Article
Biochemical Research Methods
Muhammad Tahir, Muhammad Sardaraz, Zahid Mehmood, Muhammad Saud Khan
Summary: This paper proposed an efficient error estimation computational model ESREEM to assess error rates in NGS data. The model is based on a probabilistic error model integrated with Hidden Markov Model, and experimental results show that it efficiently estimates errors compared to state-of-the-art algorithms.
CURRENT BIOINFORMATICS
(2021)
Review
Biochemistry & Molecular Biology
Sushmaa Chandralekha Selvakumar, K. Auxzilia Preethi, Kehinde Ross, Deusdedit Tusubira, Mohd Wajid Ali Khan, Panagal Mani, Tentu Nageswara Rao, Durairaj Sekar
Summary: Personalized or precision medicine combines genetic information with phenotypic and environmental characteristics to tailor healthcare to individuals, enabled by cancer genome sequencing. The advantages of NGS, such as limited sample requirements and the development of biomarkers, have accelerated personalized medicine.
Article
Virology
Laila Sara Arroyo Muhr, Daniel Guerendiain, Kate Cuschieri, Karin Sundstrom
Summary: NGS technology provides powerful opportunities for HPV genomics research, but rigorous validation and quality assurance procedures are essential to ensure reliable interpretation of results. Recommendations for optimizing sequencing data yield and curated bioinformatical procedures are crucial for robust analysis of HPV genotypes and mutations. International standards for quality assurance in HPV NGS should be developed to enhance testing and diagnostics in global efforts.
Review
Medicine, General & Internal
Syahzuwan Hassan, Rosnah Bahar, Muhammad Farid Johan, Ezzeddin Kamil Mohamed Hashim, Wan Zaidah Abdullah, Ezalia Esa, Faidatul Syazlin Abdul Hamid, Zefarina Zulkafli
Summary: Thalassemia is a highly heterogeneous disease with over a thousand recorded mutation types worldwide. Conventional PCR-based DNA analysis for thalassemia diagnosis is time-consuming and resource-intensive due to phenotype variability, disease complexity, and test limitations. Advanced molecular techniques such as next-generation sequencing (NGS) and third-generation sequencing (TGS) offer more suitable and valuable options for DNA analysis of thalassemia. The continuous improvement of sequencing methods and bioinformatics tools, particularly for identifying copy number variations and homologous genes, will lead to more accurate thalassemia detection.
Review
Genetics & Heredity
Muntazir Mushtaq, Aejaz Ahmad Dar, Umer Basu, Basharat Ahmad Bhat, Rakeeb Ahmad Mir, Sanskriti Vats, M. S. Dar, Anshika Tyagi, Sajad Ali, Monika Bansal, Gyanendra Kumar Rai, Shabir Hussain Wani
Summary: Plant pathology has been revolutionized by next-generation sequencing technologies, enabling fast, cost-effective, and reliable diagnostics for pathogens. NGS has advanced research and diagnostics of plant infecting viromes, bridging plant virology with genome editing technologies, and holds potential for improving plant health. Integration of NGS with CRISPR-based genome editing technologies is poised to revolutionize combating deadly plant viruses at the genomic level.
FRONTIERS IN GENETICS
(2021)
Review
Microbiology
Muhammad Shafiq Shahid, Muhammad Naeem Sattar, Zafar Iqbal, Amir Raza, Abdullah M. Al-Sadi
Summary: In recent years, next-generation sequencing (NGS) and CRISPR-Cas technologies have revolutionized plant virology. NGS allows for rapid sequencing and deciphering of viral metagenomes, while CRISPR-Cas enables the development of effective virus resistance approaches.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Immunology
Lauren M. Walker, Andrea R. Shiakolas, Rohit Venkat, Zhaojing Ariel Liu, Steven Wall, Nagarajan Raju, Kelsey A. Pilewski, Ian Setliff, Amyn A. Murji, Rebecca Gillespie, Nigel A. Makoah, Masaru Kanekiyo, Mark Connors, Lynn Morris, Ivelin S. Georgiev
Summary: The development of novel technologies for discovering human monoclonal antibodies has been extremely valuable in combating infectious diseases. LIBRA-seq with epitope mapping is a next-generation sequencing technology that can determine residue-level epitopes for thousands of single B cells simultaneously, making it an efficient tool for high-throughput identification of antibodies against specific antigen epitopes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Virology
Manasi Majumdar, Cristina Celma, Elaine Pegg, Krunal Polra, Jake Dunning, Javier Martin
Summary: The study focused on a detection method for enteroviruses using NGS analysis of clinical samples, showing high concordance with conventional Sanger sequencing and good sensitivity and specificity for different EV types. The NGS method identified previously untyped EVs and potential co-infections, demonstrating its potential for comprehensive EV detection and genetic analysis.
Review
Biochemistry & Molecular Biology
Muhammad Furqan Ashraf, Dan Hou, Quaid Hussain, Muhammad Imran, Jialong Pei, Mohsin Ali, Aamar Shehzad, Muhammad Anwar, Ali Noman, Muhammad Waseem, Xinchun Lin
Summary: Crop production is a major challenge in providing food for the projected 10 billion individuals in 2050. Utilizing genomics and metabolomics strategies can help enhance crop yield and generate stress-tolerant plants. Next-generation sequencing innovation has laid the foundation for understanding genetic potential and improving crops. The application of NGS and metabolomics can improve crop suitability and nutritional value.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Yen-Yi Liu, Bo-Han Chen, Chih-Chieh Chen, Chien-Shun Chiou
Summary: This study evaluated the robustness of different read lengths, read depths, and assemblers in recovering genes from reference genomes. The quality of assemblies was found to be mainly affected by read depth, regardless of the assembler used. Recommendations for cutoff values and cost-effective combinations for cgMLST were provided.
Article
Oncology
Juan A. Santamaria-Barria, Chikako Matsuba, Adam Khader, Anthony J. Scholar, Mary Garland-Kledzik, Trevan D. Fischer, Richard Essner, Matthew P. Salomon, Joshua M. V. Mammen, Melanie Goldfarb
Summary: This study analyzed melanoma samples and identified age-related mutational differences, as well as potential targetable mutations for personalized therapies.
JOURNAL OF SURGICAL ONCOLOGY
(2023)
Article
Genetics & Heredity
Vista Sohrab, Cristina Lopez-Diaz, Antonio Di Pietro, Li-Jun Ma, Dilay Hazal Ayhan
Summary: TEfinder is a simple tool developed for the detection of new TE insertions with minimal software and input file dependencies. The tool has been tested in evolving populations of Fusarium oxysporum and shown to effectively detect new TE insertion events, making it accessible and practical for TE analysis.
Review
Fisheries
Li Lian Wong, Siti Aisyah Razali, Zulaikha Mat Deris, Muhd Danish-Daniel, Min Pau Tan, Siti Azizah Mohd Nor, Hongyu Ma, Wang Min, Liang Yantao, Md Asaduzzaman, Yeong Yik Sung, Zhanjiang Liu, Patrick Sorgeloos, Yves Van de Peer, Nor Afiqah-Aleng
Summary: High-throughput sequencing technologies have been widely applied in aquaculture research, providing important data support for disease management, breeding programs, etc.
Article
Microbiology
Sheng-Han Wu, Yu-Xin Xiao, Hseuh-Chien Hsiao, Ruwen Jou
Summary: The study developed and validated a targeted next-generation sequencing (tNGS) method for drug-resistant tuberculosis, which can comprehensively detect drug resistance to 14 anti-TB drugs, show high concordance with traditional detection methods, and significantly reduce turnaround time, providing more clinical information for personalized treatment.
MICROBIOLOGY SPECTRUM
(2022)
Review
Neurosciences
Behrouz Shademan, Cigir Biray Avci, Masoud Nikanfar, Alireza Nourazarian
Summary: The NGS method is crucial for identifying genetic causes of neurodegenerative diseases like Alzheimer's and Parkinson's by quickly and accurately diagnosing them. With its ability to cater to individual genome variations, NGS has transformed personalized medicine and treatment strategies. However, the NGS method also has its own limitations.
NEUROMOLECULAR MEDICINE
(2021)
Article
Plant Sciences
Xiaolei Niu, Meiliang Zhou, Christiaan V. Henkel, G. Paul H. van Heusden, Paul J. J. Hooykaas
Article
Biotechnology & Applied Microbiology
I. C. R. M. Kolder, S. J. van der Plas-Duivesteijn, G. Tan, G. F. Wiegertjes, M. Forlenza, A. T. Guler, D. Y. Travin, M. Nakao, T. Moritomo, I. Irnazarow, J. T. den Dunnen, S. Y. Anvar, H. J. Jansen, R. P. Dirks, M. Palmblad, B. Lenhard, C. V. Henkel, H. P. Spaink
Article
Endocrinology & Metabolism
Erik Burgerhout, Yuki Minegishi, Sebastiaan A. Brittijn, Danielle L. de Wijze, Christiaan V. Henkel, Hans J. Jansen, Herman P. Spaink, Ron P. Dirks, Guido E. E. J. M. van den Thillart
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2016)
Review
Food Science & Technology
Harald M. I. Kerkkamp, R. Manjunatha Kini, Alexey S. Pospelov, Freek J. Vonk, Christiaan V. Henkel, Michael K. Richardson
Article
Multidisciplinary Sciences
Niels van Tol, Martijn Rolloos, Johan E. Pinas, Christiaan V. Henkel, Dieuwertje Augustijn, Paul J. J. Hooykaas, Bert J. van der Zaal
Article
Oncology
E. Alghisi, M. Distel, M. Malagola, V. Anelli, C. Santoriello, L. Herwig, A. Krudewig, C. V. Henkel, D. Russo, M. C. Mione
Article
Cell Biology
Eirill Ager-Wick, Christiaan V. Henkel, Trude M. Haug, Finn-Arne Weltzien
PHYSIOLOGICAL GENOMICS
(2014)
Article
Multidisciplinary Sciences
Daan Mes, Arjan P. Palstra, Christiaan Henkel, Ian Mayer, Marco A. Vindas
ROYAL SOCIETY OPEN SCIENCE
(2020)
Article
Multidisciplinary Sciences
Francesca Bertolini, Michelle Grace Pinto Jorgensen, Christiaan Henkel, Sylvie Dufour, Jonna Tomkiewicz
Article
Multidisciplinary Sciences
Khadeeja Siddique, Eirill Ager-Wick, Romain Fontaine, Finn-Arne Weltzien, Christiaan V. Henkel
Summary: The pituitary is an important vertebrate endocrine gland producing essential peptide hormones that regulate various physiological and developmental processes. Single-cell sequencing in medaka revealed distinct cell types in the pituitary involved in the production of specific peptide hormones, providing a valuable reference for pituitary biology research in fish and vertebrates.
Review
Endocrinology & Metabolism
Romain Fontaine, Muhammad Rahmad Royan, Christiaan Henkel, Kjetil Hodne, Eirill Ager-Wick, Finn -Arne Weltzien
Summary: This review discusses the discovery history, technical limitations, origin, and biological role of multi-hormonal cells in the vertebrate pituitary, providing a comprehensive review of pituitary plasticity.
FRONTIERS IN NEUROENDOCRINOLOGY
(2022)
Article
Endocrinology & Metabolism
Muhammad Rahmad Royan, Khadeeja Siddique, Rasoul Nourizadeh-Lillabadi, Finn-Arne Weltzien, Christiaan Henkel, Romain Fontaine
Summary: Using single cell transcriptomics, two distinct prolactin-expressing cell types were discovered in Japanese medaka. Small satellite lactotrope cell clusters were also found in the medaka pituitary, which develop early during development and increase in cell number throughout life. These satellite clusters are not directly related to the stem cell-like lactotropes.
GENERAL AND COMPARATIVE ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Eirill Ager-Wick, Gersende Maugars, Kristine von Krogh, Romain Fontaine, Finn-Arne Weltzien, Christiaan Henkel
Summary: The pituitary is an important endocrine gland in all vertebrates, playing a role in both organismal homeostasis and physiological adaptation. It coordinates sexual maturation by producing and releasing hormones that stimulate gonad development. A study was conducted on the developmental dynamics of the pituitary in the model fish medaka (Oryzias latipes), where 68 female fish were sampled for their pituitary and ovaries. Histological examination of the ovaries and RNA-seq analysis of the pituitary glands were performed to determine the timing of hormone production priorities and provide a comprehensive resource for their regulation.
Article
Biology
M. Liem, T. Regensburg-Tuink, C. Henkel, H. Jansen, H. Spaink
Summary: Using only three ONT flow cells, thousands of organisms, including bacteriophages, were identified, with a large part at species level. Genomes could be assembled from environmental samples with Flye, resulting in >1 Mbp contigs in several cases and a near complete genome for a Thioglobus singularis species. k-mer analysis revealed that a significant portion of the data represented species not yet deposited in the database. This approach is suitable for scalable genomic investigations and provides a new platform for education in biodiversity.
BMC RESEARCH NOTES
(2021)
Article
Microbiology
Christiaan Henkel, Amke den Dulk-Ras, Xiaorong Zhang, Paul J. J. Hooykaas
GENOME ANNOUNCEMENTS
(2014)