All Stories

  1. Cancer-associated fibroblast signature and SMAD4 mutation in resistance to adjuvant chemotherapy in stage III colon cancer patients

    Article • European Journal of Cancer, March 2026, Elsevier

    Dr. Sanne Abeln

  2. Beyond olfaction: New insights into human odorant binding proteins

    Article • Protein Science, January 2026, Wiley

    Dr. Sanne Abeln

  3. Distinct cerebrospinal fluid proteomic signatures define clinicopathological subtypes of sporadic Creutzfeldt-Jakob disease and predict patient survival

    Article • Acta Neuropathologica Communications, December 2025, Springer Science + Business Media

    Dr. Sanne Abeln

  4. Explainable AI in healthcare: to explain, to predict, or to describe?

    Article • Diagnostic and Prognostic Research, December 2025, Springer Science + Business Media

    Dr. Sanne Abeln

  5. PLM-eXplain: divide and conquer the protein embedding space

    Article • Bioinformatics, November 2025, Oxford University Press (OUP)

    Dr. Sanne Abeln

  6. Disentangled and Interpretable Multimodal Attention Fusion for Cancer Survival Prediction

    Article • September 2025, Springer Science + Business Media

    Dr. Sanne Abeln

  7. Condition-dependent, amorphous protein agglomerates control cytoplasmic rheology

    Article • June 2025, openRxiv

    Dr. Sanne Abeln

  8. Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data

    Article • PLoS Computational Biology, May 2025, PLOS

    Dr. Sanne Abeln

  9. Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers

    Article • npj Precision Oncology, May 2025, Springer Science + Business Media

    Dr. Sanne Abeln

  10. FAIR data for optical tweezers experiments

    Article • Biophysical Journal, April 2025, Elsevier

    Dr. Sanne Abeln

  11. Data‐driven evaluation of suitable immunogens for improved antibody selection

    Article • Protein Science, March 2025, Wiley

    Dr. Sanne Abeln

  12. Neurofilament Light Chain under the Lens of Structural Mass Spectrometry

    Article • ACS Chemical Neuroscience, January 2025, American Chemical Society (ACS)

    Dr. Sanne Abeln

  13. Probing the effect of the disordered flank regions on amyloid fibril growth and proliferation

    Article • RSC Advances, January 2025, Royal Society of Chemistry

    Dr. Sanne Abeln

  14. Tumor break load quantitates structural variant-associated genomic instability with biological and clinical relevance across cancers

    Article • December 2024, Cold Spring Harbor Laboratory Press

    Dr. Sanne Abeln

  15. Odorant Binding Proteins Facilitate the Gas‐Phase Uptake of Odorants Through the Nasal Mucus

    Article • Chemistry - A European Journal, December 2024, Wiley

    Dr. Sanne Abeln

  16. High Prevalence of Chromosomal Rearrangements and LINE Retrotranspositions Detected in Formalin-Fixed, Paraffin-Embedded Colorectal Cancer Tissue

    Article • Journal of Molecular Diagnostics, December 2024, Elsevier

    Dr. Sanne Abeln

  17. Considerations in the search for epistasis

    Article • Genome Biology, November 2024, Springer Science + Business Media

    Dr. Sanne Abeln

  18. Data-driven evaluation of suitable immunogens for improved antibody selection

    Article • October 2024, Cold Spring Harbor Laboratory Press

    Dr. Sanne Abeln

  19. The GFAP proteoform puzzle: How to advance GFAP as a fluid biomarker in neurological diseases

    Article • Journal of Neurochemistry, September 2024, Wiley

    Dr. Sanne Abeln

  20. CIBRA identifies genomic alterations with a system-wide impact on tumor biology

    Article • Bioinformatics, September 2024, Oxford University Press (OUP)

    Dr. Sanne Abeln

  21. Comparison of sequence- and structure-based antibody clustering approaches on simulated repertoire sequencing data

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Dr. Sanne Abeln

  22. The immunological landscape of peripheral blood in glioblastoma patients and immunological consequences of age and dexamethasone treatment

    Article • Frontiers in Immunology, January 2024, Frontiers

    Dr. Sanne Abeln

  23. PatchProt: hydrophobic patch prediction using protein foundation models

    Article • Bioinformatics Advances, January 2024, Oxford University Press (OUP)

    Dr. Sanne Abeln

  24. Proteome encoded determinants of protein sorting into extracellular vesicles

    Article • Journal of Extracellular Biology, January 2024, Wiley

    Dr. Sanne Abeln

  25. Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)

    Article • Proteins Structure Function and Bioinformatics, December 2023, Wiley

    Dr. Sanne Abeln

  26. Structural flexibility and heterogeneity of recombinant human glial fibrillary acidic protein (GFAP)

    Article • October 2023, Wiley

    Dr. Sanne Abeln

  27. Methods to Discover and Validate Biofluid-Based Biomarkers in Neurodegenerative Dementias

    Article • Molecular & Cellular Proteomics, October 2023, Elsevier

    Dr. Sanne Abeln

  28. Deciphering Protein Secretion from the Brain to Cerebrospinal Fluid for Biomarker Discovery

    Article • Journal of Proteome Research, August 2023, American Chemical Society (ACS)

    Dr. Sanne Abeln

  29. Discovery of novel CSF biomarkers to predict progression in dementia using machine learning

    Article • Scientific Reports, April 2023, Springer Science + Business Media

    Dr. Sanne Abeln

  30. Clusters of co-abundant proteins in the brain cortex associated with fronto-temporal lobar degeneration

    Article • Alzheimer s Research & Therapy, March 2023, Springer Science + Business Media

    Dr. Sanne Abeln

  31. Proteome encoded determinants of protein sorting into extracellular vesicles

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Dr. Sanne Abeln

  32. Discovery of novel CSF biomarkers to predict progression in dementia using machine learning

    Article • December 2022, Research Square

    Dr. Sanne Abeln

  33. Therapeutic potential of compounds targeting SARS-CoV-2 helicase

    Article • Frontiers in Chemistry, December 2022, Frontiers

    Dr. Sanne Abeln

  34. Tumour break load is a biologically relevant feature of genomic instability with prognostic value in colorectal cancer

    Article • European Journal of Cancer, December 2022, Elsevier

    Dr. Sanne Abeln

  35. INFLECT: an R-package for cytometry cluster evaluation using marker modality

    Article • BMC Bioinformatics, November 2022, Springer Science + Business Media

    Dr. Sanne Abeln

  36. Bioinformatics tools and data resources for assay development of fluid protein biomarkers

    Article • Biomarker Research, November 2022, Springer Science + Business Media

    Dr. Sanne Abeln

  37. Clusters of co-regulated proteins in brain cortex associate with fronto-temporal lobar degeneration

    Article • November 2022, Research Square

    Dr. Sanne Abeln

  38. Multi-task learning to leverage partially annotated data for PPI interface prediction

    Article • Scientific Reports, June 2022, Springer Science + Business Media

    Dr. Sanne Abeln

  39. Impact of pathogenic mutations of the GLUT1 glucose transporter on solute carrier dynamics using ComDYN enhanced sampling

    Article • F1000Research, June 2022, Faculty of 1000, Ltd.

    Dr. Sanne Abeln

  40. Methods included

    Article • Communications of the ACM, May 2022, ACM (Association for Computing Machinery)

    Dr. Sanne Abeln

  41. PIPENN: protein interface prediction from sequence with an ensemble of neural nets

    Article • Bioinformatics, February 2022, Oxford University Press (OUP)

    Dr. Sanne Abeln

  42. How sticky are our proteins? Quantifying hydrophobicity of the human proteome

    Article • Bioinformatics Advances, January 2022, Oxford University Press (OUP)

    Dr. Sanne Abeln

  43. PIPENN: Protein Interface Prediction with an Ensemble of Neural Nets

    Article • September 2021, Cold Spring Harbor Laboratory Press

    Dr. Sanne Abeln

  44. SeRenDIP-CE: sequence-based interface prediction for conformational epitopes

    Article • Bioinformatics, May 2021, Oxford University Press (OUP)

    Dr. Sanne Abeln

  45. SeRenDIP-CE: Sequence-based Interface Prediction for Conformational Epitopes

    Article • November 2020, Cold Spring Harbor Laboratory Press

    Dr. Sanne Abeln

  46. The hydrophobic effect characterises the thermodynamic signature of amyloid fibril growth

    Article • PLoS Computational Biology, May 2020, PLOS

    Dr. Sanne Abeln

  47. The potential use of big data in oncology

    Article • Oral Oncology, November 2019, Elsevier

    Dr. Sanne Abeln

  48. Tailor-made multiple sequence alignments using the PRALINE 2 alignment toolkit

    Article • Bioinformatics, August 2019, Oxford University Press (OUP)

    Dr. Sanne Abeln

  49. Abstract 1738: Characterization of structural variants within MACROD2 in the pathogenesis of colorectal cancer

    Article • Cancer Research, July 2019, American Association for Cancer Research (AACR)

    Dr. Sanne Abeln

  50. SeRenDIP: SEquential REmasteriNg to DerIve profiles for fast and accurate predictions of PPI interface positions

    Article • Bioinformatics, May 2019, Oxford University Press (OUP)

    Dr. Sanne Abeln

  51. Impact of pathogenic mutations of the GLUT1 glucose transporter on channel dynamics using ConsDYN enhanced sampling

    Article • F1000Research, March 2019, Faculty of 1000, Ltd.

    Dr. Sanne Abeln

  52. Protein Three-Dimensional Structure Prediction

    Article • January 2019, Elsevier

    Dr. Sanne Abeln

  53. Motif-Aware PRALINE: Improving the alignment of motif regions

    Article • PLoS Computational Biology, November 2018, PLOS

    Dr. Sanne Abeln

  54. The characteristics of molten globule states and folding pathways strongly depend on the sequence of a protein

    Article • Molecular Physics, July 2018, Taylor & Francis

    Wan Fokkink, Dr. Sanne Abeln

  55. Training for translation between disciplines: a philosophy for life and data sciences curricula

    Article • Bioinformatics, June 2018, Oxford University Press (OUP)

    Dr. Sanne Abeln

  56. Aurora kinase A (AURKA) interaction with Wnt and Ras-MAPK signalling pathways in colorectal cancer

    Article • Scientific Reports, May 2018, Springer Science + Business Media

    Dr. Sanne Abeln

  57. Systematically linking tranSMART, Galaxy and EGA for reusing human translational research data

    Article • F1000Research, August 2017, Faculty of 1000, Ltd.

    Mr Chao Zhang, Dr. Sanne Abeln, Stefan Payralbe, Ward Weistra, Rita Azevedo, Luiz Olavo Bonino da Silva Santos

  58. GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes

    Article • F1000Research, July 2017, Faculty of 1000, Ltd.

    Dr. Sanne Abeln

  59. Abstract A07: Detection of structural variants and recurrent breakpoint genes in colorectal adenoma-to-carcinoma progression

    Article • Cancer Research, January 2017, American Association for Cancer Research (AACR)

    Dr. Sanne Abeln

  60. Integration of EGA secure data access into Galaxy

    Article • F1000Research, December 2016, Faculty of 1000, Ltd.

    Dr. Sanne Abeln, Mr Chao Zhang

  61. Multiple Sequence Alignment

    Article • November 2016, Springer Science + Business Media

    Dr. Sanne Abeln

  62. Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping

    Article • Scientific Reports, October 2016, Nature

    Dr. Sanne Abeln

  63. GeneBreak: detection of recurrent DNA copy number aberration-associated chromosomal breakpoints within genes

    Article • F1000Research, September 2016, Faculty of 1000, Ltd.

    Dr. Sanne Abeln

  64. ECCB 2016: The 15th European Conference on Computational Biology

    Article • Bioinformatics, September 2016, Oxford University Press (OUP)

    Dr. Sanne Abeln

  65. Mechanical Unfolding of an Autotransporter Passenger Protein Reveals the Secretion Starting Point and Processive Transport Intermediates

    Article • ACS Nano, June 2016, American Chemical Society (ACS)

    Dr. Sanne Abeln

  66. BioASF: a framework for automatically generating executable pathway models specified in BioPAX

    Article • Bioinformatics, June 2016, Oxford University Press (OUP)

    Dr. Sanne Abeln

  67. Consistent Treatment of Hydrophobicity in Protein Lattice Models Accounts for Cold Denaturation

    Article • Physical Review Letters, February 2016, American Physical Society (APS)

    Dr. Sanne Abeln

  68. Mapping the Protein Fold Universe Using the CamTube Force Field in Molecular Dynamics Simulations

    Article • PLoS Computational Biology, October 2015, PLOS

    Dr. Sanne Abeln, Professor Michele Vendruscolo

  69. High Prevalence and Clinical Relevance of Genes Affected by Chromosomal Breaks in Colorectal Cancer

    Article • PLOS One, September 2015, PLOS

    Dr. Sanne Abeln

  70. metaModules identifies key functional subnetworks in microbiome-related disease

    Article • Bioinformatics, September 2015, Oxford University Press (OUP)

    Dr. Sanne Abeln

  71. Explaining disease using big data: How valid is your pathway?

    Article • July 2015, Institute of Electrical & Electronics Engineers (IEEE)

    Dr. Sanne Abeln

  72. The Hydrophobic Temperature Dependence of Amino Acids Directly Calculated from Protein Structures

    Article • PLoS Computational Biology, May 2015, PLOS

    Dr. Sanne Abeln

  73. Quantifying the Displacement of Mismatches in Multiple Sequence Alignment Benchmarks

    Article • PLOS One, May 2015, PLOS

    Dr. Sanne Abeln

  74. NGS-eval: NGS Error analysis and novel sequence VAriant detection tooL

    Article • Nucleic Acids Research, April 2015, Oxford University Press (OUP)

    Dr. Sanne Abeln

  75. Competition between surface adsorption and folding of fibril-forming polypeptides

    Article • Physical Review E, February 2015, American Physical Society (APS)

    Dr. Sanne Abeln

  76. Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

    Article • Bioinformatics, February 2014, Oxford University Press (OUP)

    Dr. Sanne Abeln

  77. A Simple Lattice Model That Captures Protein Folding, Aggregation and Amyloid Formation

    Article • PLOS One, January 2014, PLOS

    Professor Michele Vendruscolo, Dr. Sanne Abeln

  78. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

    Article • Bioinformatics, November 2013, Oxford University Press (OUP)

    Dr. Sanne Abeln

  79. Exploring Fold Space Preferences of New-born and Ancient Protein Superfamilies

    Article • PLoS Computational Biology, November 2013, PLOS

    Dr. Sanne Abeln

  80. Interplay between Folding and Assembly of Fibril-Forming Polypeptides

    Article • Physical Review Letters, July 2013, American Physical Society (APS)

    Dr. Sanne Abeln

  81. Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds

    Article • Briefings in Bioinformatics, April 2013, Oxford University Press (OUP)

    Dr. Sanne Abeln

  82. Comparing clustering and pre-processing in taxonomy analysis

    Article • Bioinformatics, September 2012, Oxford University Press (OUP)

    Dr. Sanne Abeln

  83. Correction

    Article • Biophysical Journal, August 2011, Elsevier

    Dr. Sanne Abeln

  84. Accounting for Protein-Solvent Contacts Facilitates Design of Nonaggregating Lattice Proteins

    Article • Biophysical Journal, February 2011, Elsevier

    Dr. Sanne Abeln

  85. Multiple alignment of transmembrane protein sequences

    Article • January 2010, Springer Science + Business Media

    Dr. Sanne Abeln

  86. Disordered Flanks Prevent Peptide Aggregation

    Article • PLoS Computational Biology, December 2008, PLOS

    Dr. Sanne Abeln

  87. Using Phylogeny to Improve Genome-Wide Distant Homology Recognition

    Article • PLoS Computational Biology, January 2007, PLOS

    Dr. Sanne Abeln

  88. Linking evolution of protein structures through fragments

    Article • BMC Systems Biology, January 2007, Springer Science + Business Media

    Dr. Sanne Abeln

  89. Fold usage on genomes and protein fold evolution

    Article • Proteins Structure Function and Bioinformatics, July 2005, Wiley

    Dr. Sanne Abeln, Charlotte Deane

  90. How old is your fold?

    Article • Bioinformatics, June 2005, Oxford University Press (OUP)

    Dr. Sanne Abeln

  91. Using phylogeny to improve genome wide distant homology recognition

    Article • PLoS Computational Biology, January 2005, PLOS

    Dr. Sanne Abeln