Highlighted Publications
Cosmic kidney disease: an integrated pan-omic, physiological and morphological study into spaceflight-induced renal dysfunction. Nature Communications. 2024 June. Keith Siew, Kevin A Nestler, Charlotte Nelson, Sergio Baranzini. PMCID: PMC11167060
Biomedical knowledge graph-optimized prompt generation for large language models. Bioinformatics. 2024 Sep 02; 40(9). Soman K, Rose PW, Morris JH, Akbas RE, Smith B, Peetoom B, Villouta-Reyes C, Cerono G, Shi Y, Rizk-Jackson A, Israni S, Nelson CA, Huang S, Baranzini SE. PMID: 39288310; PMCID: PMC11441322
Leveraging electronic health records and knowledge networks for Alzheimer's disease prediction and sex-specific biological insights. Nat Aging. 2024 Mar; 4(3):379-395. Tang AS, Rankin KP, Cerono G, Miramontes S, Mills H, Roger J, Zeng B, Nelson C, Soman K, Woldemariam S, Li Y, Lee A, Bove R, Glymour M, Aghaeepour N, Oskotsky TT, Miller Z, Allen IE, Sanders SJ, Baranzini S, Sirota M. PMID: 38383858; PMCID: PMC10950787.
Early detection of Parkinson's disease through enriching the electronic health record using a biomedical knowledge graph. Front Med (Lausanne). 2023; 10:1081087. Soman K, Nelson CA, Cerono G, Goldman SM, Baranzini SE, Brown EG. PMID: 37250641; PMCID: PMC10217780.
The scalable precision medicine open knowledge engine (SPOKE): a massive knowledge graph of biomedical information. Bioinformatics. 2023 02 03; 39(2). Morris JH, Soman K, Akbas RE, Zhou X, Smith B, Meng EC, Huang CC, Cerono G, Schenk G, Rizk-Jackson A, Harroud A, Sanders L, Costes SV, Bharat K, Chakraborty A, Pico AR, Mardirossian T, Keiser M, Tang A, Hardi J, Shi Y, Musen M, Israni S, Huang S, Rose PW, Nelson CA, Baranzini SE. PMID: 36759942; PMCID: PMC9940622.
Time-aware Embeddings of Clinical Data using a Knowledge Graph. Pac Symp Biocomput. 2023; 28:97-108. Soman K, Nelson CA, Cerono G, Baranzini SE. PMID: 36540968; PMCID: PMC9782808.
A biomedical open knowledge network harnesses the power of AI to understand deep human biology. AI Mag. 2022; 43(1):46-58. Baranzini SE, Börner K, Morris J, Nelson CA, Soman K, Schleimer E, Keiser M, Musen M, Pearce R, Reza T, Smith B, Herr BW, Oskotsky B, Rizk-Jackson A, Rankin KP, Sanders SJ, Bove R, Rose PW, Israni S, Huang S. PMID: 36093122; PMCID: PMC9456356.
Embedding electronic health records onto a knowledge network recognizes prodromal features of multiple sclerosis and predicts diagnosis. J Am Med Inform Assoc. 2022 01 29; 29(3):424-434. Nelson CA, Bove R, Butte AJ, Baranzini SE. PMID: 34915552; PMCID: PMC8800523.
Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases
Charlotte A. Nelson, Ana Uriarte Acuna, Amber M. Paul, Ryan T. Scott, Atul J. Butte, Egle Cekanaviciute, Sergio E. Baranzini, Sylvain V. Costes. Life 12 Jan 2021.
Mechanical Ventilation Stimulates Expression of the SARS-Cov-2 Receptor ACE2 in the Lung and May Trigger a Vicious Cycle
Sui Huang, Arja Kaipainen, Michael Strasser, Sergio Baranzini. Preprints Online: 26 May 2020.
Integrating biomedical research and electronic health records to create knowledge-based biologically meaningful machine-readable embeddings
Charlotte A Nelson, Atul J Butte, Sergio E Baranzini. Nat Commun 2019 Jul 10.
Systematic integration of biomedical knowledge prioritizes drugs for repurposing
Daniel Scott Himmelstein, Antoine Lizee, Christine Hessler, Leo Brueggeman, Sabrina L Chen, Dexter Hadley, Ari Green, Pouya Khankhanian, Sergio E Baranzini. Elife 2017 Sep 22.
iCTNet2: integrating heterogeneous biological interactions to understand complex traits
Lili Wang, Daniel S Himmelstein, Adam Santaniello, Mousavi Parvin, Sergio E Baranzini. F1000Res 2015 Aug 5.
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes
Daniel S Himmelstein, Sergio E Baranzini. PLoS Comput Biol 2015 Jul 9.