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Biochemistry & Molecular Biology
Sanjida H. Rangwala, Anatoliy Kuznetsov, Victor Ananiev, Andrea Asztalos, Evgeny Borodin, Vladislav Evgeniev, Victor Joukov, Vadim Lotov, Ravinder Pannu, Dmitry Rudnev, Andrew Shkeda, Eric M. Weitz, Valerie A. Schneider
Summary: NCBI is an archive that provides free access to biological sequence data and literature, where staff scientists analyze user-submitted data to generate gene and SNP annotation. Their flagship genome browser GDV integrates with various resources and offers a platform for customized analysis and visualization.
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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.
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Biochemical Research Methods
Weize Xu, Quan Zhong, Da Lin, Ya Zuo, Jinxia Dai, Guoliang Li, Gang Cao
Summary: CoolBox is an open-source toolkit for visual analysis of genomics data, highly compatible with Python ecosystem, featuring a user-friendly interface, allowing users to generate high-quality visualization plots and explore their data in a flexible, programmable, and user-friendly way.
BMC BIOINFORMATICS
(2021)
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Biochemical Research Methods
Ana M. Vasconcelos, Maria Beatriz Carmo, Beatriz Ferreira, Ines Viegas, Margarida Gama-Carvalho, Antonio Ferreira, Andreia J. Amaral
Summary: IsomiR Window is a platform developed to identify, quantify, and explore isomiR expression in small RNA-seq datasets. It includes a pipeline for data processing and a user-friendly interface, integrating various softwares for analysis and a new algorithm for detecting different types of isomiRs. The tool has been shown to accurately detect isomiRs with high confidence and has practical applications in studying miRNA variants in disease pathways.
BMC BIOINFORMATICS
(2021)
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)
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Biochemistry & Molecular Biology
Kerry A. Mullan, Liesl M. Bramberger, Prithvi Raj Munday, Gabriel Goncalves, Jerico Revote, Nicole A. Mifsud, Patricia T. Illing, Alison Anderson, Patrick Kwan, Anthony W. Purcell, Chen Li
Summary: ggVolcanoR is an R-based Shiny application that allows customizable generation and visualization of volcano plots, correlation plots, upset plots, and heatmaps for differential expression datasets. It provides practical options for analyzing and comparing dysregulated genes/proteins across multiple datasets, and offers a downloadable list of filtered dysregulated expression data for downstream pathway analysis. The source code is available on GitHub and a webserver is freely accessible for academic purposes.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
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Genetics & Heredity
Frieder Hadlich, Henry Reyer, Michael Oster, Nares Trakooljul, Eduard Murani, Siriluck Ponsuksili, Klaus Wimmers
Summary: Commercial and customized microarrays are valuable tools for analyzing holistic expression patterns, but require integration of the latest genomic information. This study presents a comprehensive workflow using the rePROBE R package to assign probes and annotate probe sets based on up-to-date genomic and transcriptomic data. The workflow reveals updated probe assignments and annotations for various livestock species and human, with a focus on providing a detailed basis for comprehensive analyses such as eQTL studies.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
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Computer Science, Artificial Intelligence
Marie Destandau, Caroline Appert, Emmanuel Pietriga
Summary: The article introduces the concept of semantic paths for obtaining meaningful information about RDF resources through analyzing chains of triples, and implementing a navigation strategy based on aggregation to determine the most readable representation. S-Paths is a browsing tool that systematically identifies the best rated view for a given set of resources.
Review
Biochemical Research Methods
Maxwell W. Libbrecht, Rachel C. W. Chan, Michael M. Hoffman
Summary: SAGA algorithms are widely used for understanding genome activity and gene regulation by partitioning the genome based on epigenomic datasets and assigning labels to segments. They function in an unsupervised manner like clustering algorithms, discovering categories of activity such as promoters and enhancers, without prior knowledge of known genomic elements.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Robert Schoepflin, Uira Souto Melo, Hossein Moeinzadeh, David Heller, Verena Laupert, Jakob Hertzberg, Manuel Holtgrewe, Nico Alavi, Marius-Konstantin Klever, Julius Jungnitsch, Emel Comak, Seval Tuerkmen, Denise Horn, Yannis Duffourd, Laurence Faivre, Patrick Callier, Damien Sanlaville, Orsetta Zuffardi, Romano Tenconi, Nehir Edibe Kurtas, Sabrina Giglio, Bettina Prager, Anna Latos-Bielenska, Ida Vogel, Merete Bugge, Niels Tommerup, Malte Spielmann, Antonio Vitobello, Vera M. Kalscheuer, Martin Vingron, Stefan Mundlos
Summary: The study characterizes structural variations in a cohort of individuals with complex genomic rearrangements, finding breakpoints enriched in inactive regions leading to chromatin domain fusions. By combining short- and long-read genome sequencing with Hi-C, large-scale genomic rearrangements are identified, impacting gene expression and three-dimensional chromatin architecture. The study reveals an enrichment of breakpoints in lamina-associated domains and reshuffling of topologically associating domains, suggesting different mechanisms at play in allelic imbalanced gene expression around breakpoints.
NATURE COMMUNICATIONS
(2022)
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Genetics & Heredity
Mikaela Koutrouli, Evangelos Karatzas, Katerina Papanikolopoulou, Georgios A. Pavlopoulos
Summary: NORMA is a web tool for interactive network annotation visualization and topological analysis, capable of handling multiple networks and annotations simultaneously. It provides precalculated annotations and automated community detection algorithms, allowing users to generate publication-ready figures by adjusting network views and selecting groups of interest.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2022)
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Biochemical Research Methods
Benjamin Hepp, Violette Da Cunha, Florence Lorieux, Jacques Oberto
Summary: BAGET 2.0 is an updated web service that allows access to the sequence and synteny of any gene from completely sequenced bacteria and archaea in just three mouse clicks, and it can also process user-provided annotated genomes.
Article
Biotechnology & Applied Microbiology
Thomas Roder, Simone Oberhaensli, Noam Shani, Remy Bruggmann
Summary: OpenGenomeBrowser is a self-hostable, open-source platform for managing access to genomic data and simplifying comparative genomics analyses. It offers a wide range of features, including generation of phylogenetic trees, comparison of gene loci, browsing of biochemical pathways, and execution of BLAST searches.
Article
Biochemical Research Methods
Guangyu Yang, Leslie Cope, Zitong He, Liliana Florea
Summary: This study introduces a toolkit called Jutils for visualizing differential splicing events at the intron level. Jutils is method-agnostic, converting outputs from different tools into a unified representation to create heatmaps, sashimi plots, and Venn diagrams. The tool is lightweight and relies solely on a unified data file for visualizations.
Article
Multidisciplinary Sciences
Shuyan Ji, Fengling Chen, Paula Stein, Jiacheng Wang, Ziming Zhou, Lijuan Wang, Qing Zhao, Zili Lin, Bofeng Liu, Kai Xu, Fangnong Lai, Zhuqing Xiong, Xiaoyu Hu, Tianxiang Kong, Feng Kong, Bo Huang, Qiujun Wang, Qianhua Xu, Qiang Fan, Ling Liu, Carmen J. Williams, Richard M. Schultz, Wei Xie
Summary: OBOX, a PRD-like homeobox domain transcription factor family, is a key regulator of mouse zygotic genome activation and early embryogenesis. OBOX facilitates RNA polymerase II preconfiguration, leading to the transition of gene expression during early embryonic development.
Article
Anatomy & Morphology
Natalia Vilor-Tejedor, Gregory Operto, Tavia E. Evans, Carles Falcon, Marta Crous-Bou, Carolina Minguillon, Raffaele Cacciaglia, Marta Mila-Aloma, Oriol Grau-Rivera, Marc Suarez-Calvet, Diego Garrido-Martin, Sebastian Moran, Manel Esteller, Hieab H. Adams, Jose Luis Molinuevo, Roderic Guigo, Juan Domingo Gispert
BRAIN STRUCTURE & FUNCTION
(2020)
Article
Biochemistry & Molecular Biology
Lihua Jiang, Meng Wang, Shin Lin, Ruiqi Jian, Xiao Li, Joanne Chan, Guanlan Dong, Huaying Fang, Aaron E. Robinson, Michael P. Snyder
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Biochemistry & Molecular Biology
Adam Frankish, Mark Diekhans, Irwin Jungreis, Julien Lagarde, Jane E. Loveland, Jonathan M. Mudge, Cristina Sisu, James C. Wright, Joel Armstrong, If Barnes, Andrew Berry, Alexandra Bignell, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomas Di Domenico, Sarah Donaldson, Ian T. Fiddes, Carlos Garcia Giron, Jose Manuel Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martinez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinuri Xu, Yucheng T. Yang, Andrew Yates, Daniel Zerbino, Yan Zhang, Jyoti S. Choudhary, Mark Gerstein, Roderic Guigo, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek
Summary: The GENCODE project annotates human and mouse genes and transcripts with high accuracy, using experimental data and bioinformatic tools, and continues to improve annotation infrastructure and tools for the human and mouse genomes. This includes manual annotation for the mouse reference genome, targeted improvements for SARS-CoV-2 related genes, collaborative projects for reference annotation databases, and the first GENCODE supervised automated annotation of lncRNAs.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Multidisciplinary Sciences
Diego Garrido-Martin, Beatrice Borsari, Miquel Calvo, Ferran Reverter, Roderic Guigo
Summary: Alternative splicing is a fundamental step in eukaryotic mRNA biogenesis, and the comprehensive catalog of splicing QTLs in the human genome generated through analysis of the GTEx dataset provides insight into splicing regulation mechanisms and disease mechanisms.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Olivia M. de Goede, Daniel C. Nachun, Nicole M. Ferraro, Michael J. Gloudemans, Abhiram S. Rao, Craig Smail, Tiffany Y. Eulalio, Francois Aguet, Bernard Ng, Jishu Xu, Alvaro N. Barbeira, Stephane E. Castel, Sarah Kim-Hellmuth, YoSon Park, Alexandra J. Scott, Benjamin J. Strober, Christopher D. Brown, Xiaoquan Wen, Ira M. Hall, Alexis Battle, Tuuli Lappalainen, Hae Kyung Im, Kristin G. Ardlie, Sara Mostafavi, Thomas Quertermous, Karla Kirkegaard, Stephen B. Montgomery
Summary: This study systematically characterized 14,100 lncRNA genes across 49 tissues for 101 complex genetic traits using GTEx project data, identifying 1,432 lncRNA gene-trait associations, 800 of which were not explained by neighboring protein-coding genes. The findings revealed associations between lncRNA and various diseases and traits.
Article
Biochemistry & Molecular Biology
Bertrand Fouks, Philipp Brand, Hung N. Nguyen, Jacob Herman, Francisco Camara, Daniel Ence, Darren E. Hagen, Katharina J. Hoff, Stefanie Nachweide, Lars Romoth, Kimberly K. O. Walden, Roderic Guigo, Mario Stanke, Giuseppe Narzisi, Mark Yandell, Hugh M. Robertson, Nikolaus Koeniger, Panuwan Chantawannakul, Michael C. Schatz, Kim C. Worley, Gene E. Robinson, Christine G. Elsik, Olav Rueppell
Summary: This study compared the genomes of three different subgenera of honey bees and revealed a complex gene regulation pattern and the role of positive selection in adaptive evolution among honey bee species.
Article
Multidisciplinary Sciences
Svetlana Kalmykova, Marina Kalinina, Stepan Denisov, Alexey Mironov, Dmitry Skvortsov, Roderic Guigo, Dmitri Pervouchine
Summary: The ability of nucleic acids to form double-stranded structures is essential for all living systems, with long-range RNA structures containing conserved complementary regions abundant in human protein-coding genes. PCCRs, mainly located within introns, have a distinct splicing pattern and may affect splicing widely.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Beatrice Borsari, Pablo Villegas-Miron, Silvia Perez-Lluch, Isabel Turpin, Hafid Laayouni, Alba Segarra-Casas, Jaume Bertranpetit, Roderic Guigo, Sandra Acosta
Summary: The study explored the correlation between the genomic location of active enhancers and tissue-specific gene expression, revealing that tissue-specific enhancers are enriched in intronic regions and control genes involved in tissue-specific functions. The results suggest that the genomic location of active enhancers is crucial for the tissue-specific control of gene expression, with the transition from developmental to adult stages showing a continuum of intergenic to intronic enhancers.
Article
Clinical Neurology
Natalia Vilor-Tejedor, Iacopo Ciampa, Gregory Operto, Carles Falcon, Marc Suarez-Calvet, Marta Crous-Bou, Mahnaz Shekari, Eider M. Arenaza-Urquijo, Marta Mila-Aloma, Oriol Grau-Rivera, Carolina Minguillon, Gwendlyn Kollmorgen, Henrik Zetterberg, Kaj Blennow, Roderic Guigo, Jose Luis Molinuevo, Juan Domingo Gispert
Summary: This study found that in the asymptomatic stages of the Alzheimer's continuum, ePVS in the CS region is specifically associated with tau pathophysiology, neurodegeneration, and synaptic dysfunction, while there is no association with ePVS in the BG region.
ALZHEIMERS RESEARCH & THERAPY
(2021)
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Genetics & Heredity
Iacopo Ciampa, Gregory Operto, Carles Falcon, Carolina Minguillon, Manuel Castro de Moura, David Pineyro, Manel Esteller, Jose Luis Molinuevo, Roderic Guigo, Arcadi Navarro, Juan Gispert, Natalia Vilor-Tejedor
Summary: The study revealed a significant association between the BIN1-rs744373 polymorphism and ePVS in the centrum semiovale, showing increased risk for G allele carriers, particularly in APOE-epsilon 4 carriers. This suggests that genetic predisposition for Alzheimer's disease may influence the enlargement of perivascular spaces in the brain.
Article
Genetics & Heredity
Anna Vlasova, Toni Hermoso Pulido, Francisco Camara, Julia Ponomarenko, Roderic Guigo
Summary: Functional annotation is essential for enhancing the biological relevance of predicted features in genomic sequences, and improving gene structural annotation. The pipeline FA-nf, implemented in Nextflow, integrates various annotation approaches for producing multiple files and reports efficiently. It can be easily parallelized and deployed in a Linux computational environment, ensuring full reproducibility through software containerization.
Article
Biotechnology & Applied Microbiology
Diego Garrido-Martin, Miquel Calvo, Ferran Reverter, Roderic Guigo
Summary: This article introduces an analysis method for multidimensional phenotypic data in large cohorts of genotyped individuals, which has high computational efficiency and significant judging ability, and performs well in QTL mapping and GWAS.
Article
Biochemistry & Molecular Biology
Natalia Vilor-Tejedor, Diego Garrido-Martin, Blanca Rodriguez-Fernandez, Sander Lamballais, Roderic Guigo, Juan Domingo Gispert
Summary: Imaging genetic studies aim to investigate how genetic information influences brain structure and function by analyzing the correlation and association between genetic variants and brain measurements. While univariate approaches have been successful, the development and application of multivariate methods become crucial when dealing with multiple brain phenotypes and genetic data.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
