Unsupervised and semi-supervised ML/AI with iterative experimentation for rapid identification of targeted alphaviral small molecules
NEWS
Congratulations to graduate research assistant Swastika Tenkila Purushotham, on successful defense of her Computer Engineering MS dissertation, “Advancing Drug Discovery and Disease Understanding through Knowledge Graphs and Machine Learning Techniques”, December 2024 graduation, and co-authorship of related new paper, now available via MedArxiv pre-print.
Congratulation to Dr. Jeremiah Abok, on his successful Chemistry and Chemical Biology PhD dissertation defense, on February 26, 2025, entitled “Drug Targets Illumination: An Evidence-Based Data Analytics and Informatics Approach to Hypothesis Generation Through Clinical Trials and Genomic Variants”. Dr. Abok’s research was supervised by PhD advisor Prof. Jeremy Edwards, and Prof. Jeremy Yang. For more information, see publication preprints: [1] and [2].
The CFDE Summer Internship at UNM (June-July 2025) is an NIH CFDE sponsored program, organized by the IDG Data Coordinating Center (DCC) at the University of New Mexico (UNM), and focused on effective use and integration of Common Fund (CF) datasets for biomedical discovery. To learn more, and to apply, see the CFDE Summer Internship at UNM Home Page
SEMINAR: “Exploring structure-activity relationships (SAR) in curated PubChem sources with potential AI/ ML applications,” Christopher Southan, Honorary Professor at the University of Edinburgh, Fellow of the BPS, RSC, and RSB, Adjunct Associate Professor, UNM. WEDNESDAY, JANUARY 22, 2025, NOON, Innovation, Discovery and Training Complex (IDTC) Room 2135. SOM IM – Seminar Announcement Flyer 8 x11,
New publication: “Detecting Opioid Use Disorder in Health Claims Data With Positive Unlabeled Learning“, Praveen Kumar, Fariha Moomtaheen, Scott A. Malec, Jeremy J. Yang, Cristian G. Bologa, Kristan A Schneider. Published: 11 Dec 2024, IEEE Journal of Biomedical and Health Informatics
TID Division Administrator Tonya Morgan has been recognized for her outstanding performance by receiving the School of Medicine Dean’s Staff Award for 2024, presented by Dean Finn at a ceremony on November 21, 2024, and including a trophy and $1000.
New publication: “Positive Unlabeled Learning Selected Not At Random (PULSNAR): class proportion estimation without the selected completely at random assumption” Praveen Kumar, Fariha Moomtaheen, Scott A. Malec, Jeremy J Yang, Cristian G. Bologa, Kristan A Schneider. Published: 5 Nov 2024, PeerJ Computer Science 10:e2451
New publication: “Detecting Opioid Use Disorder in Health Claims Data with Positive Unlabeled Learning”,
Praveen Kumar, Fariha Moomtaheen, Scott A. Malec, Jeremy J. Yang, Cristian G. Bologa, Kristan A. Schneider, Yiliang Zhu, Mauricio Tohen, Gerardo Villarreal, Douglas J. Perkins, Elliot M. Fielstein, Sharon E. Davis, Michael E. Matheny, Christophe Gerard Lambert.
Published: 25 Sept 2024, Last Modified: 25 Sept 2024IEEE BHI’24
New publication: “TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets,” Vincent T. Metzger, Daniel C. Cannon, Jeremy J. Yang, Stephen L. Mathias, Cristian G. Bologa, Anna Waller, Stephan C. Schürer, Dusica Vidović, Keith J. Kelleher, Timothy K. Sheils, Lars Juhl Jensen, Christophe G. Lambert, Tudor I. Oprea, Jeremy S. Edwards. PeerJ, published June 25, 2024.
New Publication, “Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus” by Jeremy J. Yang, Aaron Goff, David J. Wild, Ying Ding, Ayano Annis, Randy kerber, Brian Foote, Anurag Passi, Joel L. Duerksen, Shelly London, Ana C. Puhl, Thomas R.Lane, Miriam Braunstein, Simon J. Waddell, Sean Ekins
Tuberculosis,
Accepted 24 February 2024, Available online 27 February 2024.
New Publication, “Authophagy dark genes: Can we find them with machine learning?” by Mohsen Ranjbar, Jeremy J. Yang, Praveen Kumar, Daniel R. Byrd, Elaine L. Bearer, Tudor I. Oprea
New Grant, “Deriving high-quality evidence from national healthcare databases to improve suicidality detection and treatment outcomes in PTSD” Project Leader- Christophe Lambert Start Date- 12/23/22 End Date- 11/30/26
Read the press release, “Hidden Patterns” by Michael Haederle, February 10, 2023
New Publication, “DrugCentral 2023 extends human clinical data and integrates veterinary drugs” by Tudor I Oprea
New Publication, “Pharos 2023: an integrated resource for the understudied human proteome“, by
New Publication by Christophe Lambert and Team. Congratulations!
“Using Machine Learning Imputed Outcomes to Assess Drug-Dependent Risk of Self-Harm in Patients with Bipolar Disorder: A Comparative Effectiveness Study“. https://doi.org/10.2196/24522
Christophe Lambert: Linkedin Article
New Publication, “A machine learning platform to estimate, anti-SARS-CoV-2 activities” by Tudor Oprea, MD, PhD and Team:
Govinda B. C, Giovanni Bocci, Srijan Verma, Md Mahmudulla Hassan, Jayme_Holmes, Jeremy J. Yang & Suman Sirimulla.
-Nature Machine Intelligence Publication
-Redial 2020 Web Application
-HSC NewsRoom Article
Bioinformatics and Drug Discovery 3rd Edition, Editors: Dr. Larson & Dr. Oprea. Congratulations!
This third edition volume expands on the previous editions with new topics that cover drug discovery through translational bioinformatics, informatics, clinical research informatics, as well as clinical informatics. The chapters discuss new methods to study target identification, genome analysis, cheminformatics,
COVID Corner
Daily UNM Global Health COVID-19 Briefings– Including a daily compilation of curated news and literature that are sent out to help inform government, healthcare and research officials, and even members of the public. To Subscribe to the above COVID-19 Briefings
How to Prepare a Compound Collection Prior to Virtual Screening.
Virtual screening is a well-established technique that has proven to be successful in the identification of novel biologically active molecules, including drug repurposing. Whether for ligand-based or for structure-based virtual screening, a chemical collection needs to be properly processed prior
Comparison of 71 bipolar disorder pharmacotherapies for kidney disorder risk: The potential hazards of polypharmacy
Read Article Newly observed KD occurred in 14,713 patients. No regimen had significantly lower risk of KDs than “No drug”. The HR estimates ranged 0.86–2.66 for “all” KDs and 0.87–5.30 for “severe” KDs. As additional drugs were combined to compare
Our Publications Section
Here you can search Publications by Author. Cristian Bologa Ph.D. PubMed Google Scholar Jayme Holmes, PubMed Christophe Lambert, Ph.D. VIVO Orcid Pubmed Google Scholar Stephen Mathias, Ph.D. VIVO Google Scholar Tudor Oprea, M.D., Ph.D. PubMed Google Scholar BioSketch Avinash Sahu, Ph.D. UNMCCC Google
TID: Published Books
Bioinformatics and Drug Discovery 3rd Edition, Editors: Dr. Larson & Dr. OpreaCover Design: Jayme Holmes Buy on Amazon Dr. Kroth’s Book Available! Health Care USA, Ninth Edition. Dr. Lambert’s book available, “Human Genome Informatics”. Human Genome Informatics: Translating Genes into
UNM scientist Dr. Tudor Oprea: Artificial intelligence can aid COVID-19 research
UNM Scientists Studying Ways to Repurpose Older Drugs to Treat COVID-19 Infection. Read more
A.I. in GPCR Research
Listen to the podcast:http://www.drgpcr.com/episode-18-a.i.-and-gpcr-with-dr.-yamina-berchiche/
(IDG) Druggablegenome.net
The goal of the Illuminating the Druggable Genome (IDG) program is to improve our understanding of the properties and functions of proteins that are currently unannotated within the three most commonly drug-targeted protein families: G-protein coupled receptors, ion channels, and
Follow link: DrugCentral.org
DrugCentral is online drug information resource created and maintained by Division of Translational Informatics at University of New Mexico. DrugCentral provides information on active ingredients chemical entities, pharmaceutical products, drug mode of action, indications, pharmacologic action. We monitor FDA, EMA,
Repurposing
Drug Repurposing Projects Ketorolac Virtual screening by TiD identified the R-enantiomer of ketorolac as a hit for blocking GTPase activation in response to growth factor stimulus. Ketorolac is a nonsteroidal anti-inflammatory drug (NSAID) used for pain relief under the trade
Digital Assets
FACILITIES AND OTHER RESOURCES UNIVERSITY OF NEW MEXICO Translational Informatics Division The Translational Informatics Division (TID) is housed in the Innovation Discovery & Training Complex (IDTC) together with the UNM Center for Molecular Discovery (UNMCMD). TID is part of the
Cheminformatics
Cheminformatics is the application of informatics and computation to chemistry. Historically, cheminformatics has been associated with drug discovery science. Cheminformatics encompasses a wide range of foundational disciplines and computational technologies, from graph theory based molecular representations, to machine learning based
Translational Bioinformatics
Translational Bioinformatics (TBI): The science of leveraging biomolecular data into clinical medicine. Here is a much longer definition from the American Medical Informatics Association site. Translational Bioinformatics is the development of storage, analytic, and interpretive methods to optimize the transformation
Clinical Informatics
Fellowship NOW Being Offered at UNM The Department of Internal Medicine is starting a new Clinical Informatics Fellowship. For more information, click HERE Clinical Informatics is the application of health information technologies to help in the quality of health care,
Data Science
Please click on images to the right to learn more about some of TiD's innovative applications such as the recently developed TiNEX, our legacy Public Apps, and Carlsbad One. For more TiDware, see the tab at the top of this page.
