Computational Biology

Recent Discoveries

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Machine learning helps plant science turn over a new leaf

LA JOLLA—Father of genetics Gregor Mendel spent years tediously observing and measuring pea plant traits by hand in the 1800s to uncover the basics of genetic inheritance. Today, botanists can track the traits, or phenotypes, of hundreds or thousands of plants much more quickly, with automated camera systems. Now, Salk researchers have helped speed up plant phenotyping even more, with machine-learning algorithms that teach a computer system to analyze three-dimensional shapes of the branches and leaves of a plant. The study, published in Plant Physiology on October 7, 2019, may help scientists better quantify how plants respond to climate change, genetic mutations or other factors.


Salk’s Tatyana Sharpee elected 2018 Fellow of American Physical Society

LA JOLLA—Salk Associate Professor Tatyana Sharpee, a member of the Computational Neurobiology Laboratory, has been elected a 2018 Fellow of the American Physical Society (APS) for her outstanding contribution to physics. In particular, she is granted this honor for “advancing our understanding of how neurons represent sensory signals and make decisions by pioneering new methods for analyzing neural responses to natural stimuli and uncovered organizing principles for closed loop behaviors,” according to the organization.


Researchers train robotic gliders to soar

LA JOLLA—The words “fly like an eagle” are famously part of a song, but they may also be words that make some scientists scratch their heads. Especially when it comes to soaring birds like eagles, falcons and hawks, who seem to ascend to great heights over hills, canyons and mountain tops with ease. Scientists realize that upward currents of warm air assist the birds in their flight, but they don’t know how the birds find and navigate these thermal plumes.


Fruit fly brains inform search engines of the future

LA JOLLA—Every day, websites you visit and smartphone apps that you use are crunching huge sets of data to find things that resemble each other: products that are similar to your past purchases; songs that are similar to tunes you’ve liked; faces that are similar to people you’ve identified in photos. All these tasks are known as similarity searches, and the ability to perform these massive matching games well—and fast—has been an ongoing challenge for computer scientists.


Salk computational neurobiologist receives NSF grant to study how brain processes sound

LA JOLLA—Salk Associate Professor Tatyana Sharpee has been awarded a grant of approximately $950,000 over 4 years by the National Science Foundation to study how the brain processes complex sounds. This grant is part of a multi-national project together with groups in France and Israel.


How plant architectures mimic subway networks

LA JOLLA—It might seem like a tomato plant and a subway system don’t have much in common, but both, it turns out, are networks that strive to make similar tradeoffs between cost and performance.


How plants grow like human brains

LA JOLLA—Plants and brains are more alike than you might think: Salk scientists discovered that the mathematical rules governing how plants grow are similar to how brain cells sprout connections. The new work, published in Current Biology on July 6, 2017, and based on data from 3D laser scanning of plants, suggests there may be universal rules of logic governing branching growth across many biological systems.


How the brain recognizes what the eye sees

LA JOLLA—If you think self-driving cars can’t get here soon enough, you’re not alone. But programming computers to recognize objects is very technically challenging, especially since scientists don’t fully understand how our own brains do it.


How cells divide tasks and conquer work

LA JOLLA—Despite advances in neuroscience, the brain is still very much a black box—no one even knows how many different types of neurons exist. Now, a scientist from the Salk Institute has used a mathematical framework to better understand how different cell types divide work among themselves.


The Internet and your brain are more alike than you think

LA JOLLA—Although we spend a lot of our time online nowadays—streaming music and video, checking email and social media, or obsessively reading the news—few of us know about the mathematical algorithms that manage how our content is delivered. But deciding how to route information fairly and efficiently through a distributed system with no central authority was a priority for the Internet’s founders. Now, a Salk Institute discovery shows that an algorithm used for the Internet is also at work in the human brain, an insight that improves our understanding of engineered and neural networks and potentially even learning disabilities.


Salk scientists adapt computer program to gauge eye spasm severity

LA JOLLA—If two clinicians observe the same patient with blepharospasm—uncontrollable muscle contractions around the eye—they’ll often come away with two different conclusions on the severity of the patient’s symptoms. That’s because the rating scales for blepharospasm are notoriously subjective and unreliable.


Memory capacity of brain is 10 times more than previously thought

LA JOLLA—Salk researchers and collaborators have achieved critical insight into the size of neural connections, putting the memory capacity of the brain far higher than common estimates. The new work also answers a longstanding question as to how the brain is so energy efficient and could help engineers build computers that are incredibly powerful but also conserve energy.


Terrence Sejnowski receives Swartz Prize for Theoretical and Computational Neuroscience

LA JOLLA–The Society for Neuroscience (SfN), an organization of nearly 40,000 scientists and clinicians, will award the Swartz Prize for Theoretical and Computational Neuroscience to Terrence Sejnowski, Salk professor and head of the Computational Neurobiology Laboratory.


Tatyana Sharpee named to NSF team trying to crack olfactory code

LA JOLLA–Since the early 19th century, scientists have worked to unravel the mystery of olfaction, our sense of smell.


Brain-based algorithms make for better networks

LA JOLLA–When it comes to developing efficient, robust networks, the brain may often know best.
Researchers from the Salk Institute for Biological Studies and Carnegie Mellon University have, for the first time, determined the rate at which the developing brain eliminates unneeded connections between neurons during early childhood.


How the brain balances risk-taking and learning

LA JOLLA–If you had 10 chances to roll a die, would you rather be guaranteed to receive $5 for every roll ($50 total) or take the risk of winning $100 if you only roll a six?


Salk Institute welcomes four new faculty

LA JOLLA—The Salk Institute is pleased to welcome a new full professor and three new assistant professors, all exceptional leaders in their respective fields. The new faculty will facilitate innovative and collaborative breakthroughs in understanding human health and disease.