Article
Biochemistry & Molecular Biology
Jiyao Wang, Philippe Youkharibache, Aron Marchler-Bauer, Christopher Lanczycki, Dachuan Zhang, Shennan Lu, Thomas Madej, Gabriele H. Marchler, Tiejun Cheng, Li Chuin Chong, Sarah Zhao, Kevin Yang, Jack Lin, Zhiyu Cheng, Rachel Dunn, Sridhar Acharya Malkaram, Chin-Hsien Tai, David Enoma, Ben Busby, Nicholas L. Johnson, Francesco Tabaro, Guangfeng Song, Yuchen Ge
Summary: iCn3D was initially developed as a web-based 3D molecular viewer and evolved into a full-featured interactive structural analysis software. By sharing URLs, users can share annotated molecular scenes and underlying data. Recently, Python and Node.js are used to systematically analyze large structural datasets.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Mads Valdemar Anderson, Jakob Haldrup, Emil Aagaard Thomsen, Jonas Holst Wolff, Jacob Giehm Mikkelsen
Summary: Prime editing is a precise genome editing technology that uses pegRNAs as guide molecules and editing templates. pegIT is a user-friendly web tool for rapid design of various user-defined edits.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biology
Daniel Castillo-Secilla, Juan Manuel G. Galvez, Francisco Carrillo-Perez, Marta Verona-Almeida, Daniel Redondo-Sanchez, Francisco Manuel Ortuno, Luis Javier Herrera, Ignacio Rojas
Summary: KnowSeq is a powerful software designed to automate and integrate bioinformatic tools for complex gene expression analysis and disease gene signature identification. It provides a unified environment, advanced algorithms, automatic HTML report generation, and biological knowledge extraction to assist decision-making processes.
COMPUTERS IN BIOLOGY AND MEDICINE
(2021)
Article
Biochemistry & Molecular Biology
Xiaoli Chen, Shaojie Zhang
Summary: The functions of non-coding RNAs are dependent on their 3D structures, making it critical to compare RNA 3D structures in order to analyze their functions. In this study, we identified a phenomenon where two non-coding RNAs may have similar substructures when their sequence order is rotated. To address this, we developed a software tool called CircularSTAR3D to detect circular matched substructures in RNA 3D structures. Our computational experiments on a non-redundant RNA structure dataset revealed the ubiquity of circular matching. We also demonstrated the usefulness of CircularSTAR3D in detecting conserved substructures missed by regular alignment tools.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biochemical Research Methods
Ji-Hye Choi, Hui-Seon Choi, Seong-Ho Cho, Ji-Hye Lee, Hyun Goo Woo
Summary: Researchers can utilize the user-friendly web service Cancer Genome Viewer (CGV) to connect, integrate, and analyze cancer genomic data and pharmacogenomic data. They can customize the selection of samples to be analyzed using pre-defined options from multiple datasets. CGV also provides pre-calculated drug response scores, aiding in the discovery of new cancer targets and therapeutics.
Article
Biology
Theo Sanderson
Summary: The COVID-19 pandemic has generated an unprecedented amount of sequencing data for SARS-CoV-2, leading to the need for a scalable tool for exploring phylogenetic trees. Taxonium is a new tool that uses WebGL to enable the exploration of large trees with millions of nodes in the browser. This article describes the insights gained from analyzing a tree of five million sequences and provides a tool for exploring a public tree of over five million SARS-CoV-2 sequences.
Article
Chemistry, Multidisciplinary
Noelia Vallez, Jose Luis Espinosa-Aranda, Anibal Pedraza, Oscar Deniz, Gloria Bueno
Summary: Microscopy scanners and AI techniques have advanced biomedicine, but challenges arise from the variety of digital file formats used. DICOM stands out as a standard that transcends internal image formats, but its clinical use is limited. This paper presents the first web viewer system that integrates WSI DICOM images and AI models, aiming to bridge the gap and improve CAD WSI processing tasks.
APPLIED SCIENCES-BASEL
(2023)
Article
Biochemistry & Molecular Biology
Gerard Minuesa, Cristina Alsina, Juan Antonio Garcia-Martin, Juan Carlos Oliveros, Ivan Dotu
Summary: MoiRNAiFold is a versatile and user-friendly tool for de novo synthetic RNA design, based on Constraint Programming, with the ability to handle multiple design constraints and quality measures, and improve features for RNA regulation control of gene expression. Demonstrated to outperform any previous software in benchmarking structural RNA puzzles from EteRNA.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
David Borland, Carolyn M. McCormick, Niyanta K. Patel, Oleh Krupa, Jessica T. Mory, Alvaro A. Beltran, Tala M. Farah, Carla F. Escobar-Tomlienovich, Sydney S. Olson, Minjeong Kim, Guorong Wu, Jason L. Stein
Summary: Segmentor is an open-source tool designed for reliable, efficient, and user-friendly manual annotation and refinement of objects within 3D light sheet microscopy images, particularly nuclei. It employs a hybrid 2D-3D approach for visualizing and segmenting objects, with features for automatic region splitting to streamline the process of 3D segmentation. Editing simultaneously in 2D and 3D using Segmentor significantly decreases time spent on manual annotations without affecting accuracy.
BMC BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Patrick Adelberger, Klaus Eckelt, Markus J. Bauer, Marc Streit, Christian Haslinger, Thomas Zichner
Summary: A main task in computational cancer analysis is to identify patient subgroups based on metadata attributes or genomic markers, and the web-based cohort analysis tool Coral is designed to support this task by allowing users to interactively create, refine, and compare cohorts. Coral also visualizes the evolution of cohorts and provides intuitive access to prevalence information, as well as the ability to store, share, and reproduce findings. It is pre-loaded with data from over 128,000 samples from various cancer research projects.
Article
Biochemical Research Methods
Eloi Durant, Francois Sabot, Matthieu Conte, Mathieu Rouard
Summary: Pangenomics has evolved to study all sequences available, with linear representations being a suitable option for user-friendliness. Panache is a tool for visualizing gene-based and sequence-based pangenomes, using a linear layout similar to genome browsers.
Article
Engineering, Civil
Susanna Grasso, Pierluigi Claps, Daniele Ganora, Andrea Libertino
Summary: To reduce the impact of droughts and increase the resilience of regional water systems, various competing demands need to be reconciled. Planners and practitioners would benefit from using the most recent data and easily accessible analysis tools for sustainable and efficient water resource management.
WATER RESOURCES MANAGEMENT
(2021)
Article
Mathematical & Computational Biology
Seonggyun Han, Jaehang Shin, Hyeim Jung, Jane Ryu, Habtamu Minassie, Kwangsik Nho, Insong Koh, Younghee Lee
Summary: Alzheimer's disease is a neurodegenerative disorder with complex biological mechanisms, and comprehensive investigations with multi-omics data from different brain regions can help understand the disease progression. ADAS-viewer is a web platform that integrates various omics data to identify functional changes and potential biomarkers of AD across multiple brain regions.
NPJ SYSTEMS BIOLOGY AND APPLICATIONS
(2021)
Article
Biochemical Research Methods
Adam C. Knapp, Luis Sordo Vieira, Reinhard Laubenbacher, Julia Chifman
Summary: Introducing SteadyCellPhenotype, a browser-based interface for analyzing ternary biological networks. It provides tools for deterministically finding all steady states of a network and simulating and visualizing trajectories with high-quality graphics for publication. Simulations help approximate the size of attractor basins, while deterministic simulations of trajectories near specified points allow exploration of the system's behavior in that neighborhood.
Article
Biochemical Research Methods
Ning Wang, Sofia Khan, Laura L. L. Elo
Summary: VarSCAT is a tool for annotating the sequence contexts of genomic variants, including breakpoint ambiguities, flanking bases of variants, wildtype/mutated DNA sequences, variant nomenclatures, distances between adjacent variants, tandem repeat regions, and custom annotation with user customizable options. It is more versatile and customizable than currently available methods for annotating variants in short tandem repeat (STR) regions or insertions and deletions (indels) with breakpoint ambiguity. Analysis using VarSCAT revealed the presence of breakpoint ambiguities in more than 75% of high-confidence human germline and clinically relevant indels, and showed that over 80% of human germline small variants in STR regions are indels correlated with STR motif sizes.
PLOS COMPUTATIONAL BIOLOGY
(2023)