Article
Biochemistry & Molecular Biology
Pora Kim, Hua Tan, Jiajia Liu, Haeseung Lee, Hyesoo Jung, Himanshu Kumar, Xiaobo Zhou
Summary: The study introduces FusionGDB 2.0, a database with updated functional annotations of fusion genes, which is crucial for understanding genomic breakage context and developing therapeutic strategies. FusionGDB 2.0 provides comprehensive information on human fusion genes and their characteristics, making it a valuable resource for diverse human genomic studies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Yabing Song, Jianbin Wang
Summary: ggcoverage is an R package for visualizing and annotating genome coverage of multi-groups and multi-omics. It supports various input file formats and provides reliable and efficient methods for read normalization, consensus peaks generation, and track data loading. ggcoverage offers multiple available annotations and allows customization of plots with ggplot2. Additionally, it supports visualization and annotation of protein coverage.
BMC BIOINFORMATICS
(2023)
Article
Multidisciplinary Sciences
Ka Ming Nip, Saber Hafezqorani, Kristina K. Gagalova, Readman Chiu, Chen Yang, Rene L. Warren, Inanc Birol
Summary: Long-read sequencing technologies have greatly improved, but there is little focus on reference-free transcriptome assembly methods. In this study, the authors introduce RNA-Bloom2, a reference-free method for long-read transcriptome sequencing data. They demonstrate its competitive assembly quality compared to reference-based methods, as well as its lower memory and runtime requirements. They also showcase its application in assembling a transcriptome sample of Sitka spruce, setting the groundwork for large-scale comparative transcriptomics without readily available genome assemblies.
NATURE COMMUNICATIONS
(2023)
Article
Entomology
Takako Mochizuki, Mika Sakamoto, Yasuhiro Tanizawa, Hitomi Seike, Zhen Zhu, Yi Jun Zhou, Keisuke Fukumura, Shinji Nagata, Yasukazu Nakamura
Summary: We identified neuropeptides and their genomic loci in Gryllus bimaculatus, improving the draft genome annotation and facilitating research. Genome annotation is essential for supporting studies, but often lacks tissue-specific or low-expression genes. Through reference mapping, de novo transcriptome assembly, and manual curation, we annotated 41 neuropeptides in the cricket. These annotation methods can be applied to other insects and provide useful infrastructures for neuropeptide studies.
Article
Biochemical Research Methods
Hue Reardon, Anney Che, Brian T. Luke, Sarangan Ravichandran, Jack R. Collins, Uma S. Mudunuri
Summary: AVIA is a web application that allows users to annotate and visualize genomic variant data, investigate functional significance of genetic alterations, and conduct comparative analysis across samples, genes, and pathways. The latest version, AVIA 3.0, offers more filtering options and new services, allowing for greater flexibility in data management.
Article
Plant Sciences
Qihang Yang, Tao Liu, Tong Wu, Tianyu Lei, Yuxian Li, Xiyin Wang
Summary: Analyzing the genome structures of Gramineae plants and linking duplicated genes to specific polyploidization events is crucial for understanding plant biology and evolution. This study analyzed 29 well-assembled Gramineae genome sequences and constructed an online database, GGDB, which provides a platform for exploring genome changes and functional innovation in Gramineae plants.
Article
Biochemical Research Methods
Andrew J. Olson, Doreen Ware
Summary: TRaCE ranks transcripts at gene loci using annotation edit distance from RNA-seq samples, elects a canonical transcript through multiple rounds of voting based on relevance criteria, and identifies common isoforms or prioritizes alternative transcripts expressed in specific contexts from the provided expression data set.
Article
Multidisciplinary Sciences
Rebecca J. Rockett, Jenny Draper, Mailie Gall, Eby M. Sim, Alicia Arnott, Jessica E. Agius, Jessica Johnson-Mackinnon, Winkie Fong, Elena Martinez, Alexander P. Drew, Clement Lee, Christine Ngo, Marc Ramsperger, Andrew N. Ginn, Qinning Wang, Michael Fennell, Danny Ko, Linda Huston, Lukas Kairaitis, Edward C. Holmes, Matthew N. O'Sullivan, Sharon C-A Chen, Jen Kok, Dominic E. Dwyer, Vitali Sintchenko
Summary: The study reveals the co-infection of SARS-CoV-2 variants Omicron and Delta in two patients with chronic kidney disease, highlighting the importance of integrated genomic surveillance in vulnerable populations.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Beatrice Amos, Cristina Aurrecoechea, Matthieu Barba, Ana Barreto, Evelina Y. Basenko, Wojciech Bazant, Robert Belnap, Ann S. Blevins, Ulrike Bohme, John Brestelli, Brian P. Brunk, Mark Caddick, Danielle Callan, Lahcen Campbell, Mikkel B. Christensen, George K. Christophides, Kathryn Crouch, Kristina Davis, Jeremy DeBarry, Ryan Doherty, Yikun Duan, Michael Dunn, Dave Falke, Steve Fisher, Paul Flicek, Brett Fox, Bindu Gajria, Gloria Giraldo-Calderon, Omar S. Harb, Elizabeth Harper, Christiane Hertz-Fowler, Mark J. Hickman, Connor Howington, Sufen Hu, Jay Humphrey, John Iodice, Andrew Jones, John Judkins, Sarah A. Kelly, Jessica C. Kissinger, Dae Kun Kwon, Kristopher Lamoureux, Daniel Lawson, Wei Li, Kallie Lies, Disha Lodha, Jamie Long, Robert M. MacCallum, Gareth Maslen, Mary Ann McDowell, Jaroslaw Nabrzyski, David S. Roos, Samuel S. C. Rund, Stephanie Wever Schulman, Achchuthan Shanmugasundram, Vasily Sitnik, Drew Spruill, David Starns, Christian J. Stoeckert, Sheena Shah Tomko, Haiming Wang, Susanne Warrenfeltz, Robert Wieck, Paul A. Wilkinson, Lin Xu, Jie Zheng
Summary: VEuPathDB project is a bioinformatics resource center funded by the National Institutes of Health, supporting over 500 organisms including invertebrate vectors, eukaryotic pathogens, and hosts. It integrates over 1700 pre-analyzed datasets, providing advanced search capabilities, visualizations, and analysis tools, with standardized workflows for researchers to access Omics data and bioinformatic analyses.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Microbiology
Ursula Oggenfuss, Daniel Croll
Summary: Transposable elements (TEs) are engines of evolution and have important impacts on pathogen evolution. We analyzed numerous high-quality genomes of a fungal wheat pathogen species and found that the reactivation and activity of TEs were primarily driven by specific factors such as proximity to genes.
Article
Plant Sciences
Cheng Zou, Surya Sapkota, Rosa Figueroa-Balderas, Jeff Glaubitz, Dario Cantu, Brewster F. Kingham, Qi Sun, Lance Cadle-Davidson
Summary: Fine mapping of quantitative trait loci (QTL) is essential in modern breeding practice. This study presents a multitiered haplotypic marker system that improves fine mapping accuracy and successfully identifies a grapevine downy mildew resistance locus. The strategy combines different resolutions of genome sequencing and integrates high-density genetic information to pinpoint the genetic basis of QTLs.
Article
Genetics & Heredity
Meili Chen, Yingke Ma, Song Wu, Xinchang Zheng, Hongen Kang, Jian Sang, Xingjian Xu, Lili Hao, Zhaohua Li, Zheng Gong, Jingfa Xiao, Zhang Zhang, Wenming Zhao, Yiming Bao
Summary: The Genome Warehouse (GWH) is a public repository that houses genome assembly data for various species and offers web services for data submission, storage, release, and sharing. With a uniform quality control procedure, GWH accepts full and partial genome sequences and visualizes released data using JBrowse, serving as an important resource for global research activities.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Multidisciplinary Sciences
Yao Zhou, Zhiyang Zhang, Zhigui Bao, Hongbo Li, Yaqing Lyu, Yanjun Zan, Yaoyao Wu, Lin Cheng, Yuhan Fang, Kun Wu, Jinzhe Zhang, Hongjun Lyu, Tao Lin, Qiang Gao, Surya Saha, Lukas Mueller, Zhangjun Fei, Thomas Stadler, Shizhong Xu, Zhiwu Zhang, Doug Speed, Sanwen Huang
Summary: Constructing a graph pangenome of tomato can improve the estimation of heritability for complex traits, identify more causal structural variants, and facilitate the identification of genetic factors underlying agronomically important traits. This study advances our understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.
Article
Multidisciplinary Sciences
Tewodros Gebresilase, Chris Finan, Daniel Suveges, Tesfaye Sisay Tessema, Abraham Aseffa, Gail Davey, Konstantinos Hatzikotoulas, Eleftheria Zeggini, Melanie J. Newport, Fasil Tekola-Ayele
Summary: The study confirmed the association between the HLA class II region and podoconiosis through a second GWAS, indicating that abnormal induction and regulation of immune responses mediated by HLA may play a key role in its pathogenesis.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Matthew R. Lueder, Regina Z. Cer, Miles Patrick, Logan J. Voegtly, Kyle A. Long, Gregory K. Rice, Kimberly A. Bishop-Lilly
Summary: Manual Annotation Studio (MAS) is a software tool designed to improve the efficiency of manual functional annotation for prokaryotic and viral genomes. It allows users to upload, edit, and track annotations, provides structure to projects, and reduces errors. MAS can interface with HPC clusters, support multiple users, and export data in various formats.
Article
Biochemistry & Molecular Biology
Benoit Piegu, Sassan Asgari, Dennis Bideshi, Brian A. Federici, Yves Bigot
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2015)
Review
Biochemistry & Molecular Biology
Benoit Piegu, Solenne Bire, Peter Arensburger, Yves Bigot
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2015)
Article
Biotechnology & Applied Microbiology
Sebastien Guizard, Benoit Piegu, Peter Arensburger, Florian Guillou, Yves Bigot
Article
Genetics & Heredity
Solenne Bire, Sophie Casteret, Benoit Piegu, Linda Beauclair, Nathalie Moire, Peter Arensbuger, Yves Bigot
Article
Virology
Benoit Piegu, Sebastien Guizard, Tatsinda Spears, Corinne Cruaud, Arnault Couloux, Dennis K. Bideshi, Brian A. Federici, Yves Bigot
ARCHIVES OF VIROLOGY
(2014)
Article
Biotechnology & Applied Microbiology
Romain Blanc-Mathieu, Bram Verhelst, Evelyne Derelle, Stephane Rombauts, Francois-Yves Bouget, Isabelle Carre, Annie Chateau, Adam Eyre-Walker, Nigel Grimsley, Herve Moreau, Benoit Piegu, Eric Rivals, Wendy Schackwitz, Yves Van de Peer, Gwenael Piganeau
Review
Genetics & Heredity
Solenne Bire, Sophie Casteret, Ahmed Arnaoty, Benoit Piegu, Thierry Lecomte, Yves Bigot
Article
Biotechnology & Applied Microbiology
Benoit Piegu, Sebastien Guizard, Tatsinda Spears, Corinne Cruaud, Arnault Couloux, Dennis K. Bideshi, Brian A. Federici, Yves Bigot
JOURNAL OF GENERAL VIROLOGY
(2013)
Article
Biotechnology & Applied Microbiology
Benoit Piegu, Sebastien Guizard, Tan Yeping, Corinne Cruaud, Sassan Asgari, Dennis K. Bideshi, Brian A. Federici, Yves Bigot
JOURNAL OF GENERAL VIROLOGY
(2014)
Article
Zoology
Benoit Piegu, Sebastian Guizard, Tatsinda Spears, Corinne Cruaud, Arnault Couloux, Dennis K. Bideshi, Brian A. Federici, Yves Bigot
JOURNAL OF INVERTEBRATE PATHOLOGY
(2014)
Article
Medicine, Research & Experimental
Julien Lejeune, Benoit Piegu, Valerie Gouilleux-Gruart, Marc Ohresser, Herve Watier, Gilles Thibault
Article
Biochemistry & Molecular Biology
Yves Bigot, Benoit Piegu, Sophie Casteret, Frederick Gavory, Dennis K. Bideshi, Brian A. Federici
MOLECULAR PHYLOGENETICS AND EVOLUTION
(2013)
Article
Biochemical Research Methods
Sarah-Anne David, Benoit Piegu, Christelle Hennequet-Antier, Maelle Pannetier, Tiphaine Aguirre-Lavin, Sabine Crochet, Thierry Bordeau, Nathalie Courousse, Aurelien Brionne, Yves Bigot, Anne Collin, Vincent Coustham
BIOLOGICAL PROCEDURES ONLINE
(2017)
Article
Genetics & Heredity
Benoit Piegu, Sebastien Guizard, Tan Yeping, Corinne Cruaud, Arnault Couloux, Dennis K. Bideshi, Brian A. Federici, Yves Bigot
STANDARDS IN GENOMIC SCIENCES
(2014)