Katy Borner

Katy Borner
Indiana University Bloomington | IUB · Department of Information and Library Science

About

394
Publications
128,457
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
10,769
Citations
Citations since 2017
71 Research Items
5418 Citations
201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
201720182019202020212022202302004006008001,000
Additional affiliations
August 1999 - present
Indiana University Bloomington
Position
  • Victor H. Yngve Professor of Information Science

Publications

Publications (394)
Article
Cells respond to many stressors by senescing, acquiring stable growth arrest, morphologic and metabolic changes, and a proinflammatory senescence-associated secretory phenotype. The heterogeneity of senescent cells (SnCs) and senescence-associated secretory phenotype are vast, yet ill characterized. SnCs have diverse roles in health and disease and...
Article
Full-text available
Seventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data ac...
Article
Diabetic kidney disease (DKD) is the leading cause of end-stage kidney disease (ESKD). Prognostic biomarkers reflective of underlying molecular mechanisms are critically needed for effective management of DKD. A three-marker panel was derived from a proteomics analysis of plasma samples by an unbiased machine learning approach from participants (N...
Preprint
Full-text available
A bstract The human body is made up of about 37 trillion cells (adults). Each cell has its own unique role and is affected by its neighboring cells and environment. The NIH Human BioMolecular Atlas Program (HuBMAP) aims at developing a 3D atlas of human body consisting of organs, vessels, tissues to singe cells with all 3D spatially registered in a...
Preprint
Full-text available
The Human Reference Atlas (HRA) is defined as a comprehensive, three-dimensional (3D) atlas of all the cells in the healthy human body. It is compiled by an international team of experts that develop standard terminologies linked to 3D reference objects describing anatomical structures. The third HRA release (v1.2) covers spatial reference data and...
Article
Full-text available
Background: Image-based machine learning tools hold great promise for clinical applications in pathology research. However, the ideal end-users of these computational tools (e.g., pathologists and biological scientists) often lack the programming experience required for the setup and use of these tools which often rely on the use of command line i...
Article
The Human BioMolecular Atlas Program (HuBMAP) aims to create a computable, open Human Reference Atlas (HRA) [1]. This HRA will redefine our understanding of the human body by recovering multi-scale tissue organization from the human body to the single cell resolution. In the initial three years of the project, we created an authoritative ontology o...
Preprint
Full-text available
More than 150 scientists from 17 consortia are collaborating on an international project to build a Human Reference Atlas, which maps all 37 trillion cells in the healthy adult human body. The initial release of this atlas provided hierarchical lists of the anatomical structures, cell types, and biomarkers in 11 organs. Here, we describe the method...
Article
Full-text available
Virtual reality (VR) has seen increased use for training and instruction. Designers can enable VR users to gain insights into their own performance by visualizing telemetry data from their actions in VR. Our ability to detect patterns and trends visually suggests the use of data visualization as a tool for users to identify strategies for improved...
Preprint
The CCF Organ VR Gallery lets the user explore 21 human organs, journeying from the Whole Body, to the Organ, to the Cell stage and back, presented in real-world size and 3D. The user discovers hidden regions by exploding and collapsing organs into their individual anatomical structures. We show cell type populations for a kidney using a data-drive...
Preprint
Full-text available
Several international consortia are collaborating to construct a human reference atlas, which is a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, integrating and...
Preprint
Full-text available
Virtual reality (VR) has seen increased use for training and instruction. Designers can enable VR users to gain insights into their own performance by visualizing telemetry data from their actions in VR. Our ability to detect patterns and trends visually suggests the use of data visualization as a tool for users to identify strategies for improved...
Article
The Human Reference Atlas (HRA) aims to map all of the cells of the human body to advance biomedical research and clinical practice. This Perspective presents collaborative work by members of 16 international consortia on two essential and interlinked parts of the HRA: (1) three-dimensional representations of anatomy that are linked to (2) tables t...
Article
Full-text available
Working with organs and extracted tissue blocks is an essential task in many medical surgery and anatomy environments. In order to prepare specimens from human donors for further analysis, wet-bench workers must properly dissect human tissue and collect metadata for downstream analysis, including information about the spatial origin of tissue. The...
Article
The number, size and complexity of ‘big science’ projects are growing — as are the size, complexity and value of the data sets and software services they produce. In this context, big data gives a new way to analyse, understand, manage and communicate the inner workings of collaborations that often involve thousands of experts, thousands of scholar...
Article
BACKGROUND . The increasing availability of digital data on scholarly inputs and outputs – from research funding, productivity, and collaboration to paper citations and scientist mobility – offers unprecedented opportunities to explore the structure and evolution of science. The science of science (SciSci) offers a quantitative understanding of the...
Preprint
Full-text available
Working with organs and tissue blocks is an essential task in medical environments. In order to prepare specimens for further analysis, wet-bench workers must dissect tissue and collect spatial metadata. The Registration User Interface (RUI) was developed to allow stakeholders in the Human Biomolecular Atlas Program (HuBMAP) to register tissue bloc...
Preprint
Full-text available
Responding to the U.S. opioid crisis requires a holistic approach supported by evidence from linking and analyzing multiple data sources. This paper discusses how 20 available resources can be combined to answer pressing public health questions related to the crisis. It presents a network view based on U.S. geographical units and other standard con...
Article
Full-text available
Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. This paper presents new funding, publication, and scholarly network metrics and visualizations that were validated via expert surveys. The metrics and visualizations e...
Article
Full-text available
Scholarly organizations bring together experts to move forward specific areas of scientific endeavor. More than 5,000 scholarly societies exist world-wide yet little is known about the composition, evolution, and collaboration of experts within these organizations. This study presents general methods to study the evolution of a biomedical organizat...
Preprint
Full-text available
Effective adoption of online platforms for teaching, learning, and skill development is essential to both academic institutions and workplaces. Adoption of online learning has been abruptly accelerated by COVID19 pandemic, drawing attention to research on pedagogy and practice for effective online instruction. Online learning requires a multitude o...
Preprint
Recent advances in highly multiplexed imaging have enabled the comprehensive profiling of complex tissues in healthy and diseased states, facilitating the study of fundamental biology and human disease in spatially-resolved contexts at subcellular resolution. However, current computational infrastructure to distribute and visualize these data on th...
Preprint
Full-text available
The National Institutes of Health's (NIH) Human Biomolecular Atlas Program (HuBMAP) aims to create a comprehensive high-resolution atlas of all the cells in the healthy human body. Multiple laboratories across the United States are collecting tissue specimens from different organs of donors who vary in sex, age, and body size. Integrating and harmo...
Preprint
Full-text available
Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. The resulting data-driven decision support helps set proper research and development (R&D) priorities; develop future S&T investment strategies; monitor key authors, o...
Preprint
Full-text available
Understanding the emergence, co-evolution, and convergence of science and technology (S&T) areas offers competitive intelligence for researchers, managers, policy makers, and others. The resulting data-driven decision support helps set proper research and development (R&D) priorities; develop future S&T investment strategies; monitor key authors, o...
Article
Full-text available
Background Effective treatment strategies exist for substance use disorder (SUD), however severe hurdles remain in ensuring adequacy of the SUD treatment (SUDT) workforce as well as improving SUDT affordability, access and stigma. Although evidence shows recent increases in SUD medication access from expanding Medicaid availability under the Afford...
Poster
Full-text available
The Complex Networks and Systems NSF Research Traineeship (CNS-NRT) is an interdisciplinary multifaceted STEM program with a rigorous dual-PhD degree focus, emphasizing collaborative skills and workforce development. This complex institutional training model requires comprehensive evolutionary systems thinking and modeling, and novel data visualiza...
Preprint
Full-text available
Effective treatment strategies exist for substance use disorder (SUD), however severe hurdles remain in ensuring adequacy of the SUD treatment (SUDT) workforce as well as improving SUDT affordability, access and stigma. Although evidence shows recent increases in SUD medication access from expanding Medicaid availability under the Affordable Care A...
Article
Full-text available
Learning analytics and visualizations make it possible to examine and communicate learners’ engagement, performance, and trajectories in online courses to evaluate and optimize course design for learners. This is particularly valuable for workforce training involving employees who need to acquire new knowledge in the most effective manner. This pap...
Data
Learner trajectory network processing pipeline. Supporting information describes the Learner Trajectory Network Processing Pipeline used for analysis and visualizations introduced in this paper, and provides links to related protocol and GitHub repository. (DOCX)
Data
Data dictionary for learner trajectory network processing pipeline. Appendix provides a data dictionary for the outputs generated by each script of the processing pipeline. (DOCX)
Data
Sample data outputs of learner trajectory network processing pipeline. Dataset includes five files that were generated by the data processing pipeline based on course and student data from the MITxPro course, Architecture of Complex Systems, Fall 2016. (ZIP)
Article
Full-text available
In the information age, the ability to read and construct data visualizations becomes as important as the ability to read and write text. However, while standard definitions and theoretical frameworks to teach and assess textual, mathematical, and visual literacy exist, current data visualization literacy (DVL) definitions and frameworks are not co...
Article
Full-text available
Rapid research progress in science and technology (S&T) and continuously shifting workforce needs exert pressure on each other and on the educational and training systems that link them. Higher education institutions aim to equip new generations of students with skills and expertise relevant to workforce participation for decades to come, but their...
Preprint
Full-text available
This paper analyzes the impact of air transport connectivity and accessibility on scientific collaboration. Numerous studies demonstrated that the likelihood of collaboration declines with increase in distance between potential collaborators. These works commonly use simple measures of physical distance rather than actual flight capacity and freque...
Article
Within museums and science centers, the visual presentation of data represents a timely, relevant, and formidable interpretive challenge. Tackling this challenge head on, however, means employing a series of principles that position educators to support learners of all skill levels in interpreting data visualizations more generally. In this article...
Article
Full-text available
Climb atop shoulders and wait for funerals. That, suggested Newton and then Planck, is how science advances (more or less). We’ve come far since then, but many notions about how people and practices, policies, and resources influence the course of science are still more rooted in traditions and intuitions than in evidence. We can and must do better...
Article
Full-text available
Countries, research institutions, and scholars are interested in identifying and promoting high-impact and transformative scientific research. This paper presents a novel set of text- and citation-based metrics that can be used to identify high-impact and transformative works. The 11 metrics can be grouped into seven types: Radical-Generative, Radi...
Article
Full-text available
The whys and wherefores of SciSci The science of science (SciSci) is based on a transdisciplinary approach that uses large data sets to study the mechanisms underlying the doing of science—from the choice of a research problem to career trajectories and progress within a field. In a Review, Fortunato et al. explain that the underlying rationale is...
Article
Full-text available
Most maps of science use a network layout; few use a landscape metaphor. Human users are trained in reading geospatial maps, yet most have a hard time reading even simple networks. Prior work using general networks has shown that map-based visualizations increase recall accuracy of data. This paper reports the result of a comparison of two comparab...
Article
Full-text available
Many universities invest substantial resources in the design, deployment, and maintenance of campus-based cyberinfrastructure (CI). To justify the expense, it is important that university administrators and others understand and communicate the value of these internal investments in terms of scholarly impact. This paper introduces two visualization...
Article
Full-text available
Network visualizations, a particular kind of data visualization, can be a useful way to visually represent the relationships in real or theoretical social, physical or biological systems. Network data can be generated and analyzed without being visualized, but the visualizations are often more compelling and may be more easily understood than numbe...
Chapter
Full-text available
Network visualizations, a particular kind of data visualization, can be a useful way to visually represent the relationships in real or theoretical social, physical, or biological systems. Network data can be generated and analyzed without being visualized, but the visualizations are often more compelling and may be more easily understood than numb...
Article
Full-text available
Background Alzheimer’s disease neuroimaging initiative (ADNI) is a landmark imaging and omics study in AD. ADNI research literature has increased substantially over the past decade, which poses challenges for effectively communicating information about the results and impact of ADNI-related studies. In this work, we employed advanced information vi...
Data
Number of publications versus author position. (A) Number of publications versus author position: For each point, the x-axis value indicates the position of an author, and the y-axis value is the number of papers this author published at this author rank. For example, an author with three first author papers and one second author paper contributes...
Data
Top journals of ADNI publications. Top journals or conference proceedings ranked by the number of ADNI publications. Wordle visualization in top-right lists top and other journals size and color coded by the number of ADNI publications. (DOCX)
Data
Processed and cleaned ADNI publication citation data, including those used for visualization. (XLSX)
Data
Correlation of SJR to Impact Factor for ADNI publication journals. (A) compares the distribution of the normalized SCImago Journal Rank (SJR) and Impact Factors (Jrank − mean(Jrank)/StDev(Jrank)). (B) is a line fit plot of regression analysis of journal SJR and Impact Factor values that are within two standard deviations of the mean difference betw...
Data
Statistics of co-publication networks. (A) Number of co-publications over time, that is, the total number of edges (blue bar) or the sum of edge weights (orange bar) over years. Blue bars represent the number of unique edges: if there are multiple co-publications (i.e., edge weight > 1) between two institutions, the collaboration/edge is counted on...
Data
World-wide geospatial map of publication co-occurrence network. Co-affiliation network overlaid on a geospatial map shows collaborating organizations affiliated with ADNI in world-wide based on co-authored publications. Only organizations with at least 4 publications are shown; organizations with at least 30 publications or that are a Core ADNI res...
Data
Sub-network of hubs from co-publication networks over time. Sub-networks were extracted from the full co-publication networks, where only nodes with degree ≥ 30 were included. Both size and color of node were from the original co-publication network. Node were labeled by the institution name. (DOCX)
Data
Keyword co-occurrence network focused on major ADNI themes. Nodes represent keywords relevant to major ADNI themes, including MRI, PET, other biological biomarkers, clinical and neuropsychological assessment, genetics, and disease and progression. Edges denote the joint appearance of keywords in a publication. Nodes are colored based on the themes...
Data
SJR Groups. For each SJR Groups, five example journals from each group were selected based on the total number of publications that they received. (DOCX)
Data
Annual SCImago Journal Rankings and annual citation counts. Plot of shows annual SCImago Journal Rankings and annual citation counts for the journals that have published at least 5 papers related to ADNI in at least 3 years, between 2006 and 2014. Journals are grouped by a heuristic categorization system derived from the Scopus journal subject cate...
Article
Full-text available
Increasingly, our everyday environments become more and more connected and “smart”. Intelligent Interactive Systems (IIS) is an umbrella term to describe environments that are characterized by their ability to process data and generate responsive behavior using sensors, actuators, and microprocessors. Sentient Architecture generates an artful, imag...
Poster
Full-text available
The Clarivate Analytics Web of Science (WoS) has served as a research dataset for more than 9,000 scholarly articles in the past 15 years alone—across a wide a range of fields and disciplines from toxicology to computer science to economics. Scientists and scholars have been particularly interested in the WoS citation network, a massive graph conta...
Article
It appears paradoxical that science is producing outstanding new results and theories at a rapid rate at the same time that researchers are identifying serious problems in the practice of science that cause many reports to be irreproducible and invalid. Certainly the practice of science needs to be improved and scientists are now pursuing this goal...
Conference Paper
Interactive data visualizations known as macroscopes have great potential as tools for exploring, understanding, and communicating science [1]. Macroscopes empower individuals to interact with data in order to better understand it from multiple perspectives. Joël de Rosnay [2] first introduced the concept of the macroscope in his 1979 book, The Mac...
Conference Paper
Understanding the financial and intellectual value of campus-based cyberinfrastructure (CI) to the institutions that invest in such CI is intrinsically difficult. Given today's financial pressures, there is often administrative pressure questioning the value of campus-based and campus-funded CI resources. In this paper we describe new financial ana...
Article
Along with significant opportunities, Massively Open Online Courses (MOOCs) provide major challenges to students (keeping track of course materials and effectively interacting with teachers and fellow students), teachers (managing thousands of students and supporting their learning progress), researchers (understanding how students interact with ma...
Article
Full-text available
The Million Dollar List (MDL, online at http://www.milliondollarlist.org) is a compilation of publicly announced charitable donations of $1 million or more from across the United States since 2000; as of December 2016, the database contains close to 80,000 gifts made by U.S. individuals, corporations, foundations, and other grant-making nonprofit o...
Article
Full-text available
Objective: We sought to depict the topical, geospatial, and temporal diffusion of the 2015 North American Menopause Society position statement on the nonhormonal management of menopause-associated vasomotor symptoms released on September 21, 2015, and its associated press release from September 23, 2015. Methods: Three data sources were used: on...
Article
Understanding the value of campus-based cyberinfrastructure (CI) to the institutions that invest in such CI is intrinsically difficult. Given today’s financial pressures, administrative support for campus- based CI centers offering resources to local campus users is under constant budgetary pressure. This is partly due to the difficulty in obtainin...