{"id":654808,"date":"2026-08-25T01:42:14","date_gmt":"2026-08-25T01:42:14","guid":{"rendered":"https:\/\/www.europesays.com\/ie\/654808\/"},"modified":"2026-08-25T01:42:14","modified_gmt":"2026-08-25T01:42:14","slug":"new-tool-for-big-data-analysis-facilitates-biological-discovery","status":"publish","type":"post","link":"https:\/\/www.europesays.com\/ie\/654808\/","title":{"rendered":"New Tool for Big Data Analysis Facilitates Biological Discovery"},"content":{"rendered":"

Original story from the University of Basel (Switzerland).<\/a><\/p>\n

A new software tool, Bonsai, makes sense of high-dimensional datasets by presenting the data within a tree framework, aiding the discovery of hidden patterns.<\/strong><\/p>\n

Modern biology research can now generate valuable data on an unprecedented scale. But there is one major obstacle: making sense of these complex high-dimensional datasets. A team at the University of Basel<\/a> (Switzerland) has developed a new tool that can provide accurate pictures of the structures hiding within highly complex datasets. By helping scientists uncover hidden patterns in the data, the software will help to make new scientific discoveries.<\/p>\n

Over the past decade, biology has entered the era of \u2018big data\u2019. Today\u2019s high-throughput technologies generate vast datasets that capture the identities and multi-dimensional characteristics of cells. Using single-cell RNA sequencing, for example, researchers can measure the activity of tens of thousands of genes in hundreds of thousands or even millions of individual cells. Similar large-scale datasets are now produced in many fields of biology, from genetics and cancer research to neuroscience.<\/p>\n

These data promise to provide fundamental new insights into how cells develop, communicate and change during disease. However, analyzing and interpreting such complex datasets remains a big challenge that researchers continue to struggle with. \u201cPeople are good at recognizing patterns in two or three dimensions,\u201d explained Erik van Nimwegen, senior author of the paper. \u201cBut we simply can\u2019t make a picture of a dataset that exists in 10,000 dimensions, and lack intuition for what kind of structures can even exist\u00a0in such high-dimensional spaces.\u201d<\/p>\n

Now, researchers present their newly developed software tool, called Bonsai, which visualizes high-dimensional data on a tree. They demonstrate that this visualization provides a faithful picture of the structure in the data, including how cells are related and how they may have developed from precursor cells.<\/p>\n

\"\"Redrawing the brain\u2019s molecular blueprint: 3D genome mapping and AI reveal more about Alzheimer\u2019s pathology<\/strong><\/a><\/p>\n

Using a combination of single-cell genome mapping, spatial transcriptomics and AI, researchers have identified chromatin alterations as a component of Alzheimer\u2019s disease pathology.<\/p>\n

A tree instead of a flat map<\/p>\n

Most popular tools force data with thousands of dimensions into a two-dimensional map. Although these methods are used in virtually every study, researchers appreciate that such pictures invariably distort the data, making it impossible to tell whether the displayed relationships between cells are true or artifacts created by forcing the data into a two-dimensional visualization. Bonsai overcomes this problem.<\/p>\n

\u201cInstead of creating a flat map, our tool builds a branching tree, with individual cells at the leaves of the branches,\u201d shared first author Daan de Groot. \u201cCrucially, the distances along the branches accurately reflect how closely cells are related in the high-dimensional space.\u201d The team tested the software on both simulated and real single-cell RNA sequencing datasets. Compared to existing methods, Bonsai reconstructs developmental pathways vastly more accurately, preserves the true relationships between cells, and identifies similar cells much more reliably.\u201d<\/p>\n

From better pictures to new discoveries<\/p>\n

When the researchers analyzed human blood cells, Bonsai not only automatically recovered the known relationships between different blood cell types but also uncovered a novel subtype of a type of immune cells, known as natural killer (NK) cells. The molecular signature of this new subtype of NK cells revealed that they originate from a lineage (called the myeloid lineage) that is different from the so-called lymphoid lineage that all NK cells were thought to derive from.<\/p>\n

\u201cThis example shows why faithful representation and visualization of complex data matters,\u201d concluded van Nimwegen. \u201cWhen you can trust the picture, you have a much better chance of making new discoveries.\u201d<\/p>\n

Because Bonsai can be applied to any type of high-dimensional data, including not only gene expression and chromatin state data but also medical data, data from microbiology (i.e. species composition), or data from neuroscience (i.e. neural firing patterns), the researchers believe Bonsai can be a valuable tool for scientists across the life sciences.<\/p>\n

The Bonsai software is freely available to the research community at:\u00a0https:\/\/bonsai.unibas.ch\/<\/a><\/strong><\/p>\n

This article has been republished from the following\u00a0materials<\/a>.\u00a0Material may have been edited for length and\u00a0house style. For further information, please contact the cited source. Our press release publishing policy can be accessed\u00a0here<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"Original story from the University of Basel (Switzerland). A new software tool, Bonsai, makes sense of high-dimensional datasets…\n","protected":false},"author":2,"featured_media":654809,"comment_status":"","ping_status":"","sticky":false,"template":"","format":"standard","meta":{"footnotes":"","_share_on_mastodon":"0"},"categories":[77],"tags":[79656,18,19,17,133,864],"class_list":["post-654808","post","type-post","status-publish","format-standard","has-post-thumbnail","category-science","tag-dna-analysis","tag-eire","tag-ie","tag-ireland","tag-science","tag-software"],"share_on_mastodon":{"url":"","error":""},"_links":{"self":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/654808","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/comments?post=654808"}],"version-history":[{"count":0,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/posts\/654808\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media\/654809"}],"wp:attachment":[{"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/media?parent=654808"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/categories?post=654808"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.europesays.com\/ie\/wp-json\/wp\/v2\/tags?post=654808"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}