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Algorithmic Information Dynamics: A Computational Approach to Causality with Applications to Living Systems

Zenil, Hector

2023

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Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis

Proceedings of the National Academy of Sciences - PNAS, 2017-02, Vol.114 (9), p.E1678-E1687

2017

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Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box

NPJ systems biology and applications, 2022-02, Vol.8 (1), p.9-9, Article 9

2022

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RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases

Frontiers in molecular biosciences, 2022-08, Vol.9, p.916128-916128

2022

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Computational disease modeling - fact or fiction?

BMC systems biology, 2009-06, Vol.3 (1), p.56-56, Article 56

2009

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DNA Methylation Signatures of Multiple Sclerosis Occur Independently of Known Genetic Risk and Are Primarily Attributed to B Cells and Monocytes

International journal of molecular sciences, 2023-08, Vol.24 (16), p.12576

2023

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Data-driven bioinformatics to disentangle cells within a tissue microenvironment

Trends in cell biology, 2022-06, Vol.32 (6), p.467-469

2022

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Translating single-cell genomics into cell types

Nature machine intelligence, 2023-01, Vol.5 (1), p.11-12

Tegner, Jesper N.

2023

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Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation

iScience, 2022-05, Vol.25 (5), p.104225, Article 104225

2022

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DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows

Genome biology and evolution, 2021-10, Vol.13 (10)

2021

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Evolving Neural Networks through a Reverse Encoding Tree

2020 IEEE Congress on Evolutionary Computation (CEC), 2020, p.1-10

2020

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A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

Entropy (Basel, Switzerland), 2018-08, Vol.20 (8), p.605

2018

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A Review of Graph and Network Complexity from an Algorithmic Information Perspective

Entropy (Basel, Switzerland), 2018-07, Vol.20 (8), p.551

2018

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The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation

Scientific reports, 2015-10, Vol.5 (1), p.15029-15029, Article 15029

2015

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Causal deconvolution by algorithmic generative models

Nature machine intelligence, 2019-01, Vol.1 (1), p.58-66

2019

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Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

Journal of autoimmunity, 2013-03, Vol.41, p.6-16

2013

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Low-algorithmic-complexity entropy-deceiving graphs

Physical review. E, 2017-07, Vol.96 (1-1), p.012308-012308, Article 012308

2017

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Dynamics and heterogeneity of brain damage in multiple sclerosis

PLoS computational biology, 2017-10, Vol.13 (10), p.e1005757-e1005757

2017

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Methods of information theory and algorithmic complexity for network biology

Seminars in cell & developmental biology, 2016-03, Vol.51, p.32-43

2016

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The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

Entropy (Basel, Switzerland), 2019-06, Vol.21 (6), p.560

2019

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Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients

Scientific reports, 2019-08, Vol.9 (1), p.11996, Article 11996

2019

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TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells

Frontiers in immunology, 2019-11, Vol.10, p.2708-2708

2019

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Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

BMC biology, 2018-05, Vol.16 (1), p.47-47, Article 47

2018

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Algorithmic Probability-Guided Machine Learning on Non-Differentiable Spaces

Frontiers in artificial intelligence, 2021-01, Vol.3, p.567356-567356

2021

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Human macrophages induce CD4+Foxp3+ regulatory T cells via binding and re‐release of TGF‐β

Immunology and cell biology, 2016-09, Vol.94 (8), p.747-762

2016

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Algorithmic Information Dynamics: A Computational Approach to Causality with Applications to Living Systems

Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis

Deep neural network prediction of genome-wide transcriptome signatures – beyond the Black-box

RNA-sequencing and mass-spectrometry proteomic time-series analysis of T-cell differentiation identified multiple splice variants models that predicted validated protein biomarkers in inflammatory diseases

Computational disease modeling - fact or fiction?

DNA Methylation Signatures of Multiple Sclerosis Occur Independently of Known Genetic Risk and Are Primarily Attributed to B Cells and Monocytes

Data-driven bioinformatics to disentangle cells within a tissue microenvironment

Translating single-cell genomics into cell types

Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation

DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows

Evolving Neural Networks through a Reverse Encoding Tree

A Decomposition Method for Global Evaluation of Shannon Entropy and Local Estimations of Algorithmic Complexity

A Review of Graph and Network Complexity from an Algorithmic Information Perspective

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation

Causal deconvolution by algorithmic generative models

Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression

Low-algorithmic-complexity entropy-deceiving graphs

Dynamics and heterogeneity of brain damage in multiple sclerosis

Methods of information theory and algorithmic complexity for network biology

The Thermodynamics of Network Coding, and an Algorithmic Refinement of the Principle of Maximum Entropy

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients

TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3

Algorithmic Probability-Guided Machine Learning on Non-Differentiable Spaces

Human macrophages induce CD4+Foxp3+ regulatory T cells via binding and re‐release of TGF‐β

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