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Publications

[1]
K. Zhu et al., "TGFβ signaling mediates microglial resilience to spatiotemporally restricted myelin degeneration," Nature Neuroscience, 2026.
[2]
P. Rodin-Mörch et al., "A chromosome-level genome assembly of the European green toad (Bufotes viridis)," G3 : Genes, Genomes, Genetics, vol. 15, no. 3, 2025.
[3]
D. Lutgen et al., "A mosaic of modular variation at a single gene underpins convergent plumage coloration," Science, vol. 390, no. 6770, pp. 8005, 2025.
[4]
A. Venkat et al., "AAnet Resolves a Continuum of Spatially Localized Cell States to Unveil Intratumoral Heterogeneity," Cancer Discovery, vol. 15, no. 10, pp. 2139-2165, 2025.
[5]
J. Zhong et al., "adiposetissue.org : A knowledge portal integrating clinical and experimental data from human adipose tissue," Cell Metabolism, vol. 37, no. 3, pp. 566-569, 2025.
[6]
R. M. Buckley et al., "Analysis of canine gene constraint identifies new variants for orofacial clefts and stature," Genome Research, vol. 35, no. 5, pp. 1080-1093, 2025.
[7]
A. Tsyben et al., "Cell-intrinsic metabolic phenotypes identified in patients with glioblastoma, using mass spectrometry imaging of 13C-labelled glucose metabolism," Nature Metabolism, vol. 7, no. 5, 2025.
[8]
C. Fei et al., "Comparative Analysis of Salivary and Serum Inflammatory Mediator Profiles in Patients With Rheumatoid Arthritis and Periodontitis," Mediators of Inflammation, vol. 2025, no. 1, 2025.
[9]
T. Li et al., "Computational pathology annotation enhances the resolution and interpretation of breast cancer spatial transcriptomics data," npj Precision Oncology, vol. 9, no. 1, 2025.
[10]
A. Miraldo et al., "Data of the Insect Biome Atlas: a metabarcoding survey of the terrestrial arthropods of Sweden and Madagascar," Scientific Data, vol. 12, no. 1, 2025.
[11]
M. Zamboni et al., "Decoding Injury Responsive Enhancers In The Cns For Cell State Targeting," Glia, vol. 73, pp. E1268-E1268, 2025.
[12]
M. D. Luecken et al., "Defining and benchmarking open problems in single-cell analysis," Nature Biotechnology, vol. 43, no. 7, pp. 1035-1040, 2025.
[13]
B. E. Langer, C. Notredame and F. Bonath, "Empowering bioinformatics communities with Nextflow and nf-core," Genome Biology, vol. 26, no. 1, 2025.
[14]
S. Gudmundsson et al., "Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database," Nature Communications, vol. 16, no. 1, 2025.
[15]
Q. Deng et al., "Genetic Adaptation to Brackish Water and Spawning Season in European Cisco," Molecular Ecology, vol. 34, no. 20, 2025.
[16]
S. Kolmodin Dahlberg et al., "Hidden network preserved in Slide-tags data allows reference-free spatial reconstruction," Nature Communications, vol. 16, no. 1, 2025.
[17]
E. Iwaszkiewicz-Eggebrecht et al., "High-throughput biodiversity surveying sheds new light on the brightest of insect taxa," Proceedings of the Royal Society of London. Biological Sciences, vol. 292, no. 2046, 2025.
[18]
J. Freestone et al., "How to Train a Postprocessor for Tandem Mass Spectrometry Proteomics Database Search While Maintaining Control of the False Discovery Rate," Journal of Proteome Research, vol. 24, no. 5, pp. 2266-2279, 2025.
[19]
K. Mrozik, "Improving DNA barcode error handling accuracy in network-based spatial transcriptomics," , 2025.
[20]
N. Sharma et al., "In-depth patient-specific analysis of tumor heterogeneity in melanoma brain metastasis : Insights from spatial transcriptomics and multi-region bulk sequencing," Translational Oncology, vol. 59, 2025.
[21]
J. Gleeson et al., "Isoform-level profiling of m6A epitranscriptomic signatures in human brain," Science Advances, vol. 11, no. 32, 2025.
[22]
B. C. Brown et al., "Large-scale causal discovery using interventional data sheds light on gene network structure in k562 cells," Nature Communications, vol. 16, no. 1, 2025.
[23]
X. Hu et al., "Leveraging Disease Relevant Transcriptomes From TOPMed LTRC Improves Polygenic Transcriptome Risk Prediction for COPD," American Journal of Respiratory and Critical Care Medicine, vol. 211, 2025.
[24]
F. Li et al., "LIPA, a risk locus for coronary artery disease : decoding the variant-to-function relationship," European Heart Journal, vol. 46, no. 48, pp. 5273-5288, 2025.
[25]
R. De Paoli-Iseppi et al., "Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain," Genome Biology, vol. 26, no. 1, 2025.
[26]
D. P. R. Herlemann et al., "Low impact of Zostera marina meadows on sediment and water microbiota under brackish conditions," Environmental Microbiome, vol. 20, no. 1, 2025.
[27]
P. Truong, "Machine Learning Models in Proteomics and Phylogenetics," Doctoral thesis Stockholm : KTH Royal Institute of Technology, TRITA-CBH-FOU, 2025:18, 2025.
[28]
B. A. Emery et al., "MEA-seqX : High-Resolution Profiling of Large-Scale Electrophysiological and Transcriptional Network Dynamics," Advanced Science, vol. 12, no. 20, 2025.
[29]
P. Bjärterot et al., "Met-ID: An Open-Source Software for Comprehensive Annotation of Multiple On-Tissue Chemical Modifications in MALDI-MSI," Analytical Chemistry, vol. 97, no. 16, pp. 9033-9041, 2025.
[30]
Y. Perez-Riverol et al., "Open-Source and FAIR Research Software for Proteomics," Journal of Proteome Research, vol. 24, no. 5, pp. 2222-2234, 2025.
[31]
S. M. Salas et al., "Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows," Nature Methods, vol. 22, no. 4, pp. 813-823, 2025.
[32]
E. L. Ivansson et al., "Oral contraceptive use increases bone density and reduces the risk of osteoporosis," European Journal of Epidemiology, vol. 40, no. 9, pp. 1123-1131, 2025.
[33]
T. Cheng et al., "Pain in idiopathic scoliosis not associated with known genetic variants for pain," Pain Reports, vol. 10, no. 1, 2025.
[34]
J. Lapin et al., "Pairwise Attention : Leveraging Mass Differences to Enhance De Novo Sequencing of Mass Spectra," Journal of Proteome Research, 2025.
[35]
N. Bhalla, "Patterns of Life : Advancing Spatial Omics for a Better Understanding of Metabolic Tissues," Doctoral thesis Stockholm : KTH Royal Institute of Technology, TRITA-CBH-FOU, 2025:11, 2025.
[36]
A. Kampe et al., "Precision Omics Initiative Sweden (PROMISE) will integrate research with healthcare," Nature Medicine, 2025.
[37]
J. Vasicek et al., "ProHap Explorer: Visualizing Haplotypes in Proteogenomic Datasets," IEEE Computer Graphics and Applications, 2025.
[38]
R. L. P. Santos-Cortez et al., "Rare and low-frequency variants in families with otitis media," Journal of Molecular Medicine, vol. 103, no. 5, pp. 559-570, 2025.
[39]
P. Rentzsch et al., "Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes," Genome Research, vol. 35, no. 10, pp. 2316-2325, 2025.
[40]
K. Lavrichenko et al., "Recommendations for bioinformatics in clinical practice," Genome Medicine, vol. 17, no. 1, 2025.
[41]
D. Schwochow et al., "RNA-seq analysis identifies key genes enhancing hoof strength to withstand barefoot racing in Standardbred trotters," BMC Genomics, vol. 26, no. 1, 2025.
[42]
Y. A. Choi et al., "Secure and federated quantitative trait loci mapping with privateQTL," Cell Genomics, vol. 5, no. 2, 2025.
[43]
D. Schulte et al., "Simultaneous polyclonal antibody sequencing and epitope mapping by cryo electron microscopy and mass spectrometry," eLIFE, vol. 14, 2025.
[44]
E. Lázár and J. Lundeberg, "Spatial architecture of development and disease," Nature reviews genetics, 2025.
[45]
A. B. Firsova et al., "Spatial single-cell atlas reveals regional variations in healthy and diseased human lung," Nature Communications, vol. 16, no. 1, 2025.
[46]
S. Saarenpää, "Spatial Transcriptomics across kingdoms," Doctoral thesis Stockholm, Sweden : KTH Royal Institute of Technology, TRITA-CBH-FOU, 2025:5, 2025.
[47]
D. L. Croteau et al., "Spatial transcriptomics reveals an unexpected impact of tau and tau pathology on the expression of transthyretin," Frontiers in Aging Neuroscience, vol. 17, 2025.
[48]
E. Lázár et al., "Spatiotemporal gene expression and cellular dynamics of the developing human heart," Nature Genetics, vol. 57, no. 11, pp. 2756-2771, 2025.
[49]
M. Minaeva et al., "Specifying cellular context of transcription factor regulons for exploring context-specific gene regulation programs," NAR Genomics and Bioinformatics, vol. 7, no. 1, 2025.
[50]
S. Gkouma et al., "Standalone single- and bi-layered human skin 3D models supported by recombinant silk feature native spatial organization," Biofabrication, vol. 17, no. 1, 2025.