All Stories

  1. Clinical Advancement Forecasting

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Mr Daniel S Himmelstein

  2. The probability of edge existence due to node degree: a baseline for network-based predictions

    Article • GigaScience, January 2024, Oxford University Press (OUP)

    Professor Casey Greene, Mr Daniel S Himmelstein

  3. Hetnet connectivity search provides rapid insights into how two biomedical entities are related

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  4. The probability of edge existence due to node degree: a baseline for network-based predictions

    Article • January 2023, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  5. Hetnet connectivity search provides rapid insights into how biomedical entities are related

    Article • GigaScience, December 2022, Oxford University Press (OUP)

    Professor Casey Greene, Mr Daniel S Himmelstein

  6. Unifying the identification of biomedical entities with the Bioregistry

    Article • Scientific Data, November 2022, Springer Science + Business Media

    Mr Daniel S Himmelstein

  7. Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts

    Article • BioData Mining, October 2022, Springer Science + Business Media

    Professor Casey Greene, Mr Daniel S Himmelstein

  8. Unifying the Identification of Biomedical Entities with the Bioregistry

    Article • July 2022, Cold Spring Harbor Laboratory Press

    Mr Daniel S Himmelstein

  9. PMLB v1.0: an open-source dataset collection for benchmarking machine learning methods

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

    Mr Daniel S Himmelstein

  10. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations

    Article • May 2020, Springer Science + Business Media

    Professor Casey Greene, Mr Daniel S Himmelstein

  11. Analysis of ISCB honorees and keynotes reveals disparities

    Article • April 2020, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  12. Reusing label functions to extract multiple types of biomedical relationships from biomedical abstracts at scale

    Article • August 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  13. Open collaborative writing with Manubot

    Article • PLoS Computational Biology, June 2019, PLOS

    Professor Casey Greene, Mr Daniel S Himmelstein

  14. Sequential compression across latent space dimensions enhances gene expression signatures

    Article • March 2019, Cold Spring Harbor Laboratory Press

    Professor Casey Greene, Mr Daniel S Himmelstein

  15. Opportunities and obstacles for deep learning in biology and medicine

    Article • Journal of The Royal Society Interface, April 2018, Royal Society Publishing

    Mr Daniel S Himmelstein, Professor Casey Greene

  16. Research: Sci-Hub provides access to nearly all scholarly literature

    Article • eLife, February 2018, eLife

    Professor Casey Greene, Mr Daniel S Himmelstein

  17. Sci-Hub provides access to nearly all scholarly literature

    Article • February 2018, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  18. Sci-Hub provides access to nearly all scholarly literature

    Article • October 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  19. Sci-Hub provides access to nearly all scholarly literature

    Article • October 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  20. Systematic integration of biomedical knowledge prioritizes drugs for repurposing

    Article • eLife, September 2017, eLife

    Mr Daniel S Himmelstein

  21. Precision annotation of digital samples in NCBI’s gene expression omnibus

    Article • Scientific Data, September 2017, Nature

    Mr Daniel S Himmelstein

  22. Sci-Hub provides access to nearly all scholarly literature

    Article • July 2017, PeerJ

    Professor Casey Greene, Mr Daniel S Himmelstein

  23. Opportunities And Obstacles For Deep Learning In Biology And Medicine

    Article • May 2017, Cold Spring Harbor Laboratory Press

    Mr Daniel S Himmelstein, Professor Casey Greene

  24. Systematic integration of biomedical knowledge prioritizes drugs for repurposing

    Article • November 2016, Cold Spring Harbor Laboratory Press

    Mr Daniel S Himmelstein

  25. Rephetio: Repurposing drugs on a hetnet [report]

    Article • November 2016, Thinklab

    Mr Daniel S Himmelstein

  26. Association of HLA Genetic Risk Burden With Disease Phenotypes in Multiple Sclerosis

    Article • JAMA Neurology, July 2016, American Medical Association (AMA)

    Mr Daniel S Himmelstein

  27. Genetic Association–Guided Analysis of Gene Networks for the Study of Complex Traits

    Article • Circulation Cardiovascular Genetics, April 2016, Wolters Kluwer Health

    Mr Daniel S Himmelstein, Professor Casey Greene

  28. Meta-analysis of genome-wide association studies reveals genetic overlap between Hodgkin lymphoma and multiple sclerosis

    Article • International Journal of Epidemiology, March 2016, Oxford University Press (OUP)

    Mr Daniel S Himmelstein, Professor Ruth Frances Jarrett

  29. iCTNet2: integrating heterogeneous biological interactions to understand complex traits

    Article • F1000Research, September 2015, Faculty of 1000, Ltd.

    Mr Daniel S Himmelstein

  30. iCTNet2: integrating heterogeneous biological interactions to understand complex traits

    Article • F1000Research, August 2015, Faculty of 1000, Ltd.

    Mr Daniel S Himmelstein

  31. Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes

    Article • PLoS Computational Biology, July 2015, PLOS

    Mr Daniel S Himmelstein

  32. Understanding multicellular function and disease with human tissue-specific networks

    Article • Nature Genetics, April 2015, Nature

    Mr Daniel S Himmelstein, Professor Casey Greene

  33. Lung cancer incidence decreases with elevation

    Article • PeerJ, January 2015, PeerJ

    Mr Daniel S Himmelstein

  34. Rephetio: Repurposing drugs on a hetnet [project]

    Article • January 2015, Thinklab

    Mr Daniel S Himmelstein

  35. Evolving hard problems: Generating human genetics datasets with a complex etiology

    Article • BioData Mining, January 2011, Springer Science + Business Media

    Mr Daniel S Himmelstein, Professor Casey Greene

  36. Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS

    Article • Bioinformatics, January 2010, Oxford University Press (OUP)

    Mr Daniel S Himmelstein, Professor Casey Greene

  37. The Informative Extremes: Using Both Nearest and Farthest Individuals Can Improve Relief Algorithms in the Domain of Human Genetics

    Article • January 2010, Springer Science + Business Media

    Mr Daniel S Himmelstein, Professor Casey Greene

  38. A Model Free Method to Generate Human Genetics Datasets with Complex Gene-Disease Relationships

    Article • January 2010, Springer Science + Business Media

    Mr Daniel S Himmelstein, Professor Casey Greene

  39. ENABLING PERSONAL GENOMICS WITH AN EXPLICIT TEST OF EPISTASIS

    Article • October 2009, World Scientific Pub Co Pte Lt

    Mr Daniel S Himmelstein