Article
Biochemical Research Methods
Alon Zivony, Rasha Kardosh, Liadh Timmins, Niv Reggev
Summary: Historically, guidelines for scientific studies have focused on minimizing risk for participants. However, studies can harm individuals and social groups indirectly through their design, reporting, and dissemination. Recent criticisms and retractions of high-profile studies highlight a lack of resources and guidance on conducting socially responsible research, leading motivated researchers to unknowingly publish work with negative social impacts. To address this, we propose 10 rules to help researchers reflect on their social responsibility and actively consider the potential social impact of their work throughout the study lifecycle.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Simon J. D. Cox, Alejandra N. Gonzalez-Beltran, Barbara Magagna, Maria-Cristina Marinescu
Summary: The paper presents ten rules for converting a legacy vocabulary into a FAIR vocabulary, emphasizing the importance of providing a unique resolvable identifier for each term. Standard representation should be returned when the web identifier is resolved, for machine-interchange and human consumption. These rules offer guidance on creating a standalone FAIR vocabulary for unambiguous data annotation, enhancing data interoperability and integration.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Jitao David Zhang
Summary: By knowing why to join, what to expect, and how to prepare, postdoctoral programs in the pharmaceutical and life science industry offer opportunities for personal and professional development.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Jessica L. Burnett, Renee Dale, Chung-Yi Hou, Gabriela Palomo-Munoz, Kaitlin Stack Whitney, Steve Aulenbach, Robert Sky Bristol, Denis Valle, Tristan P. Wellman
Summary: The use of scientific web applications in biological and environmental sciences has grown exponentially, but researchers often lack training in creating such tools. While rolling out SWApps may be simple and quick, ensuring their usefulness, usability, and sustainability is a challenge. These 10 rules provide a foundation for researchers with little to no experience in web application design and development.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Carly Strasser, Kate Hertweck, Josh Greenberg, Dario Taraborelli, Elizabeth Vu
Summary: Scientific research relies on open source software, and investing in scientific OSS requires focus on scholarly credit, labor, maintenance, governance, and community-building.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Vishal H. H. Oza, Jordan H. H. Whitlock, Elizabeth J. J. Wilk, Angelina Uno-Antonison, Brandon Wilk, Manavalan Gajapathy, Timothy C. C. Howton, Austyn Trull, Lara Ianov, Elizabeth A. A. Worthey, Brittany N. N. Lasseigne
Summary: With the increasing availability of public biological data, this article provides 10 simple rules for successfully downloading and utilizing this data, including using it purposefully, evaluating its suitability, adhering to reuse requirements and ethics, planning storage and compute requirements, properly citing the data, and making reprocessed data, models, pipelines, and code Findable, Accessible, Interoperable, and Reusable (FAIR) and sharing them. These rules serve as a guide for researchers to enhance data reuse and reproducibility.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Review
Biochemical Research Methods
Claude Pellen, Anne Le Louarn, Gilliosa Spurrier-Bernard, Evelyne Decullier, Jean-Marie Chretien, Eric Rosenthal, Gerard Le Goff, David Moher, John P. A. Ioannidis, Florian Naudet
Summary: Clinical trial data-sharing is crucial for research integrity. However, early experiences have been unsatisfactory because of improper conduct. We propose 10 rules for researchers to follow, including abiding by legal requirements, involving research participants, determining data access methods, and striving for excellence.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Biochemical Research Methods
Esther Sebastian-Gonzalez, Eva Gracia, Alejandra Moran-Ordonez, Irene Perez-Ibarra, Ana Sanz-Aguilar, Mar Sobral
Summary: Although there is an increasing awareness of the low number of women in science, especially in leadership positions and higher stages of the scientific career, more actions are urgently needed to support scientific mothers and increase gender diversity and equality in Academia. Therefore, a group of moms in science propose 10 simple rules that can be adopted by academic institutions to directly support mother scientists and avoid losing them from Academia. The implementation of these rules may also benefit other groups such as mothers-to-be, fathers, caregivers, and women in general, helping to create more diverse working environments and ultimately leading to more optimal solutions.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Editorial Material
Biochemical Research Methods
Stefan Gaillard, Tara van Viegen, Michele Veldsman, Melanie I. Stefan, Veronika Cheplygina
Summary: Failure is a crucial part of life and academia, yet it is often ignored. This article highlights the negative consequences of ignoring failure and provides strategies for learning from and dealing with it. These strategies allow academics to develop their own successful approaches to failure.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Anne M. Treasure, Siobhan Mackenzie Hall, Igor Lesko, Derek Moore, Malvika Sharan, Menno van Zaanen, Yo Yehudi, Anelda van der Walt
Summary: In recent years, mentorship programmes have been developed to address issues that cannot be solved through traditional teaching methods alone. Mentors play important roles in the growth and development of both mentors and mentees, with positive impacts that have been well-documented. However, gaining a clear overview of this field can be challenging.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Carla Bautista, Narjes Alfuraiji, Anna Drangowska-Way, Karishma Gangwani, Alida de Flamingh, Philip E. Bourne
Summary: This article emphasizes the importance of communication in scientific development and methodology. It presents 10 rules divided into three categories to help scientists engage in and improve science communication. Examples and resources are included to provide actionable strategies for involvement and engagement in science communication.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Neurosciences
Malte Woestmann, Viola S. Stoermer, Jonas Obleser, Douglas A. Addleman, Soren K. Andersen, Nicholas Gaspelin, Joy J. Geng, Steven J. Luck, MaryAnn P. Noonan, Heleen A. Slagter, Jan Theeuwes
Summary: This article discusses the principles for studying distractor suppression, including experimental design, differentiation of different types of distractor suppression, and statistical evaluation. These rules provide a concise and comprehensive synopsis of promising advances in the field, and facilitate communication between sub-disciplines.
PROGRESS IN NEUROBIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Joseph C. Ayoob, Juan S. Ramirez-Lugo
Summary: In this article, we present ten simple rules for planning, offering, running, and improving a summer research program in computational biology, which aim to support students in honing technical competencies for successful research and developing skills to become successful scientific professionals.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biochemical Research Methods
Caroline J. Wendt, G. Brooke Anderson
Summary: This article outlines 10 simple rules for finding and evaluating packages in the R software environment, covering aspects such as considering purpose, exploring online resources, assessing popularity and utility, investigating package development processes, and digging into package code.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Editorial Material
Biochemical Research Methods
Whitney M. Woelmer, L. M. Bradley, Lisa T. Haber, David H. Klinges, Abigail S. L. Lewis, Elizabeth J. Mohr, Christa L. Torrens, Kathryn I. Wheeler, Alyssa M. Willson
Summary: Successfully training oneself in an emerging field requires setting and revisiting specific goals, achieving academic and career objectives, and following simple rules for engaging with and contributing to the field.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Letter
Medicine, General & Internal
A. Cecile J. W. Janssens, Bart Penders
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2018)
Letter
Medicine, General & Internal
Paul Barach, Ronald L. Thomas, Steven E. Lipshultz
JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
(2018)
Editorial Material
Medical Ethics
Bart Penders, Sarah de Rijcke, J. Britt Holbrook
ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE
(2020)
Review
Immunology
Ronghui Yang, Bart Penders, Klasien Horstman
Article
Medical Ethics
Bart Penders, David M. Shaw
ACCOUNTABILITY IN RESEARCH-POLICIES AND QUALITY ASSURANCE
(2020)
Article
Genetics & Heredity
Bart Penders, A. Cecile J. W. Janssens
Summary: Polygenic risk scores (PRS) are distinct from other biomarkers as they are calculated, compiled or constructed through the statistical assemblage of genetic variants. How researchers frame and name PRSs impacts how we interpret and value their results. Important questions include what PRS seeks to represent, whether current ways of 'doing PRS' are optimal and responsible, and the basis for the credibility of PRS-based knowledge claims.
Article
Medical Ethics
Mohammad Hosseini, Enric Senabre Hidalgo, Serge P. J. M. Horbach, Stephan Guttinger, Bart Penders
Summary: Although adherence to Mertonian values of science can cause friction with the normative structures and practices of Open Science, new normative structures need to consider the aspirations and outcomes of Open Science practices. The intersection of Open Science practices with Mertonian values becomes complicated when interests of different groups collide. Acknowledging and exploring these tensions can inform researchers' behavior and improve their interactions with other normative structures.
ACCOUNTABILITY IN RESEARCH-ETHICS INTEGRITY AND POLICY
(2022)
Article
Communication
Bart Penders
Summary: This paper examines the importance of replication and replication studies in communication between scientists to enhance scientific credibility. However, not every epistemic culture agrees with this and there are alternative ways of organizing communication to achieve the same goal.
TIJDSCHRIFT VOOR COMMUNICATIEWETENSCHAP
(2022)
Article
Sociology
Ronghui Yang, Klasien Horstman, Bart Penders
Summary: This paper critically examines the dynamics of the Chinese food safety governance infrastructure after the melamine crisis, revealing tensions and gaps between different governance models. Despite the ideal of inclusive, transparent, and participatory governance, challenges still exist in effective problem-solving.
FOOD CULTURE & SOCIETY
(2022)
Article
Political Science
Ronghui Yang, Klasien Horstman, Bart Penders
Summary: Scholarly debates on public accountability for food safety in China aim to restore public trust and reflect on different strategies and perspectives. This analysis shows that arguments for specific accountability models and scientific expertise are intertwined, shaping a public forum for discussing supervision and accountability, risk assessment, and transparency.
JOURNAL OF CHINESE GOVERNANCE
(2022)
Article
Communication
Mu-Chi Chiu, Bart Penders
Summary: This paper explores how YouTubers promote and support health concepts, finding that they use new health concepts to replace traditional definitions, focusing on practical dietary issues and specific audiences.
FRONTIERS IN COMMUNICATION
(2021)
Article
Management
Edward J. Hackett, Erin Leahey, John N. Parker, Ismael Rafols, Stephanie E. Hampton, Ugo Corte, Diego Chavarro, John M. Drake, Bart Penders, Laura Sheble, Niki Vermeulen, Todd J. Vision
Summary: Synthesis centers facilitate research that integrates diverse theories, methods, and data to enhance the generality, applicability, and empirical soundness of scientific explanations. By comparing the topical diversity of publications, it was found that synthesis center collaborations have greater variety and evenness in their papers compared to the reference corpus, with less disparity. The origins of synthesis centers, as well as diversity measures, significantly influence the visibility of publications.
Article
Immunology
Ronghui Yang, Bart Penders, Klasien Horstman
Article
Ethics
Bart Penders, Peter Lutz, David M. Shaw, David M. R. Townend
LIFE SCIENCES SOCIETY AND POLICY
(2020)
Article
Information Science & Library Science
Bart Penders, J. Britt Holbrook, Sarah de Rijcke
