Selected publications

1997 · Inorganica Chimica Acta

A new strontium-copper ethylene glycol complex: synthesis and structure of [Sr(C2H6O2)5][Cu(C2H4O2)2]·C2H6O2

Alexander R. Pico; Carol S. Houk; Timothy J.R. Weakley; Catherine J. Page.

Inorganica Chimica Acta 258(2): 155-160 (1997).

A synthesis-and-structure study of a strontium–copper ethylene glycol complex. An early publication connecting chemical preparation with structural characterization.

This paper concerns a chemical complex; it is not presented here as a demonstration of superconductivity.

1999 · Neurocomputing

Local cortical injections of glutamate and noradrenaline alter high-frequency (245Hz) neuronal activity in rat cortex

Brent A Field; Alexander R Pico; Richard T Marrocco.

Neurocomputing 26-27: 123-130 (1999).

A study of how local cortical injections of glutamate and noradrenaline alter high-frequency neuronal activity in rat cortex. It connects chemical perturbation with the analysis of neural activity.

2001 · Neuron

Structure of the RCK Domain from the E. coli K+ Channel and Demonstration of Its Presence in the Human BK Channel

Youxing Jiang; Alexander Pico; Martine Cadene; Brian T. Chait; Roderick MacKinnon.

Neuron 29(3): 593-601 (2001).

X-ray crystallography, structure-based sequence alignment, and mutational analysis connect a bacterial potassium-channel regulatory domain to the gating machinery of the human BK channel.

2010 · Science

Structure of the Human BK Channel Ca 2+ -Activation Apparatus at 3.0 Å Resolution

Peng Yuan; Manuel D. Leonetti; Alexander R. Pico; Yichun Hsiung; Roderick MacKinnon.

Science 329(5988): 182-186 (2010).

A structural study of the human BK channel’s calcium-activation apparatus. The work describes a gating ring and calcium-binding sites, linking molecular architecture to channel regulation.

2008 · PLoS Biology

WikiPathways: pathway editing for the people

Alexander R Pico; Thomas Kelder; Martijn P van Iersel; Kristina Hanspers; Bruce R Conklin; Chris Evelo.

PLoS Biology 6(7): e184 (2008).

Introduces a community-curated approach to biological pathways, combining a wiki model with graphical pathway editing. Connects open scientific infrastructure with a practical way to organize and share biological knowledge.

2010 · BMC Bioinformatics

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

Martijn P van Iersel; Alexander R Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina Hanspers; Bruce R Conklin; Chris T Evelo.

BMC Bioinformatics 11(1): 5 (2010).

Presents a shared interface for mapping gene, protein, and metabolite identifiers across different data services. The framework separates analysis tools from individual mapping providers, supporting data integration and multi-omics workflows.

2019 · Genome Biology

Cytoscape Automation: empowering workflow-based network analysis

David Otasek; John H. Morris; Jorge Bouças; Alexander R. Pico; Barry Demchak.

Genome Biology 20(1): 185 (2019).

Connects interactive network analysis with scripted Python and R workflows through standardized interfaces. A contribution to making scientific analysis more reproducible, scalable, and reusable.

2023 · BMC Genomics

Using published pathway figures in enrichment analysis and machine learning

Min-Gyoung Shin; Alexander R. Pico.

BMC Genomics 24(1): 713 (2023).

Explores how biological pathway figures from the literature can become a resource for enrichment analysis and machine learning. Includes case studies in cancer subtype and grade prediction, connecting scientific diagrams with computational analysis.

2015 · New England Journal of Medicine

Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors

Jeanette E. Eckel-Passow et al., including Alexander R. Pico.

New England Journal of Medicine 372(26): 2499-2508 (2015).

Groups gliomas using IDH mutations, TERT promoter mutations, and 1p/19q codeletion, then examines their relationships with clinical features, survival, and inherited variation. An example of connecting molecular classification with the diversity of brain tumors.

2020 · Journal of Virology

Shared Mechanisms Govern HIV Transcriptional Suppression in Circulating CD103+ and Gut CD4+ T Cells

Steven A. Yukl et al., including Alexander R. Pico.

Journal of Virology 95(2): e01331-20 (2020).

Compares viral transcription and host-cell gene expression in blood and gut T cells to investigate HIV latency. The work links tissue-associated immune-cell states with mechanisms that may help maintain persistent infection.

2024 · European Heart Journal

Incident heart failure in chronic kidney disease: proteomics informs biology and risk stratification

Ruth F Dubin et al., including Alexander R. Pico.

European Heart Journal 45(30): 2752-2767 (2024).

Uses large-scale circulating-protein measurements to investigate heart-failure risk in people with chronic kidney disease. Connects proteomics, biological pathways, and risk models across cardiovascular and renal disease.

2024 · Nature

Fibrin drives thromboinflammation and neuropathology in COVID-19

Jae Kyu Ryu et al., including Alexander R. Pico.

Nature 633(8031): 905-913 (2024).

Investigates how interactions between fibrin and the SARS-CoV-2 spike protein contribute to inflammation and neuronal injury. Connects blood clotting, immune activation, and neuropathology; experimental antibody findings are not presented as proven treatment benefits in people.

2024 · Cell Reports

Machine learning reveals prominent spontaneous behavioral changes and treatment efficacy in humanized and transgenic Alzheimer's disease models

Stephanie R. Miller et al., including Alexander R. Pico.

Cell Reports 43(11): 114870 (2024).

Applies machine-learning analysis of spontaneous mouse behavior to humanized and transgenic Alzheimer’s disease models. Links behavioral changes with neuroinflammation and evaluates intervention effects in these models—not clinical efficacy in people.