All Stories

  1. GlyContact analyzes glycan 3D structures at scale

    Article • Nature Communications, December 2025, Springer Science + Business Media

    Daniel Bojar

  2. Bridging Worlds: Connecting Glycan Representations with Glycoinformatics via Universal Input and a Canonicalized Nomenclature

    Article • Bioinformatics Advances, December 2025, Oxford University Press (OUP)

    Daniel Bojar

  3. Serum N-glycosylation is altered in Nephropathic Cystinosis

    Article • Glycobiology, August 2025, Oxford University Press (OUP)

    Daniel Bojar

  4. GlyContact reveals structure-function relationships in glycans

    Article • June 2025, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  5. PyCycleBio: modelling non-sinusoidal-oscillator systems in temporal biology

    Article • May 2025, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  6. Seal milk oligosaccharides rival human milk complexity and exhibit functional dynamics during lactation

    Article • March 2025, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  7. Compositional data analysis enables statistical rigor in comparative glycomics

    Article • Nature Communications, January 2025, Springer Science + Business Media

    Daniel Bojar

  8. O-glycosylation contributes to mammalian glycoRNA biogenesis

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  9. Navigating the maze of mass spectra: a machine-learning guide to identifying diagnostic ions in O-glycan analysis

    Article • Analytical and Bioanalytical Chemistry, August 2024, Springer Science + Business Media

    Daniel Bojar

  10. Navigating the Maze of Mass Spectra: A Machine-Learning Guide to Identifying Diagnostic Ions in O-Glycan Analysis

    Article • July 2024, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  11. Predicting glycan structure from tandem mass spectrometry via deep learning

    Article • Nature Chemical Biology, July 2024, Springer Science + Business Media

    Daniel Bojar

  12. Ratios in Disguise, Truths Arise: Glycomics Meets Compositional Data Analysis

    Article • June 2024, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  13. Protocol for constructing glycan biosynthetic networks using glycowork

    Article • STAR Protocols, June 2024, Elsevier

    Daniel Bojar

  14. The evolving world of milk oligosaccharides: Biochemical diversity understood by computational advances

    Article • Carbohydrate Research, March 2024, Elsevier

    Daniel Bojar

  15. Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

    Article • Beilstein Journal of Organic Chemistry, February 2024, Beilstein Institut

    Daniel Bojar

  16. Syntactic Sugars: Crafting a Regular Expression Framework for Glycan Structures

    Article • February 2024, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  17. Syntactic sugars: crafting a regular expression framework for glycan structures

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

    Daniel Bojar

  18. Elucidating the Glycan-Binding Specificity and Structure ofCucumis meloAgglutinin, a New R-Type Lectin

    Article • December 2023, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  19. Decoding glycomics with a suite of methods for differential expression analysis

    Article • Cell Reports Methods, December 2023, Elsevier

    Daniel Bojar

  20. Breast Milk Oligosaccharides Contain Immunomodulatory Glucuronic Acid and LacdiNAc

    Article • Molecular & Cellular Proteomics, September 2023, Elsevier

    Daniel Bojar

  21. Decoding Glycomics: Differential Expression Reimagined

    Article • August 2023, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  22. GlycoDraw: a python implementation for generating high-quality glycan figures

    Article • Glycobiology, July 2023, Oxford University Press (OUP)

    Daniel Bojar

  23. Mammalian milk glycomes: Connecting the dots between evolutionary conservation and biosynthetic pathways

    Article • Cell Reports, July 2023, Elsevier

    Daniel Bojar

  24. Predicting glycan structure from tandem mass spectrometry via deep learning

    Article • June 2023, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  25. GlycoDraw: A Python Implementation for Generating High-Quality Glycan Figures

    Article • May 2023, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  26. Mammalian Milk Glycomes: Connecting the Dots between Evolutionary Conservation and Biosynthetic Pathways

    Article • February 2023, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  27. Breast Milk Oligosaccharides Contain Immunomodulatory Glucuronic Acid and LacdiNAc

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  28. GlyLES: Grammar-based Parsing of Glycans from IUPAC-condensed to SMILES

    Article • November 2022, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  29. Deep learning explains the biology of branched glycans from single-cell sequencing data

    Article • iScience, October 2022, Elsevier

    Daniel Bojar

  30. Glycoinformatics in the Artificial Intelligence Era

    Article • Chemical Reviews, August 2022, American Chemical Society (ACS)

    Daniel Bojar

  31. Deep Learning Explains the Biology of Branched Glycans from Single-Cell Sequencing Data

    Article • June 2022, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  32. Structural insights into host–microbe glycointeractions

    Article • Current Opinion in Structural Biology, April 2022, Elsevier

    Daniel Bojar

  33. A Useful Guide to Lectin Binding: Machine-Learning Directed Annotation of 57 Unique Lectin Specificities

    Article • ACS Chemical Biology, January 2022, American Chemical Society (ACS)

    Daniel Bojar

  34. LectinOracle: A Generalizable Deep Learning Model for Lectin–Glycan Binding Prediction

    Article • Advanced Science, December 2021, Wiley

    Daniel Bojar

  35. The Role of Fucose-Containing Glycan Motifs Across Taxonomic Kingdoms

    Article • Frontiers in Molecular Biosciences, September 2021, Frontiers

    Daniel Bojar

  36. A Useful Guide to Lectin Binding: Machine-Learning Directed Annotation of 57 Unique Lectin Specificities

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  37. LectinOracle – A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  38. The role of fucose-containing glycan motifs across taxonomic kingdoms

    Article • August 2021, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  39. Glycowork: A Python package for glycan data science and machine learning

    Article • Glycobiology, June 2021, Oxford University Press (OUP)

    Daniel Bojar

  40. Using graph convolutional neural networks to learn a representation for glycans

    Article • Cell Reports, June 2021, Elsevier

    Daniel Bojar

  41. Glycowork: A Python package for glycan data science and machine learning

    Article • April 2021, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  42. Gene switch for l‐glucose‐induced biopharmaceutical production in mammalian cells

    Article • Biotechnology and Bioengineering, March 2021, Wiley

    Daniel Bojar

  43. Using Graph Convolutional Neural Networks to Learn a Representation for Glycans

    Article • March 2021, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  44. DeepConnection: classifying momentary relationship state from images of romantic couples

    Article • Journal of Computational Social Science, January 2021, Springer Science + Business Media

    Daniel Bojar

  45. Construction of Caffeine-Inducible Gene Switches in Mammalian Cells

    Article • January 2021, Springer Science + Business Media

    Daniel Bojar

  46. Learning the language of sugars

    Article • Cell Host & Microbe, October 2020, Elsevier

    Daniel Bojar

  47. Structure Determines Function – The Role of Topology in the Functionality of Gene Circuits

    Article • Synthetic Biology, June 2020, Oxford University Press (OUP)

    Daniel Bojar

  48. SweetOrigins: Extracting Evolutionary Information from Glycans

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  49. Using Natural Language Processing to Learn the Grammar of Glycans

    Article • January 2020, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  50. The Role of Protein Engineering in Biomedical Applications of Mammalian Synthetic Biology

    Article • Small, October 2019, Wiley

    Daniel Bojar

  51. DeepConnection: Classifying Relationship State from Images of Romantic Couples

    Article • June 2019, Center for Open Science

    Daniel Bojar

  52. A CRISPR/Cas9-based central processing unit to program complex logic computation in human cells

    Article • Proceedings of the National Academy of Sciences, March 2019, Proceedings of the National Academy of Sciences

    Daniel Bojar

  53. Purity by design: Reducing impurities in bioproduction by stimulus-controlled global translational downregulation of non-product proteins

    Article • Metabolic Engineering, March 2019, Elsevier

    Daniel Bojar

  54. Speaking to nature: a deep learning representational model of proteins ushers in protein linguistics

    Article • Synthetic Biology, January 2019, Oxford University Press (OUP)

    Daniel Bojar

  55. Arch enemy no more: designing the first synthetic globular all-beta proteins with beta-arches

    Article • Synthetic Biology, January 2019, Oxford University Press (OUP)

    Daniel Bojar

  56. New adaptive laboratory evolution database highlights the need for consolidating directed evolution data

    Article • Synthetic Biology, January 2019, Oxford University Press (OUP)

    Daniel Bojar

  57. Synthetic bacterial stem cells and their multicellularity for synthetic biology and beyond

    Article • Synthetic Biology, January 2019, Oxford University Press (OUP)

    Daniel Bojar

  58. Updating the in silico human surfaceome with meta-ensemble learning and feature engineering

    Article • December 2018, Cold Spring Harbor Laboratory Press

    Daniel Bojar

  59. Programming mammalian gene expression with the antibiotic simocyclinone D8 and the flavonoid luteolin

    Article • AIChE Journal, September 2018, Wiley

    Daniel Bojar

  60. Caffeine-inducible gene switches controlling experimental diabetes

    Article • Nature Communications, June 2018, Springer Science + Business Media

    Daniel Bojar

  61. Generalized extracellular molecule sensor platform for programming cellular behavior

    Article • Nature Chemical Biology, April 2018, Springer Science + Business Media

    Daniel Bojar

  62. Designer exosomes produced by implanted cells intracerebrally deliver therapeutic cargo for Parkinson’s disease treatment

    Article • Nature Communications, April 2018, Springer Science + Business Media

    Daniel Bojar

  63. Design and applications of a clamp for Green Fluorescent Protein with picomolar affinity

    Article • Scientific Reports, November 2017, Springer Science + Business Media

    Daniel Bojar

  64. Generation of glucose-sensitive insulin-secreting beta-like cells from human embryonic stem cells by incorporating a synthetic lineage-control network

    Article • Journal of Biotechnology, October 2017, Elsevier

    Daniel Bojar

  65. Design of Synthetic Promoters for Gene Circuits in Mammalian Cells

    Article • January 2017, Springer Science + Business Media

    Daniel Bojar

  66. Crystal structures of the phosphorylated BRI 1 kinase domain and implications for brassinosteroid signal initiation

    Article • The Plant Journal, March 2014, Wiley

    Daniel Bojar