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Items: 21

1.

Reproducible big data science: A case study in continuous FAIRness.

Madduri R, Chard K, D'Arcy M, Jung SC, Rodriguez A, Sulakhe D, Deutsch E, Funk C, Heavner B, Richards M, Shannon P, Glusman G, Price N, Kesselman C, Foster I.

PLoS One. 2019 Apr 11;14(4):e0213013. doi: 10.1371/journal.pone.0213013. eCollection 2019.

2.

Participatory methods to support team science development for predictive analytics in health.

Arevian AC, Bell D, Kretzman M, Kasari C, Narayanan S, Kesselman C, Wu S, Di Capua P, Hsu W, Keener M, Pevnick J, Wells KB, Chung B.

J Clin Transl Sci. 2018 Jun;2(3):178-182. doi: 10.1017/cts.2018.313. Epub 2018 Aug 30.

3.

ERMrest: A Collaborative Data Catalog with Fine Grain Access Control.

Czajkowski K, Kesselman C, Schuler R.

Proc IEEE Int Conf Escience. 2017 Oct;2017:510-517. doi: 10.1109/eScience.2017.83. Epub 2017 Nov 16.

4.

Experiences with Deriva: An Asset Management Platform for Accelerating eScience.

Bugacov A, Czajkowski K, Kesselman C, Kumar A, Schuler RE, Tangmunarunkit H.

Proc IEEE Int Conf Escience. 2017 Oct;2017:79-88. doi: 10.1109/eScience.2017.20. Epub 2017 Nov 16.

5.

Conserved and Divergent Features of Human and Mouse Kidney Organogenesis.

Lindström NO, McMahon JA, Guo J, Tran T, Guo Q, Rutledge E, Parvez RK, Saribekyan G, Schuler RE, Liao C, Kim AD, Abdelhalim A, Ruffins SW, Thornton ME, Baskin L, Grubbs B, Kesselman C, McMahon AP.

J Am Soc Nephrol. 2018 Mar;29(3):785-805. doi: 10.1681/ASN.2017080887. Epub 2018 Feb 15.

6.

Neuroanatomical morphometric characterization of sex differences in youth using statistical learning.

Sepehrband F, Lynch KM, Cabeen RP, Gonzalez-Zacarias C, Zhao L, D'Arcy M, Kesselman C, Herting MM, Dinov ID, Toga AW, Clark KA.

Neuroimage. 2018 May 15;172:217-227. doi: 10.1016/j.neuroimage.2018.01.065. Epub 2018 Feb 3.

7.

(Re)Building a Kidney.

Oxburgh L, Carroll TJ, Cleaver O, Gossett DR, Hoshizaki DK, Hubbell JA, Humphreys BD, Jain S, Jensen J, Kaplan DL, Kesselman C, Ketchum CJ, Little MH, McMahon AP, Shankland SJ, Spence JR, Valerius MT, Wertheim JA, Wessely O, Zheng Y, Drummond IA.

J Am Soc Nephrol. 2017 May;28(5):1370-1378. doi: 10.1681/ASN.2016101077. Epub 2017 Jan 17.

8.

Predictive Big Data Analytics: A Study of Parkinson's Disease Using Large, Complex, Heterogeneous, Incongruent, Multi-Source and Incomplete Observations.

Dinov ID, Heavner B, Tang M, Glusman G, Chard K, Darcy M, Madduri R, Pa J, Spino C, Kesselman C, Foster I, Deutsch EW, Price ND, Van Horn JD, Ames J, Clark K, Hood L, Hampstead BM, Dauer W, Toga AW.

PLoS One. 2016 Aug 5;11(8):e0157077. doi: 10.1371/journal.pone.0157077. eCollection 2016.

9.

The FaceBase Consortium: a comprehensive resource for craniofacial researchers.

Brinkley JF, Fisher S, Harris MP, Holmes G, Hooper JE, Jabs EW, Jones KL, Kesselman C, Klein OD, Maas RL, Marazita ML, Selleri L, Spritz RA, van Bakel H, Visel A, Williams TJ, Wysocka J; FaceBase Consortium, Chai Y.

Development. 2016 Jul 15;143(14):2677-88. doi: 10.1242/dev.135434. Epub 2016 Jun 10.

10.

Big biomedical data as the key resource for discovery science.

Toga AW, Foster I, Kesselman C, Madduri R, Chard K, Deutsch EW, Price ND, Glusman G, Heavner BD, Dinov ID, Ames J, Van Horn J, Kramer R, Hood L.

J Am Med Inform Assoc. 2015 Nov;22(6):1126-31. doi: 10.1093/jamia/ocv077. Epub 2015 Jul 21.

11.

A system to build distributed multivariate models and manage disparate data sharing policies: implementation in the scalable national network for effectiveness research.

Meeker D, Jiang X, Matheny ME, Farcas C, D'Arcy M, Pearlman L, Nookala L, Day ME, Kim KK, Kim H, Boxwala A, El-Kareh R, Kuo GM, Resnic FS, Kesselman C, Ohno-Machado L.

J Am Med Inform Assoc. 2015 Nov;22(6):1187-95. doi: 10.1093/jamia/ocv017. Epub 2015 Jul 3.

12.

A physical sciences network characterization of non-tumorigenic and metastatic cells.

Physical Sciences - Oncology Centers Network, Agus DB, Alexander JF, Arap W, Ashili S, Aslan JE, Austin RH, Backman V, Bethel KJ, Bonneau R, Chen WC, Chen-Tanyolac C, Choi NC, Curley SA, Dallas M, Damania D, Davies PC, Decuzzi P, Dickinson L, Estevez-Salmeron L, Estrella V, Ferrari M, Fischbach C, Foo J, Fraley SI, Frantz C, Fuhrmann A, Gascard P, Gatenby RA, Geng Y, Gerecht S, Gillies RJ, Godin B, Grady WM, Greenfield A, Hemphill C, Hempstead BL, Hielscher A, Hillis WD, Holland EC, Ibrahim-Hashim A, Jacks T, Johnson RH, Joo A, Katz JE, Kelbauskas L, Kesselman C, King MR, Konstantopoulos K, Kraning-Rush CM, Kuhn P, Kung K, Kwee B, Lakins JN, Lambert G, Liao D, Licht JD, Liphardt JT, Liu L, Lloyd MC, Lyubimova A, Mallick P, Marko J, McCarty OJ, Meldrum DR, Michor F, Mumenthaler SM, Nandakumar V, O'Halloran TV, Oh S, Pasqualini R, Paszek MJ, Philips KG, Poultney CS, Rana K, Reinhart-King CA, Ros R, Semenza GL, Senechal P, Shuler ML, Srinivasan S, Staunton JR, Stypula Y, Subramanian H, Tlsty TD, Tormoen GW, Tseng Y, van Oudenaarden A, Verbridge SS, Wan JC, Weaver VM, Widom J, Will C, Wirtz D, Wojtkowiak J, Wu PH.

Sci Rep. 2013;3:1449. doi: 10.1038/srep01449.

13.

Next generation sequence analysis and computational genomics using graphical pipeline workflows.

Torri F, Dinov ID, Zamanyan A, Hobel S, Genco A, Petrosyan P, Clark AP, Liu Z, Eggert P, Pierce J, Knowles JA, Ames J, Kesselman C, Toga AW, Potkin SG, Vawter MP, Macciardi F.

Genes (Basel). 2012 Aug 30;3(3):545-75. doi: 10.3390/genes3030545.

14.

A flexible, open, decentralized system for digital pathology networks.

Schuler R, Smith DE, Kumaraguruparan G, Chervenak A, Lewis AD, Hyde DM, Kesselman C.

Stud Health Technol Inform. 2012;175:29-38.

15.

A system architecture for sharing de-identified, research-ready brain scans and health information across clinical imaging centers.

Chervenak AL, van Erp TG, Kesselman C, D'Arcy M, Sobell J, Keator D, Dahm L, Murry J, Law M, Hasso A, Ames J, Macciardi F, Potkin SG.

Stud Health Technol Inform. 2012;175:19-28.

16.

Applications of the pipeline environment for visual informatics and genomics computations.

Dinov ID, Torri F, Macciardi F, Petrosyan P, Liu Z, Zamanyan A, Eggert P, Pierce J, Genco A, Knowles JA, Clark AP, Van Horn JD, Ames J, Kesselman C, Toga AW.

BMC Bioinformatics. 2011 Jul 26;12:304. doi: 10.1186/1471-2105-12-304.

17.

Enabling collaborative research using the Biomedical Informatics Research Network (BIRN).

Helmer KG, Ambite JL, Ames J, Ananthakrishnan R, Burns G, Chervenak AL, Foster I, Liming L, Keator D, Macciardi F, Madduri R, Navarro JP, Potkin S, Rosen B, Ruffins S, Schuler R, Turner JA, Toga A, Williams C, Kesselman C; Biomedical Informatics Research Network.

J Am Med Inform Assoc. 2011 Jul-Aug;18(4):416-22. doi: 10.1136/amiajnl-2010-000032. Epub 2011 Apr 22.

18.

funcLAB/G-service-oriented architecture for standards-based analysis of functional magnetic resonance imaging in HealthGrids.

Erberich SG, Bhandekar M, Chervenak A, Kesselman C, Nelson MD.

Neuroimage. 2007;37 Suppl 1:S135-43.

PMID:
17707204
19.

Globus MEDICUS - federation of DICOM medical imaging devices into healthcare Grids.

Erberich SG, Silverstein JC, Chervenak A, Schuler R, Nelson MD, Kesselman C.

Stud Health Technol Inform. 2007;126:269-78.

PMID:
17476069
20.

Gender issues in the use of virtual environments.

Larson P, Rizzo AA, Buckwalter JG, Van Rooyen A, Kratz K, Neumann U, Kesselman C, Thiebaux M, Van Der Zaag C.

Cyberpsychol Behav. 1999;2(2):113-23. doi: 10.1089/cpb.1999.2.113.

PMID:
19178247
21.

Virtual environments for targeting cognitive processes: an overview of projects at the University of Southern California.

Rizzo AA, Buckwalter JG, Neumann U, Chua C, VAN Rooyen A, Larson P, Kratz K, Kesselman C, Thiebaux M, Humphrey L.

Cyberpsychol Behav. 1999;2(2):89-100. doi: 10.1089/cpb.1999.2.89.

PMID:
19178245

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