PRESS-NEWS.org - Press Release Distribution
PRESS RELEASES DISTRIBUTION

UCI researchers use deep learning to identify gene regulation at single-cell level

Novel ability could further understanding and treatment of diseases such as cancer

2021-01-13
(Press-News.org) Irvine, Calif., Jan. 5, 2021 -- Scientists at the University of California, Irvine have developed a new deep-learning framework that predicts gene regulation at the single-cell level.

Deep learning, a family of machine-learning methods based on artificial neural networks, has revolutionized applications such as image interpretation, natural language processing and autonomous driving. In a study published recently in Science Advances, UCI researchers describe how the technique can also be successfully used to observe gene regulation at the cellular level. Until now, that process had been limited to tissue-level analysis.

According to co-senior author Xiaohui Xie, UCI professor of computer science, the framework enables the study of transcription factor binding at the cellular level, which was previously impossible due to the intrinsic noise and sparsity of single-cell data. A transcription factor is a protein that controls the translation of genetic information from DNA to RNA; TFs regulate genes to ensure they're expressed in proper sequence and at the right time in cells.

"The breakthrough was in realizing that we could leverage deep learning and massive datasets of tissue-level TF binding profiles to understand how TFs regulate target genes in individual cells through specific signals," Xie said.

By training a neural network on large-scale genomic and epigenetic datasets, and by drawing on the expertise of collaborators across three departments, the researchers were able to identify novel gene regulations for individual cells or cell types.

"Our capability of predicting whether certain transcriptional factors are binding to DNA in a specific cell or cell type at a particular time provides a new way to tease out small populations of cells that could be critical to understanding and treating diseases," said co-senior author Qing Nie, UCI Chancellor's Professor of mathematics and director of the campus's National Science Foundation-Simons Center for Multiscale Cell Fate Research, which supported the project.

He said that scientists can use the deep-learning framework to identify key signals in cancer stem cells - a small cell population that is difficult to specifically target in treatment or even quantify.

"This interdisciplinary project is a prime example of how researchers with different areas of expertise can work together to solve complex biological questions through machine-learning techniques," Nie added.

INFORMATION:

Collaborators were Laiyi Fu, a visiting scholar in UCI's Department of Computer Science who is now a researcher in the School of Electronic and Information Engineering at China's Xi'an Jiaotong University; Lihua Zhang, a postdoctoral scholar in mathematics; and Emmanuel Dollinger, a graduate student in mathematical, computational & systems biology.

About the University of California, Irvine: Founded in 1965, UCI is the youngest member of the prestigious Association of American Universities. The campus has produced three Nobel laureates and is known for its academic achievement, premier research, innovation and anteater mascot. Led by Chancellor Howard Gillman, UCI has more than 36,000 students and offers 222 degree programs. It's located in one of the world's safest and most economically vibrant communities and is Orange County's second-largest employer, contributing $5 billion annually to the local economy. For more on UCI, visit http://www.uci.edu.

Media access: Radio programs/stations may, for a fee, use an on-campus ISDN line to interview UCI faculty and experts, subject to availability and university approval. For more UCI news, visit news.uci.edu. Additional resources for journalists may be found at communications.uci.edu/for-journalists.



ELSE PRESS RELEASES FROM THIS DATE:

Research reveals how teeth functioned and evolved in giant mega-sharks

Research reveals how teeth functioned and evolved in giant mega-sharks
2021-01-13
A pioneering study by University of Bristol researchers finds that the evolution of teeth in the giant prehistoric shark Megalodon and its relatives was a by-product of becoming huge, rather than an adaptation to new feeding habits. The iconic extinct Megalodon was the largest shark to ever roam the seas. Its name translates to 'big tooth', making reference to its massive teeth, which represent the most abundant fossil remains of the species. They are broad and triangular, nothing like the curved, blade-like teeth of the closest relatives of Megalodon. The ...

Recurrent GBM brain tumors with few mutations respond best to immunotherapy

2021-01-13
DURHAM, N.C. - Glioblastoma brain tumors are especially perplexing. Inevitably lethal, the tumors occasionally respond to new immunotherapies after they've grown back, enabling up to 20% of patients to live well beyond predicted survival times. What causes this effect has long been the pursuit of researchers hoping to harness immunotherapies to extend more lives. New insights from a team led by Duke's Preston Robert Tisch Brain Tumor Center provide potential answers. The team found that recurring glioblastoma tumors with very few mutations are far more vulnerable ...

Upper ocean temperatures hit record high in 2020

Upper ocean temperatures hit record high in 2020
2021-01-13
Even with the COVID-19-related small dip in global carbon emissions due to limited travel and other activities, the ocean temperatures continued a trend of breaking records in 2020. A new study, authored by 20 scientists from 13 institutes around the world, reported the highest ocean temperatures since 1955 from surface level to a depth of 2,000 meters. The report was published on January 13 in Advances in Atmospheric Sciences and concluded with a plea to the policymakers and others to consider the lasting damage warmer oceans can cause as they attempt to mitigate the ...

Ukraine genome survey adds missing pieces to human diversity puzzle

Ukraine genome survey adds missing pieces to human diversity puzzle
2021-01-13
Today, the largest study of genetic diversity in Ukraine was published in the open science journal GigaScience. The project was an international effort, bringing together researchers in Ukraine, the US and China and is the first fruits of this collaboration to set up a new Central Europe Center for Genomic Research in Ukraine. Led by researchers at Uzhhorod National University and Oakland University in the US, the work provides genetic understanding of the historic and pre-historic migration settlements in one of the key intersections of human trade and migration between the Eurasian peoples as well as the identification of genetic variants of medical interest in the Ukrainian population that differ ...

New study suggests that college campuses are COVID-19 superspreaders

New study suggests that college campuses are COVID-19 superspreaders
2021-01-13
College campuses are at risk of becoming COVID-19 superspreaders for their entire county, according to a new vast study which shows the striking danger of the first two weeks of school in particular. Looking at 30 campuses across the nation with the highest amount of reported cases, experts saw that over half of the institutions had spikes - at their peak - which were well above 1,000 coronavirus cases per 100,000 people per week within the first two weeks of class. In some colleges, one in five students had been infected with the virus by the end of the fall term. Four institutions had over 5,000 ...

Ovarian cancer cells adapt to their surroundings to aid tumor growth

2021-01-13
A detailed description of how ovarian cancer cells adapt to survive and proliferate in the peritoneal cavity has been published in Frontiers in Oncology. Researchers show that structures inside the cells change as the disease progresses from benign to malignant, helping the cells to grow in an otherwise hostile environment of low nutrients and oxygen. Understanding how these cellular adaptations are regulated could herald new targeted treatment options against the fifth-leading cause of cancer-related deaths in women. "Our study compared the structures inside cells representing different stages of ovarian cancer, including after aggregation, which enhances their survival," says Eva Schmelz, a Professor and Scientific Director at Virginia Tech University, USA, who led this research. "We found ...

Families' remote learning experience during lockdown more positive than widely believed

2021-01-13
The remote learning experience of parents who had their children at home in Spring 2020, as schools across the US closed during the United States' COVID-19 lockdown, was more positive than widely believed. That is the suggestion from a new study published in the Journal of School Choice, which looked at the experience of a nationally representative sample of 1,700 parents stretching right across America. On average only 44% of parents reported the online learning program required too much of parents, while 38% of parents said it was difficult for them to manage the online provisions. However, worryingly, most parents (63%) believed remote learning caused their child to fall behind. While the study focused ...

Disagreeing takes up a lot of brain real estate

2021-01-13
Yale researchers have devised a way to peer into the brains of two people simultaneously while are engaged in discussion. What they found will not surprise anyone who has found themselves arguing about politics or social issues. When two people agree, their brains exhibit a calm synchronicity of activity focused on sensory areas of the brain. When they disagree, however, many other regions of the brain involved in higher cognitive functions become mobilized as each individual combats the other's argument, a Yale-led research team reports Jan. 13 in the journal Frontiers of Human Neuroscience. "Our entire brain ...

Expert prognosis for the planet - we're on track for a ghastly future

2021-01-13
A loss of biodiversity and accelerating climate change in the coming decades coupled with ignorance and inaction is threatening the survival of all species, including our very own, according to the experts from institutions including Stanford University, UCLA, and Flinders University. The researchers state that world leaders need a 'cold shower' regarding the state of our environment, both to plan and act to avoid a ghastly future. Lead author Professor Corey Bradshaw of Flinders University in Australia says he and his colleagues have summarised the state of the natural world in stark form to help clarify the gravity of the human predicament. "Humanity is causing a ...

Need to reduce work-related stress? It's a walk in the park

2021-01-13
Tsukuba, Japan - Work causes so much stress that it's become a global public health issue. Stress's impact on mental and physical health can also hurt productivity and result in economic loss. A new study now finds that working people who regularly take walks in forests or greenspaces may have higher stress-coping abilities. In a study published in Public Health in Practice, researchers led by Professor Shinichiro Sasahara at the University of Tsukuba analyzed workers' "sense of coherence" (SOC) scores, demographic attributes, and their forest/greenspace walking habits. SOC comprises the triad of meaningfulness (finding a sense of meaning in life), comprehensibility (recognizing and understanding stress), and ...

LAST 30 PRESS RELEASES:

Breathable yet protective: Next-gen medical textiles with micro/nano networks

Frequency-engineered MXene supercapacitors enable efficient pulse charging in TENG–SC hybrid systems

Developed an AI-based classification system for facial pigmented lesions

Achieving 20% efficiency in halogen-free organic solar cells via isomeric additive-mediated sequential processing

New book Terraglossia reclaims language, Country and culture

The most effective diabetes drugs don't reach enough patients yet

Breast cancer risk in younger women may be influenced by hormone therapy

Strategies for staying smoke-free after rehab

Commentary questions the potential benefit of levothyroxine treatment of mild hypothyroidism during pregnancy

Study projects over 14 million preventable deaths by 2030 if USAID defunding continues

New study reveals 33% gap in transplant access for UK’s poorest children

Dysregulated epigenetic memory in early embryos offers new clues to the inheritance of polycystic ovary syndrome (PCOS)

IVF and IUI pregnancy rates remain stable across Europe, despite an increasing uptake of single embryo transfer

It takes a village: Chimpanzee babies do better when their moms have social connections

From lab to market: how renewable polymers could transform medicine

Striking increase in obesity observed among youth between 2011 and 2023

No evidence that medications trigger microscopic colitis in older adults

NYUAD researchers find link between brain growth and mental health disorders

Aging-related inflammation is not universal across human populations, new study finds

University of Oregon to create national children’s mental health center with $11 million federal grant

Rare achievement: UTA undergrad publishes research

Fact or fiction? The ADHD info dilemma

Genetic ancestry linked to risk of severe dengue

Genomes reveal the Norwegian lemming as one of the youngest mammal species

Early birds get the burn: Monash study finds early bedtimes associated with more physical activity

Groundbreaking analysis provides day-by-day insight into prehistoric plankton’s capacity for change

Southern Ocean saltier, hotter and losing ice fast as decades-long trend unexpectedly reverses

Human fishing reshaped Caribbean reef food webs, 7000-year old exposed fossilized reefs reveal

Killer whales, kind gestures: Orcas offer food to humans in the wild

Hurricane ecology research reveals critical vulnerabilities of coastal ecosystems

[Press-News.org] UCI researchers use deep learning to identify gene regulation at single-cell level
Novel ability could further understanding and treatment of diseases such as cancer