Article
Biotechnology & Applied Microbiology
Hongwei Wang, Xiaotian Zhang, Shuangcheng Ding, Yujie Huang, Shengyong Wang, Huili Chen, Yuhang Chen, Yuting Li
Summary: This paper describes the development of VisProDom, a new tool that allows users to visualize protein domains and transcript features together at the genome-wide level and export publication-ready figures.
Article
Multidisciplinary Sciences
Wanyanhan Jiang, Han Chen, Lian Yang, Xiaoqi Pan
Summary: When comparing means of different groups, it is necessary to explore and compare data for influencing factors or relative indices. This can be a complex and challenging process, especially for users who lack statistical knowledge and coding experience. To address this issue, we developed moreThanANOVA, an interactive, user-friendly, open-source, and cloud-based application that automates distribution tests and correlative significance tests, allowing users to customize post-hoc analysis based on their considerations.
Article
Computer Science, Software Engineering
Peter E. Morse, Anya M. Reading, Tobias Stal
Summary: In this paper, the visualization and researcher interaction of global deep Earth volume datasets are considered. A novel, interactive graphical application suite and workflow are presented, which use an intuitive 2.5D layer compositing approach. The methodology is anticipated to be used in the visualization of multiple datasets representing aspects of the Earth's deep interior and atmosphere.
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS
(2022)
Article
Biology
Patrick Koenig, Sebastian Beier, Martin Mascher, Nils Stein, Matthias Lange, Uwe Scholz
Summary: DivBrowse is a web application that allows interactive visualization and exploratory analysis of genomic diversity data stored in VCF files. It combines BLAST as an entry point with features like principal component analysis, providing a unique set of capabilities for studying genomic biodiversity datasets. The application also supports data interoperability and integration with existing web applications.
Article
Computer Science, Information Systems
Minxing Zheng, Xinran Miao, Kris Sankaran
Summary: In this study, interactive visualization and representation analysis were applied to guide the interpretation of glacier segmentation models. Activation values from a U-Net were visualized to understand and evaluate model performance. An online interface was built to provide comprehensive error analysis and enable user interaction for discovering model failure modes. The study also discussed the role of visualization in data preprocessing and model training.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2022)
Article
Biochemistry & Molecular Biology
Jingcheng Yang, Yaqing Liu, Jun Shang, Yechao Huang, Ying Yu, Zhihui Li, Leming Shi, Zihan Ran
Summary: BioVisReport is a lightweight solution that allows the rapid generation of interactive websites based on user-defined Markdown files. It facilitates reproducibility of research findings and enables further in-depth analysis. The tool offers various types of plot visualization for published data and supports flexible integration of user-developed Python plugins with multiple programming languages.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2022)
Article
Multidisciplinary Sciences
Genki Kobayashi
Summary: This article describes the assembly of mitochondrial protein-coding genes using publicly available next-generation sequencing (NGS) reads. Using a recently published pipeline, the protein-coding genes of 32 annelid species were successfully assembled from the reads deposited in the NCBI Sequence Read Archive (SRA). The assembled genes were deposited in GenBank and a phylogenetic analysis revealed the relationships of some polychaetes and leeches.
Article
Computer Science, Hardware & Architecture
Luca Rossetto, Ralph Gasser, Silvan Heller, Mahnaz Parian-Scherb, Loris Sauter, Florian Spiess, Heiko Schuldt, Ladislav Peska, Tomas Soucek, Miroslav Kratochvil, Frantisek Mejzlik, Patrik Vesely, Jakub Lokoc
Summary: In the research on video retrieval systems, dedicated retrieval competitions offer valuable insights into system performance, but are limited by set-up costs, logistics, and organization complexity. A proposed remote evaluation methodology provides statistically robust results and increases experiment replicability, making a significant contribution to open science in interactive retrieval benchmarks. Additionally, detailed evaluation reports provide new observations on previously inaccessible aspects of video retrieval.
Article
Biochemical Research Methods
Federico Marini, Annekathrin Ludt, Jan Linke, Konstantin Strauch
Summary: GeneTonic is a comprehensive toolkit for streamlining the interpretation of functional enrichment analyses in the context of differential expression, leveraging interactive visualizations and allowing users to navigate data effectively. The software is integrated with Bioconductor workflows and can accept outputs from various pathway analysis tools, offering both interactivity and reproducibility benefits to researchers.
BMC BIOINFORMATICS
(2021)
Article
Computer Science, Software Engineering
Elias Laurin Meyer, Constantin Kumaus, Michal Majka, Franz Koenig
Summary: This article describes an R-Shiny app designed for visualizing tidy, long data with multiple dimensions encountered in scientific computer simulations. The app is specifically designed for visualizing complex data structures in clinical trial simulation. It significantly speeds up the workflow and is illustrated with two examples, including the visualization of actual platform trial simulation data.
Article
Nursing
Lacey W. Heinsberg, Theresa A. Koleck, Mitali Ray, Daniel E. Weeks, Yvette P. Conley
Summary: Scientific data visualization is important for understanding data patterns and trends, and static visualizations are no longer sufficient. The availability of electronic scientific journal articles has created new opportunities for dynamic and interactive data visualization. Using the open-source programming language R and the R shiny package, dynamic and interactive scientific data visualization can be achieved.
BIOLOGICAL RESEARCH FOR NURSING
(2023)
Article
Biochemical Research Methods
Surbhi Sona, Matthew Bradley, Angela H. Ting
Summary: This passage introduces the use of software that analyzes single-cell RNA-seq data to deconvolve spatial transcriptomic spots. The protocols for implementing Seurat and Giotto packages to study cell-type distribution in a human ureter scRNA-seq dataset are provided. Additionally, the passage describes how to create an interactive web application using Seurat libraries to visualize and share the results.
Article
Environmental Sciences
J. E. H. Percival, N. Tsutsumida, D. Murakami, T. Yoshida, T. Nakaya
Summary: This paper introduces the gwpcorMapper software application for mapping geographically weighted (GW) correlation and partial correlation statistics in high-dimensional datasets. The software facilitates exploratory spatial data analysis by allowing researchers to interact with map components that describe local correlative relationships.
JOURNAL OF GEOVISUALIZATION AND SPATIAL ANALYSIS
(2022)
Article
Health Care Sciences & Services
John Del Gaizo, Ken R. Catchpole, Alexander Alekseyenko
Summary: read-tv is an open source R Shiny application for visualizing longitudinal data with unique filtering and changepoint analysis features. It addresses the need for analyzing surgical disruptions and other longitudinal data, enabling quick pattern identification for users.
Article
Mathematical & Computational Biology
Carlos Prieto, David Barrios, Angela Villaverde
Summary: Single-cell RNA sequencing (scRNA-Seq) enables quantification of transcriptomes of individual cells, and its application requires expertise in computational biology. We have developed SingleCAnalyzer, a user-friendly cloud platform for comprehensive scRNA-Seq analysis.
FRONTIERS IN BIOINFORMATICS
(2022)
Article
Biophysics
Gennady Gorin, Lior Pachter
Summary: In this study, the impact of splicing cascades on expression dynamics is investigated. The authors examine a class of processes and associated distributions that arise from bursty promoters coupled to directed acyclic graphs of splicing. They provide time-dependent joint distributions for various species, offering insights into how splicing can regulate expression dynamics. The findings are validated through the analysis of long-read sequencing data.
BIOPHYSICAL JOURNAL
(2022)
Article
Infectious Diseases
Kristjan E. Hjorleifsson, Solvi Rognvaldsson, Hakon Jonsson, Arna B. Agustsdottir, Margret Andresdottir, Kolbrun Birgisdottir, Ogmundur Eiriksson, Elias S. Eythorsson, Run Fridriksdottir, Gudmundur Georgsson, Kjartan R. Gudmundsson, Arnaldur Gylfason, Gudbjorg Haraldsdottir, Brynjar O. Jensson, Adalbjorg Jonasdotti, Aslaug Jonasdottir, Kamilla S. Josefsdottir, Nina Kristinsdottir, Borghildur Kristjansdottir, Thordur Kristjansson, Droplaug N. Magnusdottir, Runolfur Palsson, Louise le Roux, Gudrun M. Sigurbergsdottir, Asgeir Sigurdsson, Martin Sigurdsson, Gardar Sveinbjornsson, Emil Aron Thorarensen, Bjarni Thorbjornsson, Marianna Thordardottir, Agnar Helgason, Hilma Holm, Ingileif Jonsdottir, Frosti Jonsson, Olafur T. Magnusson, Gisli Masson, Gudmundur L. Norddahl, Jona Saemundsdottir, Patrick Sulem, Unnur Thorsteinsdottir, Daniel F. Gudbjartsson, Pall Melsted, Kari Stefansson
Summary: This study reconstructs the transmission tree of the third wave of SARS-CoV-2 infections in Iceland using contact tracing and viral sequence data. The results show that individuals diagnosed outside of quarantine were 89% more infectious than those diagnosed while in quarantine. Additionally, people of working age were found to be 46% more infectious than those outside of that age range.
CLINICAL MICROBIOLOGY AND INFECTION
(2022)
Article
Rheumatology
Saedis Saevarsdottir, Lilja Stefansdottir, Patrick Sulem, Gudmar Thorleifsson, Egil Ferkingstad, Gudrun Rutsdottir, Bente Glintborg, Helga Westerlind, Gerdur Grondal, Isabella C. Loft, Signe Bek Sorensen, Benedicte A. Lie, Mikael Brink, Lisbeth Arlestig, Asgeir Orn Arnthorsson, Eva Baecklund, Karina Banasik, Steffen Bank, Lena Bjorkman, Torkell Ellingsen, Christian Erikstrup, Oleksandr Frei, Inger Gjertsson, Daniel F. Gudbjartsson, Sigurjon A. Gudjonsson, Gisli H. Halldorsson, Oliver Hendricks, Jan Hillert, Estrid Hogdall, Soren Jacobsen, Dorte Vendelbo Jensen, Helgi Jonsson, Alf Kastbom, Ingrid Kockum, Salome Kristensen, Helga Kristjansdottir, Margit H. Larsen, Asta Linauskas, Ellen-Margrethe Hauge, Anne G. Loft, Bjorn R. Ludviksson, Sigrun H. Lund, Thorsteinn Markusson, Gisli Masson, Pall Melsted, Kristjan H. S. Moore, Heidi Munk, Kaspar R. Nielsen, Gudmundur L. Norddahl, Asmundur Oddsson, Thorunn A. Olafsdottir, Pall Olason, Tomas Olsson, Sisse Rye Ostrowski, Kim Horslev-Petersen, Solvi Rognvaldsson, Helga Sanner, Gilad N. Silberberg, Hreinn Stefansson, Erik Sorensen, Inge J. Sorensen, Carl Turesson, Thomas Bergman, Lars Alfredsson, Tore K. Kvien, Soren Brunak, Kristjan Steinsson, Vibeke Andersen, Ole A. Andreassen, Solbritt Rantapaa-Dahlqvist, Merete Lund Hetland, Lars Klareskog, Johan Askling, Leonid Padyukov, Ole Bv Pedersen, Unnur Thorsteinsdottir, Ingileif Jonsdottir, Kari Stefansson
Summary: This study identified causal genes for rheumatoid arthritis (RA) and its subsets through a genome-wide association study. Most of these genes encode proteins related to interferon and IL-12/23 signaling, particularly in the JAK/STAT pathway. Variants in some of these genes were found to increase or decrease the risk of seropositive RA.
ANNALS OF THE RHEUMATIC DISEASES
(2022)
Review
Biochemical Research Methods
Lambda Moses, Lior Pachter
Summary: This article reviews spatial transcriptomics research since 1987 and provides a detailed analysis of trends and applications of related technologies and methods. The study offers historical context and guidance for current research.
Correction
Biochemical Research Methods
Lambda Moses, Lior Pachter
Article
Multidisciplinary Sciences
Bjarni Halldorsson, Hannes P. Eggertsson, Kristjan H. S. Moore, Hannes Hauswedell, Ogmundur Eiriksson, Magnus O. Ulfarsson, Gunnar Palsson, Marteinn T. Hardarson, Asmundur Oddsson, Brynjar O. Jensson, Snaedis Kristmundsdottir, Brynja D. Sigurpalsdottir, Olafur A. Stefansson, Doruk Beyter, Guillaume Holley, Vinicius Tragante, Arnaldur Gylfason, Pall Olason, Florian Zink, Margret Asgeirsdottir, Sverrir T. Sverrisson, Brynjar Sigurdsson, Sigurjon A. Gudjonsson, Gunnar T. Sigurdsson, Gisli H. Halldorsson, Gardar Sveinbjornsson, Kristjan Norland, Unnur Styrkarsdottir, Droplaug N. Magnusdottir, Steinunn Snorradottir, Kari Kristinsson, Emilia Sobech, Helgi Jonsson, Arni J. Geirsson, Isleifur Olafsson, Palmi Jonsson, Ole Birger Pedersen, Christian Erikstrup, Soren Brunak, Sisse Rye Ostrowski, Gudmar Thorleifsson, Frosti Jonsson, Pall Melsted, Ingileif Jonsdottir, Thorunn Rafnar, Hilma Holm, Hreinn Stefansson, Jona Saemundsdottir, Daniel F. Gudbjartsson, Olafur T. Magnusson, Gisli Masson, Unnur Thorsteinsdottir, Agnar Helgason, Hakon Jonsson, Patrick Sulem, Kari Stefansson
Summary: A comprehensive understanding of how diversity in the human genome sequence affects phenotypic diversity relies on a reliable characterization of both sequences and phenotypic variation. In this study, whole-genome sequencing of 150,119 individuals from the UK Biobank was performed, leading to insights into the relationship between sequence variation and phenotypic traits. The analysis revealed rare variants with large effects, which were not previously identified through whole-exome sequencing and/or imputation studies.
Article
Genetics & Heredity
Gardar Sveinbjornsson, Magnus O. Ulfarsson, Rosa B. Thorolfsdottir, Benedikt A. Jonsson, Eythor Einarsson, Gylfi Gunnlaugsson, Solvi Rognvaldsson, David O. Arnar, Magnus Baldvinsson, Ragnar G. Bjarnason, Thjodbjorg Eiriksdottir, Christian Erikstrup, Egil Ferkingstad, Gisli H. Halldorsson, Hannes Helgason, Anna Helgadottir, Lotte Hindhede, Grimur Hjorleifsson, David Jones, Kirk U. Knowlton, Sigrun H. Lund, Pall Melsted, Kristjan Norland, Isleifur Olafsson, Sigurdur Olafsson, Gudjon R. Oskarsson, Sisse Rye Ostrowski, Ole Birger Pedersen, Audunn S. Snaebjarnarson, Emil Sigurdsson, Valgerdur Steinthorsdottir, Michael Schwinn, Gudmundur Thorgeirsson, Gudmar Thorleifsson, Ingileif Jonsdottir, Henning Bundgaard, Lincoln Nadauld, Einar S. Bjornsson, Ingrid C. Rulifson, Thorunn Rafnar, Gudmundur L. Norddahl, Unnur Thorsteinsdottir, Patrick Sulem, Daniel F. Gudbjartsson, Hilma Holm, Kari Stefansson
Summary: This study identified genetic variants, genes, and proteins associated with nonalcoholic fatty liver, cirrhosis, and hepatocellular carcinoma. The findings provide insights into the development of noninvasive evaluation and new therapeutic options for NAFL. Proteomics can also distinguish between NAFL and cirrhosis.
Article
Multidisciplinary Sciences
Gudmundur L. Norddahl, Pall Melsted, Kristbjorg Gunnarsdottir, Gisli H. Halldorsson, Thorunn A. Olafsdottir, Arnaldur Gylfason, Mar Kristjansson, Olafur T. Magnusson, Patrick Sulem, Daniel F. Gudbjartsson, Unnur Thorsteinsdottir, Ingileif Jonsdottir, Kari Stefansson
Summary: This study examines the immune responses elicited by different initial/booster vaccine combinations in Iceland and evaluates the effects of booster doses against Delta and Omicron infections. The findings suggest that mRNA boosters provide increased protection against both variants compared to other vaccine combinations.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Gennady Gorin, Meichen Fang, Tara Chari, Lior Pachter
Summary: We perform a thorough analysis of RNA velocity methods and propose an improved framework.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Gennady Gorin, John J. Vastola, Meichen Fang, Lior Pachter
Summary: This study investigates how cell-to-cell differences in transcription rate affect RNA count distributions. The authors introduce quantitative models to compare and contrast two biologically plausible hypotheses about transcription rate variation. They propose a framework for analyzing these models and use Bayesian model selection to identify candidate genes in single-cell transcriptomic data.
NATURE COMMUNICATIONS
(2022)
Correction
Multidisciplinary Sciences
A. Sina Booeshaghi, Eduardo da Veiga Beltrame, Dylan Bannon, Jase Gehring, Lior Pachter
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Tara Chari, Lior Pachter
Summary: Dimensionality reduction is a common method for filtering noise and identifying relevant features in large-scale data analysis. However, reducing high-dimensional datasets to just 2 or 3 dimensions can lead to significant distortion. This study shows that low-dimensional embedding of single-cell data can be counter-productive for exploratory biological analysis due to extensive distortions and inconsistent practices. Alternative approaches for targeted embedding and feature exploration are discussed to enable hypothesis-driven biological discovery.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Gennady Gorin, John J. Vastola, Lior Pachter
Summary: Recent experimental developments in genome-wide RNA quantification show great potential for systems biology. However, a unified mathematical framework is needed to comprehensively study the biology of living cells, taking into account technical variations in genomics assays and the stochasticity of single-molecule biology. In this paper, we review different models for RNA transcription processes and present a framework that integrates these phenomena through the manipulation of generating functions. Finally, we provide simulated scenarios and biological data to demonstrate the implications and applications of this approach.
Article
Biophysics
Gennady Gorin, Lior Pachter
Summary: Single-cell RNA sequencing data can be modeled using Markov chains to gain genome-wide insights into transcriptional physics. However, accurate analysis of the data requires careful consideration of noise sources. A length-based model of capture bias is proposed to explain the over-representation of long pre-mRNA transcripts in sequencing data, which may lead to false-positive observations. This model provides concordant parameter trends and helps identify systematic, mechanistically interpretable technical and biological differences in paired data sets.
BIOPHYSICAL REPORTS
(2023)
Article
Biochemical Research Methods
Petur Helgi Einarsson, Pall Melsted
Summary: We propose a compression scheme and its implementation in BUStools software for BUS files. Our algorithm achieves smaller file sizes and faster compression and decompression speeds compared to gzip. We evaluated our algorithm on 533 BUS files from scRNA-seq experiments, resulting in a 8.3x reduction in file size and a compressed dataset size of 122GB.
