Article
Biochemical Research Methods
Ze-Gang Wei, Xu Chen, Xiao-Dan Zhang, Hao Zhang, Xing-Guo Fan, Hong-Yan Gao, Fei Liu, Yu Qian
Summary: Recent advances in sequencing technology have led to a large amount of sequencing data, and clustering analysis is a powerful tool to study this data. However, comparison studies of clustering methods have limitations, and this study aims to provide a comprehensive benchmark for sequence clustering methods, helping biological analyzers choose appropriate algorithms and motivating algorithm designers to develop more efficient approaches.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2023)
Article
Biochemistry & Molecular Biology
Rachel A. Swenie, Brian P. Looney, Yi-Hong Ke, Jorge A. Rojas, Marc A. Cubeta, Gitta J. Langer, Rytas Vilgalys, Patrick B. Matheny
Summary: In this study, a multi-locus pooled sequencing method using PacBio long-read high-throughput sequencing was developed and evaluated. The method successfully recovered multiple sequence variants of fungi species, providing accurate multi-locus sequence data. The method also allowed for the recovery of alleles from polymorphic samples and multi-organism specimens.
MOLECULAR ECOLOGY RESOURCES
(2023)
Article
Plant Sciences
Jiyeong Choi, Anya Clara Osatuke, Griffin Erich, Kristian Stevens, Min Sook Hwang, Maher Al Rwahnih, Marc Fuchs
Summary: Pawpaw trees in New York were found to be infected with tobacco ringspot virus (TRSV) and tomato ringspot virus (ToRSV) based on high-throughput sequencing and testing. The study also revealed high similarity between different isolates of these viruses in pawpaw trees.
Article
Biotechnology & Applied Microbiology
Tony P. Huang, Zachary J. Heins, Shannon M. Miller, Brandon G. Wong, Pallavi A. Balivada, Tina Wang, Ahmad S. Khalil, David R. Liu
Summary: Directed evolution has been used to create new compact Cas9 variants that can target most pyrimidine-rich PAM sequences. These variants were evolved using phage-assisted noncontinuous evolution and eVOLVER-supported phage-assisted continuous evolution. The resulting variants showed improved target specificity and activity in human cells compared to existing variants.
NATURE BIOTECHNOLOGY
(2022)
Article
Biochemical Research Methods
Natalie J. Wu-Woods, Jacob T. Barlow, Florian Trigodet, Dustin G. Shaw, Anna E. Romano, Bana Jabri, A. Murat Eren, Rustem F. Ismagilov
Summary: This study introduces a microbial-enrichment method (MEM) that enables the removal of host DNA in human intestinal biopsies and allows for the characterization of low-abundance microbial taxa. The method provides deeper insights into the high-throughput characterization of the gut microbiome and demonstrates the construction of metagenome-assembled genomes from human intestinal biopsies.
Article
Biotechnology & Applied Microbiology
Brianne Edwards, Eli D. Hornstein, Nathan J. Wilson, Heike Sederoff
Summary: This study developed a simple method using T-DNA-specific primers and high-throughput sequencing to identify transgene insertion sites in the T-1 generation of any crop transformed via Agrobacterium. The example using allohexaploid oil-seed plant Camelina sativa demonstrated the feasibility of determining insertion site location of two transgenes. This new methodology allows for early selection of desirable transgene location and copy number to generate homozygous lines within two generations.
Article
Plant Sciences
Xudong Fan, Zunping Zhang, Chen Li, Fang Ren, Guojun Hu, Baodong Zhang, Yafeng Dong
Summary: A putative new marafivirus, named grapevine-associated marafivirus (GaMV), was identified in a 'Jumeigui' grapevine showing obvious vein-clearing symptoms. The complete genome sequence of GaMV was determined and it showed significant homology with other marafiviruses. GaMV was found to be graft-transmissible and phylogenetic analysis revealed its position as a novel species within the genus Marafivirus.
Article
Virology
Izabela Fabianska, Stefan Borutzki, Benjamin Richter, Hon Q. Tran, Andreas Neubert, Dietmar Mayer
Summary: High-throughput sequencing (HTS) is effective in detecting both known and unknown viruses in samples, providing support for determining the safety of biological products such as vaccines. Due to the complexity of bioinformatics, standardized and reliable methods are necessary for managing HTS data. The LABRADOR analysis pipeline demonstrates reliable detection of viruses in mixtures of model viruses, vaccines, and clinical samples.
Article
Multidisciplinary Sciences
Shuhei Yasumoto, Toshiya Muranaka
Summary: Genome editing is a powerful breeding technique that introduces mutations into specific gene sequences in genomes. However, there is still no widely authorized method for detecting foreign genes in genome-edited crops.
SCIENTIFIC REPORTS
(2023)
Review
Microbiology
Mark Paul Selda Rivarez, Ana Vucurovic, Natasa Mehle, Maja Ravnikar, Denis Kutnjak
Summary: The pace of tomato virus discovery has increased in the past decade due to the use of high-throughput sequencing (HTS), but further characterization lags behind, especially for economically devastating viruses. There are at least 312 virus, satellite virus, or viroid species associated with tomato, the highest number recorded for any plant, according to databases and literature review.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Virology
Meripet Polat Yamanaka, Susumu Saito, Kazuyoshi Hosomichi, Yoko Aida
Summary: A novel proviral DNA-capture sequencing method was developed to investigate the integration of bovine leukemia virus (BLV) in B-cell lymphoma lines. The method successfully detected the BLV proviral integration sites and provided comprehensive information on the proviral structure. This study contributes to the understanding of BLV-induced leukemogenesis and provides a potential tool for early screening of BLV-infected cattle.
Article
Virology
Tomoyuki Nabeshima, Junya Abe
Summary: Vitis coignetiae samples from northern Japan were found to be infected with multiple RNA viruses, with three newly identified virus species assigned to different genera based on sequence identity and phylogenetic analysis.
Article
Biochemistry & Molecular Biology
Cornelis A. M. Wagemaker, Liesje Mommer, Eric J. W. Visser, Alexandra Weigelt, Thomas P. van Gurp, Maarten Postuma, Annemiek E. Smit-Tiekstra, Hans de Kroon
Summary: Plant interactions belowground are important and difficult to quantify accurately. The msGBS method presented in this study allows for high taxonomic resolution and parallel quantification of multiple species in root samples. Compared to qPCR, msGBS offers similar results with advantages in revealing hidden belowground interactions.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Plant Sciences
D. E. V. Villamor, K. E. Keller, R. R. Martin, I. E. Tzanetakis
Summary: This study compared virus detection using high throughput sequencing (HTS) and standard protocols in berry selections. HTS showed superior detection capabilities for variants and discovery of novel viruses. Additionally, the study found inconsistent results between the two protocols, suggesting a testing requirement of four sampling times over two growing seasons to ensure comprehensive virus detection.
Article
Plant Sciences
Leonardo Velasco, Carlos V. Padilla
Summary: Biological indexing is the primary method for certifying propagative grapevines, with HTS proposed as an alternative. Research findings indicate that HTS is more effective than biological indexing in terms of identifying viruses, saving time, and reducing costs.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Multidisciplinary Sciences
Wayne Xu, Vichithra R. B. Liyanage, Aaron MacAulay, Romina D. Levy, Kyle Curtis, Carl O. Olson, Robby M. Zachariah, Shayan Amiri, Marjorie Buist, Geoffrey G. Hicks, James R. Davie, Mojgan Rastegar
SCIENTIFIC REPORTS
(2019)
Article
Genetics & Heredity
Sanzida Jahan, Tasnim H. Beacon, Shihua He, Carolina Gonzalez, Wayne Xu, Genevieve P. Delcuve, Shuo Jia, Pingzhao Hu, James R. Davie
Article
Oncology
Shujun Huang, Wayne Xu, Pingzhao Hu, Ted M. Lakowski
Article
Biochemistry & Molecular Biology
Sanzida Jahan, Tasnim H. Beacon, Wayne Xu, James R. Davie
BIOCHEMISTRY AND CELL BIOLOGY
(2020)
Article
Biochemistry & Molecular Biology
Kent A. Shefchek, Nomi L. Harris, Michael Gargano, Nicolas Matentzoglu, Deepak Unni, Matthew Brush, Daniel Keith, Tom Conlin, Nicole Vasilevsky, Xingmin Aaron Zhang, James P. Balhoff, Larry Babb, Susan M. Bello, Hannah Blau, Yvonne Bradford, Seth Carbon, Leigh Carmody, Lauren E. Chan, Valentina Cipriani, Alayne Cuzick, Maria Della Rocca, Nathan Dunn, Shahim Essaid, Petra Fey, Chris Grove, Jean-Phillipe Gourdine, Ada Hamosh, Midori Harris, Ingo Helbig, Maureen Hoatlin, Marcin Joachimiak, Simon Jupp, Kenneth B. Lett, Suzanna E. Lewis, Craig McNamara, Zoe M. Pendlington, Clare Pilgrim, Tim Putman, Vida Ravanmehr, Justin Reese, Erin Riggs, Sofia Robb, Paola Roncaglia, James Seager, Erik Segerdell, Morgan Similuk, Andrea L. Storm, Courtney Thaxon, Anne Thessen, Julius O. B. Jacobsen, Julie A. McMurry, Tudor Groza, Sebastian Koehler, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres, David Osumi-Sutherland
NUCLEIC ACIDS RESEARCH
(2020)
Article
Plant Sciences
Ana Borrego-Benjumea, Adam Carter, James R. Tucker, Zhen Yao, Wayne Xu, Ana Badea
Article
Biology
Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M. Good, Malachi Griffith, Obi L. Griffith, Kristina Hanspers, HiErni Ng Hermjakob, Toby S. Hudson, Kevin Hybiske, Sarah M. Keating, Magal Manske, Michael Mayers, Daniel Mietchen, Elvira Mitraka, Alexander R. Pico, Timothy Putman, Anders Riutta, Nuria Queralt-Rosinach, Lynn M. Schriml, Thomas Shafee, Denise Slenter, Ralf Stephan, Katherine Thornton, Ginger Tsueng, Roger Tu, Sabah Ul-Hasan, Egon Willighagen, Chunlei Wu, Andrew Su
Article
Genetics & Heredity
Tasnim H. Beacon, Wayne Xu, James R. Davie
Article
Biochemical Research Methods
Zhen Yao, Frank M. You, Amidou N'Diaye, Ron E. Knox, Curt McCartney, Colin W. Hiebert, Curtis Pozniak, Wayne Xu
BMC BIOINFORMATICS
(2020)
Article
Genetics & Heredity
Wayne Xu, James R. Tucker, Wubishet A. Bekele, Frank M. You, Yong-Bi Fu, Raja Khanal, Zhen Yao, Jaswinder Singh, Brian Boyle, Aaron D. Beattie, Francois Belzile, Martin Mascher, Nicholas A. Tinker, Ana Badea
Summary: The genome sequence of Canadian two-row malting barley cultivar AAC Synergy was assembled for the first time using a combination of sequencing technologies, resulting in a contiguous assembly with high gene completeness. This represents an important genomic resource for barley research in Canada.
G3-GENES GENOMES GENETICS
(2021)
Review
Medicine, Research & Experimental
Deepak R. Unni, Sierra A. T. Moxon, Michael Bada, Matthew Brush, Richard Bruskiewich, J. Harry Caufield, Paul A. Clemons, Vlado Dancik, Michel Dumontier, Karamarie Fecho, Gustavo Glusman, Jennifer J. Hadlock, Nomi L. Harris, Arpita Joshi, Tim Putman, Guangrong Qin, Stephen A. Ramsey, Kent A. Shefchek, Harold Solbrig, Karthik Soman, Anne E. Thessen, Melissa A. Haendel, Chris Bizon, Christopher J. Mungall
Summary: Graph-based data models are increasingly used in clinical, biomedical, and translational science projects for knowledge representation. However, knowledge discovery across these knowledge graphs has remained challenging due to data heterogeneity and complexity, proliferation of ad hoc data formats, and a lack of a universally accepted standardization model. The Biolink Model is an open-source model that addresses these challenges by formalizing relationships between data structures in translational science, supporting integration and interoperability of biomedical knowledge graphs.
CTS-CLINICAL AND TRANSLATIONAL SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Ray Stefancsik, James P. P. Balhoff, Meghan A. A. Balk, Robyn L. L. Ball, Susan M. M. Bello, Anita R. R. Caron, Elissa J. J. Chesler, Vinicius de Souza, Sarah Gehrke, Melissa Haendel, Laura W. W. Harris, Nomi L. L. Harris, Arwa Ibrahim, Sebastian Koehler, Nicolas Matentzoglu, Julie A. A. McMurry, Christopher J. J. Mungall, Monica C. C. Munoz-Torres, Tim Putman, Peter Robinson, Damian Smedley, Elliot Sollis, Anne E. E. Thessen, Nicole Vasilevsky, David O. O. Walton, David Osumi-Sutherland
Summary: The Ontology of Biological Attributes (OBA) is a standardized and species-independent framework that can integrate various observable biological traits with different biological data. OBA has a modular design, allowing users and data integrators to classify and infer trait terms based on domain-specific ontologies for cells, anatomical entities, and other relevant entities. The logical axioms in OBA also bridge the gap between Mendelian phenotypes, GWAS, and quantitative traits computationally.
Article
Biochemical Research Methods
J. Harry Caufield, Tim Putman, Kevin Schaper, Deepak R. Unni, Harshad Hegde, Tiffany J. Callahan, Luca Cappelletti, Sierra A. T. Moxon, Vida Ravanmehr, Seth Carbon, Lauren E. Chan, Katherina Cortes, Kent A. Shefchek, Glass Elsarboukh, Jim Balhoff, Tommaso Fontana, Nicolas Matentzoglu, Richard M. Bruskiewich, Anne E. Thessen, Nomi L. Harris, Monica C. Munoz-Torres, Melissa A. Haendel, Peter N. Robinson, Marcin P. Joachimiak, Christopher J. Mungall, Justin T. Reese
Summary: KG-Hub is a platform for constructing, exchanging, and reusing knowledge graphs. It provides standardized construction processes, easy integration of biomedical ontologies, cached data sources, version control, and automatic updating. Current projects using KG-Hub cover various domains such as COVID-19 research, drug repurposing, microbial-environmental interactions, and rare disease research. KG-Hub also offers tools for analyzing, manipulating, and integrating machine learning into the graphs.
Article
Biochemistry & Molecular Biology
Tim E. Putman, Kevin Schaper, Nicolas Matentzoglu, Vincent P. Rubinetti, Faisal S. Alquaddoomi, Corey Cox, J. Harry Caufield, Glass Elsarboukh, Sarah Gehrke, Harshad Hegde, Justin T. Reese, Ian Braun, Richard M. Bruskiewich, Luca Cappelletti, Seth Carbon, Anita R. Caron, Lauren E. Chan, Christopher G. Chute, Katherina G. Cortes, Vinicius De Souza, Tommaso Fontana, Nomi L. Harris, Emily L. Hartley, Eric Hurwitz, Julius O. B. Jacobsen, Madan Krishnamurthy, Bryan J. Laraway, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Kathleen R. Mullen, Shawn T. O'Neil, Kent A. Shefchek, Ray Stefancsik, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Patricia L. Whetzel, David Osumi-Sutherland, Damian Smedley, Peter N. Robinson, Christopher J. Mungall, Melissa A. Haendel, Monica C. Munoz-Torres
Summary: The Monarch Initiative aims to bridge the gap between genetic variations, environmental determinants, and phenotypic outcomes by developing an integrated platform with open ontologies, semantic data models, and knowledge graphs. It provides advanced analysis tools and curated datasets for clinical diagnosis and understanding disease mechanisms.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Mathematical & Computational Biology
Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M. Gyori, Melissa Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad B. Hegde, Amelia L. Hoyt, Charles T. Hoyt, Dazhi Jiao, Ernesto Jimenez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim Putman, Nuria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H. Wagner, Christopher J. Mungall
Summary: This paper introduces the "Simple Standard for Sharing Ontological Mappings (SSSOM)" standard, which addresses issues in mapping different representations of objects in different databases by enhancing readability of metadata, defining an easy-to-use table-based format, and implementing open collaborative workflows. The standard provides reference tools and software libraries for handling mappings.
DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION
(2022)
Article
Virology
Naiqing Xu, Xinen Tang, Xin Wang, Miao Cai, Xiaowen Liu, Xiaolong Lu, Shunlin Hu, Min Gu, Jiao Hu, Ruyi Gao, Kaituo Liu, Yu Chen, Xiufan Liu, Xiaoquan Wang
Summary: This study found that the H9N2 subtype avian influenza virus has a high airborne transmissibility, while the H7N9 virus does not. The Hemagglutinin protein of the H9N2 virus was found to play a key role in replication, stability, and airborne transmission.
Article
Virology
Samar S. Ewies, Sabry M. Tamam, Ahmed S. Abdel-Moneim, Sherin R. Rouby
Summary: Contagious ecthyma (CE) is a highly contagious viral disease of sheep and goats worldwide. The study provided a clinical description of CE and screened for genetic variation in the B2L gene. Infected sheep exhibited anorexia and oral lesions, while inoculated chicken embryos showed pock lesions. The B2L gene was successfully amplified and found to be highly conserved.
Article
Virology
Yigal Farnoushi, Dan Heller, Avishai Lublin
Summary: In recent years, new variants of avian reovirus (ARV) have caused a variety of symptoms in chickens worldwide, including viral arthritis/tenosynovitis. This study analyzed emerging ARV variants in Israel and found significant genetic diversity. Most ARV isolates in Israel belonged to genotypic cluster 5 (GC5). The study suggests that Israel has not experienced the emergence of new ARV variants since the introduction of the live vaccine (ISR-7585), but ongoing monitoring is needed due to the continuous emergence of ARV variants.
Article
Virology
Shigeru Tajima, Michiyo Kataoka, Yuki Takamatsu, Hideki Ebihara, Chang-Kweng Lim
Summary: Yokose virus (YOKV), a bat-associated flavivirus, was found to replicate at a slower rate in mosquito cells compared to other mosquito-borne flaviviruses. Specific nucleotide mutations in the virus were identified to enhance its proliferation ability in mosquito cells.
Article
Virology
Alejandra Borjabad, Baojun Dong, Wei Chao, David J. Volsky, Mary Jane Potash
Summary: This study investigated HIV brain disease using a mouse model, and found that poly I:C can reverse associated cognitive impairment and reduce virus burden. The results also revealed transcriptional changes related to neuronal function and innate immune responses.
Article
Virology
Ching-Hung Lin, Feng-Cheng Hsieh, Meilin Wang, Chieh Hsu, Hsuan-Wei Hsu, Chun-Chun Yang, Cheng-Yao Yang, Hung-Yi Wu
Summary: This study demonstrates that the synthesis of coronavirus subgenomic mRNA is not solely determined by the sequence homology between the leader TRS and TRS-B, but also by the disassociation of the coronavirus polymerase from the viral genome. This finding provides a new insight into the transcription mechanism of coronaviruses.
Article
Virology
Nicholas S. Kron, Benjamin W. Neuman, Sathish Kumar, Patricia L. Blackwelder, Dayana Vidal, Delphina Z. Walker-Phelan, Patrick D. I. Gibbs, Lynne A. Fieber, Michael C. Schmale
Summary: Two recent studies documented the genome of a novel virus in marine animals, finding that the virus is widespread in apparently healthy animals but not highly expressed in neurons. The studies also identified viral replication factories and high levels of defective genomes in chronically infected animals.
Article
Virology
Andrew M. Ramey, Laura C. Scott, Christina A. Ahlstrom, Evan J. Buck, Alison R. Williams, Mia Kim Torchetti, David E. Stallknecht, Rebecca L. Poulson
Summary: We successfully detected and characterized highly pathogenic avian influenza viruses in hunter-harvested wild waterfowl samples from western Alaska. Genomic analysis revealed three independent viral introductions into Alaska. Our findings demonstrate the utility and potential limitations of using molecular processing approaches directly on original swab samples for viral research and monitoring.
Article
Virology
Ting Gong, Dongdong Wu, Yongzhi Feng, Xing Liu, Qi Gao, Xiaoyu Zheng, Zebu Song, Heng Wang, Guihong Zhang, Lang Gong
Summary: This study discovered that quercetin can inhibit PEDV replication both in vivo and in vitro, and alleviate the clinical symptoms and intestinal injury caused by the virus. This provides a new direction for the development of PED antiviral drugs.
Article
Virology
Min Zhu, Hao Zeng, Jianqiao He, Yaohui Zhu, Pingping Wang, Jianing Guo, Jinfan Guo, Huabo Zhou, Yifeng Qin, Kang Ouyang, Zuzhang Wei, Weijian Huang, Ying Chen
Summary: The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study found that the introduction of EA H1N1 internal genes into H9N2 virus restored the replication capability and resulted in extreme virulence in some cases. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.
