Publications and Presentations  

Publications

1. Murphy F, Bar-Sinai M, Martone ME. A tool for assessing alignment of biomedical data repositories with open, FAIR, citation and trustworthy principles. PLoS One. 2021 Jul 9;16(7):e0253538. doi: 10.1371/journal.pone.0253538. PMID: 34242248; PMCID: PMC8270168.
2. Hsu CN, Chang CH, Poopradubsil T, Lo A, William KA, Lin KW, Bandrowski A, Ozyurt IB, Grethe JS, Martone ME. Antibody Watch: Text mining antibody specificity from the literature. PLoS Comput Biol. 2021 May 27;17(5):e1008967. doi: 10.1371/journal.pcbi.1008967. PMID: 34043624; PMCID: PMC8189493..
3. Menke J, Roelandse M, Ozyurt B, Martone M, Bandrowski A. The Rigor and Transparency Index Quality Metric for Assessing Biological and Medical Science Methods. iScience. 2020 Oct 20;23(11):101698. doi: 10.1016/j.isci.2020.101698. PMID: 33196023; PMCID: PMC7644557.
4. Lin, Dawei, et al. The TRUST Principles for digital repositories. Sci Data. 2020 May 14;7(1):144. doi: 10.1038/s41597-020-0486-7. PMID: 32409645; PMCID: PMC7224370.
5. Hsu C-N, Chang C-H, Poopradubsil T , Lo A, William KA , Lin K-W, Bandrowski A, Ozyurt IB , Grethe JS , Martoneet ME. Resource Reports: Using text mining of the biomedical literature to build a database of known antibody issues (P212). Mol Biol Cell. 2020 Dec 15;  31(26): Supplement: 2020 ASCB Annual Meeting Abstract POSTERS-134. doi: 10.1091/mbc.E20-10-0665 (poster presentation abstract)
6. Lin K-W, Bandrowski A, McKenna NJ, Grethe JS, Martone ME. Educating Biomedical Students on Rigor and Reproducibility in Scientific Research: NIDDK Information  Network (dkNET) Summer of Data Student Internship Program (P926). Mol Biol Cell. 2020 Dec 15;  31(26): Supplement: 2020 ASCB Annual Meeting Abstract POSTERS-590. doi: 10.1091/mbc.E20-10-0665 (poster presentation abstract)
7. Ozyurt, IB. On the effectiveness of small, discriminatively pre-trained language representation models for biomedical text mining. Proceedings of the First Workshop on Scholarly Document Processing. 2020 Nov: 104-112; doi: 10.18653/v1/2020.sdp-1.12
   
8. Kellman BP, Zhang Y, Logomasini E, Meinhardt E, Godinez-Macias KP, Chiang AWT, Sorrentino JT, Liang C, Bao B, Zhou Y, Akase S, Sogabe I, Kouka T, Winzeler EA, Wilson IBH, Campbell MP, Neelamegham S, Krambeck FJ, Aoki-Kinoshita KF, Lewis NE. A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR). Beilstein J Org Chem. 2020 Oct 27;16:2645-2662. doi: 10.3762/bjoc.16.215. PMID: 33178355; PMCID: PMC7607430. (summer internship student)
9. Menke J, Roelandse M, Ozyurt B, Martone M, Bandrowski A. The Rigor and Transparency Index Quality Metric for Assessing Biological and Medical Science Methods. iScience. 2020 Oct 20;23(11):101698. doi: 10.1016/j.isci.2020.101698. PMID: 33196023; PMCID: PMC7644557.
10. Ochsner SA, Pillich RT, McKenna NJ. Consensus transcriptional regulatory networks of coronavirus-infected human cells. Sci Data. 2020 Sep 22;7(1):314. doi: 10.1038/s41597-020-00628-6. PMID: 32963239; PMCID: PMC7509801.
11. Hsu C-N, Chang C-H, Poopradubsil T, Lo A, William KA, Lin K-W,  Bandrowski A, Ozyurt IB, Grethe JS, Martone ME. Antibody Watch: Text Mining Antibody Specificity from the Literature. arXiv.org. 2020 Nov 12;  arXiv:2008.01937v2 [cs.CL].(preprint)
12. Lin D, Crabtree J, Dillo I, Downs RR, Edmunds R, Giaretta D, De Giusti M, L'Hours H, Hugo W, Jenkyns R, Khodiyar V, Martone ME, Mokrane M, Navale V, Petters J, Sierman B, Sokolova DV, Stockhause M, Westbrook J. The TRUST Principles for digital repositories. Sci Data. 2020 May 14;7(1):144. doi: 10.1038/s41597-020-0486-7. PMID: 32409645; PMCID: PMC7224370.
13. Hsu CN et al. Comparing the Use of Research Resource Identifiers and Natural Language Processing for Citation of Databases, Software, and Other Digital Artifacts. Computer in Science & Engineering. 2020 March-April; 22(2): 22-32. DOI: 10.1109/MCSE.2019.2952838
14. Lin K-W, Bandrowski AE, Guo V, Hsu C-N, Ozyurt IB, Pascual L, Grethe JS, Martone ME. Improving Scientific Rigor and Reproducibility: Check Research Resources Information When Planning Experiments Using dkNET. The FASEB Journal. 2020 April 20; 34 (S1): 1. doi:10.1096/fasebj.2020.34.s1.04748 (poster presentation abstract)
15. Ochsner SA, McKenna NJ. No Dataset Left Behind: Mechanistic Insights into Thyroid Receptor Signaling Through Transcriptomic Consensome Meta-Analysis. Thyroid. 2020 Apr; 30(4):621-639. doi: 10.1089/thy.2019.0307. Epub 2020 Jan 29. PMID: 31910096; PMCID: PMC7187985.
16. Ozyurt IB, Bandrowski AE, and Grethe JS, Bio-AnswerFinder: a system to find answers to questions from biomedical texts, Database, Volume 2020, 2020, baz137, https://doi.org/10.1093/database/baz137
17. Fenner M et al. A Data Citation Roadmap for Scholarly Data Repositories. Sci. Data, 2019 April 1; 6(1):28. doi: https://doi.org/10.1038/s41597-019-0031-8
18. Babic Z, Capes-Davis A, Martone ME, Bairoch A, Ozyurt IB, Gillespie TH, Bandrowski AE. Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines. Elife. 2019 Jan 29;8. pii: e41676. doi: 10.7554/eLife.41676.
19. Ozyurt, I. B., & Grethe, J. S. Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. Database, 2018. doi:10.1093/database/bay130
20. Ochsner S et al. The Signaling pathways Project: An Integrated 'Omics Knowledgebase for Mammalian Cellular Signaling Pathways. bioRxiv Preprint. 2018. doi: https://doi.org/10.1101/401729
21. Hsu CN, Bandrowski AE, Grethe JS, Martone ME. Assessing Value of Biomedical Digital Repositories. PeerJ Preprints. 2017; 5:e2688v1 https://doi.org/10.7287/peerj.preprints.2688v3
22. McMurry J et al. Identifiers for the 21st Century: How to Design, Provision, and Reuse Persistent Identifiers to Maximize Utility and Impact of Life Science Data. PLOS Biology, 2017 Jun 29; 15(6), e2001414. doi:10.1371/journal.pbio.2001414. eCollection 2017 Jun. PMID: 28662064
23. Lin KW et al. The NIDDK Information Network (dkNET) - A Community Research Data and Resource Discovery Portal. ISN’s Forefronts Symposium on the Metabolome and Microbiome in Kidney Disease, 2016 Sep. 23-25, San Diego, CA.
24. Wilkinson MD et al. The FAIR Guiding Principles for scientific data management and stewardship. Sci. Data. 2016 Mar 15; 3:160018 doi:10.1038/sdata.2016.18. PMID: 26978244
25. Grethe JS and Martone ME. The NIDDK Information Network - a Community Discovery Portal for Researchers: Finding Data, Materials, and Tools Relevant to Your Research. Levine-Riggs Symposium. 2016 Mar. 7, Long Beach, CA and Endocrine Society 98th Annual Meeting and Expo. 2016 Apr. 3, Boston, MA.
26. Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. Resource Disambiguator for the Web: Extracting Biomedical Resources and Their Citations from the Scientific Literature. PLoS One. 2016 Jan 5;11(1):e0146300. DOI: 10.1371/journal.pone.0146300. PMID: 26730820.
27. Whetzel PL, Grethe JS, Banks DE, Martone ME. The NIDDK Information Network: A Community Portal for Finding Data, Materials, and Tools for Researchers Studying Diabetes, Digestive, and Kidney Diseases. PLoS ONE. 2015 Sep 22;10(9):e0136206. doi: 10.1371/journal.pone.0136206. eCollection 2015. PMID: 26393351
28. Bandrowski A et al. The Resource Identification Initiative: A cultural shift in publishing. Version 2. F1000Res. 2015 May 29 [revised 2015 Nov 19]; 4(134). doi: 10.12688/f1000research.6555.2. eCollection 2015. PMID: 26594330
29. Ferguson AR, Nielson JL, Cragin MH, Bandrowski AE, Martone ME. Big Data from Small Data: Data-Sharing in the "Long Tail" of Neuroscience. Nat. Neurotic. 2014 Oct 28; do:10.1038/nn.3838. PMID: 25349910.

Software

1. Banks, Davis et al.. (2015). The SciCrunch Portal. Zenodo. 10.5281/zenodo.30627
   
2. Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. (2015). resource_disambiguator: resource_disambiguator. Zenodo. 10.5281/zenodo.20560
3. Ozyurt IB, Grethe JS, Martone ME, Bandrowski AE. (2015). rdw: RDW. Zenodo. 10.5281/zenodo.20557
   

Presentations

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