Breaking News
August 14, 2018 - American Heart Association Urges Screen Time Limits for Youth
August 14, 2018 - Brief interventions during routine care reduce alcohol use among men with HIV
August 14, 2018 - New genome analysis could identify people at higher risk of common deadly diseases
August 14, 2018 - NIH grant for Mount Sinai to study use of inhaled corticosteroids for treatment of sickle cell disease
August 14, 2018 - Daicel supplies free nanodiamond samples to international researchers
August 14, 2018 - Switching anti-psychotic drugs in first-episode schizophrenia patients does not improve clinical outcomes
August 14, 2018 - Study to examine whether modulating gut bacteria can improve cardiac function in heart failure patients
August 14, 2018 - One out of two children not getting enough nutrients needed for their health
August 14, 2018 - Mono-antiplatelet therapy after aortic heart valve replacements may work as well as two drugs
August 14, 2018 - Aid-in-dying patient chooses his last day
August 14, 2018 - Exercise Really Can Chase Away the Blues, to a Point
August 14, 2018 - Surgical mesh implants may cause autoimmune disorders
August 14, 2018 - Researchers develop revolutionary zebrafish model to gain more insight into bone diseases
August 14, 2018 - Researchers discover secret communication hotline between breast cancers and normal cells
August 14, 2018 - Study examines how a person adapts to visual field loss after stroke
August 14, 2018 - Researchers show how specialized nucleic acid-based nanostructures could help target cancer cells
August 14, 2018 - Reducing opioid prescriptions for one operation can also spill over to other procedures
August 14, 2018 - E-cigarettes not so safe but still better than cigarettes
August 14, 2018 - Researchers find link between common ‘harmless’ virus and cardiovascular damage
August 14, 2018 - Initiation of PIMs associated with higher risk of fracture-specific hospitalizations and mortality
August 14, 2018 - Genetically modified mosquitoes and special bed nets help tackle deadly diseases
August 14, 2018 - Advances in treating hep C lead to new option for transplant patients
August 14, 2018 - Study finds quality of doctor-patient discussions about lung cancer screening to be ‘poor’
August 14, 2018 - MSU researchers uncover the effects of aging on regenerative ability of kidneys
August 14, 2018 - Better conditioning, throwing mechanics can help reduce elbow injuries in young baseball pitchers
August 14, 2018 - Brain game doesn’t offer brain gain
August 14, 2018 - Reproductive choices facing women with disabilities require careful consideration
August 14, 2018 - Scientists pinpoint the cause of a rare childhood seizure disorder
August 14, 2018 - Lumpectomy plus radiation associated with reduced risk of breast cancer death, study finds
August 14, 2018 - UAB study shows how ion channel differentiates newborn and mature neurons in the brain
August 14, 2018 - Experts highlight key knowledge gaps that need to be addressed in Ebola vaccine research
August 14, 2018 - Discovery could lead to new drugs against infection and inflammation
August 14, 2018 - Infection Prevention Differs Between Small, Large Hospitals
August 14, 2018 - Mom still matters—In study, young adults tended to prioritize parents over friends
August 14, 2018 - Deep brain stimulation might benefit those with severe alcoholism, preliminary studies show
August 14, 2018 - Study finds increased rate of repeat pregnancies in women with intellectual and developmental disabilities
August 14, 2018 - Lighter sedation fails to reduce risk of postoperative delirium in older patients
August 13, 2018 - Asking better questions about person’s memory could improve doctors’ understanding of patients
August 13, 2018 - U.S. Trauma Doctors Push for Stricter Gun Controls
August 13, 2018 - Asthma and flu: a double whammy
August 13, 2018 - 5 Questions: Donna Zulman on engaging high-need patients in intensive outpatient programs | News Center
August 13, 2018 - Behavioral Nudges Lead to Drop in Prescriptions of Potent Antipsychotic
August 13, 2018 - Potential New Class of Drugs May Reduce Cardiovascular Risk by Targeting Gut Microbes
August 13, 2018 - How to get your kids to eat better
August 13, 2018 - The importance of hearing your patients
August 13, 2018 - Transmission of F. tularensis unlikely to happen through the food chain
August 13, 2018 - Researchers discover epigenetic mechanism underlying ischemic cardiomyopathy
August 13, 2018 - Adolescent health programs receive only a tiny share of international aid, finds research
August 13, 2018 - Fracture risk increases by 30% after gastric bypass, study shows
August 13, 2018 - Quality-improvement project to standardize feeding practices helps micro preemies gain weight
August 13, 2018 - Long-term cannabinoid exposure impairs memory, study shows
August 13, 2018 - New intervention to reduce risk of HIV in young transgender women
August 13, 2018 - Japan human trial tests iPS cell treatment for Parkinson’s
August 13, 2018 - Altered nitrogen metabolism may contribute to emergence of new cancer mutations
August 13, 2018 - Cycling provides greatest health benefits, study finds
August 13, 2018 - Scientists discover biomarker for kidney cancer
August 13, 2018 - New test predicts the risk of serious disease before symptoms appear
August 13, 2018 - Cianna Medical receives FDA 510(k) clearance to extend indication of SCOUT reflector for use in soft tissue localization
August 13, 2018 - Ground-breaking discovery offers new hope for treatment of Alzheimer’s, other neurological diseases
August 13, 2018 - Medical nutrition therapy provided by RDNs benefits patients with chronic kidney disease
August 13, 2018 - Prenatal Tdap vaccination not linked with increased risk of autism in children, study shows
August 13, 2018 - One-Third of Canadian Patients Get Hip Fx Repair Within 24 Hours
August 13, 2018 - ANA (Antinuclear Antibody) Test: MedlinePlus Lab Test Information
August 13, 2018 - Traffic jams in the brain
August 13, 2018 - NIH awards $6.5 million to establish multi-institution biomedical technology resource center
August 13, 2018 - New marker in the blood could help predict person’s risk of developing kidney cancer
August 13, 2018 - New biomarker may provide clues to create diagnostic tool for hypoglycemia-associated autonomic failure
August 13, 2018 - Oxidative Stress Hampers Blood Vessel Dilation in Men
August 13, 2018 - Parents’ Religious Beliefs May Affect Kids’ Suicide Risk: Study
August 13, 2018 - Measure of belly fat in older adults is linked with cognitive impairment
August 13, 2018 - FDA permits marketing of first mobile medical app for contraceptive use to prevent pregnancy
August 13, 2018 - NUS scientists develop new technology to customize optimal drug ‘cocktail’ for myeloma patients
August 13, 2018 - Disordered eating behaviors up for overweight young adults
August 13, 2018 - Connection between Alzheimer’s disease and degenerative eye diseases
August 13, 2018 - Employer expectation of checking email during nonwork hours affects health of workers and families
August 13, 2018 - Rotavirus vaccination reduces infant diarrhea deaths by 34% in rural Malawi
August 13, 2018 - Approval of drug derived from cannabis not necessarily a win for weed
August 13, 2018 - Study shows COPD risk in women with asthma can be reduced
August 13, 2018 - FIND and genedrive announce study agreement to evaluate HCV ID Kit
August 13, 2018 - One in two people putting their eye health at risk during summer, says eye research charity
Researchers develop new dynamic statistical model to follow gene expressions over time

Researchers develop new dynamic statistical model to follow gene expressions over time

image_pdfDownload PDFimage_print

Researchers at Carnegie Mellon University have developed a new dynamic statistical model to visualize changing patterns in networks, including gene expression during developmental periods of the brain.

Published in the Proceedings of the National Academy of Sciences, the model now gives researchers a tool that extends past observing static networks at a single snapshot in time, which is hugely beneficial since network data are usually dynamic. The analysis of network data–or the study of relationships from a large-scale view–is an emerging field of statistics and data science.

“For any dataset with a dynamic component, people can now use this in a powerful way to find communities that persist and change over time,” said Kathryn Roeder, the UPMC Professor of Statistics and Life Sciences in the Dietrich College of Humanities and Social Sciences. “This will be very helpful in understanding how certain diseases and disorders progress. For example, we know that certain genes are responsible for autism and can use our model to give us insight into at what point the disorder begins developing.”

The model, Persistent Communities by Eigenvector Smoothing (PisCES), combines information across a series of networks, longitudinally, to strengthen the inference for each period. The CMU team used PisCES to follow neural gene expressions from conception through adulthood in rhesus monkey brains to find out what genes work together during different points of development.

“Our visualization method combines two different existing tools: community detection, which is a popular tool for static network data, and sankey plots, which are often used to visualize ‘flows’ of information. Our visualization organizes the actors of the network into communities that evolve over time and then depicts the evolving community memberships as a series of flows between the communities,” said David Choi, assistant professor of statistics and information systems at the Heinz College of Information Systems and Public Policy.

Their analysis revealed the existence of change points as well as periods of persistent gene community structure, including a dynamic community of genes involved in neural projection guidance that was highly active during the mid to late fetal period. This particular community includes many genes associated with risk for autism.

“Essentially our goal was to add ‘smoothing’ to community detection to eliminate the ‘noise,’ and we were able to do that,” Choi said.

Although the team piloted the model by visualizing the changing patterns in the ways that genes work together, the hope is that the method could be applied to social networks, dynamic diffusion networks in physics and other relational situations.

“The model is really flexible, and we are already starting to use it with fMRI data to understand how regions of the brain interconnect and change over time,” said Fuchen Liu, a Ph.D. student in the Department of Statistics and Data Science.

Developing a new dynamic statistical model to follow neural gene expressions over time is one of the many brain research breakthroughs to happen at Carnegie Mellon. CMU has created some of the first cognitive tutors, helped to develop the Jeopardy-winning Watson, founded a groundbreaking doctoral program in neural computation, and is the birthplace of artificial intelligence and cognitive psychology. Building on its strengths in biology, computer science, psychology, statistics and engineering, CMU launched BrainHub, an initiative that focuses on how the structure and activity of the brain give rise to complex behaviors.

Tagged with:

About author

Related Articles