Article
Veterinary Sciences
Tingting Li, Wenhui Li, Nianzhang Zhang, Zigang Qu, John A. Ohiolei, Li Li, Hongbin Yan, Wanzhong Jia, Baoquan Fu
Summary: The study investigated the immune responses to Chinese Tibet Trichinella spiralis infection in Tibetan pigs with different doses over a 49-day tracking period. Results showed that the larval numbers of T. spiralis in Tibetan pigs increased with infective dose, and the anti-Trichinella IgG levels peaked at 49 days post-infection. Cytokine kinetics revealed a high level of mixed Th1/Th2 cytokines in Tibetan pigs infected with T. spiralis.
BMC VETERINARY RESEARCH
(2021)
Article
Parasitology
Banucicek Yucesan, Dilek Guldemir, Cahit Babur, Selcuk Kilic, Ayse Cakmak
Summary: This study successfully conducted whole-genome sequencing of T. gondii for the first time in Turkey, providing important data for better understanding this pathogen.
Article
Biochemistry & Molecular Biology
Markus Pfenninger, Philipp Schoennenbeck, Tilman Schell
Summary: Accurate estimation of genome sizes is essential in biodiversity genomics, and this study introduces a method that can estimate genome size from the number of sequenced bases and mean sequencing depth. Simulations demonstrate that even from low-coverage genome drafts, reasonable estimates can be obtained using this method. Comparison with flow cytometry estimates suggests that both methods provide similar and interchangeable results.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Oncology
Tyler Shugg, Reynold C. Ly, Wilberforce Osei, Elizabeth J. Rowe, Caitlin A. Granfield, Ty C. Lynnes, Elizabeth B. Medeiros, Jennelle C. Hodge, Amy M. Breman, Bryan P. Schneider, S. Cenk Sahinalp, Ibrahim Numanagic, Benjamin A. Salisbury, Steven M. Bray, Ryan Ratcliff, Todd C. Skaar
Summary: This study assessed the accuracy of the Aldy computational method in extracting pharmacogenomics genotypes from whole genome sequencing (WGS) and whole exome sequencing (WES) data. The results showed that Aldy achieved over 99% accuracy in calling diplotypes for major pharmacogenes from both WGS and WES data, supporting its importance in clinical applications.
FRONTIERS IN ONCOLOGY
(2023)
Article
Parasitology
Xiaoxiang Hu, Xiaolei Liu, Chen Li, Yulu Zhang, Chengyao Li, Yanfeng Li, Yingxi Chen, Heng Guo, Xue Bai, Mingyuan Liu
Summary: The gene expression patterns in response to Trichinella infection in murine myocytes were most pronounced during early infection, with a sharp increase in differentially expressed genes at 10 days post-infection. However, the initial reaction steadied in later stages of infection. This dataset provides valuable insight into how pathogens evade host defenses and survive in the mammalian environment.
PARASITES & VECTORS
(2021)
Review
Biochemistry & Molecular Biology
Natsuko Aida, Akiko Saito, Toshifumi Azuma
Summary: The development of next-generation sequencing (NGS) has greatly improved the speed and capacity of genetic analysis, expanding its applications to include genome, epigenome, metagenome, and transcriptome analyses. Bone tissue, as a crucial unit supporting the body, is susceptible to genetic diseases. The relationship between age-related bone fragility and genetic factors has recently gained attention.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Obstetrics & Gynecology
M. D. Kilby
Summary: This paper reviews the role of NGS in investigating fetal malformations, emphasizing the importance of prospective case selection and informative pre-test counseling, as well as the crucial role of regulated laboratory sequencing and bioinformatic pathways in clinical practice.
BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY
(2021)
Article
Genetics & Heredity
Wei Li, Xiaggojiang Chen, Mengmeng Zheng, Yin Wang, Xingchen Zhou, Haiyang Li, Guolong Zhou, Bichun Li
Summary: The complete mitogenome sequence of Sinogastromyzon szechuanensis was obtained using next generation sequencing and confirmed via overlap-PCR method. The genome consisted of 13 protein-coding genes, 2 ribosomal RNA genes, 23 transfer RNA genes, and 1 control region, with a slight A-T skew in the overall nucleotide composition of the heavy strand. Mitochondrial genome analyses based on ML analyses yielded identical phylogenetic trees.
MITOCHONDRIAL DNA PART B-RESOURCES
(2021)
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
Genetics & Heredity
Alexandra Emms, James Castleman, Stephanie Allen, Denise Williams, Esther Kinning, Mark Kilby
Summary: Congenital malformations diagnosed by ultrasound screening have an underlying genetic cause in many cases. Next generation sequencing as a secondary prenatal genetic test offers additional diagnostic yield for congenital abnormalities potentially associated with genetic causes, especially in cases involving cardiac and neurological anomalies, large nuchal translucency, and non-immune fetal hydrops. The use of exome sequencing has shown significant incremental yield in single-system anomalies, making it a valuable tool for routine clinical care in fetuses with congenital abnormalities.
Article
Parasitology
Dilek Guldemir, Selma Usluca, Ayse Serpil Nalbantoglu
Summary: This study successfully obtained a high-quality whole-genome sequence of Leishmania infantum for the first time in Turkey, providing a basis for research on cutaneous leishmaniosis. The Lin_TR01 strain is the first strain to be isolated from cutaneous leishmaniosis, which is of significant research value.
ACTA PARASITOLOGICA
(2021)
Article
Microbiology
Madjid Morsli, Christine Zandotti, Aurelie Morand, Philippe Colson, Michel Drancourt
Summary: In this case report, metagenomic next-generation sequencing successfully identified Echovirus 12 as an etiological agent of acute meningitis in pediatric population, highlighting the potential of this method in improving the accuracy of viral diagnosis.
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.
Article
Virology
Josep Quer, Sergi Colomer-Castell, Carolina Campos, Cristina Andres, Maria Pinana, Maria Francesca Cortese, Alejandra Gonzalez-Sanchez, Damir Garcia-Cehic, Marta Ibanez, Tomas Pumarola, Francisco Rodriguez-Frias, Andres Anton, David Tabernero
Summary: Virus pandemics are inevitable and have been accelerated by human activities. To effectively control and prevent pandemics, it is crucial to develop barriers based on knowledge rather than physical walls. Next-generation sequencing has proven to be a powerful tool in detecting and identifying infectious agents, developing vaccines and antiviral drugs, and understanding viral transmission dynamics and variants.
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
Infectious Diseases
Luke B. B. Hecht, Peter C. Thompson, Elizabeth S. Lavin, Dante S. Zarlenga, Benjamin M. Rosenthal
INFECTION GENETICS AND EVOLUTION
(2016)
Article
Infectious Diseases
Benjamin M. Rosenthal, Detiger Dunams-Morel, Gyorgyi Ostoros, Kalman Molnar
INFECTION GENETICS AND EVOLUTION
(2016)
Article
Parasitology
Shiv K. Verma, David S. Lindsay, Benjamin M. Rosenthal, Jitender P. Dubey
PARASITOLOGY RESEARCH
(2016)
Article
Parasitology
X. Bai, X. L. Wang, B. Tang, H. N. Shi, P. Boireau, B. Rosenthal, X. P. Wu, M. Y. Liu, X. L. Liu
VETERINARY PARASITOLOGY
(2016)
Article
Multidisciplinary Sciences
Hernan Lorenzi, Asis Khan, Michael S. Behnke, Sivaranjani Namasivayam, Lakshmipuram S. Swapna, Michalis Hadjithomas, Svetlana Karamycheva, Deborah Pinney, Brian P. Brunk, James W. Ajioka, Daniel Ajzenberg, John C. Boothroyd, Jon P. Boyle, Marie L. Darde, Maria A. Diaz-Miranda, Jitender P. Dubey, Heather M. Fritz, Solange M. Gennari, Brian D. Gregory, Kami Kim, Jeroen P. J. Saeij, Chunlei Su, Michael W. White, Xing-Quan Zhu, Daniel K. Howe, Benjamin M. Rosenthal, Michael E. Grigg, John Parkinson, Liang Liu, Jessica C. Kissinger, David S. Roos, L. David Sibley
NATURE COMMUNICATIONS
(2016)
Article
Parasitology
S. K. Verma, D. S. Lindsay, J. D. Mowery, B. M. Rosenthal, J. P. Dubey
JOURNAL OF PARASITOLOGY
(2017)
Article
Parasitology
S. K. Verma, A. Rosypal von Dohlen, J. D. Mowery, D. Scott, B. M. Rosenthal, J. P. Dubey, D. S. Lindsay
JOURNAL OF PARASITOLOGY
(2017)
Article
Parasitology
Peter C. Thompson, Dante S. Zarlenga, Ming-Yuan Liu, Benjamin M. Rosenthal
Article
Parasitology
Camila K. Cerqueira-Cezar, Peter C. Thompson, Shiv Kumar Verma, Joseph Mowery, Rafael Calero-Bernal, Fernando H. Antunes Murata, David R. Sinnett, Caroline Van Hemert, Benjamin M. Rosenthal, Jitender P. Dubey
PARASITOLOGY RESEARCH
(2017)
Article
Parasitology
Shiv K. Verma, Camila K. Cerqueira-Cezar, Fernando H. A. Murat, Matthew J. Lovallo, Benjamin M. Rosenthal, Jitender P. Dubey
VETERINARY PARASITOLOGY
(2017)
Article
Parasitology
R. Calero-Bernal, N. F. Mauroo, S. W. Hui, T. Kuiken, M. W. G. van de Bildt, A. W. de Jong, A. D. M. E. Osterhaus, L. Sims, A. Gendron-Fitzpatrick, D. Carmena, C. K. Cerqueira-Cezar, B. M. Rosenthal, J. P. Dubey
VETERINARY PARASITOLOGY
(2017)
Article
Parasitology
Fernando H. Antunes Murata, Camila K. Cerqueira-Cezar, Peter C. Thompson, Keshaw Tiwari, Joseph D. Mowery, Shiv K. Verma, Benjamin M. Rosenthal, Ravindra N. Sharma, Jitender P. Dubey
PARASITOLOGY RESEARCH
(2018)
Article
Parasitology
Weilin Zeng, Ling Sun, Zheng Xiang, Na Li, Jie Zhang, Yongshu He, Qing Li, Fang Yang, Jingling Song, James Morris, Benjamin M. Rosenthal, Le Sun, Huaie Liu, Zhaoqing Yang
VETERINARY PARASITOLOGY
(2018)
Article
Biology
Luke B. B. Hecht, Peter C. Thompson, Benjamin M. Rosenthal
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2018)
Article
Veterinary Sciences
Emil Gjurcevic, Snjezana Kuzir, Branimir Bazdaric, Kresimir Matanovic, Iris Debelic, Fabio Marino, Kresimir Drasner, Benjamin M. Rosenthal
VETERINARSKI ARHIV
(2017)