BIG DATA for DISCOVERY SCIENCE
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The Big Data for Discovery Science Center (BDDS) - comprised of leading experts in biomedical imaging, genetics, proteomics, and computer science - is taking an "-ome to home" approach toward streamlining big data management, aggregation, manipulation, integration, and the modeling of biological systems across spatial and temporal scales.
 

Published

04 Nov 2016Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

Deutsch EW, Overall CM, Van Eyk JE, Baker MS, Paik YK, Weintraub ST, Lane L, Martens L, Vandenbrouck Y, Kusebauch U, Hancock WS, Hermjakob H, Aebersold R, Moritz RL, Omenn GS

04 Nov 2016Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics

Deutsch EW, Sun Z, Campbell DS, Binz PA, Farrah T, Shteynberg D, Mendoza L, Omenn GS, Moritz RL

10 Jan 2016A comprehensive Candida albicans PeptideAtlas build enables deep proteome coverage

Vialas V, Sun Z, Reales-Calderón JA, Hernáez ML, Casas V, Carrascal M, Abián J, Monteoliva L, Deutsch EW, Moritz RL, Gil C

18 Feb 2016The Pig PeptideAtlas: A resource for systems biology in animal production and biomedicine

Hesselager MO1, Codrea MC2, Sun Z3, Deutsch EW3, Bennike TB4, Stensballe A4, Bundgaard L5, Moritz RL3, Bendixen E1

06 Feb 2017I’ll Take That to Go: Big Data Bags and Minimal Identifiers for Exchange of Large, Complex Datasets

K. Chard, M. D’Arcy, B. Heavner, I. Foster, C. Kesselman, R. Madduri, A. Rodriguez, S. Soiland-Reyes, C. Goble, K. Clark, E. W. Deutsch, I. Dinov, N. Price, and A. Toga, IEEE International Conference on Big Data, Washington, DC, USA, 2016.
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05 Aug 2016Predictive Big Data Analysis: 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, and Toga, AW. PLoS ONE, 11(8):1-28, e0157077. DOI: 10.1371/journal.pone.0157077.

23 Jun 2015Controlling False Discovery Rate in Signal Space for Transformation-Invariant Thresholding of Statistical Maps

Li J, Shi Y & Toga AW. 2015. Inf Process Med Imaging, 24:125-36. PMCID: PMC4512301.

28 Aug 2015The Global Alzheimer’s Association Interactive Network

Toga AW, Neu SC, Bhatt P, Crawford KL & Ashish N. 2015. Alzheimers & Dementia, 12(1):49-54. PMID: 26318022.

01 Jan 2016The Image and Data Archive at the Laboratory of Neuro Imaging

Crawford KL, Neu SC & Toga AW. 2015. NeuroImage, 124(Pt B):1080-3. PMCID: PMC4644502.

04 Sep 2015State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet

Deutsch EW, Sun Z, Campbell D, Kusebauch U, Chu CS, Mendoza L, Shteynberg D, Omenn GS & Moritz RL. 2015. J Proteome Res, 14(9):3461-73. PMCID: PMC4755269.

04 Sep 2015Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification

Omenn GS, Lane L, Lundberg EK, Beavis RC, Nesvizhskii AI & Deutsch EW. 2015. J Proteome Res, 14(9):3452-60. PMCID: PMC4755311.

29 Apr 2015The Globus Galaxies platform: delivering science gateways as a service

Madduri R, Chard K, Chard R, Lacinski L, Rodriguez A, Sulakhe D, Kelly D, Dave U & Foster I. 2015. Concurrency Computat.: Pract. Exper, 27(16):4344-60. doi: 10.1002/cpe.3486.

20 Aug 2015Cost-Aware Elastic Cloud Provisioning for Scientific Workloads

Chard R, Chard K, Bubendorfer K, Lacinski L, Madduri R & Foster I 2015. 8th International Conference on Cloud Computing (CLOUD), New York City, NY, 2015, 971-974. doi: 10.1109/CLOUD.2015.130.

26 Oct 2015Cost-Aware Cloud Provisioning

Chard R, Chard K, Bubendorfer K, Lacinski L, Madduri R & Foster I 2015. 11th IEEE International Conference on e-Science (e-Science), Munich, 2015, 136-144. doi: 10.1109/eScience.2015.67.

26 Oct 2015Globus Data Publication as a Service: Lowering Barriers to Reproducible Science

Chard K, Pruyne J, Blaiszik B, Ananthakrishnan R, Tuecke S & Foster I. 2015. 11th IEEE International Conference on e-Science (e-Science), Munich, 2015, 401-10. doi: 10.1109/eScience.2015.68.

02 Jun 2016The Discovery Cloud: Accelerating and Democratizing Research on a Global Scale

Foster I, Chard K & Tuecke S. 2016. Accepted to the IEEE International Conference on Cloud Engineering (IC2E).

21 Jul 2016An Automated Tool Profiling Service for the Cloud

Chard R, Chard K, Ng B, Bubendorfer K, Rodriguez A, Madduri R & Foster I 2016. Accepted to the 16th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing.

16 Jun 2016Data Centric Discovery with a Data-Oriented Architecture

Schuler R, Kesselman C & Czajkowski K. The Science of Cyberinfrastructure: Research, Experience, Applications and Models (SCREAM-15) Workshop.

10 Aug 2015Espaliers: A Visualization Method for Big Data

Robinson M, Eley G, Vockley JG, Niederhuber JE & Glusman G 2015. JSM Proceedings, Statistical Computing Section. Alexandria, VA: American Statistical Association.

01 Mar 2016Methodological challenges and analytic opportunities for modeling and interpreting Big Healthcare Data

Managing, processing and understanding big healthcare data is challenging, costly and demanding. Without a robust fundamental theory for representation, analysis and inference, a roadmap for uniform handling and analyzing of such complex data remains elusive. In this article, we outline various big data challenges, opportunities, modeling methods and software techniques for blending complex healthcare data, advanced analytic tools, and distributed scientific computing.
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04 May 2015Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment

Woo, Dinov, Hobel, Zamanyan, Choi, Thomson, Toga. For the Alzheimer's Disease Neuroimaging Initiative‡ , Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment. 4 MAY 2015; DOI: 10.1111/jon.12252

17 Jul 2015SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information

Syed S Husain, Alexandr Kalinin, Anh Truong, Ivo D Dinov, SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information. Journal of Big Data. 17 Jul 2015; DOI 10.1186/s40537-015-0018-z.

26 Jun 2015Probability Distributome : a web computational infrastructure for exploring the properties, interrelations, and applications of probability distributions

Ivo D. Dinov, Kyle Siegrist, Dennis K. Pearl, Alexandr Kalinin, Nicolas Christou, Probability Distributome : a web computational infrastructure for exploring the properties, interrelations, and applications of probability distributions. Computational Statistics. 26 Jun 2015;

12 Jan 2015Gene interactions and structural brain change in early-onset Alzheimer's disease subjects using the pipeline environment

Moon SW, Dinov ID, Zamanyan A, Shi R, Genco A, Hobel S, Thompson PM, Toga AW, Alzheimer's Disease Neuroimaging Initiative (ADNI). Gene interactions and structural brain change in early-onset Alzheimer's disease subjects using the pipeline environment. Psychiatry Investig. 2015 Jan;12(1):125-35. PubMed PMID: 25670955; PubMed Central PMCID: PMC4310910

01 Jan 2015Studying Ventricular Abnormalities in Mild Cognitive Impairment with Hyperbolic Ricci Flow and Tensor-based Morphometry

Shi J, Stonnington CM, Thompson PM, Chen K, Gutman B, Reschke C, Baxter LC, Reiman EM, Caselli RJ, Wang Y, Alzheimer's Disease Neuroimaging Initiative. Studying ventricular abnormalities in mild cognitive impairment with hyperbolic Ricci flow and tensor-based morphometry. Neuroimage. 2015 Jan 1;104:1-20. PubMed PMID: 25285374; PubMed Central PMCID: PMC4252650

12 Feb 2015Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline

Slagel J, Mendoza L, Shteynberg D, Deutsch EW, Moritz RL. Processing shotgun proteomics data on the Amazon cloud with the trans-proteomic pipeline. Mol Cell Proteomics. 2015 Feb;14(2):399-404. PubMed PMID: 25418363; PubMed Central PMCID: PMC4350034.

27 Jun 2015Sharing big biomedical data

Toga, AW, Dinov, ID. (2015) Sharing big biomedical data. Journal of Big Data., 2(7):1-12. DOI: 10.1186/s40537-015-0016-1

4 May 2015Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

Woo MS, Dinov, ID, Hobel, S, Zamanyan, A, Choi, YC, Thompson, PM, Toga, AW and Alzheimer's Disease Neuroimaging Initiative (ADNI) (2015) Structural Brain Changes in Early-Onset Alzheimer's Disease Subjects Using the LONI Pipeline Environment. Journal of Neuroimaging., in press. DOI: 10.1111/jon.12252

29 Jan 2015Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics

Deutsch EW, Mendoza L, Shteynberg D, Slagel J, Sun Z, Moritz RL. Trans-Proteomic Pipeline, a standardized data processing pipeline for large-scale reproducible proteomics informatics. Proteomics Clin Appl. 2015 Jan 29;PubMed PMID: 25631240; NIHMSID: 669315.

21 Jul 2015Big 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 2015 Big Biomedical Data as the Key Resource for Discovery Science. JAMIA.