Curriculum Vitae

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Andrew B. Caldwell

Research Scientist, Bioinformatics and Systems Biology

UC San Diego

Subramaniam Lab, Department of Bioengineering

9500 Gilman Drive

La Jolla, CA 92093

Systems Biologist working on neurodevelopment and neurodegeneration focusing on experimental methods in sequencing, bioinformatics data processing and analysis, chromatin dynamics, -omics data integration, and systems-level mechanistic disease models.

Degrees

PhD in Biochemistry, UC San Diego, 2014
Towards a Quantitative Understanding of TNF's Signaling Functions

MS in Biochemistry, UC San Diego, 2010

BS in Chemistry and Biochemistry, Seattle Pacific University, 2008

Publications

  • Valdes P*, Caldwell AB*, Qing L, Fitzgerald MQ, Ramachandran S, Karch CM, Dominantly Inherited Alzheimer Network (DIAN), Galasko DR, Yuan SH, Wagner SL, Subramaniam S. 2025. Integrative multiomics reveals common endotypes across PSEN1, PSEN2, and APP mutations in familial Alzheimer's disease. Alzheimer's Research & Therapy 17,5. Valdes et al. 2025
  • Valdes P, Henry KW, Fitzgerald MQ, Muralidharan K, Caldwell AB, Ramachandran S, Goldstein LSB, Mobley WC, Galasko DR, Subramaniam S. 2023. Limitations of the human iPSC-derived neuron model for early-onset Alzheimer's disease. Molecular Brain 16,75. Valdes et al. 2023
  • Patel AO, Caldwell AB, Ramachandran S, Subramaniam S. 2023. Endotype Characterization Reveals Mechanistic Differences Across Brain Regions in Sporadic Alzheimer's Disease. Journal of Alzheimer's Disease Reports 7, 1:957-972. Patel et al. 2023
  • Dwivedi I, Caldwell AB*, Zhou D*, Wu W, Subramaniam S, Haddad GG. 2023. Methadone alters transcriptional programs associated with synapse formation in human cortical organoids. Translational Psychiatry 13, 151. Dwivedi et al. 2023
  • Caldwell AB, Anantharaman BG, Ramachandran S, Nguyen P, Liu Q, Trinh I, Galasko D, Desplats PA, Wagner SL, Subramaniam S. 2022. Transcriptomic profiling of sporadic Alzheimer's disease patients. Molecular Brain 15:83. Caldwell et al. 2022
  • Azad P, Caldwell AB, Ramachandran S, Spann NJ, Akbari A, Villafuerte FC, Bermudez D, Zhao H, Poulson O, Zhou D, Bafna V, Subramaniam S, Haddad GG. 2022. ARID1B, a molecular suppressor of erythropoiesis, is essential for the prevention of Monge's disease. Experimental & Molecular Medicine 54:777–787. Azad et al. 2022
  • Caldwell AB, Qing L, Zhang C, Schroth GP, Galasko DR, Rynearson KD, Tanzi RE, Yuan SH, Wagner SL, Subramaniam S. 2022. Endotype reversal as a novel strategy for screening drugs targeting familial Alzheimer's disease. Alzheimer's & Dementia, alz12553. Caldwell et al. 2022
  • Caldwell AB, Qing L, Schroth GP, Galasko DR, Yuan SH, Wagner SL, Subramaniam S. 2020. Dedifferentiation and neuronal repression define familial Alzheimer's disease. Science Advances 6, 46, eaba5933. Caldwell et al. 2020
  • Caldwell AB, Cheng Z, Vargas JA, Birnbaum H, Hoffmann A. 2014. Network dynamics determine the autocrine and paracrine signaling functions of TNF. Genes & Development 28:2120-2133. Caldwell et al. 2014
  • Culpepper DJ, Maddox MK, Caldwell AB, McFarland BJ. 2011. Systematic mutation and thermodynamic analysis of central tyrosine pairs in polyspecific NKG2D receptor interactions. Molecular Immunology 48:516-523. Culpepper et al. 2011

Software

  • Choudhary KS, Caldwell AB, Subramaniam S. 2021. DEGenR: An R Shiny app for differential gene expression and enrichment analysis (Version v1.0.0). Zenodo doi.org/10.5281/zenodo.4815134. DEGenR v1.0.0

Reviews

  • Shih VF, Tsui R, Caldwell AB, Hoffmann A. 2011. A single NFκB system for both canonical and non-canonical signaling. Cell Research 21: 86-102. Shih et al. 2011

Interested in collaborating with me?

I'm always open to discussing new projects, research collaborations, or interesting opportunities.

Let's talk