David Jimenez-Morales

David Jimenez-Morales

Bioinformatics Lead & Research Scientist

Leading computational biology research at Stanford University, specializing in multi-omic data analysis, proteomics, and systems biology. PhD in Bioinformatics with extensive experience in developing bioinformatics tools and pipelines.
But why am I doing research?

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About Me

Education

2006 - 2013

PhD Bioinformatics

Department of Bioengineering, University of Illinois at Chicago

2003 - 2004

MSc Computational Biology

Universidad Complutense de Madrid

1993 - 1998

BSc Biology

Universidad de Granada

Current Position

Bioinformatics Lead

The Ashley Lab

Department of Medicine, Division of Cardiovascular Medicine

Stanford University

View Stanford Profile

Research Highlights

Evolution Beta Barrel Research
Transmembrane regions of beta-barrel membrane proteins
djm-diagrams: my graphical representations of amino acid substitutions
Systems Biology Modeling: integrative analytical strategy for multi-omics data
FluOMICS Research
Characterization of functional cavities in the proteome
Defining functional cavities: Active site pockets and craters
We defined a new metric for caveties in proteins: CharDen (Charge Density)
The CharDen is very different between functional sites and non-functional sites (craters)
PreLysCar: Prediction of lysine carboxylation in proteins
Structural motifs for Lysine Carboxylation
Performance of PreLysCar
I made available a web-based tool for predicting lysine carboxylation in proteins
PreLysCar is part of CCP4
Early career: Proteomics in Spain (and my first professional art work)

Research Experience

2022 - Present

Bioinformatics Lead

The Ashley Lab, Stanford University

Lead organization-wide data initiatives (MoTrPAC, COVID-omics); own multi-omics engineering and analysis across multi-tissue in-vivo and clinical studies; champion FAIR principles; manage and mentor a high-performing analyst team; architect cloud-native multi-omics software (OmicsPipelines).

2021 - 2022

Senior Research Engineer (Academic Research Staff)

The Ashley Lab, Stanford University

Advanced research engineering supporting clinical and translational projects; drove implementation of FAIR-aligned workflows; contributed to large-scale multi-omics integration and production-grade pipeline development.

2018 - 2021

Senior Computational Biologist

The Ashley Lab, Stanford University

Developed cloud-native proteomics and genomics analytics; created the Bioconductor package artMS; designed and implemented an EHR-derived clinical severity scale enabling COVID-19 outcome modeling.

2015 - 2018

Computational Lead (Researcher)

The Krogan Lab, UCSF

Led the bioinformatics team; delivered >20 collaborations across infectious diseases, cancer, diabetes, and neurodegeneration; built modeling frameworks integrating RNA-seq, large-scale proteomics (abundance, phospho, ubiquitin, AP-MS) and functional genomics (RNAi, CRISPRi) to prioritize disease genes; secured funding and developed the multi-omics tool bioNeNa; contributed to R01/U19/U54/P50 grants.

2016 - 2018

Visiting Scientist

Gladstone Institutes, San Francisco, CA

Collaborative research position at the prestigious Gladstone Institutes.

2013 - 2018

Bioengineering Department Affiliate

Department of Bioengineering, University of Illinois-Chicago

Maintained academic affiliation with the Bioengineering Department.

2014 - 2015

Research Associate - Software Developer & Bioinformatics Specialist

dictyBase, Center for Genetic Medicine, Northwestern University

Redesigned and implemented the new dictyBase interface; led Agile-oriented development; managed biological databases and Oracle→PostgreSQL data migration; contributed to successful NIH renewals (dictyBase & Dicty Stock Center).

2013 - 2015

Visiting Research Associate

Shannon Hackett's Lab, Bird Division, The Field Museum of Natural History

Research collaboration in evolutionary biology and computational approaches.

2013 - 2014

Visiting Instructor

Eisenberg Lab, Dept. of Molecular Biophysics & Physiology, Rush University Medical Center

Studied polarity patterns in protein cores and links to active sites; used APBS to evaluate electrostatic properties; taught BIOE480 (Intro to Bioinformatics) and BIOE481 (Bioinformatics Lab).

2006 - 2013

PhD Graduate Student

Prof. Jie Liang's Lab, Dept. of Bioengineering, University of Illinois at Chicago

Developed physicochemical metrics for protein cavities and their functional links; created a computational method predicting lysine carboxylation (PreLysCar; also at CCP4) revealing broader prevalence; analyzed enzyme structure–function with metabolite concentrations and fluxes.

2003 - 2005

Research Assistant

Proteomics Unit & Department of Microbiology II, Universidad Complutense de Madrid – Parque Científico de Madrid

Research in proteomics and microbiology at the Madrid Science Park.

1998 - 2000

Research Assistant

Department of Microbiology I, Faculty of Medicine, Universidad Complutense de Madrid

Early research experience in microbiology and medical sciences.

Publications

📄 Check my preprints from bioRxiv and medRxiv

Peer-reviewed Journals (0)

Other Publications

Abstracts & Communications (0)

Books (0)

Popular Science Articles (0)

PhD Thesis

Computing

Bioinformatics Tools

  • OmicsPipelines — Conceived, directed, and supervised a user-friendly cloud-native platform enabling genomic, transcriptomic, and proteomic analyses without deep cloud expertise.
  • R package: artMS — Analytical R Tools for Mass Spectrometry. GitHub · Bioconductor
  • R package: MotrpacBicQC — Primary/secondary QC for MoTrPAC CAS datasets (MoTrPAC).
  • CAS→BIC Data Transfer QC Monitor — Real-time QC monitor of datasets submitted and processed by the MoTrPAC BIC.
  • bioNeNa — The FluOMICS bioNetwork Navigator for exploring large-scale datasets (currently unfunded and limited).
  • TB OMICS EXPLORER — Multi-omics profiling of primary macrophages during Mycobacterium tuberculosis infection (publication).
  • MIDTOD — Metabolite Identification Through Orthogonal Datasets (under development).
  • PreLysCar — Predictor of Lysine Carboxylation; also available within CCP4.
  • bbTM-ST — Beta-barrel TransMembrane Search Tool.

Skills

  • Operating Systems: Unix/Linux, macOS. Virtual computing: Docker, Vagrant.
  • Cloud Computing: Google Cloud Platform (GCP), AWS, Azure.
  • Pipeline/Workflow: WDL, Cromwell.
  • Programming: R (Shiny), Python, Perl, Bash, HTML/CSS/JS, Ruby on Rails, PHP, Matlab, C/C++, Java.
  • Bioinformatics Packages: Sequence (BLAST, MEME-MAST, ClustalW, T-Coffee, HMMER, HHsearch); structures (PyMOL, VMD, RasMol, Dino, SPDBV); MD (NAMD); interactions (MiNT, Osprey); genomics (MAKER, FastQC, ALLPATHS-LG, Circos, GeneMark, QIIME, Galaxy).
  • Databases: PostgreSQL, MySQL, SQL; GMOD Chado schema; NoSQL: Neo4j; search: Elasticsearch.
  • GMOD Tools: JBrowse, WebApollo, InterMine.
  • Others: Git/GitHub; design (Photoshop); statistics (R, SAS, SPSS).

Web Design & Development

  • 2017 — Krogan Lab, UCSF, San Francisco, CA
  • 2016 — FluOMICS, UCSF, San Francisco, CA
  • 2016 — New dictyBase, Northwestern University, Chicago, IL
  • 2015 — dictyMeeting 2015, Northwestern University, Chicago, IL
  • 2003 — Proteomics Unit, UCM-PCM, Madrid, Spain
  • 2002, 2005 — Spanish Network of Apoptosis (APORED), CIB-CSIC

Software Administration

  • 2002–2005 — Spanish Network of Apoptosis (APORED), CIB-CSIC — Administrator of BSCW workspace; co-admin of APORED email list; admin of Apobecarios list; website updates.

Teaching

Workshop Instructor

  • Association of Biomolecular Resource Facilities (ABRF) — March 2021
    Using R in Proteomics Core: from QC to Data Analysis — Course page · Slides

Courses as Instructor

  • Department of Bioengineering, University of Illinois at Chicago
    Fall 2010 — BIOE480: Introduction to Bioinformatics
  • Department of Bioengineering, University of Illinois at Chicago
    Fall 2012 — BIOE481: Bioinformatics Laboratory

Courses as Teaching Assistant

  • Department of Bioengineering, University of Illinois at Chicago
    Spring 2013 — BIOE250: Clinical Problems in Bioengineering
  • Department of Bioengineering, University of Illinois at Chicago
    Fall 2012 — BIOE481: Bioinformatics Laboratory
  • Department of Bioengineering, University of Illinois at Chicago
    Fall 2010, 2012 — BIOE480: Introduction to Bioinformatics
  • Department of Bioengineering, University of Illinois at Chicago
    Spring 2007 — BIOE455: Intro to Cell and Tissue Engineering
  • Department of Bioengineering, University of Illinois at Chicago
    Fall 2006 — BIOE240: Modeling Physiological Data & Systems

Awards & Recognition

Google Cloud Research Innovators Program Participant

2024

Google Cloud

  • Selected as one of 23 researchers for innovative ideas and commitment to solving challenging problems using AI and cloud computing.
  • Collaborating with experts and peers to accelerate groundbreaking projects.
  • Gained access to Google Cloud technology, cloud credits, and networking opportunities.

U19AI135972: "FluOMICS, The Next Generation"

2018–2022

NIH/NIAID

Co-PI Modeling Core. Co-PI Data Management and Bioinformatics Core (DMBC).

Pilot Project (U19AI106754): "Development of a web-based computational tool for integrating and navigating systems biology data and models"

2017–2018

NIH/NIAID

Principal Investigator.

Beca Talentia Excellence Grant

2008–2010

Regional Ministry for Innovation, Science and Enterprise, Junta de Andalucía, Spain

Get In Touch

Connect With Me

I'm always interested in discussing new research opportunities, collaborations, or bioinformatics challenges.

🏢 Stanford Profile 💻 GitHub