Publications by authors named "Jesper Tegner"

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An integrative analysis reveals coordinated reprogramming of the epigenome and the transcriptome in human skeletal muscle after training.
Maléne E Lindholm, Francesco Marabita, David Gomez-Cabrero, Helene Rundqvist, Tomas J Ekström, Jesper Tegnér, Carl Johan Sundberg

December 2014

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Multimodal foundation transformer models for multiscale genomics.
Sumeer Ahmad Khan, Xabier Martínez-de-Morentin, Abdel Rahman Alsabbagh, Alberto Maillo, Vincenzo Lagani, Jesper Tegner

Nat Methods· December 2025

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Leveraging network motifs to improve artificial neural networks.
Haoling Zhang, Chao-Han Huck Yang, Hector Zenil, Pin-Yu Chen, Yue Shen

Nat Commun· December 2025

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Characterization of the bone marrow architecture of multiple myeloma using spatial transcriptomics.
Emma Muiños-Lopez, Ana Rosa Lopez-Perez, Laura Sudupe, Amaia Vilas-Zornoza, Sarai Sarvide, Jesper Tegner

Commun Biol· November 2025

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Uncovering the regulatory landscape of early human B cell lymphopoiesis and its implications in the pathogenesis of B-ALL.
Núria Planell, Xabier Martínez-de-Morentin, Daniel Mouzo, David Lara-Astiaso, Amaia Vilas-Zornoza, Jesper Tegner

Sci Adv· October 2025

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GeneSetCluster 2.0: a comprehensive toolset for summarizing and integrating gene-sets analysis.
Asier Ortega-Legarreta, Alberto Maillo, Daniel Mouzo, Ana Rosa López-Pérez, Lara Kular, Jesper Tegner

BMC Bioinformatics· August 2025

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NLRP3-mediated glutaminolysis controls microglial phagocytosis to promote Alzheimer's disease progression.
Róisín M McManus, Max P Komes, Angelika Griep, Francesco Santarelli, Stephanie Schwartz

Immunity· February 2025

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Benchmarking cross-species single-cell RNA-seq data integration methods: towards a cell type tree of life.
Huawen Zhong, Wenkai Han, David Gomez-Cabrero, Jesper Tegner, Xin Gao

Nucleic Acids Res· January 2025

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Reviewability and supportability: New complementary principles to empower research software practices.
Haoling Zhang, Alberto Maillo, Sumeer Ahmad Khan, Xabier Martínez-de-Morentin, Robert Lehmann

Comput Struct Biotechnol J· December 2024

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ClustAll: An R package for patient stratification in complex diseases.
Asier Ortega-Legarreta, Sara Palomino-Echeverria, Estefania Huergo, Vincenzo Lagani, Narsis A Kiani, Jesper Tegner

PLoS Comput Biol· December 2024

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A comparative analysis of blastoid models through single-cell transcriptomics.
Ali Balubaid, Samhan Alsolami, Narsis A Kiani, David Gomez-Cabrero, Mo Li, Jesper Tegner

iScience· November 2024

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Latent space arithmetic on data embeddings from healthy multi-tissue human RNA-seq decodes disease modules.
Hendrik A de Weerd, Dimitri Guala, Mika Gustafsson, Jane Synnergren, Jesper Tegnér

Patterns (N Y)· November 2024

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A robust clustering strategy for stratification unveils unique patient subgroups in acutely decompensated cirrhosis.
Sara Palomino-Echeverria, Estefania Huergo, Asier Ortega-Legarreta, Eva M Uson Raposo, Ferran Aguilar, Jesper Tegner

J Transl Med· June 2024

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Generation of iPSC lines (KAIMRCi003A, KAIMRCi003B) from a Saudi patient with Dravet syndrome carrying homozygous mutation in the CPLX1 gene and heterozygous mutation in SCN9A.
Maryam Alowaysi, Mohammad Al-Shehri, Amani Badkok, Hanouf Attas, Doaa Aboalola, Jesper Tegner

Hum Cell· March 2024

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HLA-based banking of induced pluripotent stem cells in Saudi Arabia.
Maryam Alowaysi, Robert Lehmann, Mohammad Al-Shehri, Moayad Baadhaim, Hajar Alzahrani, Jesper Tegner

Stem Cell Res Ther· December 2023

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Generation of myoglobin (MB)-knockout human embryonic stem cell (hESC) line (KAIMRCe002-A-1S) using CRISPR/Cas9 technology.
Maryam Alowaysi, Mohammad Al-Shehri, Moayad Baadhaim, Hajar AlZahrani, Doaa Aboalola, Jesper Tegner

Stem Cell Res· September 2023

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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.
Alexandre Xavier, Vicki E Maltby, Ewoud Ewing, Maria Pia Campagna, Sean M Burnard, Jesper N Tegner

Int J Mol Sci· August 2023

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scAEGAN: Unification of single-cell genomics data by adversarial learning of latent space correspondences.
Sumeer Ahmad Khan, Robert Lehmann, Xabier Martinez-de-Morentin, Alberto Maillo, Vincenzo Lagani, Jesper Tegner

PLoS One· February 2023

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Approximations of algorithmic and structural complexity validate cognitive-behavioral experimental results.
Hector Zenil, James A R Marshall, Jesper Tegnér

Front Comput Neurosci· January 2023

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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.
Rasmus Magnusson, Olof Rundquist, Min Jung Kim, Sandra Hellberg, Chan Hyun Na

Front Mol Biosci· August 2022

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Data-driven bioinformatics to disentangle cells within a tissue microenvironment.
Jesper N Tegner, David Gomez-Cabrero

Trends Cell Biol· June 2022

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Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.
Jin Ye, Isabel A Calvo, Itziar Cenzano, Amaia Vilas, Xabier Martinez-de-Morentin, Jesper N Tegner

iScience· May 2022

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Deep neural network prediction of genome-wide transcriptome signatures - beyond the Black-box.
Rasmus Magnusson, Jesper N Tegnér, Mika Gustafsson

NPJ Syst Biol Appl· February 2022

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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.
Szabolcs Éliás, Angelika Schmidt, David Gomez-Cabrero, Jesper Tegnér

J Immunol Res· December 2021

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DNA Transposon Expansion is Associated with Genome Size Increase in Mudminnows.
Robert Lehmann, Aleš Kovařík, Konrad Ocalewicz, Lech Kirtiklis, Andrea Zuccolo, Jesper N Tegner

Genome Biol Evol· October 2021

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Deep characterization of paired chromatin and transcriptomes in four immune cell types from multiple sclerosis patients.
Sunjay Jude Fernandes, Matilda Ericsson, Mohsen Khademi, Maja Jagodic, Tomas Olsson

Epigenomics· October 2021

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