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Current and future directions in network biology.

Zitnik M, Li MM, Wells A, Glass K, Morselli Gysi D, Krishnan A, Murali TM, Radivojac P, Roy S, Baudot A, Bozdag S, Chen DZ, Cowen L, Devkota K, Gitter A, Gosline SJC, Gu P, Guzzi PH, Huang H, Jiang M, Kesimoglu ZN, Koyuturk M, Ma J, Pico AR, Pržulj N, Przytycka TM, Raphael BJ, Ritz A, Sharan R, Shen Y, Singh M, Slonim DK, Tong H, Yang XH, Yoon BJ, Yu H, Milenković T. Zitnik M, et al. Among authors: cowen l. Bioinform Adv. 2024 Aug 14;4(1):vbae099. doi: 10.1093/bioadv/vbae099. eCollection 2024. Bioinform Adv. 2024. PMID: 39143982 Free PMC article.

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GLIDER: function prediction from GLIDE-based neighborhoods.

Devkota K, Schmidt H, Werenski M, Murphy JM, Erden M, Arsenescu V, Cowen LJ. Devkota K, et al. Among authors: cowen lj. Bioinformatics. 2022 Jun 27;38(13):3395-3406. doi: 10.1093/bioinformatics/btac322. Bioinformatics. 2022. PMID: 35575379 Free PMC article.

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Network propagation: a universal amplifier of genetic associations.

Cowen L, Ideker T, Raphael BJ, Sharan R. Cowen L, et al. Nat Rev Genet. 2017 Sep;18(9):551-562. doi: 10.1038/nrg.2017.38. Epub 2017 Jun 12. Nat Rev Genet. 2017. PMID: 28607512 Review.

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Bioinformatics of Corals: Investigating Heterogeneous Omics Data from Coral Holobionts for Insight into Reef Health and Resilience.

Cowen LJ, Putnam HM. Cowen LJ, et al. Annu Rev Biomed Data Sci. 2022 Aug 10;5:205-231. doi: 10.1146/annurev-biodatasci-122120-030732. Epub 2022 May 10. Annu Rev Biomed Data Sci. 2022. PMID: 35537462 Review.

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MEDFORD: A human- and machine-readable metadata markup language.

Shpilker P, Freeman J, McKelvie H, Ashey J, Fonticella JM, Putnam H, Greenberg J, Cowen L, Couch A, Daniels NM. Shpilker P, et al. Among authors: cowen l. Database (Oxford). 2022 Aug 17;2022:baac065. doi: 10.1093/database/baac065. Database (Oxford). 2022. PMID: 35976727 Free PMC article.

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Assessment of network module identification across complex diseases.

Choobdar S, Ahsen ME, Crawford J, Tomasoni M, Fang T, Lamparter D, Lin J, Hescott B, Hu X, Mercer J, Natoli T, Narayan R; DREAM Module Identification Challenge Consortium; Subramanian A, Zhang JD, Stolovitzky G, Kutalik Z, Lage K, Slonim DK, Saez-Rodriguez J, Cowen LJ, Bergmann S, Marbach D. Choobdar S, et al. Among authors: cowen lj. Nat Methods. 2019 Sep;16(9):843-852. doi: 10.1038/s41592-019-0509-5. Epub 2019 Aug 30. Nat Methods. 2019. PMID: 31471613 Free PMC article.

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TT3D: Leveraging precomputed protein 3D sequence models to predict protein-protein interactions.

Sledzieski S, Devkota K, Singh R, Cowen L, Berger B. Sledzieski S, et al. Among authors: cowen l. Bioinformatics. 2023 Nov 1;39(11):btad663. doi: 10.1093/bioinformatics/btad663. Bioinformatics. 2023. PMID: 37897686 Free PMC article.

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Compressive genomics for protein databases.

Daniels NM, Gallant A, Peng J, Cowen LJ, Baym M, Berger B. Daniels NM, et al. Among authors: cowen lj. Bioinformatics. 2013 Jul 1;29(13):i283-90. doi: 10.1093/bioinformatics/btt214. Bioinformatics. 2013. PMID: 23812995 Free PMC article.

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Contrastive learning in protein language space predicts interactions between drugs and protein targets.

Singh R, Sledzieski S, Bryson B, Cowen L, Berger B. Singh R, et al. Among authors: cowen l. Proc Natl Acad Sci U S A. 2023 Jun 13;120(24):e2220778120. doi: 10.1073/pnas.2220778120. Epub 2023 Jun 8. Proc Natl Acad Sci U S A. 2023. PMID: 37289807 Free PMC article.

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Evaluation of fluorescence-based viability stains in cells dissociated from scleractinian coral Pocillopora damicornis.

Roger LM, Adarkwa Darko Y, Bernas T, White F, Olaosebikan M, Cowen L, Klein-Seetharaman J, Lewinski NA. Roger LM, et al. Among authors: cowen l. Sci Rep. 2022 Sep 12;12(1):15297. doi: 10.1038/s41598-022-19586-7. Sci Rep. 2022. PMID: 36097278 Free PMC article.

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