Article
Computer Science, Software Engineering
Theophanis Tsandilas
Summary: Information visualization research has developed powerful systems that allow users to create custom data visualizations without textual programming. However, existing visualization authoring systems often assume that users want to generate visual representations they already have in mind, rather than explore designs. StructGraphics enables designers to create data-agnostic and fully reusable visualization designs by drawing graphics on a canvas and structuring visual properties independent of specific datasets.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2021)
Article
Public, Environmental & Occupational Health
Denisa Krejci, Matej Karolyi, Lucie Pehalova, Jakub Scavnicky, Michaela Zapletalova, Ivana Katinova, Jaroslav Sterba, Jan Stary, Lenka Snajdrova, Martin Komenda, Ladislav Dusek
Summary: The study developed a new web portal called the Czech Childhood Cancer Information System to provide information on childhood cancer epidemiology in the country. By validating data from multiple sources, the portal offers basic information on childhood cancer including incidence, mortality, and overall survival rates through interactive reports.
JMIR PUBLIC HEALTH AND SURVEILLANCE
(2021)
Article
Biochemistry & Molecular Biology
Shuangbin Xu, Zehan Dai, Pingfan Guo, Xiaocong Fu, Shanshan Liu, Lang Zhou, Wenli Tang, Tingze Feng, Meijun Chen, Li Zhan, Tianzhi Wu, Erqiang Hu, Yong Jiang, Xiaochen Bo, Guangchuang Yu
Summary: ggtreeExtra is a universal tool for visualizing tree data, supporting various data types and visualization methods. By integrating evolutionary statistics and external data, it extends the applications of phylogenetic trees in different disciplines.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Article
Computer Science, Artificial Intelligence
Bernardo Breve, Loredana Caruccio, Stefano Cirillo, Vincenzo Deufemia, Giuseppe Polese
Summary: This paper introduces a tool for visualizing RFDS discovered from a data stream, which allows exploration of results for different types of RFDS and uses quantitative measures to monitor the evolution of discovery results. The tool enables comparison of RFDS discovered across multiple executions and provides visual manipulation operators for dynamically composing and filtering results.
Article
Computer Science, Interdisciplinary Applications
Diego A. Espinoza, Ryland D. Mortlock, Samson J. Koelle, Chuanfeng Wu, Cynthia E. Dunbar
Summary: Clonal tracking methods provide insights into cellular output, but the lack of analysis tools has hindered standardized frameworks. The barcodeR package now offers diverse tools for analyzing and visualizing clonal tracking data, proving useful in exploring longitudinal patterns and lineage relationships in various studies.
NATURE COMPUTATIONAL SCIENCE
(2021)
Article
Computer Science, Software Engineering
Richen Liu, Xiaodong Wen, Meng Jiang, Guang Yang, Chuyu Zhang, Xiaojian Chen
Summary: The proposed client-server based collaborative visualization system, comprising a 3D volume explorer and a 2D slice analyzer, enables domain experts to leverage their domain knowledge to illustrate different parts of the data efficiently.
SOFTWARE-PRACTICE & EXPERIENCE
(2021)
Article
Computer Science, Information Systems
Rik Eshuis
Summary: Data-centric process management enables knowledge workers to perform knowledge-intensive processes flexibly. Process templates, manually modified to suit the context of specific cases, are a key component. Extracting reusable fragments from process variants enhances efficiency and improves the quality of complex data-centric processes.
IEEE TRANSACTIONS ON SERVICES COMPUTING
(2023)
Article
Multidisciplinary Sciences
Antonia Moll, Lisa Marie Ramirez, Momchil Ninov, Juliane Schwarz, Henning Urlaub, Markus Zweckstetter
Summary: Alzheimer's disease is a neurodegenerative disorder characterized by the misfolding and aggregation of Tau protein. This study reveals that the Hsp70 and Hsp90 chaperones play a critical role in regulating Tau and that their interaction depends on Tau's aggregation-prone region. The findings highlight the importance of the Hsp70/Hsp90 multichaperone complex in neurodegenerative diseases.
NATURE COMMUNICATIONS
(2022)
Article
Computer Science, Software Engineering
Aditeya Pandey, Sehi L'Yi, Qianwen Wang, Michelle A. Borkin, Nils Gehlenborg
Summary: The interpretation of genomics data relies on visualization tools. However, the wide range of visualization techniques and tasks poses a challenge for analysts. Existing visualization recommendation systems are not designed to handle domain-specific problems. To address this, GenoREC is designed as a novel visualization recommendation system for genomics, enabling analysts to choose effective visualizations based on their data and tasks.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Biochemical Research Methods
Alexander L. Cope, Felicity Anderson, John Favate, Michael Jackson, Amanda Mok, Anna Kurowska, Junchen Liu, Emma MacKenzie, Vikram Shivakumar, Peter Tilton, Sophie M. Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F. Lareau, Premal Shah, Edward W. J. Wallace
Summary: riboviz 2 is an updated software package for comprehensive analysis and visualization of Ribo-seq data. It utilizes the Nextflow workflow management system for end-to-end processing and has been extensively tested on diverse species and library preparation strategies.
Article
Biochemistry & Molecular Biology
Sandra Schilbach, Shintaro Aibara, Christian Dienemann, Frauke Grabbe, Patrick Cramer
Summary: This study reveals the high-resolution structure of the transcription initiation complex and the mechanism of DNA opening, crucial for promoter-initiated transcription. TFIIE facilitates initiation by supporting the clamp head loop and regulating the TFIIH translocase.
Article
Chemistry, Multidisciplinary
Fan Yang, Guogeng Jia, Jiuzhou Guo, Yuan Liu, Chu Wang
Summary: Activity-based protein profiling (ABPP) is a powerful tool for annotating protein functions and discovering targets of bioactive ligands. In this study, we combined data-independent acquisition (DIA) MS with ABPP to develop a label-free quantitative chemical proteomic method called DIA-ABPP. With good reproducibility and high accuracy, DIA-ABPP allows for high-throughput quantification, enabling comprehensive profiling of functional proteomes and interactions with bioactive small molecules.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Computer Science, Artificial Intelligence
Weiner de Oliveira, Regina Braga, Jose Maria N. David, Victor Stroele, Fernanda Campos, Gabriellla Castro
Summary: Provenance is a central challenge in computational systems for establishing reliability and security. This paper presents the Visionary framework, which utilizes ontology, complex network analysis, and software visualization to assist in the understanding and use of provenance data. The framework is designed for supporting experiment reproducibility, result interpretation, and problem diagnosis, and can be adapted to any system that uses the PROV provenance model.
KNOWLEDGE AND INFORMATION SYSTEMS
(2022)
Article
Biology
Tejas Guha, Elana J. Fertig, Atul Deshpande
Summary: Reduced-dimension or spatial in situ scatter plots are commonly used in bioinformatics research to present phenomena or cell-conditions of interest in single-cell data. However, using color as the only visual cue for differentiating cell groups becomes less useful as the complexity of the information increases, especially for readers with color-vision deficiencies (CVDs). In this paper, the authors introduce scatterHatch, an R package that creates easily interpretable scatter plots by redundantly coding cell groups using colors and patterns. Simulations demonstrate that scatterHatch plots are more accessible than simple scatter plots for various types of CVDs.
Article
Multidisciplinary Sciences
Katherine S. H. Beckham, Christina Ritter, Grzegorz Chojnowski, Daniel S. Ziemianowicz, Edukondalu Mullapudi, Mandy Rettel, Mikhail M. Savitski, Simon A. Mortensen, Jan Kosinski, Matthias Wilmanns
Summary: The ESX-5 type VII secretion system is a membrane-spanning protein complex crucial to the virulence of mycobacterial pathogens. The high-resolution structure of the 2.1-megadalton ESX-5 core complex reveals a dynamic, secretion-competent conformation of the pore with flexibility for accommodating targeted protein secretion, suggesting that a highly dynamic state of the pore may be a fundamental principle of bacterial secretion machineries.
Article
Biochemistry & Molecular Biology
Molly A. Bogue, Vivek M. Philip, David O. Walton, Stephen C. Grubb, Matthew H. Dunn, Georgi Kolishovski, Jake Emerson, Gaurab Mukherjee, Timothy Stearns, Hao He, Vinita Sinha, Beena Kadakkuzha, Govindarajan Kunde-Ramamoorthy, Elissa J. Chesler
NUCLEIC ACIDS RESEARCH
(2020)
Article
Cell Biology
Xiaowei Wang, Nanhong Lou, Allison Eberhardt, Yujia Yang, Peter Kusk, Qiwu Xu, Benjamin Forstera, Sisi Peng, Meng Shi, Antonio Ladron-de-Guevara, Christine Delle, Bjorn Sigurdsson, Anna L. R. Xavier, Ali Erturk, Richard T. Libby, Lu Chen, Alexander S. Thrane, Maiken Nedergaard
SCIENCE TRANSLATIONAL MEDICINE
(2020)
Article
Ophthalmology
Alison Heffer, Victor Wang, Jayanth Sridhar, Steven E. Feldon, Richard T. Libby, Collynn F. Woeller, Ajay E. Kuriyan
TRANSLATIONAL VISION SCIENCE & TECHNOLOGY
(2020)
Article
Cell Biology
Olivia J. Marola, Stephanie B. Syc-Mazurek, Gareth R. Howell, Richard T. Libby
CELL DEATH & DISEASE
(2020)
Article
Multidisciplinary Sciences
Alison M. Heffer, Victor Wang, Richard T. Libby, Steven E. Feldon, Collynn F. Woeller, Ajay E. Kuriyan
Review
Immunology
Con Sullivan, Brandy-Lee Soos, Paul J. Millard, Carol H. Kim, Benjamin L. King
Summary: The zebrafish model is a powerful tool for studying host-virus interactions and inflammation, allowing for focused studies on the innate immune system response to viral infection and revealing significant genetic conservation with the human genome. This model offers opportunities for intensive studies aimed at understanding conserved host responses to viral infection.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Michael P. Wilczek, Aiden M. C. Pike, Sophie E. Craig, Melissa S. Maginnis, Benjamin L. King
Summary: This study examines the mutations in the noncoding control region (NCCR) of JC polyomavirus (JCPyV) and their influence on viral transcription. It was found that the number of transcription factor binding sites (TFBS) significantly increased in patients with progressive multifocal leukoencephalopathy (PML), especially in samples isolated from the cerebrospinal fluid. These findings suggest that the rearrangements in NCCR can impact disease outcome by altering viral gene transcription.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Cell Biology
Stephanie B. Syc-Mazurek, Hongtian Stanley Yang, Olivia J. Marola, Gareth R. Howell, Richard T. Libby
Summary: This study identifies the downstream transcriptional networks important for apoptotic signaling after retinal injury, which may be crucial for understanding the progression of neurodegeneration.
CELL DEATH & DISEASE
(2022)
Article
Cell Biology
Olivia J. Marola, Gareth R. Howell, Richard T. Libby
Summary: Endothelin signaling is suggested to play an important role in glaucoma, causing death of retinal ganglion cells (RGC). The study found that endothelin ligands induce RGC death through a mechanism initiated by vascular mural cells, possibly involving vasoconstriction and pathological consequences.
CELL DEATH DISCOVERY
(2022)
Editorial Material
Cell Biology
Olivia J. Marola, Sarah E. R. Yablonski, Peter G. Shrager, Robert W. Nickells, Richard T. Libby
CELL DEATH DISCOVERY
(2022)
Article
Multidisciplinary Sciences
Victor Wang, Alison Heffer, Elisa Roztocil, Steven E. Feldon, Richard T. Libby, Collynn F. Woeller, Ajay E. Kuriyan
Summary: Cigarette smoke exposure affects the TNF alpha/NF kappa B/Snail pathway in RPE cells, increasing the risk of PVR. In a mouse model, injection of ARPE-19 cells pre-treated with CSE resulted in more severe PVR formation. These findings provide important insights into the mechanisms of PVR and potential pharmacological interventions.
Article
Biochemistry & Molecular Biology
Molly A. Bogue, Robyn L. Ball, Vivek M. Philip, David O. Walton, Matthew H. Dunn, Georgi Kolishovski, Anna Lamoureux, Matthew Gerring, Hongping Liang, Jake Emerson, Tim Stearns, Hao He, Gaurab Mukherjee, John Bluis, Sejal Desai, Beth Sundberg, Beena Kadakkuzha, Govindarajan Kunde-Ramamoorthy, Elissa J. Chesler
Summary: The Mouse Phenome Database (MPD) is a biomedical data repository supported by the US National Institutes of Health, which collects and manages phenotype and genotype data from mouse experiments worldwide. With rich metadata and a suite of analysis tools, MPD enables users to analyze and visualize these data within and across studies and populations.
NUCLEIC ACIDS RESEARCH
(2023)
Meeting Abstract
Ophthalmology
Ajay E. Kuriyan, Alison Heffer, Victor Wang, Hua He, Megha Mahabole, Steven E. Feldon, Richard T. Libby, Scheffer C. G. Tseng, Collynn Woeller
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Biology
Ellen Hartig, Shusen Zhu, Benjamin L. King, James A. Coffman
BMC RESEARCH NOTES
(2020)
Meeting Abstract
Ophthalmology
Victor Wang, Alison Heffer, Steven E. Feldon, Richard T. Libby, Collynn Woeller, Ajay E. Kuriyan
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2020)