PARMESAN: An AI-Based Predictive Tool to Find New Treatments for Genetic Disorders

To discover new treatments for genetic disorders, scientists need a thorough knowledge of prior literature to determine the best gene/protein targets and the most promising drugs to test. However, biomedical literature is growing at an explosive rate and often contains conflicting information, making it increasingly time-consuming for researchers to conduct a complete and thorough review.

To address this challenge, Cole Deisseroth, a graduate student enrolled in the M.D./Ph.D. program and mentored by Drs. Huda Zoghbi and Zhandong Liu at the Jan and Duncan Neurological Research Institute (Duncan NRI) at Texas Children's Hospital and Baylor College of Medicine, led a study to generate a natural language processing (NLP) tool called PARsing ModifiErS via Article aNnotations (PARMESAN). This new tool can search for up-to-date information, assemble it into a central knowledge base, and even predict likely drugs that could correct specific protein imbalances. A description of the tool and its capabilities was published recently in the American Journal of Human Genetics.

"PARMESAN offers a wonderful opportunity for scientists to speed up the pace of their research and thus, accelerate drug discovery and development," Howard Hughes Medical Institute investigator, Dr. Huda Zoghbi, who is also the founding director of Duncan NRI and distinguished service professor at Baylor College, added.

This artificial intelligence (AI)-powered tool scans through public biomedical literature databases (PubMed and PubMed Central), to identify and rank descriptions of gene-gene and drug-gene regulatory relationships. However, what stands out about PARMESAN in particular is its ability to leverage curated information to predict undiscovered relationships.

"The unique feature of PARMESAN is that it not only identifies existing gene-gene or drug-gene interactions based on the available literature but also predicts putative novel drug-gene relationships by assigning an evidence-based score to each prediction," Dr. Zhandong Liu, Chief of Computation Sciences at Texas Children's Hospital and associate professor at Baylor College of Medicine, noted.

PARMESAN's AI algorithms analyze studies that describe the contributions of various players involved in a multistep genetic pathway. Then it assigns a weighted numerical score to each reported interaction. Interactions that are consistently and frequently reported in the literature receive higher scores, whereas interactions that are either weakly supported or appear to be contradicted between different studies are assigned lower scores.

PARMESAN currently provides predictions for more than 18,000 target genes, and benchmarking studies have suggested that the highest-scoring predictions are over 95% accurate.

"By pinpointing the most promising gene and drug interactions, this tool will allow researchers to identify the most promising drugs at a faster rate and with greater accuracy," Cole Deisseroth, said.

Deisseroth CA, Lee WS, Kim J, Jeong HH, Dhindsa RS, Wang J, Zoghbi HY, Liu Z.
Literature-based predictions of Mendelian disease therapies.
Am J Hum Genet. 2023 Oct 5;110(10):1661-1672. doi: 10.1016/j.ajhg.2023.08.018

Most Popular Now

MEDICA 2024 + COMPAMED 2024: Adapted Hal…

11 - 14 November 2024, Düsseldorf, Germany. The final preparations for MEDICA 2024 and COMPAMED 2024 in Düsseldorf have begun. A total of more than 5,500 exhibitors from approximately 70 countries...

AI does Not Necessarily Lead to more Eff…

The use of artificial intelligence (AI) in hospitals and patient care is steadily increasing. Especially in specialist areas with a high proportion of imaging, such as radiology, AI has long...

Commission Joins Forces with Venture Cap…

The Commission has launched a Trusted Investors Network bringing together a group of investors ready to co-invest in innovative deep-tech companies in Europe together with the EU. The Union's investment...

Why the NHS is Seeking to Make Media Ser…

Opinion Article by Dean Moody, Healthcare Services Director, Airwave Healthcare. Tim Kelsey and Martha Lane Fox called for WiFi to be made available free of charge throughout the NHS back in...

An AI-Powered Pipeline for Personalized …

Ludwig Cancer Research scientists have developed a full, start-to-finish computational pipeline that integrates multiple molecular and genetic analyses of tumors and the specific molecular targets of T cells and harnesses...

Wearable Cameras Allow AI to Detect Medi…

A team of researchers says it has developed the first wearable camera system that, with the help of artificial intelligence (AI), detects potential errors in medication delivery. In a test whose...

Philips and Medtronic Advocacy Partnersh…

Royal Philips (NYSE: PHG, AEX: PHIA), a global leader in health technology, and Medtronic Neurovascular, a leading innovator in neurovascular therapies, today announced a strategic advocacy partnership. Delivering timely stroke...

AI could Transform How Hospitals Produce…

A pilot study led by researchers at University of California San Diego School of Medicine found that advanced artificial intelligence (AI) could potentially lead to easier, faster and more efficient...

New AI Tool Predicts Protein-Protein Int…

Scientists from Cleveland Clinic and Cornell University have designed a publicly-available software and web database to break down barriers to identifying key protein-protein interactions to treat with medication. The computational tool...

Great Start for Ideas and Innovations: D…

8 - 10 April 2025, Berlin, Germany. From 15 October to 15 November 2024, the DMEA invites experts from business, science, politics and practice to actively participate in shaping the congress...

Start-Ups will Once Again Have a Starrin…

11 - 14 November 2024, Düsseldorf, Germany. The finalists in the 16th Healthcare Innovation World Cup and the 13th MEDICA START-UP COMPETITION have advanced from around 550 candidates based in 62...

AI for Real-Rime, Patient-Focused Insigh…

A picture may be worth a thousand words, but still... they both have a lot of work to do to catch up to BiomedGPT. Covered recently in the prestigious journal Nature...