Gene regulatory network of human GM-CSF secreting T helper cells

Authors: S. Elias, A. Schmidt, D. Gomez-Cabrero, J. Tegner
T helper cells Gene regulatory network

STATegra: a comprehensive multi-omics dataset of B-cell differentiation in mouse

Authors: D. Gomez-Cabreroc, S. Tarazona, I. Ferreirós-Vidal, R. Ramirez, A. Schmidt, T. Reijmers, (...), J. Tegner, A. Conesa
Mouse Chromatin structure

On the prediction of protein abundance from RNA

Authors: R. Magnusson, O. Rundquist, M. Kim, S. Hellberg, C. Na, M. Benson, D. Gomez-Cabrero, I. Kochum, J. Tegner, at al.
Protein abundance RNA Complex diseases

Deriving Disease Modules from the Compressed Transcriptional Space Embedded in a Deep Auto-encoder

Authors: S. Dwivedi, A. Tjarnberg, J. Tegner, M. Gustafsson
Disease modules Deep Auto-encoder Disease-related genes

TcellSubC: an atlas of the subcellular proteome of human T cells

Authors: R. Joshi, C. Stadler, R. Lehmann, J. Lehtiö, J. Tegner, A. Schmidt, M. Vesterlund
TcellSubC Subcellular Proteome Human T cells

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

Authors: M. Menden, D. Wang, M. Mason, B. Sjalai, AstraZeneca-Sanger Drug Combination DREAM Consortium, at al.
Cancer research Drug antagonism Pharmacogenomic screen

Associations of Plasma 3-Methylhistidine with Frailty Status in French Cohorts of the FRAILOMIC Initiative

Authors: B. Kochlik, W. Stuetz, K. Peres, C. Feart, J. Tegner, L. Rodriguez-Manãs, T. Grune, D. Weber
Frailty Aging Methylhistidine Biomarkers Muscle protein turnover

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

Authors: S. Fernandes, H. Morikawa, E. Ewing, S. Ruhrmann, R. Joshi, V. Lagani, N. Karathanasis, M. Khademi, N. Planell, A. Schmidt, I. Tsamardinos, T. Olsson, F. Piehl, I. Kochum, M. Jagodic, J. Tegner, D. Gomez-Cabrero
T cells Multiple sclerosis RNA-seq

Exhaustion of CD4+ T-cells mediated by the Kynurenine Pathway in Melanoma

Authors: S.R. Pour, H. Morikawa, N. Kiani, M. Yang, A. Azimi, G. Shafi, M. Shang, R. Baumgartner, D. Ketelhuth, M. Kamleh, C.E. Weelock, A. Lundqvist, J. Hansson, J. Tegner
CD4+ T cells Melanoma Kynurenine Pathway

DNA methylation changes in brains from multiple sclerosis patients

Authors: L. Kular, M. Needhamsen, M. Zeitelhofer-Adzemovich, T. Kramarova, D. Gomez-Cabrero, E. Ewing, E. Picket, J. Tegner, S. Beck, F. Piehl, L. Brundin, M. Jagodic
DNA methylation Multiple sclerosis

Paired ATAC Seq and RNA Seq in blood derived CD4, CD8, CD14 and CD19 cells of MS patients and healthy controls

Authors: S.J. Fernandes, M. Eriksson, M.Khademi, T. Olsson, D. Gomez-Cabrero, I. Kockum, J. Tegner
Multiple sclerosis Immune cells ATAC Seq RNA sequencing (RNA-Seq) DNA methylation Omics integration

Algorithmic probability-guided supervised Machine Learning on non-differentiable spaces

Authors: S. Hernández-Orozco, H. Zenil, J. Riendel, A. Uccello, N. Kiani, J. Tegner

Challenges in the multivariate analysis of mass cytometry data: the effect of randomization

Authors: G. Papoutsoglou, V. Lagani, A. Schmidt, K. Tsirlis, D. Gomez-Cabrero, J. Tegner, I. Tsamardinos
Mass cytometry Pre‐processing High dimensional Data analysis Randomization Clustering algorithms

Neuronal methylation reveals CREB-asociated neuro-axonal impairment in Multiple Sclerosis

Authors: L. Kular Et Al.
Multiple sclerosis Neurons DNA methylation DNA hydroxymethylation Axonal guidance Synaptic plasticity CREB Neurodegeneration

The thermodynamics of network coding, and an algorithmic refinement of the principle of maximum entropy

Authors: H. Zenil, N.A. Kiani, J. Tegnér
Second law of thermodynamics Reprogrammability Algorithmic complexity Generative mechanisms Deterministic systems Algorithmic randomness

Causal deconvolution by algorithmic generative models

Authors: H. Zenil, N. Kiani, A.A. Zea, J. Tegnér
Algorithmic generative models Algorithmic probability Algorithmic framework

Combining evidence from four immune cell types identifies DNA methylation patterns that implicate functionally distinct pathways during Multiple Sclerosis progression

Authors: E. Ewing, L. Kular, S.J. Fernandes, N. Karathanasis, V. Lagani, S. Ruhrmann, I. Tsamardinos, J. Tegner, F. Piehl, D. Gomez-Cabrero, M. Jagodic
450 K DNA methylation EPIC Epigenetics Immune cells Multiple sclerosis

Feedforward regulation of Myc coordinates lineage-speciifc with housekeeping gene expression during B cell progenitor cell differentiation

Authors: I. Ferreirós-Vidal, T. Carroll, (...) J. Tegner*, M. Merkenschlager*, D. Gomez-Cabrero
Cell differentiation B cells Gene expression Gene regulation Transcription factors Cell metabolism

Phosphatase inhibitor PPP1R11 modulates resistance of human T cells toward Treg‐mediated suppression of cytokine expression

Authors: R.N. Joshi, S.J. Fernandes, M.-M. Shang, N.A. Kiani, D. Gomez‐Cabrero, J. Tegnér, A. Schmidt
CD4 T cell T cell resistance Immune suppression Immunotherapy Phosphatase Regulatory T cell

MAPK pathways and B cells overactivation in multiple sclerosis revealed by phospoproteomics and genomic analysis

Authors: E. Kotelnikova, N.A. Kiani, (...), J. Tegner, P. Villoslada
Multiple sclerosis Phosphoproteomics Signaling pathways B cells Autoimmunity

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