New RFA Supports Researchers to Contribute Pediatric Data to the Human Cell Atlas

We are all familiar with changes early in life — those that are easily seen and others that are more difficult to detect or pinpoint. Growth charts show our bones getting longer, our immune system is trained via vaccination or exposure to diseases like chickenpox, many of us have allergies that then mysteriously subside as we grow, and puberty induces changes in our hormones and with it, changes in many organ systems. The processes are clear, as well as many diseases associated with them, but the cell types and how these cell types arise and change throughout these processes are not. …


What We Learned by Listening to Researchers, Imaging Scientists, and Bioimage Analysts

CZI’s imaging team wants to help all researchers measure, visualize, and quantify the biological processes underlying health and disease. To reach this goal, we work closely with the scientific community to understand what holds them back and collaborate to improve current systems. CZI supports imaging scientists that increase collaboration between biologists and technology experts, software fellows that maintain critical software tools, biologists who use imaging, and disruptive imaging technologies that will improve our mechanistic understanding of health and disease.

We heard from the scientific community about challenges using bioimaging software — tools that help researchers draw insights from the images their microscopes capture. As we considered what solutions might be possible, we wanted to better understand the experiences of the bioimaging user community: How do these individuals work together and how do their perspectives align? …


20 New Grants Advancing Open Science

The maintenance of scientific open source software is unlike scientific papers or other traditional forms of research outputs. Scientific papers don’t incur additional costs or labor to the authors the more they are used or cited. In contrast, the most mature scientific tools and software libraries become increasingly more challenging to maintain the larger their user base.

“Code, while it’s being traded, appraised, or exchanged, assumes its static form, with all the properties that we’d expect of a commodity. But once it finds users, code springs to life, switching to an active state and incurring hidden costs.” …


Key Tools and Research Outputs from the Computable Knowledge Project

In 2017, the University of Massachusetts Amherst’s Information Extraction and Synthesis Laboratory (IESL) was awarded the Computable Knowledge grant. In partnership with CZI’s Meta team, this work advanced state-of-the-art technology to extract knowledge from scientific publications to explore new ways to construct and reason over scientific knowledge bases.

Biomedical research papers are published at a staggering rate. Every day, more than 4,000 new papers are posted to services such as PubMed and bioRxiv. Amidst the current coronavirus pandemic, the world is more aware than ever of the need to accelerate scientific progress. …


A Conversation with Rahul Satija on the Seurat Software Toolkit

Within the last decade, techniques for collecting and analyzing single-cell data have come to constitute a major, fast-moving field in biomedicine. The ability to tease out individual, molecular differences in large populations of cells is providing essential information on cellular function in health and disease, allowing researchers to glean insights on protein expression and many other variables across different cell states and modalities.

Collecting complex data on single cells is one matter. Being able to integrate and interpret that data is another — which is where the work of genomicist and computational biologist Rahul Satija comes in.

In 2015, Satija — then at the Broad Institute in Cambridge, Massachusetts — and colleagues (including his postdoctoral supervisor, Aviv Regev) launched the first version of Seurat, a software toolkit for biomedical researchers. Named for the famed pointillist artist Georges Seurat, who painstakingly combined discrete dots of paint into a unified image, the open source software harmonizes and integrates multiple single-cell datasets. It can, for example, help researchers combine data collected using disparate experimental methods from varying cell populations. At the time of Seurat’s initial publication, Satija moved to the New York Genome Center (NYGC) to start his own lab. …


Supporting Tissue Diversity for the Human Cell Atlas

Researchers worldwide are working together to create a common reference map of all human cells that will allow us to better understand and treat disease: the Human Cell Atlas (HCA). The HCA is already making an impact — for example, researchers used initial cell atlas data from the nose and airway to identify cells that may be entry points for SARS-CoV2. Scientists have also used reference data from many organ systems to begin to clarify the complex pathology associated with COVID-19. Yet to be truly useful as a reference atlas for the human body, the HCA must be broadly representative of race, ethnicity, ancestry, and other determinants of health. …


Integrating Monitoring and Evaluation Into Science Philanthropy

In September 2016, Priscilla Chan and Mark Zuckerberg made a bold announcement — they were going to expand their philanthropic organization, the Chan Zuckerberg Initiative, into basic science. The mission for the work in basic science was just as ambitious — to support the science and technology that would make it possible to cure, prevent, or manage all disease by the end of the century.

Successful achievement of this goal will be transformational for the world, but the path to get there is risky and long. We can’t wait 80 years to know whether we pursued the right strategies and took the right steps to achieve our desired outcomes. We need to demonstrate progress along the way and use evidence to determine what is and isn’t working as we continue our journey. As we forge ahead in our work, we want to seize opportunities for learning and use these learnings to shape our strategies and activities to accelerate scientific progress, best serve the communities and fields in which we work, and drive us toward the greatest impact. …


A Conversation with Gentry Patrick and Gene Yeo

More than 300 biomedical researchers came together virtually this summer for CZI’s annual Neurodegeneration Challenge Network meeting. While there was plenty of cutting-edge research on the agenda, there was also critical dialogue about the field itself, including a conversation about fostering diversity, equity, and inclusion (DEI) in science with Gentry Patrick and Gene Yeo, who are both professors at the University of California, San Diego (UC San Diego). …


Announcing Collaborative Pairs Pilot Projects, Our Newest Neurodegeneration Challenge Network Grantees

The Chan Zuckerberg Initiative believes that the strongest scientific teams incorporate a wide range of lived experiences that guide them to the most important unsolved problems, and that the greatest advances in science come from interdisciplinary, collaborative work across disciplines. We launched the CZI Neurodegeneration Challenge Network (NDCN) in 2018 with the vision of building a new type of interdisciplinary collaborative research community, one that brings together biologists, computational scientists, engineers, and physicians from across broad research areas who are motivated by collaboration and open science to solve neurodegeneration.

Neurodegeneration is one of society’s most critical issues — millions of people worldwide suffer from diseases like Alzheimer’s, Parkinson’s, ALS, multiple sclerosis, Huntington’s, and many others. Over the next 30 years, the rates of these diseases are projected to grow. Moreover, there are few effective treatments or cures for neurodegenerative diseases, and in most cases, we still don’t fully understand the underlying causes or biology. …


Ivan Marazzi didn’t set out to study neurodegenerative diseases. As a virologist, he studies how cells respond to pathogens, particularly a family of RNA viruses that includes influenza. So he knows these amazingly diverse organisms are full of surprises. Still, his most recent discovery — an act of microbial espionage that hasn’t been documented before — has given him a new appreciation of their biology and the evolutionary adaptations that have given rise to it.

Working with a multinational research team, Marazzi found that some viruses steal genetic material from human cells and combine it with their own to make genes that are part virus, part human. Using this tactic, the viruses can generate a new set of genes — genes that may make them more infectious or better at evading an immune system bent on eliminating tiny invaders. …

About

Chan Zuckerberg Science Initiative

Supporting the science and technology that will make it possible to cure, prevent, or manage all diseases by the end of the century.

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