Digital Research Services - University of Edinburgh’s Post

New single-platform solution achieves nearly perfect assemblies of complete human and plant chromosomes without any gaps. Oxford Nanopore Technologies (ONT) 'Duplex' sequencing uses just one platform for chromosome-scale genome assemblies. The study shows that nanopore sequencing can generate accurate and long sequencing reads, leading to high-quality, consistent genome assemblies. By using only one sequencing platform, researchers can produce chromosome-scale haplotypes and phased assemblies without using multiple platforms. The high-quality, accurate, and long sequencing reads generated by nanopore sequencing technologies enable researchers to overcome challenges associated with gaps in genome assemblies, leading to more comprehensive and reliable genomic data. This increase in the accessibility of high-quality reference genomes and enhanced genome assembly techniques offers a promising option compared to traditional sequencing methods. Overall, the research highlights how nanopore sequencing, through techniques like Duplex sequencing, can significantly impact genomics and agriculture by providing a powerful tool for achieving complete and accurate genome assemblies across a wide range of species, beyond human genomes. Title: Gapless Assembly Of Complete Human And Plant Chromosomes Using Only Nanopore Sequencing Reviewer: Sangeeta B. Rating: ⭐⭐⭐ Authors: Zhigui Bao, Shujun Ou, Sara Goodwin, Rhie Arang, Dick Roelofs, Koen Nijbroek, Doreen Ware,  Michael Schatz, Sanwen Huang, Karen Miga, Alexander H.J. Wittenberg, Adam Phillippy To the Review: https://lnkd.in/ehD8CCQH

𝗢𝗽𝗲𝗻 𝗮𝗰𝗰𝗲𝘀𝘀 (𝗢𝗔) 𝗶𝘀 𝗿𝗲𝘃𝗼𝗹𝘂𝘁𝗶𝗼𝗻𝗶𝘇𝗶𝗻𝗴 𝘀𝗰𝗶𝗲𝗻𝘁𝗶𝗳𝗶𝗰 𝗱𝗶𝘀𝗰𝗼𝘃𝗲𝗿𝘆 𝗯𝘆 𝗿𝗲𝗺𝗼𝘃𝗶𝗻𝗴 𝗽𝗮𝘆𝘄𝗮𝗹𝗹𝘀 𝘁𝗵𝗮𝘁 𝗵𝗶𝗻𝗱𝗲𝗿 𝗮𝗰𝗰𝗲𝘀𝘀 𝘁𝗼 𝗿𝗲𝘀𝗲𝗮𝗿𝗰𝗵. This shift not only democratizes knowledge but also accelerates innovation across various fields. 𝗧𝗵𝗲 𝗢𝗽𝗲𝗻 𝗔𝗰𝗰𝗲𝘀𝘀 𝗔𝗱𝘃𝗮𝗻𝘁𝗮𝗴𝗲 Faster Discoveries: The Human Genome Project exemplifies OA's impact, making genomic data freely available and leading to rapid advancements in personalized medicine and genetic research. Enhanced Collaboration: Platforms like arXiv allow researchers to share preprints, fostering global collaboration and speeding up the dissemination of new ideas2. Broader Reach: During the COVID-19 pandemic, open access facilitated real-time sharing of critical research, accelerating vaccine development and public health responses2. 𝗦𝗰𝗶𝗩𝗲𝗻𝗶𝗮’𝘀 𝗥𝗼𝗹𝗲 𝗦𝗰𝗶𝗩𝗲𝗻𝗶𝗮 𝗰𝗼𝗻𝗻𝗲𝗰𝘁𝘀 𝘀𝗰𝗶𝗲𝗻𝘁𝗶𝘀𝘁𝘀 𝘄𝗶𝘁𝗵 𝗼𝗽𝗲𝗻-𝗮𝗰𝗰𝗲𝘀𝘀-𝗳𝗿𝗶𝗲𝗻𝗱𝗹𝘆 𝗽𝗹𝗮𝘁𝗳𝗼𝗿𝗺𝘀, 𝗲𝗻𝗮𝗯𝗹𝗶𝗻𝗴 𝘁𝗵𝗲𝗺 𝘁𝗼 𝗲𝗻𝗴𝗮𝗴𝗲 𝗶𝗻 𝘁𝗵𝗶𝘀 𝘁𝗿𝗮𝗻𝘀𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝘃𝗲 𝗺𝗼𝘃𝗲𝗺𝗲𝗻𝘁. By facilitating access to research, SciVenia enhances collaboration and innovation, ensuring that knowledge benefits everyone. 𝗝𝗼𝗶𝗻 𝘁𝗵𝗲 𝗺𝗼𝘃𝗲𝗺𝗲𝗻𝘁 𝗳𝗼𝗿 𝗼𝗽𝗲𝗻 𝗮𝗰𝗰𝗲𝘀𝘀! 𝗧𝗼𝗴𝗲𝘁𝗵𝗲𝗿, 𝘄𝗲 𝗰𝗮𝗻 𝗯𝗿𝗲𝗮𝗸 𝗱𝗼𝘄𝗻 𝗯𝗮𝗿𝗿𝗶𝗲𝗿𝘀 𝘁𝗼 𝘀𝗰𝗶𝗲𝗻𝘁𝗶𝗳𝗶𝗰 𝗸𝗻𝗼𝘄𝗹𝗲𝗱𝗴𝗲 𝗮𝗻𝗱 𝗮𝗰𝗰𝗲𝗹𝗲𝗿𝗮𝘁𝗲 𝗱𝗶𝘀𝗰𝗼𝘃𝗲𝗿𝘆 𝗳𝗼𝗿 𝗮 𝗯𝗲𝘁𝘁𝗲𝗿 𝗳𝘂𝘁𝘂𝗿𝗲. #OpenAccess #ScientificDiscovery #Innovation #Collaboration #SciVenia

📣Speaker Spotlight! Thrilled to share that Carlos D. Bustamante will be one of our distinguished guest speakers at the symposium hosted by UAB Marnix E. Heersink School of Medicine & University of Miami Herbert Business School at the University of Miami's Intelligent Computer Systems Research Institute ✍️When ? April 26-27, 2024 📍Where? University of Miami Herbert Business School 🎓What? “Unlock the Power of AI in Healthcare: A Transformative Symposium for Leaders” https://lnkd.in/ecmWJ9iT 💡Brief Bio Highlights Dr. Carlos Bustamante, a distinguished population geneticist, is a co-founder and the CEO & President of Galatea Bio Inc. His expertise extends to serving as a Board Member and Scientific Advisor at Etalon Dx, Board Member at EdenRoc Sciences, and Advisor at Digitalis Ventures, among other roles in organizations like Embark and Genomelink. Dr. Bustamante's academic contributions were recognized early in his career, leading to his faculty position at Cornell University from 2002 to 2009, and subsequently at Stanford University School of Medicine and University of Miami. His research, which lies at the intersection of #computationalbiology, mathematical #genetics, and evolutionary #genomics, has earned him several honors, including the Sloan Research Fellowship and a MacArthur Fellowship. Dr. Bustamante has significantly influenced the field through his work on human population genomics and #globalhealth, contributing to the development of statistical and computational resources for genomic studies. He holds advanced degrees from Harvard University and has been a guiding force for over 50 post-doctoral fellows and graduate students, co-authoring hundreds of peer-reviewed papers. #leadership #thoughtleadership #influencer #topvoice #strategy #healthtech #precisionhealth #healthcare #genomics #smarthealth #digitalhealth #virtualhealth #speaker #artificialintelligence #llm #innovation #populationhealth #publichealth #globalhealth

There’s no better way to start the week than at the Bioinformatics & IT Strategy Meeting happening right now at Le Meridien Boston Cambridge! Today, leaders and innovators in bioinformatics and IT are coming together to explore groundbreaking technologies and forge new partnerships. Stay tuned as we bring you updates from the event, highlight key discussions, and share insights from some of the brightest minds in the field. Don’t miss out on the chance to see how these collaborations today will lead to the innovations of tomorrow! #Bioinformatics #ITStrategy #BostonEvents #Networking #Collaboration #HealthcareInnovation

Freedom, yeah! Freedom for the researchers to access knowledge! Freedom for the researchers to work with integrity! Freedom for the researchers to publish their work! Freedom… yeah? But researcher's degrees of freedom is not as straightforward as it may seem, especially when striving for standardization and inter- and intra-lab reproducibility. In this blog, we will explore the concept of researcher's degrees of freedom and its impact in metagenomics workflows. Read our new blog here: https://lnkd.in/dbepnFJk #Metagenomics #OpticalMapping #ResearchIntegrity #MicrobiomeProfiling #MicrobiomeServices

Journal of Consumer Research: Conspiracy Beliefs and Consumption: The Role of Scientific Literacy "Conspiracy theories pose risks to consumers, businesses, and society. The present research investigates the role of scientific literacy in a variety of conspiracy beliefs with implications for consumer well-being and sustainability (e.g., regarding coronavirus disease 2019 [COVID-19], genetically modified organisms, and climate change). In contrast to the mixed effects of education in prior work, we find that scientific literacy undermines conspiracy beliefs and, in turn, conspiracy-related behaviors. This finding is explained by people’s ability to use two dimensions of scientific literacy—scientific knowledge and reasoning—to accurately assess conspiracy evidence. For robustness, we assess scientific literacy through both measurement and manipulation (i.e., interventions), identify two moderators (evidence strength and narration) that attenuate the effect, and further validate our theorizing using national and international datasets (regarding COVID-19 vaccination and Google search, respectively). We discuss the implications of our findings for consumers, companies, nonprofit organizations, and governments." #conspiracytheories https://lnkd.in/eprEDPww

Alan Moore's perspective on artists can certainly be applied to scientists. The issue of scientific integrity is a significant one, especially when it comes to the intersection of academia, industry, and powerful interests. The pressure to publish in high-impact journals and secure funding has, over time, eroded some of the foundational principles of scientific inquiry—those of curiosity, transparency, and integrity. Instead, we see an increasing focus on metrics like citation counts, impact factors, and corporate partnerships. In fields like medicine and pharmacology, this issue is even more acute due to the enormous financial stakes involved. This has led to several ethical concerns, from the manipulation of clinical trial data to the suppression of negative results that could harm a drug’s marketability. The pharmaceutical industry, in particular, has faced criticism for its influence over research, funding, and even public policy. Regulatory agencies have also come under fire for being too closely aligned with the industries they’re supposed to oversee. This situation creates a cycle where innovation is driven by profit rather than genuine need, leading to issues of trust, especially in public health. As for the integrity of scientists themselves, the pressure to secure funding can sometimes push even the most well-meaning researchers into ethical gray areas. Alan Moore’s call for artists—and by extension, scientists—to remember their true power is a reminder that the role of science in society is not to serve corporate or governmental interests, but to seek truth, improve human lives, and push the boundaries of knowledge. True integrity in science involves maintaining independence from these external pressures and ensuring that research is conducted transparently, with a focus on public good rather than private gain. It's about the accountability of scientists not just to their peers but to the societies they serve. It's a challenge that the scientific community continues to grapple with, and while there are certainly voices pushing for reform, systemic change is difficult in a landscape so dominated by profit-driven models. The question of how to restore integrity in science is deeply tied to questions of funding, power, and the role of research in society. Encouraging open science, reducing the emphasis on impact factors, and ensuring greater transparency in the publication process are just some of the steps that can help re-center science as a tool for public good rather than corporate gain. Conclusion, Sir Terry: Bringing a bit of Vimes' relentless sense of justice and Weatherwax's no-nonsense wisdom back into the scientific field would definitely be a great step forward! (edited excerpt from a dialogue with DELPHI 6 Chandaka)

Did you know a Nature survey found that 70% of surveyed researchers had tried, but ultimately failed, to reproduce another scientist's results?🤯 Worse yet, more than 50% reported having failed to reproduce their own experiments!😧(Nature,2016.) https://lnkd.in/e-z9dicQ The #reproducibilitycrisis is hindering humanity's progress forward.The reproducibility crisis is a shared burden. We all feel the effects, whether we are researchers ourselves or members of the general public who benefit from scientific research. As a community we can collaborate and work together to carry #lifesciences research forward by helping drive innovation, and in turn create a more efficient ecosystem for scientific progress to thrive. Here are three of the ways SCINET is doing our part; 💪building advanced tools to assist researchers in the management and promotion of IP 💼fostering efficient licensing processes to streamline the journey from research to practice 🤝🏻encouraging efficient lines of communication for interdisciplinary collaboration Join us on our journey and help make a positive impact on life sciences research! 🔬🧬 Join the SCINET newsletter: https://lnkd.in/dGfVxVAJ

The PREDICTOM project recently launched a new data catalog designed to make its valuable research datasets more accessible to the global scientific community. This initiative aims to foster greater collaboration and transparency in the early detection of dementia by providing an open, user-friendly platform for researchers to explore and utilize critical data. We’re proud to be one of 30 international partners driving this revolutionary joint effort. Together, we’re paving the way for innovative research that will transform how we detect and manage cognitive decline. 🤝 Other key partners include: Altoida, Inc., Alzheimer Europe, ALZpath Inc., Centre for Research & Technology Hellas (CERTH), Lygature, Fraunhofer IIS, GN Group, Medical Research Institute La Fe (IIS La Fe), Stavanger University Hospital, icometrix, JOANNEUM RESEARCH, King's College London, KLINIKUM DER UNIVERSITAT MUNCHEN, Ludwig-Maximilians-Universität München (Ludwig Maximilian University of Munich), Muhdo Health, NICE - National Institute for Health and Care Excellence, Pharmacoidea Ltd., Qairnel, Universitätsklinikum Erlangen, University of Geneva, Vrije Universiteit Brussel. Learn more about PREDICTOM and its new data catalog: https://hubs.ly/Q02QMp4p0

Last week, I had the privilege of attending #BioIT in Boston. As I dive back into the current work week, I feel invigorated by the depth of knowledge, innovation, and collaboration conveyed over those 3 days. It's truly remarkable to see how the intersection of biology and information technology is reshaping the landscape of life sciences. From engaging discussions on precision medicine to groundbreaking advancements in bioinformatics, each session was a testament to the immense potential we hold to revolutionize healthcare and beyond. The convergence of big data analytics, AI-driven insights, and genomics is paving the way for personalized treatments, disease prevention, and sustainable solutions for a healthier world. But beyond the cutting-edge technologies and scientific breakthroughs, what truly stood out for me was the sense of community and shared purpose that permeated every interaction. Meeting passionate individuals from diverse backgrounds, exchanging ideas, and forging new connections underscored the collaborative spirit driving progress in the field. I'm looking forward to future collaborations and innovations in this dynamic realm! Let's continue to push the boundaries, leverage technology for good, and unlock the mysteries of life for the betterment of humanity. 💡 #BioIT #LifeSciences #Innovation #Collaboration #whatsciencecando 💡