Jeremy Joseph Yang, PhD

	Jeremy Joseph Yang, PhD Research Associate Professor University of New Mexico, SoM, DoIM, Translational Informatics Division \| LinkedIn \| ORCID \| VIVO \| Zoom:Personal ~ UNM ~ IU
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Bio

	Research Associate Professor in the UNM School of Medicine, Department of Internal Medicine, Translational Informatics Division. Focused on biomedical and biomolecular data science, cheminformatics, and bioinformatics. Projects include Illuminating the Druggable Genome (IDG), DrugCentral and Common Fund Data Ecosystem. Past projects include Badapple, CARLSBAD and BARD, Data Commons, and informatics support for the UNMCMD. See our Public Web Apps, several of which I develop and maintain.
	Adjunct Professor since 2022. PhD, Informatics (Dissertation: "Evidence evaluation in biomedical knowledge graphs for pharmaceutical discovery", 2022), advised by Prof. David Wild, who leads the Integrative Data Science Lab (IDSL) and Crisis Technologies Innovation Lab in the Indiana University School of Informatics, Computing and Engineering.
	VP of Life Sciences Informatics at Data2Discovery, IU spin-off company focused on knowledge graph methods and technologies, founded by David Wild and Ying Ding.

Publications:

Node-degree aware edge sampling mitigates inflated classification performance in biomedical random walk-based graph representation learning , Cappelletti et al., Bioinformatics Advances, 2024.
Computational drug repositioning identifies niclosamide and tribromsalan as inhibitors of Mycobacterium tuberculosis and Mycobacterium abscessus, Yang, Goff, et al., Tuberculosis, 2024.
Overview of the Knowledge Management Center for Illuminating the Druggable Genome, Oprea, et al., Drug Discovery Today, 2024.
Toxicology knowledge graph for structural birth defects, Evangelista, et al., Communications Medicine, 3, 98, 2023.
Autophagy dark genes: Can we find them with machine learning?, Ranjbar, et al., Natural Sciences, 2023.
Pharos 2023: an integrated resource for the understudied human proteome, Kelleher, et al., Nucleic Acids Research, 2023.
DrugCentral 2023 extends human clinical data and integrates veterinary drugs, Avram, et al., Nucleic Acids Research, 2023.
Knowledge graph analytics platform with LINCS and IDG for Parkinson's disease target illumination, Yang et al., BMC Bioinformatics, 2022.
Getting Started with the IDG KMC Datasets and Tools, Kropiwnicki et al., Current Protocols, 2022.
TIGA: Target illumination GWAS analytics, Yang et al., Bioinformatics, 2021.
A machine learning platform to estimate anti-SARS-CoV-2 activities, Govinda et al., Nature Machine Intelligence, 2021.
Analyzing knowledge entities about COVID-19 using entitymetrics, Yu et al., Scientometrics volume 126, 2021.
TCRD and Pharos 2021: mining the human proteome for disease biology, T. Sheils et al., Nucleic Acids Research, 2020.
edge2vec: Representation learning using edge semantics for biomedical knowledge discovery, Zheng Gao et al, BMC Bioinformatics, 2019.
DrugCentral 2018: an update , O. Ursu et al., Nucleic Acids Research, 2018.
Unexplored therapeutic opportunities in the human genome, T.I. Oprea et al., Nature Reviews Drug Disc, 2018.
"PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets", Djokic-Petrovic et al., J Biomed Semantics, 2017.
Formalizing drug indications on the road to therapeutic intent, SJ Nelson et al., J Am Med Inform Assoc, 2017.
TIN-X: Target Importance and Novelty Explorer, D.C. Cannon et al., Bioinformatics, 2017.
Badapple: promiscuity patterns from noisy evidence , J.J. Yang et al., J. Cheminfo., 2016.
Novel Phenotypic Outcomes Identified for a Public Collection of Approved Drugs from a Publicly Accessible Panel of Assays, J. Lee, et al, PLoS ONE, 2015.
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types, E.A. Howe et al., Nucleic Acids Res, 2015.
The CARLSBAD Database: A Confederated Database of Chemical Bioactivities, S.L. Mathias et al., Database, 2013.
Analysis and hit filtering of a very large library of compounds screened against Mycobacterium tuberculosis, S. Ekins et al., Mol. BioSyst., 2010.

Talks:

Evidence evaluation in biomedical knowledge graphs for pharmaceutical discovery, UNM HSLIC Biomedical Informatics Seminar Series (BioMISS), October 5, 2023.
Knowledge graph analytics platform combining LINCS and IDG for drug target illumination, presented at the ISMB-ECCB Bioinformatics Open Source Conference (BOSC2021), July 25-30, 2021.
DrugCentralDb and BioClients: Dockerized PostgreSql with Python API-tizer (VIDEO), UNM Tech Days, June 4, 2020.
Illuminating the Druggable Genome with Knowledge Engineering and Machine Learning, 14th Annual NMBIST Symposium Integrative Omics, March 14-15, 2019.
Bibliological data science and drug discovery, ACS National Meeting in Philadelphia, Aug 21, 2016.
The Language Diversity of Computing, UNM Biomedical Info Seminar Series, Oct 15, 2015.
Molecular scaffolds are special and useful guides for discovery, ACS National Meeting, Sept. 8, 2013, Indianapolis, IN.
The BADAPPLE promiscuity plugin for BARD: Evidence-based promiscuity scores, ACS National Meeting, Sept. 9, 2013, Indianapolis, IN.
How am I supposed to organize a protein database when I can't even organize my address book?, CINF Flash session, ACS National Meeting, March 25, 2012, San Diego, CA.
Cheminformatics Software Development Case Studies, guest lecture given via webcast to SOIC I571 "Chemical Information Technology" class on Oct 24, 2011.
Applications in Biocomputing, UNM Cyberinfrastructure Day, April 22, 2010.

Posters:

Illuminating the Druggable Genome (IDG) scientific use cases powered by the CFDE Data Distillery biomedical knowledge graph, integrating multiple Common Fund datasets, Common Fund Data Ecosystem (CFDE) Meeting, Mar 19-20, 2024.
Independent study in biomedical data science, CFDE edition (ISBDS-CFDE): an online summer training course featuring IDG scientific use case research plan templates, Common Fund Data Ecosystem (CFDE) Meeting, Mar 19-20, 2024.
Clinically relevant precision molecular biomarker illumination powered by Cerner Real World Data, Common Fund Data Ecosystem (CFDE) Meeting, Mar 19-20, 2024.
TIGA: Target Illumination GWAS Analytics, IDG Annual Meeting, Feb 9-11, 2021.
Mining ClinicalTrials.gov via CTTI AACT for drug target hypotheses, IDG F2F Meeting, Arlington, VA, February 2020.
TIN-X v2: modernized architecture with REST API for sustainability & interoperability, IDG Annual Meeting, Arlington, VA, March 2019.
Exfiles: Sex-Specific Gene Expression Profiles Explorer, 2018, scientific use case for NIH Data Commons Pilot Project Consortium (DCPPC).
Badapple: promiscuity patterns from noisy evidence (poster for UNM Staff Research Expo, Jan 27,2017.)
Open Phenotypic Drug Discovery Resource, Open PHACTS: Linking life science data, Feb 18-19, 2016, Vienna, Austria.
Development of a Screening Informatics System at the UNM Center for Molecular Discovery, ACS National Meeting, March 26, 2012, San Diego, CA.
CARLSBAD: Confederated Annotated Research Libraries of Small-molecule Biological Activity Data, OpenEye CUP meeting, Santa Fe, NM, 2012.
UNM Division of Biocomputing public web applications: Computational tools for cheminformatics and molecular discovery, ChemAxon US User Group Meeting, Boston, September 13-15, 2010.
RMSD: routine measure stirs doubts, 230th National ACS meeting, Washington DC, 2005.
Canonicalized systematic nomenclature in cheminformatics, 229th National ACS Meeting, San Diego, 2005.

Teaching:

Independent Study in Biomedical Data Science

Project templates available in bioinformatics, cheminformatics, systems biology and other areas.
Offered as BIOM505 (Biomedical Sciences Special Topics: "Ind Study Biomed Data Sci") For more information: ISBDS Course Home Page.

UNM:BIOMED_505, "Introduction to Biocomputing". Bioinformatics, cheminformatics, computational structure and ligand based drug discovery informatics via online community resources and methods, This online graduate course was and offered 2007-2019. I served as course coordinator 2008-2019, with responsibilities including instruction, advisement, curricular maintenance and updates, and software support.
IU:INFO_I-590, "Topics in Informatics: Data Science for Drug Discovery, Health and Translational Medicine": This innovative data science course was introduced by Prof. Wild in 2013 and updated for 2017 by Prof. Joanne Luciano, assisted by JT Wolohan and myself as associate instructor.
IU:INFO_I-590, "Applied Data Science ": The classic data science workflow is the framework for understanding how to apply data wrangling, semantics, machine learning and other skills in realistic scenarios. Developed by Prof. Joanne Luciano in 2017, assisted by JT Wolohan, Kaicheng Yang, and myself as associate instructor.
IU:INFO_I-590, "Real World Data Science ". Developed by Prof. Wild, Prof. Luciano, and industry partner Sara Bigelow, in collaboration with Lilly, with de-identified clinical trials datasets, employing analysis tools KNIME and Tableau. Associate instructor, spring 2018.

Miscellaneous:

LINKS
Some publicly available software:
- BioClients (GitHub|PyPI) - Python package to access biomedical APIs.
- RDKit-Tools (GitHub|PyPI) - Python package of tools for use with RDKit.
- CFChemDb (GitHub) - CFDE Chemical Db and Dev System
- Badapple (GitHub) - Bioassay data associative promiscuity prediction learning engine.