost-effective, and can be easily carried for field viral disease surveillance.
Article
Biochemistry & Molecular Biology
Liliana Florea, Lindsay Payer, Corina Antonescu, Guangyu Yang, Kathleen Burns
Summary: Alu exonization events contribute to 5% of alternatively spliced exons in the human genome, and computational methods have been developed to detect Alu sequences in mRNA transcripts. Analysis of 117 GTEx human frontal cortex samples revealed hundreds of Alu-containing mRNAs, including both fixed Alu loci and polymorphic Alu elements. This unique resource provides valuable insights into the characteristics and tissue-specific expression patterns of Alu-containing mRNAs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Genetics & Heredity
Rebecca J. Hertzman, Pooja Deshpande, Shay Leary, Yueran Li, Ramesh Ram, Abha Chopra, Don Cooper, Mark Watson, Amy M. Palubinsky, Simon Mallal, Andrew Gibson, Elizabeth J. Phillips
Summary: Type B adverse drug reactions are iatrogenic immune-mediated syndromes with mechanisms that are not fully understood. Single-cell platforms have provided tools to examine heterogeneous immune cell populations, but the requirement for advanced bioinformatics expertise limits their application.
FRONTIERS IN GENETICS
(2021)
Article
Genetics & Heredity
Tithi S. Trivedi, Maulikkumar P. Patel, Vishal Nanavaty, Archana U. Mankad, Rakesh M. Rawal, Saumya K. Patel
Summary: This study used high-throughput sequencing and bioinformatics analysis to uncover miRNAs in Holarrhena pubescens, an effective medicinal plant from the Indian subcontinent. The miRNAs were found to potentially regulate specific human genes and play a role in various biological processes and signaling pathways, with associations to several diseases. The study provides new insight into the potential mechanism of action underlying the medicinal properties of this plant species.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2023)
Article
Cell Biology
Alex Hildebrandt, Benedikt Kirchner, Agnes S. Meidert, Florian Brandes, Anja Lindemann, Gero Doose, Alexander Doege, Rolf Weidenhagen, Marlene Reithmair, Gustav Schelling, Michael W. Pfaffl
Summary: The study analyzed serum-derived miRNA profiles from patients and volunteers to identify potential biomarkers for atherosclerosis. The differential expression analysis found 27 differentially expressed miRNAs in patients compared to healthy volunteers, with specific miRNA fingerprints for different atherosclerotic manifestations. Overrepresentation analysis revealed relevant biological processes related to atherosclerosis, indicating the potential of these miRNAs as biomarker candidates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Hui Ma, Tao Li, Xuefeng Xie, Long Jiang, Jingwei Ye, Chenjia Gong, Hanwei Jiang, Suixing Fan, Huan Zhang, Baolu Shi, Beibei Zhang, Xiaohua Jiang, Yang Li, Jianteng Zhou, Jianze Xu, Xingxia Zhang, Xiaoning Hou, Hao Yin, Yuanwei Zhang, Qinghua Shi
Summary: This study found that RAD51AP2 plays a specific role in the formation of crossovers on XY chromosomes in the pseudoautosomal region, and its mutation leads to compromised DSB repair in PARs.
Article
Cell Biology
Ao Ma, Aurang Zeb, Imtiaz Ali, Daren Zhao, Asad Khan, Beibei Zhang, Jianteng Zhou, Ranjha Khan, Huan Zhang, Yuanwei Zhang, Ihsan Khan, Wasim Shah, Haider Ali, Abdul Rafay Javed, Hui Ma, Qinghua Shi
Summary: In this study, homozygous variants in CFAP61 were found to be associated with Multiple morphological abnormalities of the flagella (MMAF) and male infertility. The study revealed severe disorganization of axonemal ultrastructures in spermatozoa from patients, along with the absence of certain key components. These findings emphasize the essential role of the CFAP61 gene in normal sperm flagellum structure in humans.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Medicine, General & Internal
Hira Jamil, Adeela Awan, Atif Akbar, Muhammad Babar, Sana Akhtar, Rana Khalid Iqbal, Furhan Iqbal
Summary: This study found a significant association between the presence of rs1799883 in the fatty acid binding protein-2 gene and the absence of the glutathione S-transferase mu gene with the development of type 2 diabetes.
JOURNAL OF THE PAKISTAN MEDICAL ASSOCIATION
(2022)
Article
Cell Biology
Jianze Xu, Jianing Gao, Junyan Liu, Xue Huang, Huan Zhang, Ao Ma, Jingwei Ye, Xingxia Zhang, Yang Li, Gang Yang, Hao Yin, Ranjha Khan, Tao Li, Suixing Fan, Xiaohua Jiang, Yuanwei Zhang, Hanwei Jiang, Hui Ma, Qinghua Shi
Summary: This study reveals that ZFP541 is essential for the suppression of DNA double-strand break (DSB) formation after mid-pachytene stage in meiosis. Deletion of Zfp541 gene in mice leads to abnormal recruitment of DSB machinery, resulting in massive DSBs and meiotic arrest at the diplotene stage. ZFP541 functions as a transcriptional regulator in pachytene spermatocytes, maintaining the repression of genes related to meiotic DSB formation and ensuring meiosis progression.
Article
Microbiology
Salama Al-Hamidhi, Asia Parveen, Furhan Iqbal, Muhammad Asif, Naheed Akhtar, Elshafie Elshafie, Albano Beja-Pereira, Hamza A. Babiker
Summary: The study found that the genetic structure of Theileria annulata in Pakistan is similar to that in Oman, Tunisia, and Turkey, showing a high level of genetic diversity. The genotypes of the parasite in these countries are geographically sub-structured. The parasite populations in Oman, Indian Subcontinent (Pakistan), Africa (Tunisia), and Europe (Turkey) overlap, indicating some level of parasite gene flow between neighboring countries.
Article
Biochemistry & Molecular Biology
Chenjia Gong, Tanveer Abbas, Zubair Muhammad, Jianteng Zhou, Ranjha Khan, Hui Ma, Huan Zhang, Qinghua Shi, Baolu Shi
Summary: The MSH5 c.1126del mutation may cause meiotic recombination failure and infertility in humans. The study of human spermatocytes also reveals the importance of MutS γ in synapsis and meiotic recombination.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Conghui Tian, Lingxiao Shen, Chenjia Gong, Yunxia Cao, Qinghua Shi, Gang Zhao
Summary: This study achieved low-concentration cryopreservation of preantral follicles by using microencapsulation and nanowarming. The research found that this method improved the viability of preantral follicles and maintained their ability to form cavities, compared to conventional water bath warming. Furthermore, it showed no significant impact on in vitro fertilization and embryo transfer.
NATURE COMMUNICATIONS
(2022)
Article
Parasitology
Nusrat Yasmeen, Muhammad Kashif, Tehreem Arif, Adil Khan, Muhammad Ali, Muzaffar Ali Khan, Muhammad Farooq, Mourad Ben Said, Furhan Iqbal
Summary: In this study, a total of 593 ticks were collected from one-humped camels in two tehsils of Layyah district, Punjab, Pakistan, in order to investigate their diversity, prevalence, and distribution. The results showed that camels located in Tehsil Choubara had a significantly higher tick infestation rate compared to camels from Tehsil Layyah. It was also observed that older camels were more prone to tick infestation. Hyalomma and Rhipicephalus were the two genera identified, with Hyalomma genus being the most prevalent.
VETERINARY PARASITOLOGY- REGIONAL STUDIES AND REPORTS
(2023)
Article
Agriculture, Dairy & Animal Science
Muhammad Sheraz, Fakhur Ud Din, Muhammad Saad Un Nabi, Sana Rao, Bisma Shafiq, Ghulam Murtaza, Muhammad Farooq, Furhan Iqbal
Summary: The study investigated the genotype and allelic frequency of SNP at 222 G > A in HSP70 and at ex6-7390T22G in the HSP90 gene in 204 sheep from Punjab. The tetra-primer amplification refractory mutation system-polymerase chain reaction (T-ARMS-PCR) revealed significant genotype frequency variation in the HSP70 gene, while the allelic frequency remained unaffected. The study suggests the genotypic screening of sheep before selection as breeders to improve the profitability and sustainability of animal production systems in Pakistan.
ANIMAL BIOTECHNOLOGY
(2023)
Article
Agriculture, Dairy & Animal Science
Ambar Rafiq, Gul Zareen, Sana Akbar, Muhammad Asif, Nadeem Ahmed, Nashra Bibi, Ume Habiba, Asmat Ullah Khan, Rehan Sadiq Shaikh, Furhan Iqbal
Summary: The aim of this study was to report the genotype and allelic frequency at rs438228855 in SLC35A3 receptor gene and its association with complex vertebral malformation (CMV) in enrolled Pakistani cattle. The results showed non-significant variations in allelic and genotype frequency at rs438228855 among the three cattle breeds. The heterozygous (GT) genotype was most abundant, followed by the wild type (GG) genotype, and the mutant genotype (TT) was not observed. The study also found significant differences in various hematological parameters between the cattle breeds, but no association with the genotype at rs438228855 was observed.
REPRODUCTION IN DOMESTIC ANIMALS
(2023)
Article
Genetics & Heredity
Kainat Arshad, Uzma Ishfaq, Muhammad Asif, Atif Akbar, Kehkashan Fatima Pitafi, Muhammad Rehan Mulghani, Uzman Shaheen, Suleman Saeed, Muhammad Arif, Ahsan Bashir, Muhammad Farooq, Alan Henry Brook, Furhan Iqbal
Summary: This study investigates the genotypes of GSTM1, GSTT1, and SNP rs1695 in GSTP1 genes and their associations with the incidence of chronic periodontal disease (CP). The results show that the absence of GSTM1, the presence of GSTT1, and the presence of the mutant allele (G) at rs1695 in GSTP1 are significantly associated with CP.
Article
Medicine, Research & Experimental
Ao Ma, Jianteng Zhou, Haider Ali, Tanveer Abbas, Imtiaz Ali, Zubair Muhammad, Sobia Dil, Jing Chen, Xiongheng Huang, Hui Ma, Daren Zhao, Beibei Zhang, Yuanwei Zhang, Wasim Shah, Basit Shah, Ghulam Murtaza, Furhan Iqbal, Muzammil Ahmad Khan, Asad Khan, Qing Li, Bo Xu, Limin Wu, Huan Zhang, Qinghua Shi
Summary: This study identified two mutations in the CFAP57 gene associated with MMAF, and further research revealed that these mutations disrupted the assembly of inner dynein arms in sperm flagella, leading to male infertility.
Article
Public, Environmental & Occupational Health
Asia Taqadus, Chien-Chun Chiou, Itzel Amaro-Estrada, Muhammad Asif, Nasreen Nasreen, Ghafoor Ahmad, Javaid Iqbal, Muhammad Ali, Adil Khan, Furhan Iqbal, Chien-Chin Chen
Summary: The present study aims to report the molecular prevalence of A. ovis in 1200 asymptomatic goats from four districts of Punjab, Pakistan. The results showed that 184 out of 1200 (15%) goat blood samples were infected with A. ovis. Risk factors associated with the prevalence of A. ovis and phylogeny of the bacterium were also documented. This study provides important insights for developing integrated control policies against A. ovis.
VECTOR-BORNE AND ZOONOTIC DISEASES
(2023)
Article
Zoology
Shahid Iqbal, Zulha Javed, Mushtaq Hussain Zahid, Qurat ul Ane Gillani, Furhan Iqbal
Summary: This study investigated the effects of ethanolic extracts of Pongamia pinnata (L.) Pierre leaves and Eucalyptus camaldulensis Dehnh leaves on hematological parameters and biochemical components of blood serum in male albino mice. The results showed that the P. pinnata leaf extract significantly increased cholesterol and triglyceride levels, while the E. camaldulensis leaf extract significantly reduced white blood cells, platelets, and alanine aminotransferase, and increased mean corpuscular hemoglobin levels. Both extracts showed a potential to disturb the blood biochemistry of healthy male albino mice, with more pronounced effects observed with the E. camaldulensis leaf extract.
PAKISTAN JOURNAL OF ZOOLOGY
(2023)
Article
Andrology
Muhammad Zubair, Ranjha Khan, Ao Ma, Uzma Hameed, Mazhar Khan, Tanveer Abbas, Riaz Ahmad, Jian-Teng Zhou, Wasim Shah, Ansar Hussain, Nisar Ahmed, Ihsan Khan, Khalid Khan, Yuan-Wei Zhang, Huan Zhang, Li-Min Wu, Qing-Hua Shi
Summary: Mutations in the CCDC103 gene may be a cause of severe sperm qualitative defects, which can affect male fertility.
ASIAN JOURNAL OF ANDROLOGY
(2022)
