Article
Computer Science, Software Engineering
Shreeraj Jadhav, Arie E. Kaufman
Summary: The MD-Cave is an immersive analytics system designed to support visual diagnoses performed by radiologists through enhanced stereoscopic visualizations. The system utilizes contemporary paradigms in immersive visualization and 3D interaction, making it better suited for investigating 3D volumetric data. It offers high resolution stereoscopic visualizations, 3D interactions through head and hand tracking, and a general framework that supports 3D visualization without explicit segmentation algorithms, expanding its utility to various diagnostic scenarios.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Biochemistry & Molecular Biology
Zhenyi Wang, Yanjie Zhong, Zhaofeng Ye, Lang Zeng, Yang Chen, Minglei Shi, Zhiyuan Yuan, Qiming Zhou, Minping Qian, Michael Q. Zhang
Summary: MarkovHC is a novel Markov hierarchical clustering algorithm that effectively stratifies cells, identifies cell populations, and characterizes cellular trajectories and critical points. Its application in investigating the multi-level architectures and transition processes during human embryo preimplantation development and gastric cancer procession demonstrates its effectiveness in single-cell omics studies.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Ziqi Deng, Jorge Botas, Carlos P. Cantalapiedra, Ana Hernandez-Plaza, Jordi Burguet-Castell, Jaime Huerta-Cepas
Summary: PhyloCloud is an online platform designed to host and index large collections of phylogenetic trees, providing seamless access to analyses and operations, as well as custom annotations and multiple sequence alignments.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Multidisciplinary Sciences
Yiran Chen, Ismar Volic
Summary: The Mapper graphs offer more comprehensive visualizations of the pandemic, allowing for easy comparisons of its features across time and space, while encoding a variety of geometric features of the data cloud.
Article
Chemistry, Analytical
Ming Yuan, Chunhui Li, Sheng Zhang, Yannan Xie
Summary: An Automated Power Evaluation Workbench (APEW) is developed to solve the time-consuming and error-prone manual load tuning process for Triboelectric nanogenerators (TENGs), enabling program-controlled resistance switching and power measuring. Experimental results show that the power curves obtained by APEW are almost identical to those obtained by the traditional manual switching approach, highlighting the significance of APEW in the further development of TENGs.
Article
Computer Science, Information Systems
Daniel Deutch, Amir Gilad, Tova Milo, Amit Mualem, Amit Somech
Summary: This paper proposes a novel solution to assist data scientists in exploring new datasets by identifying interesting rows based on their contribution to different columns of the entire dataframe. The solution addresses the computational challenge by focusing on semantically-related sets and provides more informative explanations. Experimental study demonstrates the usefulness of the system in various scenarios.
PROCEEDINGS OF THE VLDB ENDOWMENT
(2022)
Article
Computer Science, Software Engineering
A. Arleo, S. Miksch, D. Archambault
Summary: This paper introduces MultiDynNoS, a multi-level event-based graph layout algorithm, which can accelerate dynamic graph layout. Through comparison with existing layout techniques and experiments on algorithm extensions, MultiDynNoS demonstrates its competitiveness and contributes to opening new research directions.
COMPUTER GRAPHICS FORUM
(2022)
Article
Computer Science, Software Engineering
Qing Chen, Fuling Sun, Xinyue Xu, Zui Chen, Jiazhe Wang, Nan Cao
Summary: Despite the popularity of automated visualization tools, existing systems often do not fit the input data or meet visualization requirements, requiring additional adjustments. Therefore, we present the VizLinter framework to help users detect and rectify defective visualizations, consisting of a visualization linter and a visualization fixer.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Biochemistry & Molecular Biology
Lisanna Paladin, Martina Bevilacqua, Sara Errigo, Damiano Piovesan, Ivan Micetic, Marco Necci, Alexander Miguel Monzon, Maria Laura Fabre, Jose Luis Lopez, Juliet F. Nilsson, Javier Rios, Pablo Lorenzano Menna, Maia Cabrera, Martin Gonzalez Buitron, Mariane Goncalves Kulik, Sebastian Fernandez-Alberti, Maria Silvina Fornasari, Gustavo Parisi, Antonio Lagares, Layla Hirsh, Miguel A. Andrade-Navarro, Andrey Kajava, Silvio C. E. Tosatto
Summary: RepeatsDB database provides annotations and classification for protein tandem repeat structures from PDB. The new version 3.0 addresses challenges of data growth and annotation needs by introducing a hierarchical classification scheme.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Computer Science, Information Systems
Xiaojian Chen, Hailong Wang, Yu Zhu, Hansheng Wang, Mingjun Su, Shuyu Bao, Yiping Wu
Summary: This paper presents a new immersive visualization tool for better illustrating stratigraphic data, which is particularly useful for domain experts in petroleum information exploration. The tool allows for flexible interaction, enables experts to obtain desired underground flow path structures through surface queries, and supports different display modes and integration of geological information. Feedback from experts indicates that this tool contributes more to their scientific exploration of stratigraphic data compared to existing visualization tools in the field.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2022)
Article
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.
Article
Computer Science, Software Engineering
Sehi Lyi, Nils Gehlenborg
Summary: A series of recent studies have focused on designing responsive multi-view visualizations, but there are still unresolved questions. This paper presents a framework for designing responsive multi-view visualizations for genomics data. Existing genomics visualization tools rarely support responsiveness. The paper identifies usability issues and discusses approaches to address them, as well as extending the Gosling visualization grammar to support responsive constructs. The study suggests considering different input modalities in future research.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2023)
Article
Biochemical Research Methods
Lakshay Anand, Carlos M. Rodriguez Lopez
Summary: ChromoMap is an R package for the construction of interactive visualizations of chromosomes and feature-associated multi-omics data, providing flexibility and extensive application.
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Wenpin Hou, Zhicheng Ji
Summary: Palo optimizes the color palette assignment for improved visualization in single-cell and spatial genomic data analysis.
Article
Social Sciences, Interdisciplinary
Pleuntje Jellema, Margo Annemans, Ann Heylighen
Summary: Visual methods, including drawing, have value as both subjects and means of analysis in qualitative research. Researchers can actively engage with drawings to better understand and arrange data, and to supplement the traditional audio-to-text transcription process.
QUALITATIVE RESEARCH
(2022)