40.2k citations
- Harvard UniversityUS53 papers
- Massachusetts Institute of TechnologyUS36 papers
- Stanford UniversityUS12 papers
- Howard Hughes Medical InstituteUS11 papers
- Dana-Farber Cancer InstituteUS10 papers
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- University of PennsylvaniaUS10 papers
- University of WashingtonUS9 papers
- Centre National de la Recherche ScientifiqueFR8 papers
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- University of Wisconsin–MadisonUS8 papers
- Brigham and Women's HospitalUS7 papers
137 papers
Tracing protein and proteome history with chronologies and networks: folding recapitulates evolution
Gustavo Caetano-Anollés, M. Fayez Aziz, Fizza Mughal +1
Introduction: While the origin and evolution of proteins remain mysterious, advances in evolutionary genomics and systems biology are facilitating the historical exploration of the…
Autonomous Knowledge Graph Exploration with Adaptive Breadth-Depth Retrieval
Joaquín Polonuer, Lucas Vittor, Iñaki Arango +4
Retrieving evidence for language model queries from knowledge graphs requires balancing broad search across the graph with multi-hop traversal to follow relational links. Similarit…
Finding easy regions for short-read variant calling from pangenome data
Heng Li
Background: While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without s…
Evaluating Integrative Strategies for Incorporating Phenotypic Features in Spatial Transcriptomics
Levin M Moser, Ahmad Kamal Hamid, Esteban Miglietta +2
Spatial transcriptomics (ST) technologies not only offer an unprecedented opportunity to interrogate intact biological samples in a spatially informed manner, but also set the stag…
HIF: The hypergraph interchange format for higher-order networks
Martín Coll, Cliff A. Joslyn, Nicholas W. Landry +5
Many empirical systems contain complex interactions of arbitrary size, representing, for example, chemical reactions, social groups, co-authorship relationships, and ecological dep…
cp_measure: API-first feature extraction for image-based profiling workflows
Alán F. Muñoz, Tim Treis, Alexandr A. Kalinin +4
Biological image analysis has traditionally focused on measuring specific visual properties of interest for cells or other entities. A complementary paradigm gaining increasing tra…