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Daniel Himmelstein - Publications

Affiliations: 
2016- University of Pennsylvania Perelman School of Medicine 
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24 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Zietz M, Himmelstein DS, Kloster K, Williams C, Nagle MW, Greene CS. The probability of edge existence due to node degree: a baseline for network-based predictions. Gigascience. 13. PMID 38323677 DOI: 10.1093/gigascience/giae001  0.525
2023 Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. Hetnet connectivity search provides rapid insights into how biomedical entities are related. Gigascience. 12. PMID 37503959 DOI: 10.1093/gigascience/giad047  0.534
2023 Zietz M, Himmelstein DS, Kloster K, Williams C, Nagle MW, Greene CS. The probability of edge existence due to node degree: a baseline for network-based predictions. Biorxiv : the Preprint Server For Biology. PMID 36711569 DOI: 10.1101/2023.01.05.522939  0.526
2023 Himmelstein DS, Zietz M, Rubinetti V, Kloster K, Heil BJ, Alquaddoomi F, Hu D, Nicholson DN, Hao Y, Sullivan BD, Nagle MW, Greene CS. Hetnet connectivity search provides rapid insights into how two biomedical entities are related. Biorxiv : the Preprint Server For Biology. PMID 36711546 DOI: 10.1101/2023.01.05.522941  0.533
2022 Nicholson DN, Himmelstein DS, Greene CS. Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts. Biodata Mining. 15: 26. PMID 36258252 DOI: 10.1186/s13040-022-00311-z  0.509
2022 Rando HM, Boca SM, McGowan LD, Himmelstein DS, Robson MP, Rubinetti V, Velazquez R, Greene CS, Gitter A. An Open-Publishing Response to the COVID-19 Infodemic. Ceur Workshop Proceedings. 2976: 29-38. PMID 35558551  0.527
2021 Romano JD, Le TT, La Cava W, Gregg JT, Goldberg DJ, Chakraborty P, Ray NL, Himmelstein D, Fu W, Moore JH. PMLB v1.0: An open-source dataset collection for benchmarking machine learning methods. Bioinformatics (Oxford, England). PMID 34677586 DOI: 10.1093/bioinformatics/btab727  0.456
2021 Le TT, Himmelstein DS, Hippen AA, Gazzara MR, Greene CS. Analysis of scientific society honors reveals disparities. Cell Systems. 12: 900-906.e5. PMID 34555325 DOI: 10.1016/j.cels.2021.07.007  0.477
2021 Rando HM, Boca SM, McGowan LD, Himmelstein DS, Robson MP, Rubinetti V, Velazquez R, Consortium CR, Greene CS, Gitter A. An Open-Publishing Response to the COVID-19 Infodemic. Arxiv. PMID 34545336  0.527
2020 Way GP, Zietz M, Rubinetti V, Himmelstein DS, Greene CS. Compressing gene expression data using multiple latent space dimensionalities learns complementary biological representations. Genome Biology. 21: 109. PMID 32393369 DOI: 10.1186/S13059-020-02021-3  0.681
2019 Himmelstein DS, Rubinetti V, Slochower DR, Hu D, Malladi VS, Greene CS, Gitter A. Open collaborative writing with Manubot. Plos Computational Biology. 15: e1007128. PMID 31233491 DOI: 10.1371/Journal.Pcbi.1007128  0.503
2018 Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, et al. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society, Interface. 15. PMID 29618526 DOI: 10.1098/Rsif.2017.0387  0.656
2018 Himmelstein DS, Romero AR, Levernier JG, Munro TA, McLaughlin SR, Greshake Tzovaras B, Greene CS. Research: Sci-Hub provides access to nearly all scholarly literature. Elife. 7. PMID 29424689 DOI: 10.7554/Elife.32822  0.495
2017 Hadley D, Pan J, El-Sayed O, Aljabban J, Aljabban I, Azad TD, Hadied MO, Raza S, Rayikanti BA, Chen B, Paik H, Aran D, Spatz J, Himmelstein D, Panahiazar M, et al. Precision annotation of digital samples in NCBI's gene expression omnibus. Scientific Data. 4: 170125. PMID 28925997 DOI: 10.1038/Sdata.2017.125  0.34
2016 Greene CS, Himmelstein DS. Genetic Association-Guided Analysis of Gene Networks for the Study of Complex Traits. Circulation. Cardiovascular Genetics. 9: 179-84. PMID 27094199 DOI: 10.1161/Circgenetics.115.001181  0.56
2016 Himmelstein DS, Greene CS, Moore JH. Erratum to: Evolving hard problems: generating human genetics datasets with a complex etiology. Biodata Mining. 9: 9. PMID 26848312 DOI: 10.1186/S13040-016-0085-5  0.578
2015 Himmelstein DS, Baranzini SE. Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes. Plos Computational Biology. 11: e1004259. PMID 26158728 DOI: 10.1371/journal.pcbi.1004259  0.332
2015 Greene CS, Krishnan A, Wong AK, Ricciotti E, Zelaya RA, Himmelstein DS, Zhang R, Hartmann BM, Zaslavsky E, Sealfon SC, Chasman DI, FitzGerald GA, Dolinski K, Grosser T, Troyanskaya OG. Understanding multicellular function and disease with human tissue-specific networks. Nature Genetics. 47: 569-76. PMID 25915600 DOI: 10.1038/Ng.3259  0.634
2015 Himmelstein DS, Baranzini SE. Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes Plos Computational Biology. 11. DOI: 10.1371/journal.pcbi.1004259  0.329
2014 Himmelstein D, Baranzini S. Heterogeneous network link prediction prioritizes disease-associated genes F1000research. 5. DOI: 10.7490/F1000Research.1097367.1  0.349
2011 Himmelstein DS, Greene CS, Moore JH. Evolving hard problems: Generating human genetics datasets with a complex etiology. Biodata Mining. 4: 21. PMID 21736753 DOI: 10.1186/1756-0381-4-21  0.592
2011 Himmelstein DS, Greene CS, Moore JH. Evolving hard problems: Generating human genetics datasets with a complex etiology Biodata Mining. 4. DOI: 10.1186/1756-0381-4-21  0.56
2010 Greene CS, Sinnott-Armstrong NA, Himmelstein DS, Park PJ, Moore JH, Harris BT. Multifactor dimensionality reduction for graphics processing units enables genome-wide testing of epistasis in sporadic ALS. Bioinformatics (Oxford, England). 26: 694-5. PMID 20081222 DOI: 10.1093/Bioinformatics/Btq009  0.589
2010 Greene CS, Himmelstein DS, Nelson HH, Kelsey KT, Williams SM, Andrew AS, Karagas MR, Moore JH. Enabling personal genomics with an explicit test of epistasis. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 327-36. PMID 19908385  0.597
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